@article {pmid39481662, year = {2024}, author = {Liu, W and Wang, Z and Huang, Y and Liu, Y and Li, R and Wang, M and Zhang, H and Meng, C and Xiao, X}, title = {Acetylshikonin reduces the spread of antibiotic resistance via plasmid conjugation.}, journal = {International journal of antimicrobial agents}, volume = {}, number = {}, pages = {107370}, doi = {10.1016/j.ijantimicag.2024.107370}, pmid = {39481662}, issn = {1872-7913}, abstract = {The plasmid-mediated conjugative transfer of antibiotic resistance genes (ARGs) stands out as the primary driver behind the dissemination of antimicrobial resistance (AMR). Developing effective inhibitors that target conjugative transfer represents an efficient strategy for addressing the issue of AMR. Here, we studied the effect of acetylshikonin (ASK), a botanical derivative, on plasmid conjugation. The conjugative transfer of RP4-7 plasmid inter and intra species was notably reduced by ASK. The conjugation process of IncI2 and IncX4 plasmids harboring the mobile colistin resistance gene (mcr-1), IncX4 and IncX3 plasmids containing the carbapenem resistance gene (blaNDM-5), and IncFI and IncFII plasmids possessing the tetracycline resistance gene [tet(X4)] were also reduced by ASK. Importantly, the conjugative transfer frequency of mcr-1 positive IncI2 plasmid in mouse peritoneal conjugation model and gut conjugation model was reduced by ASK. The mechanism investigation showed that ASK disrupt the functionality of the bacterial cell membrane. Furthermore, the proton motive force (PMF) was dissipated. In addition, ASK blocked the electron transmission in bacteria's electron transport chain (ETC) through disturbing the quinone interaction, resulting in an insufficient energy supply for conjugation. Collectively, ASK is a potential conjugative transfer inhibitor, providing novel strategies to prevent the spread of AMR.}, } @article {pmid39481609, year = {2024}, author = {Tang, B and Hu, X and Wu, B and Zhao, G and Yue, M}, title = {Global Antimicrobial Resistance Threats: Insights from the Resurgence of Whooping Cough.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {106337}, doi = {10.1016/j.jinf.2024.106337}, pmid = {39481609}, issn = {1532-2742}, } @article {pmid39476778, year = {2024}, author = {Li, J and Sun, Y and Zhang, Q and Liu, S and Liu, P and Zhang, XX}, title = {Unveiling the potential role of virus-encoded polyphosphate kinases in enhancing phosphorus removal in activated sludge systems.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122678}, doi = {10.1016/j.watres.2024.122678}, pmid = {39476778}, issn = {1879-2448}, abstract = {While microbial phosphate removal in activated sludge (AS) systems has been extensively studied, the role of viruses in this process remains largely unexplored. In this study, we identified 149 viral auxiliary metabolic genes associated with phosphorus cycling from 2,510 viral contigs (VCs) derived from AS systems. Notably, polyphosphate kinase 1 (ppk1) and polyphosphate kinase 2 (ppk2) genes, which are primarily responsible for phosphate removal, were found in five unclassified VCs. These genes exhibited conserved protein structures and active catalytic sites, indicating a pivotal role of viruses in enhancing phosphorus removal. Phylogenetic analysis demonstrated a close relationship between viral ppk genes and their bacterial counterparts, suggesting the occurrence of horizontal gene transfer. Furthermore, experimental assays validated that viral ppk genes enhanced host phosphate removal capabilities. VCs carrying ppk genes were observed across diverse ecological and geographical contexts, suggesting their potential to bolster host functions in varied environmental and nutrient settings, spanning natural and engineered systems. These findings uncover a previously underappreciated mechanism by which viruses enhance phosphate removal in wastewater treatment plants. Overall, our study highlights the potential for leveraging virus-encoded genes to improve the efficiency of biological phosphorus removal processes, offering new insights into the microbial ecology of AS systems and the role of viruses in biogeochemical cycling.}, } @article {pmid39475308, year = {2024}, author = {Schrago, CG and Mello, B}, title = {Challenges in Assembling the Dated Tree of Life.}, journal = {Genome biology and evolution}, volume = {16}, number = {10}, pages = {}, pmid = {39475308}, issn = {1759-6653}, mesh = {*Phylogeny ; Evolution, Molecular ; Gene Transfer, Horizontal ; }, abstract = {The assembly of a comprehensive and dated Tree of Life (ToL) remains one of the most formidable challenges in evolutionary biology. The complexity of life's history, involving both vertical and horizontal transmission of genetic information, defies its representation by a simple bifurcating phylogeny. With the advent of genome and metagenome sequencing, vast amounts of data have become available. However, employing this information for phylogeny and divergence time inference has introduced significant theoretical and computational hurdles. This perspective addresses some key methodological challenges in assembling the dated ToL, namely, the identification and classification of homologous genes, accounting for gene tree-species tree mismatch due to population-level processes along with duplication, loss, and horizontal gene transfer, and the accurate dating of evolutionary events. Ultimately, the success of this endeavor requires new approaches that integrate knowledge databases with optimized phylogenetic algorithms capable of managing complex evolutionary models.}, } @article {pmid39474943, year = {2024}, author = {Sharma, P and Kishore, A and Singh, M}, title = {Single-use polyethylene terephthalate bottle-derived nanoplastics propagate antibiotic resistance in bacteria via transformation and outer membrane vesicle secretion.}, journal = {Nanoscale}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4nr02613f}, pmid = {39474943}, issn = {2040-3372}, abstract = {Plastic pollution arising from single-use plastic bottles (SUPBs) and containers leads to the formation of micro/nanoplastics (NPs). These NPs raise concerns due to their potential toxicity and interactions with microorganisms. In various environments, including our digestive system, both microorganisms and plastics coexist. The interactions between these NPs and microorganisms can have far-reaching consequences, potentially affecting the ecosystems and human health. Therefore, understanding these interactions is crucial for addressing the challenges posed by plastic pollution. This study investigated the role of NPs in propagating antibiotic resistance (AR), specifically through outer membrane vesicles (OMVs), which is a mechanism that has not been fully explored to date in terms of NPs' effects. To explore this, NPs were synthesized using polyethylene terephthalate (PET) SUPBs, mimicking the natural chemical composition of environmental nanoplastics, unlike previous studies, which used pure PET, polystyrene (PS) or other pure plastic materials. The resulting PET bottle-derived nanoplastics (PBNPs), which exhibited diverse shapes and sizes (50-850 nm), were found to facilitate horizontal gene transfer (HGT) through transformation and outer membrane vesicles (OMVs), enabling the transport of plasmids among bacteria. In transformation, PBNPs physically carried plasmids across the bacterial membrane. In another scenario, PBNPs induced oxidative stress and bacterial surface damage, which led to the upregulation of stress response-associated genes and the escalation of OMV secretion in E. coli. This novel pathway highlights how PBNPs contribute to AR gene dissemination, potentially exacerbating the global antibiotic resistance crisis. Furthermore, PBNPs mediate cross-species gene transfer from E. coli to Lactobacillus acidophilus, underscoring their impact on diverse microorganisms, including those in the human gut. Our findings suggest that nanoplastics may be an unrecognized contributor to the rising tide of antibiotic resistance, with significant consequences for human health and the environment. Molecular analyses revealed the upregulated expression of genes associated with stress response and OMV secretion, offering deeper insights into the biological mechanisms affected by PBNPs. This study offers crucial insights into the interactions of NPs and microorganisms for developing strategies to address the ecological and health implications of nanoplastic contamination.}, } @article {pmid39472795, year = {2024}, author = {Andriyanov, P and Zhurilov, P and Menshikova, A and Tutrina, A and Yashin, I and Kashina, D}, title = {Large-scale genomic analysis of Elizabethkingia anophelis.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1015}, pmid = {39472795}, issn = {1471-2164}, mesh = {*Flavobacteriaceae/genetics ; *Genome, Bacterial ; *Phylogeny ; *Genomics/methods ; Gene Transfer, Horizontal ; Humans ; Flavobacteriaceae Infections/microbiology ; Animals ; Drug Resistance, Bacterial/genetics ; }, abstract = {The recent emergence of Elizabethkingia anophelis as a human pathogen is a major concern for global public health. This organism has the potential to cause severe infections and has inherent antimicrobial resistance. The potential for widespread outbreaks and rapid global spread highlights the critical importance of understanding the biology and transmission dynamics of this infectious agent. We performed a large-scale analysis of available 540 E. anophelis, including one novel strain isolated from raw milk and sequenced in this study. Pan-genome analysis revealed an open and diverse pan-genome in this species, characterized by the presence of many accessory genes. This suggests that the species has a high level of adaptability and can thrive in a variety of environments. Phylogenetic analysis has also revealed a complex population structure, with limited source-lineage correlation. We identified diverse antimicrobial resistance factors, including core-genome and accessory ones often associated with mobile genetic elements within specific lineages. Mobilome analysis revealed a dynamic landscape primarily composed of genetic islands, integrative and conjugative elements, prophage elements, and small portion of plasmids emphasizing a complex mechanism of horizontal gene transfer. Our study underscores the adaptability of E. anophelis, characterized by a diverse range of antimicrobial resistance genes, putative virulence factors, and genes enhancing fitness. This adaptability is also supported by the organism's ability to acquire genetic material through horizontal gene transfer, primarily facilitated by mobile genetic elements such as integrative and conjugative elements (ICEs). The potential for rapid evolution of this emerging pathogen poses a significant challenge to public health efforts.}, } @article {pmid39260133, year = {2024}, author = {Xu, Q and Xie, M and Yang, X and Liu, X and Ye, L and Chen, K and Chan, EW and Chen, S}, title = {Conjugative transmission of virulence plasmid in Klebsiella pneumoniae mediated by a novel IncN-like plasmid.}, journal = {Microbiological research}, volume = {289}, number = {}, pages = {127896}, doi = {10.1016/j.micres.2024.127896}, pmid = {39260133}, issn = {1618-0623}, mesh = {*Klebsiella pneumoniae/genetics/pathogenicity ; *Plasmids/genetics ; Animals ; *Klebsiella Infections/microbiology/transmission ; Virulence/genetics ; *Conjugation, Genetic ; Mice ; *Virulence Factors/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Interleukin-1beta/genetics ; Phagocytosis ; Disease Models, Animal ; Macrophages/microbiology ; Female ; Humans ; Type IV Secretion Systems/genetics ; }, abstract = {Klebsiella pneumoniae (Kp) is increasingly recognized as a reservoir for a range of antibiotic resistance genes and a pathogen that frequently causes severe infections in both hospital and community settings. In this study, we have identified a novel mechanism of conjugative transfer of a non-conjugative virulence plasmid through the formation of a fusion plasmid between the virulence plasmid and a novel 59,162 bp IncN- plasmid. This plasmid was found to be a multidrug-resistance (MDR) plasmid and carried a T4SS cluster, which greatly facilitated the efficient horizontal transfer of the fusion plasmid between Kp strains. The fused virulence plasmid conferred the resistance of serum killing and macrophage phagocytosis to the transconjugants. Importantly, this plasmid was shown to be essential for Kp virulence in a mouse model. Mechanistic analysis revealed that the virulence factors encoded by this virulence plasmid contributed to resistance to in vivo clearance and induced a high level of proinflammatory cytokine IL-1β, which acts as an inducer for more neutrophil recruitment. The transmission of the fusion plasmid in Kp has the potential to convert it into both MDR and hypervirulent Kp, accelerating its evolution, and posing a serious threat to human health. The findings of this study provide new insights into the rapid evolution of MDR and hypervirulent Kp in recent years.}, } @article {pmid39471530, year = {2024}, author = {Qi, H and Lv, J and Liao, J and Jin, J and Ren, Y and Tao, Y and Wang, D and Alvarez, PJJ and Yu, P}, title = {Metagenomic insights into microalgae-bacterium-virus interactions and viral functions in phycosphere facing environmental fluctuations.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122676}, doi = {10.1016/j.watres.2024.122676}, pmid = {39471530}, issn = {1879-2448}, abstract = {Despite the ecological and biotechnological significance of microalgae-bacterium symbionts, the response of host-virus interactions to external environmental fluctuations and the role of viruses in phycosphere remain largely unexplored. Herein, we employed algal-bacterial granular sludge (ABGS) with varying light intensity and organic carbon loading to investigate the mechanisms of microalgae-bacterium-virus symbionts in response to environmental fluctuations. Metagenomics revealed that enhanced light intensity decreased the diversity of microalgae, so did the diversity of symbiotic bacteria and viruses. As carbon sources decreased, bacteria prompted horizontal gene transfer in phycosphere by 12.76 %-157.40 %, increased the proportion of oligotrophs as keystone species (0.00 % vs 14.29 %) as well as viruses using oligotrophs as hosts (18.52 % vs 25.00 %). Furthermore, virus-carried auxiliary metabolic genes (AMGs) and biosynthetic gene clusters (BGCs) encoding vitamin B12 synthesis (e.g., cobS), antioxidation (e.g., queC), and microbial aggregation (e.g., cysE). Additionally, phylogenetic and similarity analysis further revealed the evolutionary origin and potential horizontal transfer of the AMGs and BGCs, which could potentially enhance the adaptability of bacteria and eukaryotic microalgae. Overall, our research demonstrates that environmental fluctuations have cascading effects on the microalgae-bacteria-virus interactions, and emphasizes the important role of viruses in maintaining the stability of the phycosphere symbiotic community.}, } @article {pmid39470278, year = {2024}, author = {Scherff, N and Rothgänger, J and Weniger, T and Mellmann, A and Harmsen, D}, title = {Real-time plasmid transmission detection pipeline.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0210024}, doi = {10.1128/spectrum.02100-24}, pmid = {39470278}, issn = {2165-0497}, abstract = {UNLABELLED: The spread of antimicrobial resistance among bacteria by horizontal plasmid transmissions poses a major challenge for clinical microbiology. Here, we evaluate a new real-time plasmid transmission detection pipeline implemented in the SeqSphere[+] (Ridom GmbH, Münster, Germany) software. Within the pipeline, a local Mash plasmid database is created, and Mash searches with a distance threshold of 0.001 are used to trigger plasmid transmission early warning alerts (EWAs). Clonal transmissions are detected using core-genome multi-locus sequence typing allelic differences. The tools MOB-suite, NCBI AMRFinderPlus, CGE MobileElementFinder, pyGenomeViz, and MUMmer, integrated in SeqSphere+, are used to characterize plasmids and for visual pairwise plasmid comparisons, respectively. We evaluated the pipeline using published hybrid assemblies (Oxford Nanopore Technology/Illumina) of a surveillance and outbreak data set with plasmid transmissions. To emulate prospective usage, samples were imported in chronological order of sampling date. Different combinations of the user-adjustable parameters sketch size (1,000 vs 10,000) and plasmid size correction were tested, and discrepancies between resulting clusters were analyzed with Quast. When using a sketch size of 1,000 with size correction turned on, the SeqSphere[+] pipeline agreed with the published data and produced the same clonal and carbapenemase-carrying plasmid clusters. EWAs were in the correct chronological order. In summary, the developed pipeline presented here is suitable for integration into clinical microbiology settings with limited bioinformatics knowledge due to its automated analyses and alert system, which are combined with the GUI-based SeqSphere[+] platform. Thus, with its integrated sample database, (near) real-time plasmid transmission detection is within reach in bacterial routine-diagnostic settings when long-read sequencing is employed.

IMPORTANCE: Plasmid-mediated spread of antimicrobial resistance is a major challenge for clinical microbiology, and monitoring of potential plasmid transmissions is essential to combat further dissemination. Whole-genome sequencing is often used to surveil nosocomial transmissions but usually limited to the detection of clonal transmissions (based on chromosomal markers). Recent advances in long-read sequencing technologies enable full reconstruction of plasmids and the detection of very similar plasmids, but so far, easy-to-use bioinformatic tools for this purpose have been missing. Here, we present an evaluation of an innovative real-time plasmid transmission detection pipeline. It is integrated into the GUI-based SeqSphere[+] software, which already offers core-genome multi-locus sequence typing-based pathogen outbreak detection. It requires very limited bioinformatics knowledge, and its database, automated analyses, and alert system make it well suited for prospective clinical application.}, } @article {pmid39467614, year = {2024}, author = {Gobbo, A and Fraiture, MA and Van Poelvoorde, L and De Keersmaecker, SCJ and Garcia-Graells, C and Van Hoorde, K and Verhaegen, B and Huwaert, A and Maloux, H and Hutse, V and Ceyssens, PJ and Roosens, N}, title = {Strategy to develop and validate digital droplet PCR methods for global antimicrobial resistance wastewater surveillance.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {96}, number = {11}, pages = {e11145}, doi = {10.1002/wer.11145}, pmid = {39467614}, issn = {1554-7531}, support = {//Sciensano (contract NAP-AMR)/ ; }, mesh = {*Wastewater/microbiology ; Real-Time Polymerase Chain Reaction/methods ; Environmental Monitoring/methods ; Polymerase Chain Reaction/methods ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; }, abstract = {According to World Health Organization (WHO), antimicrobial resistance (AMR) is currently one of the world's top 10 health threats, causing infections to become difficult or impossible to treat, increasing the risk of disease spread, severe illness, disability, and death. Accurate surveillance is a key component in the fight against AMR. Wastewater is progressively becoming a new player in AMR surveillance, with the promise of a cost-effective real-time tracking of global AMR profiles in specific regions. One of the most useful analytical methods for wastewater surveillance is currently based on real-time PCR (qPCR) and digital droplet PCR (ddPCR) technologies. As stated in the EU Wastewater Treatment Directive proposal, methodological standardization, including a workflow for method development and validation, will play a crucial role in global monitoring of AMR in wastewater. However, according to our knowledge, there are currently no qPCR and ddPCR methods for AMR surveillance available that have been validated according to international standard performance criteria. Therefore, this study proposes a workflow for the development and validation of PCR-based methods for a harmonized and global AMR surveillance, including the construction of specific sequence databases and microbial collections for an efficient method development and method specificity evaluation. Following this strategy, we have developed and validated four duplex ddPCR methods responding to international standard performance criteria, focusing on seven AMR genes (ARG's), including extended spectrum beta-lactam (blaCTX-M), carbapenem (blaKPC-2/3), tetracycline (tet(M)), erythromycin (erm(B)), vancomycin (vanA), sulfonamide (sul2), and aminoglycoside (aac(3)-IV), as well as one indicator of antibiotic (multi-) resistance and horizontal gene transfer, named the class I integron (intl1). The performance of these ddPCR methods was successfully assessed for their specificity, as no false-positive and false-negative results were observed. These ddPCR methods were also considered to be highly sensitive as showing a limit of detection below 25 copies of the targets. In addition, their applicability was confirmed using 14 wastewater samples collected from two Belgian water resource recovery facilities. The proposed study represents therefore a step forward to reinforce method harmonization in the context of the global AMR surveillance in wastewater. PRACTITIONER POINTS: In the context of wastewater surveillance, no PCR-based methods for global AMR monitoring are currently validated according to international standards. Consequently, we propose a workflow to develop and validate PCR-based methods for a harmonized and global AMR surveillance. This workflow resulted here in four duplex ddPCR methods targeting seven ARGs and one general indicator for mobilizable resistance genes. The applicability of these validated ddPCR methods was confirmed on 14 wastewater samples from two Belgian water resource recovery facilities.}, } @article {pmid39459963, year = {2024}, author = {Pu, F and Zhang, N and Pang, J and Zeng, N and Baloch, FB and Li, Z and Li, B}, title = {Deciphering the Genetic Architecture of Staphylococcus warneri Prophage vB_G30_01: A Comprehensive Molecular Analysis.}, journal = {Viruses}, volume = {16}, number = {10}, pages = {}, pmid = {39459963}, issn = {1999-4915}, support = {31271818//National Natural Science Foundation of China/ ; 2023-01//International Cooperation Project of Universities in Liaoning Province/ ; 2022030673-JH5/104//Liaoning Province Rural Science and Technology Special Action Project/ ; 22-319-2-13//Shenyang Science and Technology Project/ ; 202108857002//China Scholarship Council/ ; }, mesh = {*Genome, Viral ; *Staphylococcus/virology/genetics ; *Prophages/genetics/physiology ; *Phylogeny ; *Host Specificity ; *Open Reading Frames ; *Staphylococcus Phages/genetics/classification/physiology/ultrastructure ; *Lysogeny ; DNA, Viral/genetics ; Genomics/methods ; }, abstract = {The current knowledge of Staphylococcus warneri phages is limited, with few genomes sequenced and characterized. In this study, a prophage, vB_G30_01, isolated from Staphylococcus warneri G30 was characterized and evaluated for its lysogenic host range. The phage was studied using transmission electron microscopy and a host range. The phage genome was sequenced and characterized in depth, including phylogenetic and taxonomic analyses. The linear dsDNA genome of vB_G30_01 contains 67 predicted open reading frames (ORFs), classifying it within Bronfenbrennervirinae. With a total of 10 ORFs involved in DNA replication-related and transcriptional regulator functions, vB_G30_01 may play a role in the genetics and transcription of a host. Additionally, vB_G30_01 possesses a complete set of genes related to host lysogeny and lysis, implying that vB_G30_01 may influence the survival and adaptation of its host. Furthermore, a comparative genomic analysis reveals that vB_G30_01 shares high genomic similarity with other Staphylococcus phages and is relatively closely related to those of Exiguobacterium and Bacillus, which, in combination with the cross-infection assay, suggests possible cross-species infection capabilities. This study enhances the understanding of Staphylococcus warneri prophages, providing insights into phage-host interactions and potential horizontal gene transfer.}, } @article {pmid39458330, year = {2024}, author = {Dixson, JD and Vumma, L and Azad, RK}, title = {An Analysis of Combined Molecular Weight and Hydrophobicity Similarity between the Amino Acid Sequences of Spike Protein Receptor Binding Domains of Betacoronaviruses and Functionally Similar Sequences from Other Virus Families.}, journal = {Microorganisms}, volume = {12}, number = {10}, pages = {}, pmid = {39458330}, issn = {2076-2607}, abstract = {Recently, we proposed a new method, based on protein profiles derived from physicochemical dynamic time warping (PCDTW), to functionally/structurally classify coronavirus spike protein receptor binding domains (RBD). Our method, as used herein, uses waveforms derived from two physicochemical properties of amino acids (molecular weight and hydrophobicity (MWHP)) and is designed to reach into the twilight zone of homology, and therefore, has the potential to reveal structural/functional relationships and potentially homologous relationships over greater evolutionary time spans than standard primary sequence alignment-based techniques. One potential application of our method is inferring deep evolutionary relationships such as those between the RBD of the spike protein of betacoronaviruses and functionally similar proteins found in other families of viruses, a task that is extremely difficult, if not impossible, using standard multiple alignment-based techniques. Here, we applied PCDTW to compare members of four divergent families of viruses to betacoronaviruses in terms of MWHP physicochemical similarity of their RBDs. We hypothesized that some members of the families Arteriviridae, Astroviridae, Reoviridae (both from the genera rotavirus and orthoreovirus considered separately), and Toroviridae would show greater physicochemical similarity to betacoronaviruses in protein regions similar to the RBD of the betacoronavirus spike protein than they do to other members of their respective taxonomic groups. This was confirmed to varying degrees in each of our analyses. Three arteriviruses (the glycoprotein-2 sequences) clustered more closely with ACE2-binding betacoronaviruses than to other arteriviruses, and a clade of 33 toroviruses was found embedded within a clade of non-ACE2-binding betacoronaviruses, indicating potentially shared structure/function of RBDs between betacoronaviruses and members of other virus clades.}, } @article {pmid39453690, year = {2024}, author = {Toppings, N and Marshall, M and Smirnova, AV and Sheremet, A and Pasala, AS and Nwosu, FC and Hepburn, M and Lewis, I and Coleman, NV and Dunfield, PF}, title = {Ethylene and epoxyethane metabolism in methanotrophic bacteria: comparative genomics and physiological studies using Methylohalobius crimeensis.}, journal = {Microbial genomics}, volume = {10}, number = {10}, pages = {}, pmid = {39453690}, issn = {2057-5858}, mesh = {*Ethylenes/metabolism ; *Multigene Family ; *Genomics/methods ; Oxidation-Reduction ; Methane/metabolism ; Phylogeny ; Epoxy Compounds/metabolism ; Oxygenases/genetics/metabolism ; Genome, Bacterial ; Bacterial Proteins/genetics/metabolism ; Methylococcaceae/genetics/metabolism ; }, abstract = {The genome of the methanotrophic bacterium Methylohalobius crimeensis strain 10Ki contains a gene cluster that encodes a putative coenzyme-M (CoM)-dependent pathway for oxidation of epoxyethane, based on homology to genes in bacteria that grow on ethylene and propylene as sole substrates. An alkene monooxygenase was not detected in the M. crimeensis genome, so epoxyethane is likely produced from co-oxidation of ethylene by the methane monooxygenase enzyme. Similar gene clusters were detected in about 10% of available genomes from aerobic methanotrophic bacteria, primarily strains grown from rice paddies and other wetlands. The sparse occurrence of the gene cluster across distant phylogenetic groups suggests that multiple lateral gene transfer events have occurred in methanotrophs. In support of this, the gene cluster in M. crimeensis was detected within a large genomic island predicted using multiple methods. Growth studies, reverse transcription-quantitative PCR (RT-qPCR) and proteomics were performed to examine the expression of these genes in M. crimeensis. Growth and methane oxidation activity were completely inhibited by the addition of >0.5% (v/v) ethylene to the headspace of cultures, but at 0.125% and below, the inhibition was only partial, and ethylene was gradually oxidized. The etnE gene encoding epoxyalkane:CoM transferase was strongly upregulated in ethylene-exposed cells based on RT-qPCR. Proteomics analysis confirmed that EtnE and nine other proteins encoded in the same gene cluster became much more predominant after cells were exposed to ethylene. The results suggest that ethylene is strongly inhibitory to M. crimeensis, but the bacterium responds to ethylene exposure by expressing an epoxide oxidation system similar to that used by bacteria that grow on alkenes. In the obligate methanotroph M. crimeensis, this system does not facilitate growth on ethylene but likely alleviates toxicity of epoxyethane formed through ethylene co-oxidation by particulate methane monooxygenase. The presence of predicted epoxide detoxification systems in several other wetland methanotrophs suggests that co-oxidation of ambient ethylene presents a stress for methanotrophic bacteria in these environments and that epoxyethane removal has adaptive value.}, } @article {pmid39452755, year = {2024}, author = {Sabin, SJ and Beesley, CA and Marston, CK and Paisie, TK and Gulvik, CA and Sprenger, GA and Gee, JE and Traxler, RM and Bell, ME and McQuiston, JR and Weiner, ZP}, title = {Investigating Anthrax-Associated Virulence Genes among Archival and Contemporary Bacillus cereus Group Genomes.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {10}, pages = {}, pmid = {39452755}, issn = {2076-0817}, abstract = {Bacillus anthracis causes anthrax through virulence factors encoded on two plasmids. However, non-B. anthracis organisms within the closely related, environmentally ubiquitous Bacillus cereus group (BCG) may cause an anthrax-like disease in humans through the partial adoption of anthrax-associated virulence genes, challenging the definition of anthrax disease. To elucidate these phenomena and their evolutionary past, we performed whole-genome sequencing on non-anthracis BCG isolates, including 93 archival (1967-2003) and 5 contemporary isolates (2019-2023). We produced annotated genomic assemblies and performed a pan-genome analysis to identify evidence of virulence gene homology and virulence gene acquisition by linear inheritance or horizontal gene transfer. At least one anthrax-associated virulence gene was annotated in ten isolates. Most homologous sequences in archival isolates showed evidence of pseudogenization and subsequent gene loss. The presence or absence of accessory genes, including anthrax-associated virulence genes, aligned with the phylogenetic structure of the BCG core genome. These findings support the hypothesis that anthrax-associated virulence genes were inherited from a common ancestor in the BCG and were retained or lost across different lineages, and contribute to a growing body of work informing public health strategies related to anthrax surveillance and identification.}, } @article {pmid39416196, year = {2024}, author = {Heredia, AG and Grossman, AD}, title = {Regulation of the SOS response and homologous recombination by an integrative and conjugative element.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39416196}, issn = {2692-8205}, support = {R35 GM122538/GM/NIGMS NIH HHS/United States ; R35 GM148343/GM/NIGMS NIH HHS/United States ; }, abstract = {Integrative and conjugative elements (ICEs) are mobile genetic elements that transfer between bacteria and influence host physiology and promote evolution. ICEBs1 of Bacillus subtilis modulates the host DNA damage response by reducing RecA filament formation. We found that the two ICEBs1-encoded proteins, RamT and RamA that modulate the SOS response in donors also function in recipient cells to inhibit both the SOS response and homologous recombination following transfer of the element. Expression of RamT and RamA caused a decrease in binding of the host single strand binding protein SsbA to ssDNA. We found that RamA interacted with PcrA, the host DNA translocase that functions to remove RecA from DNA, likely functioning to modulate the SOS response and recombination by stimulating PcrA activity. These findings reveal how ICEBs1 can modulate key host processes, including the SOS response and homologous recombination, highlighting the complex interplay between mobile genetic elements and their bacterial hosts in adaptation and evolution.}, } @article {pmid39452226, year = {2024}, author = {Durocher, AF and Paquet, VE and St-Laurent, RE and Duchaine, C and Charette, SJ}, title = {Impact of Predation by Ciliate Tetrahymena borealis on Conjugation in Aeromonas salmonicida subsp. salmonicida.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {10}, pages = {}, pmid = {39452226}, issn = {2079-6382}, support = {539024-2019//Natural Sciences and Engineering Research Council/ ; }, abstract = {BACKGROUND/OBJECTIVES: Antibiotic resistance gene (ARG) spread is driven by horizontal gene transfer (HGT). Ciliated protozoa may contribute to this process, as their predation has been shown to facilitate HGT in certain bacteria. Here, this phenomenon was further investigated using A. salmonicida subsp. salmonicida. This fish pathogen bears an extensive and dynamic plasmidome, suggesting a high potential for HGT.

METHODS: A. salmonicida strains carrying one of three conjugative plasmids bearing ARGs (pSN254b, pRAS1b or pAsa4b) were cocultured with a recipient, either A. salmonicida, E. coli or A. hydrophila. Conjugation rates were assessed in the presence and absence of the ciliate Tetrahymena borealis. PCR genotyping confirmed the acquisition of the conjugative plasmids and was used to verify the mobilization of other plasmids.

RESULTS: The basal rate of conjugation observed was high. Under the conditions studied, ciliate predation did not appear to influence the conjugation rate, except at higher proportions of ciliates, which typically hampered conjugation. Microscopy revealed that most bacteria were digested in these conditions. PCR screening demonstrated that small mobilizable plasmids from A. salmonicida (pAsa1, pAsa2, pAsa3, and pAsal1) were acquired by the recipients along with the conjugative plasmids, with a slight effect of the ciliates in some donor/recipient cell combination.

CONCLUSIONS: These results highlight how A. salmonicida can conjugate efficiently with different species and how complex its relationship with ciliates is.}, } @article {pmid39452131, year = {2024}, author = {Xiong, Z and Zhang, W and Yin, H and Wan, J and Wu, Z and Gao, Y}, title = {Diversity and Evolution of NLR Genes in Citrus Species.}, journal = {Biology}, volume = {13}, number = {10}, pages = {}, pmid = {39452131}, issn = {2079-7737}, support = {32060615//National Natural Science Foundation of China/ ; jxsq2020102134//Double Thousand Plan of Jiangxi Province/ ; }, abstract = {NLR genes are crucial components of the effector-triggered immunity (ETI) system, responsible for recognizing pathogens and initiating immune responses. Although NLR genes in many plant species have been extensively studied, the diversity of NLR genes in citrus remains largely unknown. Our analysis revealed significant variations in the copy numbers of NLR genes among these species. Gene duplication and recombination were identified as the major driving forces behind this diversity. Additionally, horizontal gene transfer (HGT) emerged as the principal mechanism responsible for the increase in NLR gene copy number in A. buxifolia. The citrus NLR genes were classified into four categories: TIR-NBS-LRR (TNL), CC-NBS-LRR (CNL), RPW8-NBS-LRR (RNL), and NL. Our findings indicate that TNL, RNL, and CNL genes originated from NL genes through the acquisition of TIR and RPW8 domains, along with CC motifs, followed by the random loss of corresponding domains. Phylogenetic analysis suggested that citrus NLR genes originated alongside the species and underwent adaptive evolution, potentially playing crucial roles in the global colonization of citrus. This study provides important insights into the diversity of citrus NLR genes and serves as a foundational dataset for future research aimed at breeding disease-resistant citrus varieties.}, } @article {pmid39450285, year = {2024}, author = {Agudo, R and Reche, MP}, title = {Revealing antibiotic resistance's ancient roots: insights from pristine ecosystems.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1445155}, pmid = {39450285}, issn = {1664-302X}, abstract = {The prevailing belief that antibiotic resistance mechanisms emerged with human antibiotic use has been challenged. Evidence indicates that some antibiotic resistance genes (ARGs) have a long evolutionary history, predating the advent of antibiotics in human medicine, thereby demonstrating that resistance is an ancient phenomenon. Despite extensive surveys of resistance elements in environments impacted by human activity, limited data are available from remote and pristine habitats. This minireview aims to compile the most relevant research on the origins and evolution of ARGs in these habitats, which function as reservoirs for ancient resistance mechanisms. These studies indicate that ancient ARGs functionally similar to modern resistance genes, highlighting the general role of natural antimicrobial substances in fostering the evolution and exchange of diverse resistance mechanisms through horizontal gene transfer over time. This minireview underscores that antibiotic resistance was present in ancestral microbial communities and emphasizes the ecological role of antibiotics and resistance determinants. Understanding ancient ARGs is crucial for predicting and managing the evolution of antibiotic resistance. Thus, these insights provide a foundational basis for developing new antibiotics and strategies for microbial resistance management.}, } @article {pmid39448149, year = {2025}, author = {Fang, M and Yuan, Y and Fox, EM and Wu, K and Tian, X and Zhang, L and Feng, H and Li, R and Bai, L and Wang, X and Yang, Z and Zhang, R and Wang, J}, title = {Prevalence and genomic characteristics of becAB-carrying Clostridium perfringens strains.}, journal = {Food microbiology}, volume = {125}, number = {}, pages = {104640}, doi = {10.1016/j.fm.2024.104640}, pmid = {39448149}, issn = {1095-9998}, mesh = {*Clostridium perfringens/genetics/classification/isolation & purification ; *Clostridium Infections/microbiology/epidemiology/veterinary ; China/epidemiology ; Prevalence ; Humans ; *Bacterial Toxins/genetics ; Animals ; Genome, Bacterial ; Plasmids/genetics ; Genomics ; Phylogeny ; }, abstract = {Clostridium perfringens, as a foodborne pathogen, can cause various intestinal diseases in both humans and animals according to its repertoire of toxins. In recent years, a multitude of studies have highlighted its threat to infants and young children. C. perfringens carries numerous toxins, with the newly identified BEC toxin confirmed as the second toxin to cause diarrheal illness, after CPE. However, the global dissemination of C. perfringens strains carrying becAB genes, which encode BEC toxins, has not been extensively studied. Following epidemiological surveillance of the prevalence of C. perfringens from different sources in various provinces of China, we identified two becAB-carrying strains and one strain carrying a sequence similar to becAB from distinct provinces and sources. When combined with genomic analysis of other becAB-carrying C. perfringens strains from public databases, we found that becAB was present in strains from different lineages. Our analysis of the plasmid and genetic environment corroborates previous findings on becAB-carrying strains, confirming that it currently achieves horizontal transmission through one type of evolutionarily conserved Pcp plasmid. This study provides a comprehensive analysis of the prevalence and transmission patterns of the newly emerged toxin gene locus, becAB, in C. perfringens. Despite the relatively low identification rate of becAB-carrying strains, their potential impact requires ongoing surveillance and investigation of their features, particularly their antimicrobial resistance.}, } @article {pmid39446960, year = {2024}, author = {Li, L and Ge, Z and Liu, S and Zheng, K and Li, Y and Chen, K and Fu, Y and Lei, X and Cui, Z and Wang, Y and Huang, J and Liu, Y and Duan, M and Sun, Z and Chen, J and Li, L and Shen, P and Wang, G and Chen, J and Li, R and Li, C and Yang, Z and Ning, Y and Luo, A and Chen, B and Seim, I and Liu, X and Wang, F and Yao, Y and Guo, F and Yang, M and Liu, CH and Fan, G and Wang, L and Yang, D and Zhang, L}, title = {Multi-omics landscape and molecular basis of radiation tolerance in a tardigrade.}, journal = {Science (New York, N.Y.)}, volume = {386}, number = {6720}, pages = {eadl0799}, doi = {10.1126/science.adl0799}, pmid = {39446960}, issn = {1095-9203}, mesh = {Animals ; DNA Damage ; *DNA Repair ; Gene Transfer, Horizontal ; Genome ; Mitochondrial Proteins/metabolism/genetics ; Multiomics ; NAD/metabolism ; Poly (ADP-Ribose) Polymerase-1/metabolism/genetics ; Proteome ; *Radiation Tolerance/genetics ; *Tardigrada/genetics/metabolism/radiation effects ; *Transcriptome ; }, abstract = {Tardigrades are captivating organisms known for their resilience in extreme environments, including ultra-high-dose radiation, but the underlying mechanisms of this resilience remain largely unknown. Using genome, transcriptome, and proteome analysis of Hypsibius henanensis sp. nov., we explored the molecular basis contributing to radiotolerance in this organism. A putatively horizontally transferred gene, DOPA dioxygenase 1 (DODA1), responds to radiation and confers radiotolerance by synthesizing betalains-a type of plant pigment with free radical-scavenging properties. A tardigrade-specific radiation-induced disordered protein, TRID1, facilitates DNA damage repair through a mechanism involving phase separation. Two mitochondrial respiratory chain complex assembly proteins, BCS1 and NDUFB8, accumulate to accelerate nicotinamide adenine dinucleotide (NAD[+]) regeneration for poly(adenosine diphosphate-ribosyl)ation (PARylation) and subsequent poly(adenosine diphosphate-ribose) polymerase 1 (PARP1)-mediated DNA damage repair. These three observations expand our understanding of mechanisms of tardigrade radiotolerance.}, } @article {pmid39446952, year = {2024}, author = {Sheahan, ML and Flores, K and Coyne, MJ and García-Bayona, L and Chatzidaki-Livanis, M and Holst, AQ and Smith, RC and Sundararajan, A and Barquera, B and Comstock, LE}, title = {A ubiquitous mobile genetic element changes the antagonistic weaponry of a human gut symbiont.}, journal = {Science (New York, N.Y.)}, volume = {386}, number = {6720}, pages = {414-420}, doi = {10.1126/science.adj9504}, pmid = {39446952}, issn = {1095-9203}, mesh = {Humans ; *Bacteroides fragilis/genetics ; Conjugation, Genetic ; *Gastrointestinal Microbiome/genetics ; *Gene Transfer, Horizontal ; Genetic Fitness ; Genome, Bacterial ; *Interspersed Repetitive Sequences ; *Symbiosis ; *Type VI Secretion Systems/genetics ; *DNA, Bacterial/genetics ; }, abstract = {DNA transfer is ubiquitous in the human gut microbiota, especially among species of the order Bacteroidales. In silico analyses have revealed hundreds of mobile genetic elements shared between these species, yet little is known about the phenotypes they encode, their effects on fitness, or pleiotropic consequences for the recipient's genome. In this work, we show that acquisition of a ubiquitous integrative conjugative element (ICE) encoding a type VI secretion system (T6SS) shuts down the native T6SS of Bacteroides fragilis. Despite inactivating this T6SS, ICE acquisition increases the fitness of the B. fragilis transconjugant over its progenitor by arming it with the new T6SS. DNA transfer causes the strain to change allegiances so that it no longer targets ecosystem members with the same element yet is armed for communal defense.}, } @article {pmid39443865, year = {2024}, author = {Xiong, Y and Lei, X and Xiong, Y and Liu, Y and Dong, Z and Zhao, J and Yu, Q and Ma, X}, title = {Factors contributing to organelle genomes size variation and the intracellular DNA transfer in Polygonaceae.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {994}, pmid = {39443865}, issn = {1471-2164}, support = {32271753//National Natural Science Foundation of China/ ; 2022YFQ0076//Sichuan Province regional innovation cooperation project/ ; 2023YFSY0012//Cooperation project of provincial college, and provincial school/ ; }, mesh = {*Genome, Mitochondrial ; *Genome, Chloroplast ; *Polygonaceae/genetics ; *Genome Size ; *Phylogeny ; Evolution, Molecular ; Genome, Plant ; Gene Transfer, Horizontal ; }, abstract = {The use of complete organelle genomes, including chloroplast and mitochondrial genomes, is a powerful molecular method for studying biological evolution and gene transfer. However, in the case of Polygonaceae, an important family with numerous edible, medicinal, and ornamental species, the mitochondrial genomes of only three species have been sequenced and analyzed. In this study, we present the mitochondrial and chloroplast genomes of two important Tibetan medicinal plants, Bistorta viviparum and B. macrophyllum. All the organelle genomes are assembled into a single circular structure and contain a common set of 32 protein-coding genes (PCGs). Some genes such as rps2 and ndhF were found to have high nucleotide polymorphism (Pi) in the chloroplast genomes, while cox1, mttB and rps12 showed pronounced Pi values in the mitochondrial genomes. Furthermore, our analysis revealed that most chloroplast genes and mitochondrial PCGs in Polygonaceae plants are under purifying selection. However, a few genes, including the chloroplast gene psaJ and the mitochondrial genes ccmFc, atp8 and nad4, showed positive selection in certain Polygonaceae plants, as indicated by a Ka/Ks ratio greater than one. Structural variation analysis revealed a wealth of differences between the mitochondrial genomes of five Polygonaceae species, with a particularly notable large-scale inversion observed between Reynoutria japonica and Fallopia aubertii. Furthermore, an analysis of the homologous sequences in the chloroplast and mitochondrial genomes revealed that the rps7 has been transferred from the chloroplast to the mitochondrial genome in all five Polygonaceae species. Finally, ecological niche models were constructed for B. viviparum and B. macrophyllum, indicating that mean annual temperature and altitude are the main climatic factors influencing the distribution of both species. Although the current distribution of B. viviparum is significantly wider than that of B. macrophyllum, projections suggest that the optimal growth ranges of both species will expand in the future, with B. macrophyllum potentially exceeding B. viviparum. This study not only contributes to the plastid genome database for Polygonaceae plants, but also provides theoretical insights into the adaptive evolution of these plants.}, } @article {pmid39441515, year = {2024}, author = {Cardoso, EM and Dea Lindner, J and Ferreira, FA}, title = {Genomic analysis of Salmonella Heidelberg isolated from the Brazilian poultry farms.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {39441515}, issn = {1678-4405}, abstract = {The rapid expansion of broiler chicken production in Brazil has presented significant sanitation challenges within the poultry industry. Among these challenges, Salmonella enterica subsp. enterica serotype Heidelberg stands as a contributor to global salmonellosis outbreaks. This study analyzed 13 draft genomes of Salmonella Heidelberg isolated from the pre-slaughter broiler chickens farms in Brazil. By conducting in silico analysis of these genomes, the study investigated genome similarity based on single nucleotide polymorphisms (SNPs) and identified genes encoding resistance to antimicrobials, sanitizers, and virulence factors. Furthermore, mobile genetic elements (MGE) were identified to assess their potential role in propagating genes through horizontal gene transfer. A risk classification was also applied based on the resistomes. The genomes revealed a high prevalence of genes conferring resistance to aminoglycosides, fosfomycin, sulfonamides, tetracycline, and genes linked to quaternary ammonium resistance. The study also uncovered six Salmonella pathogenicity islands (SPI) and over 100 genes encoding virulence factors. The association of MGE with antibiotic-resistant genes sul2 and blaCMY-2 raised concerns about the potential transfer to other bacteria, posing a substantial risk for spreading resistance mechanisms according to established risk protocols. Additionally, SNP analysis indicated close phylogenetic relationships among some isolates, suggesting a common origin. This study enhances our understanding of Salmonella Heidelberg strains by identifying key risk factors for transmission and revealing the association between resistance genes and MGEs. This insight provides a foundation for developing and implementing effective control, monitoring, and treatment strategies in the poultry industry.}, } @article {pmid39441253, year = {2024}, author = {Varshith, MR and Ghosh Dastidar, R and Shrilaxmi, MS and Bhattacharya, R and Jha, S and Choudhary, S and Varny, E and Carvalho, RA and John, L and Sundaramoorthy, V and Smith, CM and Damerla, RR and Herai, RH and Biswas, SR and Lal, PB and Mukhopadhyay, C and Ghosh Dastidar, S}, title = {Virulome and phylogenomic profiling of a novel Burkholderia pseudomallei strain from an Indian clinical isolate.}, journal = {Molecular genetics and genomics : MGG}, volume = {299}, number = {1}, pages = {98}, pmid = {39441253}, issn = {1617-4623}, support = {102. IFD/SAN/2549/2019-20 Dated 29-10-2019//Department of Biotechnology, Ramalingaswami re-entry Fellowship/ ; }, mesh = {*Burkholderia pseudomallei/genetics/isolation & purification/pathogenicity ; Humans ; *Melioidosis/microbiology ; *Virulence Factors/genetics ; India ; *Phylogeny ; Genome, Bacterial/genetics ; Genomic Islands/genetics ; Whole Genome Sequencing/methods ; Virulence/genetics ; }, abstract = {Highly pathogenic Burkholderia pseudomallei is the causative agent of melioidosis, a neglected tropical disease endemic in Southeast Asian tropical region. This bacterium encompasses diverse virulence factors which further undergo dynamic gene-expression flux as it transits through distinct environmental niches within the host which may lead to manifestation of differential clinical symptoms. B. pseudomallei, is classified as a Tier 1 select agent in the United States and regarded as a risk group 3 organism in India with the potential to be used as bioweapon. Considering these facts, it is vital to uncover both physiological and genetic heterogeneity of B. pseudomallei, particularly to identify any novel virulence factors that may contribute to pathogenicity. B. pseudomallei strain CM000113 was isolated from a clinical case in India, characterized it for its physiological, biochemical, and prominently genetic traits through WGS. It has a type 2 morphotype with faster doubling time and high biofilm producing capacity as compared to Pseudomonas aeruginosa. The genome size is 7.3 Mbp and it is phylogenetically close to B. pseudomallei strain Mahidol 1106a and Burkholderia mallei Turkey 2. We observed genetic heterogeneity, as key virulence factors that were identified shows sequence dissimilarity with reference strains. Additionally, presence of genomic islands, harbouring two virulence factors, GmhA and GmhB2, associated with pathogenesis indicates possibility of horizontal gene transfer. These results emphasize the need for an extensive study focusing the genome of B. pseudomallei and its associated heterogeneity, to identify molecular biomarkers aiding to develop point-of-care diagnostic kits for early diagnosis of melioidosis.}, } @article {pmid39441081, year = {2024}, author = {Li, Y and Feng, X and Chen, X and Yang, S and Zhao, Z and Chen, Y and Li, SC}, title = {PlasmidScope: a comprehensive plasmid database with rich annotations and online analytical tools.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkae930}, pmid = {39441081}, issn = {1362-4962}, support = {32061160472//NSFC-RGC Joint Research Scheme/ ; 32300527//National Natural Science Foundation of China/ ; 2022A1515110784//Guangdong Basic and Applied Basic Research Foundation/ ; 20220814183301001//Shenzhen Science and Technology Program/ ; }, abstract = {Plasmids are extrachromosomal genetic molecules that replicate independent of chromosomes in bacteria, archaea, and eukaryotic organisms. They contain diverse functional elements and are capable of horizontal gene transfer among hosts. While existing plasmid databases have archived plasmid sequences isolated from individual microorganisms or natural environments, there is a need for a comprehensive, standardized, and annotated plasmid database to address the vast accumulation of plasmid sequences. Here, we propose PlasmidScope (https://plasmid.deepomics.org/), a plasmid database offering comprehensive annotations, automated online analysis, and interactive visualization. PlasmidScope harbors a substantial collection of 852 600 plasmids curated from 10 repositories. Along with consolidated background information, PlasmidScope utilizes 12 state-of-the-art tools and provides comprehensive annotations for the curated plasmids, covering genome completeness, topological structure, mobility, host source, tRNA, tmRNA, signal peptides, transmembrane proteins and CRISPR/Cas systems. PlasmidScope offers diverse functional annotations for its 25 231 059 predicted genes from 9 databases as well as corresponding protein structures predicted by ESMFold. In addition, PlasmidScope integrates online analytical modules and interactive visualization, empowering researchers to delve into the complexities of plasmids.}, } @article {pmid39437930, year = {2024}, author = {Da, YM and Yang, XR and Li, MJ and Li, SS and Gao, ZP and Zhang, Y and Su, JQ and Zhou, GW}, title = {Promotion of antibiotic-resistant genes dissemination by the micro/nanoplastics in the gut of snail Achatina fulica.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {176829}, doi = {10.1016/j.scitotenv.2024.176829}, pmid = {39437930}, issn = {1879-1026}, abstract = {Terrestrial animal intestines are hotspots for the enrichment of micro/nano plastics (M/NPs) and antibiotic-resistant genes (ARGs). However, little is known about the further impact of M/NPs on the spread of ARGs in animal guts. This study investigates the role of M/NPs (polystyrene) with varying particle sizes (0.082, 42, and 182 μm), concentrations (10 and 100 mg/L), and exposure durations (4 and 16 days) in the ARGs dissemination via conjugation in the edible snail (Achatina fulica) gut. Combination of qPCR with 16S rRNA-based sequencing, we found that PS exposure caused intestinal cell impairment and shifts in the gut microbial community of snails. Conjugation rate increased with PS particle sizes in the snail gut. After 4 days of exposure, significantly higher conjugation rates were observed in the gut exposed to 100 mg/L PS compared to 10 mg/L, however, this trend reversed after 16 days. Consistently, the abundances of conjugation relevant genes trfA and trbB shared similar trends to the conjugation ratios in the snail gut after PS exposure. Transconjugant diversity was much lower in 10 mg/L PS groups than in 100 mg/L PS treatments. Therefore, this study suggests that the presence of M/NPs would complicate management of ARG spread. The selection pressure exerted by M/NPs may sustain or even amplify the spread of ARGs in the gut of terrestrial animals even in the absence of antibiotics. It highlights the necessity of avoiding M/NPs intake as a part of comprehensive strategy for cubing ARG dissemination in the gut of animals.}, } @article {pmid39437688, year = {2024}, author = {Zhang, B and Hu, X and Zhao, D and Wang, Y and Qu, J and Tao, Y and Kang, Z and Yu, H and Zhang, J and Zhang, Y}, title = {Harnessing microbial biofilms in soil ecosystems: Enhancing nutrient cycling, stress resilience, and sustainable agriculture.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122973}, doi = {10.1016/j.jenvman.2024.122973}, pmid = {39437688}, issn = {1095-8630}, abstract = {Soil ecosystems are complex networks of microorganisms that play pivotal roles in nutrient cycling, stress resilience, and the provision of ecosystem services. Among these microbial communities, soil biofilms, and complex aggregations of microorganisms embedded within extracellular polymeric substances (EPS) exert significant influence on soil health and function. This review delves into the dynamics of soil biofilms, highlighting their structural intricacies and the mechanisms by which they facilitate nutrient cycling, and discusses how biofilms enhance the degradation of pollutants through the action of extracellular enzymes and horizontal gene transfer, contributing to soil detoxification and fertility. Furthermore, the role of soil biofilms in stress resilience is underscored, as they form symbiotic relationships with plants, bolstering their growth and resistance to environmental stressors. The review also explores the ecological functions of biofilms in enhancing soil structure stability by promoting aggregate formation, which is crucial for water retention and aeration. By integrating these insights, we aim to provide a comprehensive understanding of the multifaceted benefits of biofilms in soil ecosystems. This knowledge is essential for developing strategies to manipulate soil biofilms to improve agricultural productivity and ecological sustainability. This review also identifies research gaps and emphasizes the need for practical applications of biofilms in sustainable agriculture.}, } @article {pmid39436807, year = {2024}, author = {Koleva, DT and Bengochea, AW and Mellor, SB and Ochoa-Fernandez, R and Nelson, DR and Møller, BL and Gillam, EMJ and Sørensen, M}, title = {Sequence diversity in the monooxygenases involved in oxime production in plant defense and signaling: a conservative revision in the nomenclature of the highly complex CYP79 family.}, journal = {The Plant journal : for cell and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/tpj.17044}, pmid = {39436807}, issn = {1365-313X}, support = {//Villum Fonden/ ; CF19-0301//Carlsbergfondet/ ; CF20-0352//Carlsbergfondet/ ; NNF21OC0071074//Novo Nordisk Fonden/ ; }, abstract = {Cytochrome P450 monooxygenases of the CYP79 family catalyze conversion of specific amino acids into oximes feeding into a variety of metabolic plant pathways. Here we present an extensive phylogenetic tree of the CYP79 family built on carefully curated sequences collected across the entire plant kingdom. Based on a monophyletic origin of the P450s, a set of evolutionarily distinct branches was identified. Founded on the functionally characterized CYP79 sequences, sequence features of the individual substrate recognition sites (SRSs) were analyzed. Co-evolving amino acid residues were identified using co-evolutionary sequence analysis. SRS4 possesses a specific sequence pattern when tyrosine is a substrate. Except for the CYP79Cs and CYP79Fs, substrate preferences toward specific amino acids could not be assigned to specific subfamilies. The highly diversified CYP79 tree, reflecting recurrent independent evolution of CYP79s, may relate to the different roles of oximes in different plant species. The sequence differences across individual CYP79 subfamilies may facilitate the in vivo orchestration of channeled metabolic pathways based on altered surface charge domains of the CYP79 protein. Alternatively, they may serve to optimize dynamic interactions with oxime metabolizing enzymes to enable optimal ecological interactions. The outlined detailed curation of the CYP79 sequences used for building the phylogenetic tree made it appropriate to make a conservative phylogenetic tree-based revision of the naming of the sequences within this highly complex cytochrome P450 family. The same approach may be used in other complex P450 subfamilies. The detailed phylogeny of the CYP79 family will enable further exploration of the evolution of function in these enzymes.}, } @article {pmid39433770, year = {2024}, author = {Yoon, EJ and Choi, YJ and Won, D and Choi, JR and Jeong, SH}, title = {Klebsiella pneumoniae, a human-dog shuttle organism for the genes of CTX-M ESBL.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {24725}, pmid = {39433770}, issn = {2045-2322}, support = {2019ER540402//Korea Disease Control and Prevention Agency/ ; }, mesh = {*Klebsiella pneumoniae/genetics/drug effects/isolation & purification ; *beta-Lactamases/genetics ; Humans ; Animals ; Dogs ; *Plasmids/genetics ; *Escherichia coli/genetics/drug effects ; *Klebsiella Infections/microbiology ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Genome, Bacterial ; Escherichia coli Infections/microbiology/veterinary ; }, abstract = {Antimicrobials reserved for human medicines are permitted for companion animals and it is important to understand multidrug-resistant pathogens recovered from companion animals in terms of epidemiological correlation with human pathogens and possibility of transmission to human-beings. Seventeen of each CTX-M-type extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) and Klebsiella pneumoniae (ESBL-KP) canine isolates were assessed. Entire genomes of the 34 isolates were sequenced. Plasmid transfer and relative growth rates were assessed at differed temperature conditions indicating the body temperature of dogs, that of human-beings, and environment. ESBL-ECs were clonally diverse, while ESBL-KPs were not. The ESBL-ECs carried the blaCTX-M-15 gene in plasmids and the blaCTX-M-14-like gene either in chromosomes or in plasmids. The ESBL-KPs possessed the blaCTX-M-15 gene in plasmids (n = 15). One of the isolates carried another blaCTX-M-15 gene in a chromosome simultaneously and the other isolate had an additional blaCTX-M-9 gene-harbouring plasmid, together. Two ESBL-KP isolates carried the blaCTX-M-14 gene in plasmids. Plasmid transfer ESBL-EC to K. pneumoniae was efficient and the differed biological costs by temperature was much more in ESBL-EC than in ESBL-KP. Intersectoral dissemination of ESBL-ECs occurred mainly by horizontal gene transfer, while that of ESBL-KPs occurred by clonal dissemination.}, } @article {pmid39321940, year = {2024}, author = {Wang, P and Li, L and Zhang, Y and Ren, D and Feng, Y and Li, X and Wu, D and Xie, B and Ma, J}, title = {Triclosan facilitates the dissemination of antibiotic resistance genes during anaerobic digestion: Focusing on horizontal transfer and microbial response.}, journal = {Bioresource technology}, volume = {413}, number = {}, pages = {131522}, doi = {10.1016/j.biortech.2024.131522}, pmid = {39321940}, issn = {1873-2976}, mesh = {*Triclosan/pharmacology ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Bioreactors ; }, abstract = {The present study aims to investigate the mechanism by which triclosan influences the dissemination of antibiotic resistance genes (ARGs) during the whole anaerobic digestion process. qPCR and metagenomic analyses revealed that triclosan facilitated ARGs dissemination in a dose- and time-dependent manner. Furthermore, integrons exhibited a significant correlation with the majority of quantified ARGs, and various ARGs were frequently linked on integron gene cassettes. Microbial community and redundancy analyses indicated that triclosan altered the components of dominant ARGs hosts Firmicutes, Synergistetes and Bacteroidetes. Path modeling analysis confirmed integrons were the main driving force for facilitating ARGs dissemination. The promoted ARGs dissemination may be associated with the increased reactive oxygen species generation, cell membrane permeability, close-connected the ARGs transfer related regulatory proteins induced by triclosan. This study broadens the understanding of triclosan facilitates ARGs dissemination through anaerobic treatment, the strategies for preventing potential risks should be proposed in practice.}, } @article {pmid39431893, year = {2024}, author = {Kim, DH and Seo, H and Jung, S and Kim, B-J}, title = {Global prevalence of Mycobacterium massiliense strains with recombinant rpoB genes (Rec-Mas) horizontally transferred from Mycobacterium abscessus: two major types, dominant circulating clone 7 and MLST ST46 sequence type.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0193524}, doi = {10.1128/spectrum.01935-24}, pmid = {39431893}, issn = {2165-0497}, abstract = {UNLABELLED: Mycobacterium abscessus is a group of emerging antimicrobial-resistant nontuberculous mycobacteria that causes severe lung disease in infected patients globally. Recently, molecular epidemiology studies have indicated that horizontal gene transfer (HGT) events in the rpoB gene are prevalent between M. abscessus subspecies. To determine the global prevalence of M. abscessus strains subjected to rpoB HGT, we performed phylogenetic inference using a 711-bp rpoB sequence extracted from 1,786 M. abscessus isolates for which the whole-genome sequence was publicly available. Our data showed that a total of 74 isolates (4.1%) from 1,786 strains are subject to rpoB HGT, which is more prevalent than strains with hsp65 HGT (19 isolates from 1,786, 1.1%). Most of these (69 isolates) belong to two major groups of Mycobacterium massiliense, of which the rpoB gene is horizontally transferred from M. abscessus (Rec-mas), dominant circulating clone 7 (DCC7) (44 isolates) and ST46 type by multilocus sequence typing (25 isolates). The Rec-mas strains of the two groups have distinct geographical patient distributions, of which the former is mainly distributed in the United States, while the latter is prevalent in Asia. Our further genome-based analysis indicated that the ST46 type is a novel DCC candidate of M. massiliense that is responsible for dissemination between noncystic fibrosis patients in Asia. In conclusion, our global phylogenetic analysis revealed two major Rec-mas clones with distinct geographical distributions, namely, DCC7 and ST46. This study provides insights into the genetic clustering and person-to-person transmission of globally dominant and area-specific strains harboring the HGT rpoB gene.

IMPORTANCE: Horizontal gene transfer (HGT) events play a pivotal role in the evolution of Mycobacterium abscessus into dominant circulating clones (DCCs), which is capable of causing patient-to-patient transmission. In particular, HGT of the rpoB gene between strains of different subspecies of M. abscessus could also compromise differentiation between strains of M. abscessus. Here, for the first time, using 1,786 M. abscessus genome sequences, we evaluated the global prevalence of M. abscessus strains subjected to rpoB HGT. We found a greater prevalence of M. abscessus subjected to rpoB HGT than to those subjected to hsp65 HGT, which is mainly due to two Rec-mas clones, dominant circulating clone 7 and ST46, which are responsible for dissemination between non-CF patients in Asia. Our data highlight the importance of rpoB HGT in the evolution of M. abscessus, particularly Mycobacterium massiliense, into virulent DCC clones.}, } @article {pmid39431819, year = {2024}, author = {Qian, Y and Lai, L and Cheng, M and Fang, H and Fan, D and Zylstra, GJ and Huang, X}, title = {Identification, characterization, and distribution of novel amidase gene aphA in sphingomonads conferring resistance to amphenicol antibiotics.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0151224}, doi = {10.1128/aem.01512-24}, pmid = {39431819}, issn = {1098-5336}, abstract = {Amphenicol antibiotics, such as chloramphenicol (CHL), thiamphenicol (TAP), and florfenicol (Ff), are high-risk emerging pollutants. Their extensive usage in aquaculture, livestock, and poultry farming has led to an increase in bacterial antibiotic resistance and facilitated the spread of resistance genes. Yet, limited research has been conducted on the co-resistance of CHL, TAP, and Ff. Herein, a novel amidase AphA was identified from a pure cultured strain that can concurrently mediate the hydrolytic inactivation of CHL, TAP, and Ff, yielding products p-nitrophenylserinol, thiamphenicol amine (TAP-amine), and florfenicol amine (Ff-amine), respectively. The antibacterial activity of these antibiotic hydrolysates exhibited a significant reduction or complete loss in comparison to the parent compounds. Notably, AphA shared less than 26% amino acid sequence identity with previously reported enzymes and exhibited high conservation within the sphingomonad species. Through enzymatic kinetic analysis, the AphA exhibited markedly superior affinity and catalytic activity toward Ff in comparison to CHL and TAP. Site-directed mutagenesis analysis revealed the indispensability of catalytic triad residues, particularly serine 153 and histidine 277, in forming crucial hydrogen bonds essential for AphA's hydrolytic activity. Comparative genomic analysis showed that aphA genes in some species are closely adjacent to various transposable elements, indicating that there is a high potential risk of horizontal gene transfer (HGT). This study established a hydrolysis resistance mechanism of amphenicol antibiotics in sphingomonads, which offers theoretical guidance and a novel marker gene for assessing the prevalent risk of amphenicol antibiotics in the environment.IMPORTANCEAmphenicol antibiotics are pervasive emerging contaminants that present a substantial threat to ecological systems. Few studies have elucidated resistance genes or mechanisms that can act on CHL, TAP, and Ff simultaneously. The results of this study fill this knowledge gap and identify a novel amidase AphA from the bacterium Sphingobium yanoikuyae B1, which mediates three typical amphenicol antibiotic inactivation, and the molecular mechanism is elucidated. The diverse types of transposable elements were identified in the flanking regions of the aphA gene, indicating the risk of horizontal transfer of this antibiotic resistance genes (ARG). These findings offer new insights into the bacterial resistance to amphenicol antibiotics. The gene reported herein can be utilized as a novel genetic diagnostic marker for monitoring the environmental fate of amphenicol antibiotics, thereby enriching risk assessment efforts within the context of antibiotic resistance.}, } @article {pmid39430728, year = {2025}, author = {Zhang, Y and Xue, B and Mao, Y and Chen, X and Yan, W and Wang, Y and Wang, Y and Liu, L and Yu, J and Zhang, X and Chao, S and Topp, E and Zheng, W and Zhang, T}, title = {High-throughput single-cell sequencing of activated sludge microbiome.}, journal = {Environmental science and ecotechnology}, volume = {23}, number = {}, pages = {100493}, pmid = {39430728}, issn = {2666-4984}, abstract = {Wastewater treatment plants (WWTPs) represent one of biotechnology's largest and most critical applications, playing a pivotal role in environmental protection and public health. In WWTPs, activated sludge (AS) plays a major role in removing contaminants and pathogens from wastewater. While metagenomics has advanced our understanding of microbial communities, it still faces challenges in revealing the genomic heterogeneity of cells, uncovering the microbial dark matter, and establishing precise links between genetic elements and their host cells as a bulk method. These issues could be largely resolved by single-cell sequencing, which can offer unprecedented resolution to show the unique genetic information. Here we show the high-throughput single-cell sequencing to the AS microbiome. The single-amplified genomes (SAGs) of 15,110 individual cells were clustered into 2,454 SAG bins. We find that 27.5% of the genomes in the AS microbial community represent potential novel species, highlighting the presence of microbial dark matter. Furthermore, we identified 1,137 antibiotic resistance genes (ARGs), 10,450 plasmid fragments, and 1,343 phage contigs, with shared plasmid and phage groups broadly distributed among hosts, indicating a high frequency of horizontal gene transfer (HGT) within the AS microbiome. Complementary analysis using 1,529 metagenome-assembled genomes from the AS samples allowed for the taxonomic classification of 98 SAG bins, which were previously unclassified. Our study establishes the feasibility of single-cell sequencing in characterizing the AS microbiome, providing novel insights into its ecological dynamics, and deepening our understanding of HGT processes, particularly those involving ARGs. Additionally, this valuable tool could monitor the distribution, spread, and pathogenic hosts of ARGs both within AS environments and between AS and other environments, which will ultimately contribute to developing a health risk evaluation system for diverse environments within a One Health framework.}, } @article {pmid39427888, year = {2024}, author = {Wang, S and Li, W and Xi, B and Cao, L and Huang, C}, title = {Mechanisms and influencing factors of horizontal gene transfer in composting system: A review.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {177017}, doi = {10.1016/j.scitotenv.2024.177017}, pmid = {39427888}, issn = {1879-1026}, abstract = {Organic solid wastes such as livestock manure and sewage sludge are important sources and repository of antibiotic resistance genes (ARGs). Composting, a solid waste treatment technology, has demonstrated efficacy in degrading various antibiotics and reducing ARGs. However, some recalcitrant ARGs (e.g., sul1, sul2) will enrich during the composting maturation period. These ARGs persist in compost products and spread through horizontal gene transfer (HGT). We analyzed the reasons behind the increase of ARGs during the maturation phase. It was found that the proliferation of ARG-host bacteria and HGT process play an important role. This article revealed that microbial physiological responses, environment factors, pollutants, and quorum sensing (QS) can all influence the HGT process in composting systems. We examined the influence of these factors on HGT in the compost system and summarized potential mechanism by analyzing the alterations in microbial communities. We comprehensively summarized the HGT hazards that these factors may present in composting systems. Finally, we summarized methods to inhibit HGT in compost, such as using additives, quorum sensing inhibitors (QSIs), microbial inoculation, and predicting HGT events. Overall, the HGT mechanism and driving force in complex composting systems are still insufficiently studied. In view of the current situation, using predictions to assess the risk of HGT in composting may be advisable.}, } @article {pmid39426452, year = {2024}, author = {Jaffer, YD and Monikh, FA and Klümper, U and Grossart, HP}, title = {Tire Wear Particles Enhance Horizontal Gene Transfer of Antibiotic Resistance Genes in Aquatic Ecosystems.}, journal = {Environmental research}, volume = {}, number = {}, pages = {120187}, doi = {10.1016/j.envres.2024.120187}, pmid = {39426452}, issn = {1096-0953}, abstract = {Microplastics (MPs) have introduced new surfaces for biofilm development and gene exchange among bacteria. We investigated Tire Wear Particles (TWPs) for their involvement in horizontal gene transfer (HGT), particularly in relation to associated metals in the matrices of TWPs. We employed red-fluorescently tagged E. coli strain as a donor with green-fluorescently tagged, broad-host-range plasmid pKJK5, resistant to trimethoprim. As a recipient, we utilized Pseudomonas sp. and a natural lake microbial community. HGT activity on TWPs was determined and compared with that on polystyrene (PS) (with and without metals), and chitosan, which was used as a natural surface. Exposure to TWPs significantly enhanced HGT frequency of antibiotic resistance gene (ARG) from donor to recipient compared to PS and chitosan, and metals of TWPs further promoted HGT. HGT frequency on TWPs with Pseudomonas sp. was found to be 10[-3] at 30 °C. in the lake community, it was similarly high already at 25 °C suggesting a higher permissiveness of the natural microbial community towards ARG at lower temperatures. This study sheds light on the potential impact of TWPs in promoting HGT, forming the basis for health risk assessments of TWPs and more generally of microplastic pollution in various aquatic ecosystems.}, } @article {pmid39417646, year = {2024}, author = {Wang, Q and Geng, L and Gao, Z and Sun, Y and Li, X and Sun, S and Luo, Y}, title = {Microalgae Enhances the Adaptability of Epiphytic Bacteria to Sulfamethoxazole Stress and Proliferation of Antibiotic Resistance Genes Mediated by Integron.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c04925}, pmid = {39417646}, issn = {1520-5851}, abstract = {The transmission of ARGs in the microalgae-associated epiphytic bacteria remains unclear under antibiotic exposure, apart from altering the microbial community structure. In this study, Chlorella vulgaris cocultured with bacteria screened from surface water was examined to explore the spread of ARGs in the presence of sulfamethoxazole (SMX). The extracellular polymers released by Chlorella vulgaris could reduce antibiotic-induced collateral damage to bacteria, thus increasing the diversity of the microalgae-associated epiphytic bacteria. The abundances of sul1 and intI1 in the phycosphere at 1 mg/L SMX dose increased by 290 and 28 times, respectively. Metagenomic sequencing further confirmed that SMX bioaccumulation stimulated the horizontal transfer of sul1 mediated by intI1 in the microalgae-associated epiphytic bacteria, while reactive oxygen species (ROS)-mediated oxidative stress induced the SOS response and thus enhanced the transformation of sul1 in the J group. This is the first study to verify that microalgae protect bacteria from antibiotic damage and hinder the spread of ARGs mediated by SOS response, while the transfer of ARGs mediated by integron is promoted due to the bioaccumulation of SMX in the phycosphere. The results contribute to present comprehensive understanding of the risk of ARG proliferation by the presence of emerging contaminants residues in river.}, } @article {pmid39417302, year = {2024}, author = {Li, J and Fang, W and Li, C and Cui, M and Qian, L and Jiang, Z and Jiang, Y and Shi, L and Xie, X and Guo, H and Li, P and Dong, Y and Xiu, W and Wang, Y and Wang, Y}, title = {Dissimilatory Iodate-Reducing Microorganisms Contribute to the Enrichment of Iodine in Groundwater.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c04455}, pmid = {39417302}, issn = {1520-5851}, abstract = {Iodate reduction by dissimilatory iodate-reducing microorganisms (DIRMs) plays a crucial role in the biogeochemical cycling of iodine on Earth. However, the occurrence and distribution of DIRMs in iodine-rich groundwater remain unclear. In this study, we isolated the dissimilatory iodate-reducing bacteriumAzonexus hydrophilusstrain NCP973 from a geogenic high-iodine groundwater of China for the first time. The analysis of genome, transcriptome, and heterologous expression revealed that strain NCP973 uses the dissimilatory iodate-reducing enzyme IdrABP1P2 to reduce dissolved or in situ sediment-bound iodate to iodide. The location of IdrABP1P2 in the conjugative plasmid of strain NCP973 implies that IdrABP1P2 could be spread by horizontal gene transfer and allow the recipient microorganisms to participate in the enrichment of iodide in aquifers. Based on the global iodine-rich groundwater metagenomes and genomes, the identification of idrA showed that phylogenetically diverse DIRMs are widely distributed not only in geogenic high-iodine groundwater of China but also in radionuclide-contaminated groundwater of USA as well as in subsurface cavern waters in Germany and Italy. Moreover, the abundance of idrA was found to be higher in groundwater with a relatively high iodine content. Collectively, these results suggest that terrestrial iodine-affected groundwater systems are another important habitat for DIRMs in addition to marine environments, and their activity in aquifers triggers the mobilization and enrichment of iodine in groundwater worldwide.}, } @article {pmid39416164, year = {2024}, author = {McKeithen-Mead, S and Anderson, ME and García-Heredia, A and Grossman, AD}, title = {Activation and modulation of the host response to DNA damage by an integrative and conjugative element.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.10.09.617469}, pmid = {39416164}, issn = {2692-8205}, abstract = {Mobile genetic elements help drive horizontal gene transfer and bacterial evolution. Conjugative elements and temperate bacteriophages can be stably maintained in host cells. They can alter host physiology and regulatory responses and typically carry genes that are beneficial to their hosts. We found that ICE Bs1 , an integrative and conjugative element of Bacillus subtilis , inhibits the host response to DNA damage (the SOS response). Activation of ICE Bs1 before DNA damage reduced host cell lysis that was caused by SOS-mediated activation of two resident prophages. Further, activation of ICE Bs1 itself activated the SOS response in a subpopulation of cells, and this activation was attenuated by the functions of the ICE Bs1 genes ydcT and yddA (now ramT and ramA , for RecA modulator). Double mutant analyses indicated that RamA functions to inhibit and RamT functions to both inhibit and activate the SOS response. Both RamT and RamA caused a reduction in RecA filaments, one of the early steps in activation of the SOS response. We suspect that there are several different mechanisms by which mobile genetic elements that generate ssDNA during their lifecycle inhibit the host SOS response and RecA function, as RamT and RamA differ from the known SOS inhibitors encoded by conjugative elements.}, } @article {pmid39415115, year = {2024}, author = {Bao, D and Chen, L and Shen, W and Xu, X and Zhu, L and Wang, Y and Wu, Y and He, X and Zhu, F and Li, H}, title = {Genomic epidemiology of ceftriaxone-resistant non-typhoidal Salmonella enterica strain in China.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {974}, pmid = {39415115}, issn = {1471-2164}, support = {LQ24H200003//Zhejiang Provincial Natural Science Foundation of China/ ; 2023KY414//Zhejiang Provincial Medical and Health Science and Technology Plan/ ; 2024KY1441//Zhejiang Provincial Medical and Health Science and Technology Plan/ ; }, mesh = {*Ceftriaxone/pharmacology ; China/epidemiology ; *Salmonella enterica/genetics/drug effects ; Humans ; *Salmonella Infections/microbiology/epidemiology/drug therapy ; *Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; *Phylogeny ; Drug Resistance, Multiple, Bacterial/genetics ; Multilocus Sequence Typing ; Microbial Sensitivity Tests ; Molecular Epidemiology ; }, abstract = {Non-typhoidal Salmonella (NTS) is one of the top causes of diarrhea worldwide. Ceftriaxone is commonly recommended as the initial treatment option for Salmonella infections due to its antibacterial effectiveness. The objective of this study was to investigate the molecular epidemiological characteristics of NTS and to compare the phenotypic and genotypic profiles of antimicrobial resistance in multidrug-resistant Salmonella strains by sequencing 329 NTS strains collected from a county-level hospital between 2018 and 2021. Multi-locus sequence typing (MLST), antimicrobial resistance genes and plasmid types were identified by BacWGSTdb 2.0 webserver. Phylogenetic analysis of all NTS strains was carried out using Snippy and Gubbins software. The transferability of ceftriaxone resistant plasmids was confirmed through plasmid conjugation assays, and verified by S1-PFGE-Southern blot assays. The predominant serotypes among all NTS strains were Typhimurium (161/329), Enteritidis (49/329) and London (45/329). The most common sequence type observed was ST34 (86/329), followed by ST19 (72/329) and ST11 (47/329). The antimicrobial resistance of Salmonella to a wide range of antimicrobials showed an overall increase. Out of these 37 (11.24%) ceftriaxone-resistant strains, with the majority of them (33/37) being blaCTX-M. The predominant plasmid types identified were IncHI2 (14/21) and IncI1 (6/21), ranging in size from 70 kb to 360 kb. The conjugation efficiency was calculated with the high conjugation efficiency of 1.1 × 10[- 5] to 9.3 × 10[- 2]. The strains varied widely, ranging from 3 to 45,024 single nucleotide polymorphisms (SNPs). There are close linkages observed among the predominant lineage, with an average of 78 SNPs between each pair of ST34 strains. The findings contribute to our understanding of the transmission and resistance mechanisms of multidrug-resistant Salmonella, thereby facilitating the development of effective control strategies.}, } @article {pmid39248569, year = {2024}, author = {Hassan, J and Hinenoya, A and Hatanaka, N and Awasthi, SP and Manjunath, GB and Rahman, N and Yamate, J and Nakamura, S and Motooka, D and Nagita, A and Faruque, SM and Yamasaki, S}, title = {A plasmid-mediated type III secretion system associated with invasiveness and diarrheagenicity of Providencia rustigianii.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0229724}, pmid = {39248569}, issn = {2150-7511}, support = {20K07483//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {*Providencia/genetics/metabolism/pathogenicity ; *Plasmids/genetics ; Humans ; *Type III Secretion Systems/genetics/metabolism ; Animals ; HeLa Cells ; *Bacterial Toxins/genetics/metabolism ; *Enterobacteriaceae Infections/microbiology ; Rabbits ; Diarrhea/microbiology ; Genome, Bacterial ; Whole Genome Sequencing ; Virulence Factors/genetics ; Virulence/genetics ; Conjugation, Genetic ; Gene Transfer, Horizontal ; }, abstract = {We have recently described a clinical isolate of Providencia rustigianii strain JH-1 carrying the genes for cytolethal distending toxin (CDT) in a conjugative plasmid. A cdtB mutant of strain JH-1, which lost CDT activity, was still found to retain invasiveness and diarrheagenicity. The strain was subjected to phenotypic and genetic analyses including whole genome sequencing (WGS) to explore the genetic determinants of the observed invasiveness and diarrheagenic properties. Analysis and annotation of WGS data revealed the presence of two distinct type III secretion systems (T3SS) in strain JH-1, one of which was located on the chromosome designated as cT3SS (3,992,833 bp) and the other on a mega-plasmid designated as pT3SS (168,819 bp). Comparative genomic analysis revealed that cT3SS is generally conserved in Providencia spp. but pT3SS was limited to a subset of Providencia spp., carrying cdt genes. Strain JH-1 was found to invade HeLa cells and induce fluid accumulation with characteristic pathological lesions in rabbit ileal loops. Remarkably, these phenomena were associated with the pT3SS but not cT3SS. The plasmid could be transferred by conjugation from strain JH-1 to other strains of P. rustigianii, Providencia rettgeri, and Escherichia coli with concomitant transfer of these virulence properties. This is the first report of a functional and mobile T3SS in P. rustigianii and its association with invasiveness and diarrheagenicity of this bacterium. These data suggest that P. rustigianii and other CDT-producing Providencia strains might carry T3SS and exert their diarrheagenic effect by exploiting the T3SS nano-machinery.IMPORTANCEThe precise mechanism of virulence of Providencia rustigianii is unclear, although some strains produce cytolethal distending toxin as a putative virulence factor. We have detected the presence of a type III secretion system (T3SS) for the first time on a plasmid in a P. rustigianii strain. Plasmid-mediated T3SS seems to be directly involved in virulence of P. rustigianii and may serve as a means of horizontal transfer of T3SS genes. Our results may have implication in understanding the mechanism of emergence of new pathogenic strains of P. rustigianii.}, } @article {pmid39414627, year = {2024}, author = {Aggarwal, T and Kondabagil, K}, title = {Proteome-scale structural prediction of the giant Marseillevirus reveals conserved folds and putative homologs of the hypothetical proteins.}, journal = {Archives of virology}, volume = {169}, number = {11}, pages = {222}, pmid = {39414627}, issn = {1432-8798}, support = {CRG/2023/00131//Science and Engineering Research Board/ ; 58/14/11/2020-BRNS/37188//Board of Research in Nuclear Sciences/ ; BT/PR35928/BRB/10/1979/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {*Proteome ; *Viral Proteins/genetics/chemistry ; *Genome, Viral/genetics ; Protein Folding ; Amino Acid Sequence ; Computational Biology/methods ; Giant Viruses/genetics/classification/chemistry ; Protein Conformation ; }, abstract = {A significant proportion of the highly divergent and novel proteins of giant viruses are termed "hypothetical" due to the absence of detectable homologous sequences in the existing databases. The quality of genome and proteome annotations often relies on the identification of signature sequences and motifs in order to assign putative functions to the gene products. These annotations serve as the first set of information for researchers to develop workable hypotheses for further experimental research. The structure-function relationship of proteins suggests that proteins with similar functions may also exhibit similar folding patterns. Here, we report the first proteome-wide structure prediction of the giant Marseillevirus. We use AlphaFold-predicted structures and their comparative analysis with the experimental structures in the PDB database to preliminarily annotate the viral proteins. Our work highlights the conservation of structural folds in proteins with highly divergent sequences and reveals potentially paralogous relationships among them. We also provide evidence for gene duplication and fusion as contributing factors to giant viral genome expansion and evolution. With the easily accessible AlphaFold and other advanced bioinformatics tools for high-confidence de novo structure prediction, we propose a combined sequence and predicted-structure-based proteome annotation approach for the initial characterization of novel and complex organisms or viruses.}, } @article {pmid39414103, year = {2024}, author = {Zhao, W and Ye, C and Li, J and Yu, X}, title = {Increased Risk of Antibiotic Resistance in Surface Water Due to Global Warming.}, journal = {Environmental research}, volume = {}, number = {}, pages = {120149}, doi = {10.1016/j.envres.2024.120149}, pmid = {39414103}, issn = {1096-0953}, abstract = {As the pace of global warming accelerates, so do the threats to human health, urgent priority among them being antibiotic-resistant infections. In the context of global warming, this review summarises the direct and indirect effects of rising surface water temperatures on the development of bacterial antibiotic resistance. First, the resistance of typical pathogens such as E. coli increased with average temperature. This is not only related to increased bacterial growth rate and horizontal gene transfer frequency at high temperatures but also heat shock responses and cumulative effects. Secondly, the acceleration of bacterial growth indirectly promotes antibiotic residues in surface water, which is conducive to the growth and spread of resistant bacteria. Furthermore, the cascading effects of global warming, including the release of nutrients into the water and the resulting increase of bacteria and algae, indirectly promote the improvement of resistance. Water treatment processes exposed to high temperatures also increase the risk of resistance in surface water. The fitness costs of antibiotic resistance under these dynamic conditions are also discussed, concluding the relationship between various factors and resistance persistence. It was expected to provide a comprehensive basis for mitigating antibiotic resistance in the face of global warming.}, } @article {pmid39412865, year = {2024}, author = {Bartlett, KV and Luo, TL and Ong, AC and Maybank, RA and Stribling, W and Thompson, B and Powell, A and Kwak, YI and Bennett, JW and Lebreton, F and Mc Gann, PT}, title = {Tn4661-mediated transfer of bla CTX-M-15 from Klebsiella michiganensis to an outbreak clone of Pseudomonas aeruginosa.}, journal = {Microbial genomics}, volume = {10}, number = {10}, pages = {}, pmid = {39412865}, issn = {2057-5858}, mesh = {*beta-Lactamases/genetics ; *Pseudomonas aeruginosa/genetics/drug effects/isolation & purification ; Humans ; *Disease Outbreaks ; *Plasmids/genetics ; *Pseudomonas Infections/microbiology/epidemiology ; Klebsiella/genetics/isolation & purification/drug effects ; DNA Transposable Elements ; Gene Transfer, Horizontal ; }, abstract = {Carriage of CTX-M-type extended-spectrum β-lactamase (ESBL) is rare in Pseudomonas aeruginosa. During routine surveillance of an endemic ST-621 P. aeruginosa at a large hospital, isolate MRSN 100690 carrying bla CTX-M-15 was cultured from a patient (P2). This was the first detection of this ESBL in the endemic ST-621 lineage. All 1 488 bacterial isolates collected from the same facility in the 12 months prior to the incidence of 100 690 were screened for the presence of bla CTX-M-15. A set of 183 isolates was identified, in which corresponding patient metadata was evaluated for spatiotemporal overlaps with P2. The resulting three isolates, along with 100 690, were long-read sequenced using the Oxford Nanopore MinION platform to determine a potential donor of bla CTX-M-15. The screen revealed a single Klebsiella michiganensis isolate, MRSN 895358, which carried an IncA/C2 plasmid harbouring bla CTX-M-15. Notably, the patient harbouring 895358, P1, occupied the same hospital room as P2 9 months prior. Genomic alignment revealed that both isolates shared an identical 80.8 kb region containing the IncA/C2 plasmid replicon and bla CTX-M-15. This region was plasmid bound in 895 358, but chromosomally bound in 100 690 due to Tn4661-mediated transposition. ESBL bla CTX-M-15 was acquired and subsequently integrated into the chromosome of a ST-621 P. aeruginosa, likely initiated by plasmid transfer from a K. michiganensis strain.}, } @article {pmid39411937, year = {2024}, author = {Sekar, G and Bahot, A and Bansode, M and Phadnis, A and Sarode, SC and Sharma, NK}, title = {Potentiation of Tumor Hallmarks by the Loss of GULO, a Vitamin C Biosynthesis Gene in Humans.}, journal = {Current molecular medicine}, volume = {}, number = {}, pages = {}, doi = {10.2174/0115665240328074241003110326}, pmid = {39411937}, issn = {1875-5666}, abstract = {Vitamin C plays a significant role in various physiological functions. Humans depend on external sources of vitamin C due to the loss of the L-gulono-γ-lactone oxidase (GULO) gene that contributes to the synthesis of vitamin C. During the evolutionary loss of the GULO gene, physical, chemical, and biological factors were different from the present environmental settings. Besides the evolutionary genetic loss of the GULO gene, there is a gap in the insightful discussion on the potential implications of the non-functional GULO gene towards the predisposition of humans to cancer that faces hostile and carcinogenic environments. Various methods by which vitamin C modulates cellular processes related to cancer, including DNA repair, epigenetic changes, and redox balance, are discussed. Furthermore, we present experimental and clinical evidence indicating that vitamin C deficiency promotes tumor growth, metastasis, and therapy resistance, emphasizing its potential as a cancer phenotypic modulator. Therapeutic implications of restoring vitamin C levels in cancer treatment range from improving the efficacy of conventional medicines to exploiting metabolic vulnerabilities in tumors. The relevance of assessing vitamin C status in cancer patients and the basis for additional research into vitamin C supplementation as an adjuvant therapy is emphasized. This paper presents a comprehensive overview of the implications associated with the functional deficiency of the GULO gene in human subjects exhibiting diverse tumor hallmarks, encompassing ECM remodeling, hypoxia, epigenetic reprogramming, oxidative stress, and drug responsiveness.}, } @article {pmid39411151, year = {2024}, author = {Meza-Padilla, I and McConkey, BJ and Nissimov, JI}, title = {Structural models predict a significantly higher binding affinity between the NblA protein of cyanophage Ma-LMM01 and the phycocyanin of Microcystis aeruginosa NIES-298 compared to the host homolog.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae082}, pmid = {39411151}, issn = {2057-1577}, abstract = {Horizontal gene transfer events between viruses and hosts are widespread across the virosphere. In cyanophage-host systems, such events often involve the transfer of genes involved in photosynthetic processes. The genome of the lytic cyanophage Ma-LMM01 infecting the toxic, bloom-forming, freshwater Microcystis aeruginosa NIES-298 contains a homolog of the non-bleaching A (nblA) gene, which was probably transferred from a cyanobacterial host. The function of the NblA protein is to disassemble phycobilisomes, cyanobacterial light-harvesting complexes that can comprise up to half of the cellular soluble protein content. NblA thus plays an essential dual role in cyanobacteria: it protects the cell from high-light intensities and increases the intracellular nitrogen pool under nutrient limitation. NblA has previously been shown to interact with phycocyanin, one of the main components of phycobilisomes. Using structural modeling and protein-protein docking, we show that the NblA dimer of Ma-LMM01 is predicted to have a significantly higher binding affinity for M. aeruginosa NIES-298 phycocyanin (αβ)6 hexamers, compared to the host homolog. Protein-protein docking suggests that the viral NblA structural model is able to bind deeper into the phycocyanin groove. The main structural difference between the virus and host NblA appears to be an additional α-helix near the N-terminus of the viral NblA, which interacts with the inside of the phycocyanin groove and could thus be considered partly responsible for this deeper binding. Interestingly, phylogenetic analyses indicate that this longer nblA was probably acquired from a different Microcystis host. Based on infection experiments and previous findings, we propose that a higher binding affinity of the viral NblA to the host phycocyanin may represent a selective advantage for the virus, whose infection cycle requires an increased phycobilisome degradation rate that is not fulfilled by the NblA of the host.}, } @article {pmid39405618, year = {2024}, author = {Tan, Y and Yu, P and Yu, Z and Xuan, F and Zhu, L}, title = {Deciphering defense system modulating bacteria-mobile genetic elements symbiosis in microbial aggregates under elevated hydraulic stress.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122590}, doi = {10.1016/j.watres.2024.122590}, pmid = {39405618}, issn = {1879-2448}, abstract = {Bacterial defense systems are under strong evolutionary pressures to defend against mobile genetic elements (MGEs), yet their distribution in microbial aggregates in engineered systems remains largely unexplored. Herein, we investigated the bacterial defensome and MGEs within activated sludge flocs (AS) and membrane-attached biofilm (MF) in a full-scale membrane bioreactor. Similar distribution pattern of bacterial defense systems (63 types) was observed in prokaryotic genome in AS and MF, including RM system (∼40 %), Cas system (∼18 %) and TA-Abi system (∼28 %), exhibiting a dependency on the genome size and bacterial taxonomy in microbial aggregates under elevated hydraulic stress (MF). In contrast to plasmid and provirus, which carried defense systems (22 types) similar to their associated hosts, virome (61 %) carried novel defense systems (40 types) absent in their associated hosts. With 54 % of which involved in MGEs geneflow network, 69 % of high quality bacterial genome bins were associated with horizontal gene transfer (HGT), facilitating the exchange of mobile core functional genes. This potentially conferred competitive advantages to hosts through habitat-specific payload genes related to biotic defense, antibiotic resistance, and nitrogen metabolism. The longer growth cycle and varied defense gene density suggested the potential defense redundancy and trade-off of metabolic expense and immunity in bacterial host-MGE symbionts. Furthermore, enhanced cooperative network modules of cross-feeding and defense were observed in the MF, potentially helped the symbiotic microbial communities in coping with hostile conditions under elevated hydraulic stress. These findings shed light on the dynamics of bacterial defense systems in host-MGE coevolution and provide new perspectives of microbial aggregates manipulation for ecological and engineering application.}, } @article {pmid39404847, year = {2024}, author = {Bethke, JH and Kimbrel, J and Jiao, Y and Ricci, D}, title = {Toxin-antitoxin systems reflect community interactions through horizontal gene transfer.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msae206}, pmid = {39404847}, issn = {1537-1719}, abstract = {Bacterial evolution through horizontal gene transfer (HGT) reflects their community interactions. In this way, HGT networks do well at mapping community interactions, but offer little toward controlling them-an important step in the translation of synthetic strains into natural contexts. Toxin-antitoxin (TA) systems serve as ubiquitous and diverse agents of selection; however, their utility is limited by their erratic distribution in hosts. Here we examine the heterogeneous distribution of TAs as a consequence of their mobility. By systematically mapping TA systems across a 10,000 plasmid network, we find HGT communities have unique and predictable TA signatures. We propose these TA signatures arise from plasmid competition and have further potential to signal the degree to which plasmids, hosts, and phage interact. To emphasize these relationships, we construct an HGT network based solely on TA similarity, framing specific selection markers in the broader context of bacterial communities. This work both clarifies the evolution of TA systems and unlocks a common framework for manipulating community interactions through TA compatibility.}, } @article {pmid39404832, year = {2024}, author = {Díaz-Martínez, C and Bolívar, A and Mercanoglu Taban, B and Kanca, N and Pérez-Rodríguez, F}, title = {Exploring the antibiotic resistance of Listeria monocytogenes in food environments - a review.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-24}, doi = {10.1080/1040841X.2024.2412007}, pmid = {39404832}, issn = {1549-7828}, abstract = {Listeria monocytogenes, a resilient bacterium in diverse food conditions, such as refrigeration, reduced water activity and low pH, poses a significant threat to the food industry and public health. In recent years, it has been documented an increase in the antibiotic resistance of zoonotic pathogens, including L. monocytogenes. This review provides new insight into the molecular mechanisms involved in both intrinsic and acquired antibiotic resistance of L. monocytogenes with an emphasis on the effect of different environmental and food-related factors. It also explores the relationship of these resistance mechanisms with virulence factors. An analysis of literature data (2009-2021) was conducted to investigate statistically and graphically potential associations between specific antibiotic resistance patterns in the pathogen and food categories using an unbiased variance analysis. The results evidenced that food type had an influence on the antibiotic resistance profiles of L. monocytogenes, with meat and vegetables being the food categories exhibiting the most prevalent profiles. The frequent detection of resistance to ampicillin, penicillin, and tetracycline (non-intrinsic resistances) indicates that specific processing conditions along the food chain may induce them. Many questions remain about the impact of food chain factors (e.g. thermal treatments, cold chain, preservatives, etc.) and food type (low pH, reduced water activity, etc.) on the antibiotic resistance patterns of the pathogen, particularly concerning food-related sources, the resistance mechanisms involved (e.g. cross-protection, horizontal gene transfer, etc.), and the evolutionary processes of antibiotic-resistant microbial populations. Metagenomics, in addition to other -omics technologies (metabolomics and transcriptomics), allows a better understanding of the processes involved in the acquisition of resistance.}, } @article {pmid39402773, year = {2024}, author = {Dunmyre, A and Vinayamohan, P and Locke, SR and Cheng, TY and Schaffner, V and Habing, G}, title = {Characterisation of Antimicrobial Resistance in Special-Fed Veal Production Environments.}, journal = {Zoonoses and public health}, volume = {}, number = {}, pages = {}, doi = {10.1111/zph.13186}, pmid = {39402773}, issn = {1863-2378}, support = {//U.S. Department of Agriculture/ ; //National Institute of Food and Agriculture/ ; //USDA National Institute of Food and Agriculture/ ; //Agricultural and Food Research Initiative Competitive Program/ ; 2018-68003-27466//Agriculture Economics and Rural Communities/ ; }, abstract = {INTRODUCTION: Antimicrobial resistance (AMR) is one of the leading public health threats globally. AMR genes can be transferred between bacteria through lateral gene transfer, and AMR organisms can spread through environments by contaminated water, agriculture and animals. Thus, widespread environmental dissemination of bacteria and lateral gene transfer facilitate AMR transmission pathways. Farm environments in dairy and calf production are known to harbour AMR bacteria that pose a risk for food contamination and to workers in direct or indirect contact with animals. Escherichia coli is present in farm environments and is known to participate in lateral gene transfer, providing a good marker of resistance genes in each environment.

METHODS: In this study, E. coli from nine cohorts of calves was isolated at different time points from nine barns, nine trailers and one slaughterhouse environment in a single special-fed veal calf production facility. The antimicrobial susceptibility to 15 antimicrobials, classified as highly or critically important by the World Health Organization, was characterised for E. coli isolates using Kirby-Bauer disk diffusion.

RESULTS: The highest proportion of isolates showing multidrug resistance was present in barn environments (51.7%), where calves were housed from their arrival at < 2 weeks of age until they were transported to slaughter. Additionally, 15 E. coli isolates were resistant to 11 of the 15 antimicrobials tested. Trailer and slaughterhouse environments had greater prevalence of resistance after accommodating calves, including resistance to third-generation cephalosporins.

CONCLUSION: These data highlight the importance of calf environments in the dissemination of resistant bacteria and gives insight into where interventions could be most effective in combatting antimicrobial-resistant bacteria that could infect humans and livestock.}, } @article {pmid39401218, year = {2024}, author = {Mazzamurro, F and Chirakadavil, JB and Durieux, I and Poiré, L and Plantade, J and Ginevra, C and Jarraud, S and Wilharm, G and Charpentier, X and P C Rocha, E}, title = {Intragenomic conflicts with plasmids and chromosomal mobile genetic elements drive the evolution of natural transformation within species.}, journal = {PLoS biology}, volume = {22}, number = {10}, pages = {e3002814}, pmid = {39401218}, issn = {1545-7885}, mesh = {*Plasmids/genetics ; *Interspersed Repetitive Sequences/genetics ; *Legionella pneumophila/genetics ; Humans ; Acinetobacter baumannii/genetics ; Phylogeny ; Evolution, Molecular ; Chromosomes, Bacterial/genetics ; Transformation, Bacterial ; Gene Transfer, Horizontal ; }, abstract = {Natural transformation is the only mechanism of genetic exchange controlled by the recipient bacteria. We quantified its rates in 786 clinical strains of the human pathogens Legionella pneumophila (Lp) and 496 clinical and environmental strains of Acinetobacter baumannii (Ab). The analysis of transformation rates in the light of phylogeny revealed they evolve by a mixture of frequent small changes and a few large quick jumps across 6 orders of magnitude. In standard conditions close to half of the strains of Lp and a more than a third in Ab are below the detection limit and thus presumably non-transformable. Ab environmental strains tend to have higher transformation rates than the clinical ones. Transitions to non-transformability were frequent and usually recent, suggesting that they are deleterious and subsequently purged by natural selection. Accordingly, we find that transformation decreases genetic linkage in both species, which might accelerate adaptation. Intragenomic conflicts with chromosomal mobile genetic elements (MGEs) and plasmids could explain these transitions and a GWAS confirmed systematic negative associations between transformation and MGEs: plasmids and other conjugative elements in Lp, prophages in Ab, and transposable elements in both. In accordance with the hypothesis of modulation of transformation rates by genetic conflicts, transformable strains have fewer MGEs in both species and some MGEs inactivate genes implicated in the transformation with heterologous DNA (in Ab). Innate defense systems against MGEs are associated with lower transformation rates, especially restriction-modification systems. In contrast, CRISPR-Cas systems are associated with higher transformation rates suggesting that adaptive defense systems may facilitate cell protection from MGEs while preserving genetic exchanges by natural transformation. Ab and Lp have different lifestyles, gene repertoires, and population structure. Nevertheless, they exhibit similar trends in terms of variation of transformation rates and its determinants, suggesting that genetic conflicts could drive the evolution of natural transformation in many bacteria.}, } @article {pmid39395971, year = {2024}, author = {Li, Z and Ran, Z and Xiao, X and Yan, C and Xu, J and Tang, M and An, M}, title = {Comparative analysis of the whole mitochondrial genomes of four species in sect. Chrysantha (Camellia L.), endemic taxa in China.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {955}, pmid = {39395971}, issn = {1471-2229}, support = {2022(072)//Guizhou Provincial Basic Research Program (Natural Science)/ ; 32360101//National Natural Science Foundation of China/ ; 31960043//National Natural Science Foundation of China/ ; }, mesh = {*Genome, Mitochondrial ; China ; *Camellia/genetics ; Phylogeny ; RNA Editing ; Genome, Plant ; Base Composition ; }, abstract = {BACKGROUND: The sect. Chrysantha Chang of plants with yellow flowers of Camellia species as the "Queen of the Tea Family", most of these species are narrowly distributed endemics of China and are currently listed Grde-II in National Key Protected Wild Plant of China. They are commercially important plants with horticultural medicinal and scientific research value. However, the study of the sect. Chrysantha species genetics are still in its infancy, to date, the mitochondrial genome in sect. Chrysantha has been still unexplored.

RESULTS: In this study, we provide a comprehensive assembly and annotation of the mitochondrial genomes for four species within the sect. Chrysantha. The results showed that the mitochondrial genomes were composed of closed-loop DNA molecules with sizes ranging from 850,836 bp (C. nitidissima) to 1,098,121 bp (C. tianeensis) with GC content of 45.71-45.78% and contained 48-58 genes, including 28-37 protein-coding genes, 17-20 tRNA genes and 2 rRNA genes. We also examined codon usage, sequence repeats, RNA editing and selective pressure in the four species. Then, we performed a comprehensive comparison of their basic structures, GC contents, codon preferences, repetitive sequences, RNA editing sites, Ka/Ks ratios, haplotypes, and RNA editing sites. The results showed that these plants differ little in gene type and number. C. nitidissima has the greatest variety of genes, while C. tianeensis has the greatest loss of genes. The Ka/Ks values of the atp6 gene in all four plants were greater than 1, indicating positive selection. And the codons ending in A and T were highly used. In addition, the RNA editing sites differed greatly in number, type, location, and efficiency. Twelve, six, five, and twelve horizontal gene transfer (HGT) fragments were found in C. tianeensis, Camellia huana, Camellia liberofilamenta, and C. nitidissima, respectively. The phylogenetic tree clusters the four species of sect. Chrysantha plants into one group, and C. huana and C. liberofilamenta have closer affinities.

CONCLUSIONS: In this study, the mitochondrial genomes of four sect. Chrysantha plants were assembled and annotated, and these results contribute to the development of new genetic markers, DNA barcode databases, genetic improvement and breeding, and provide important references for scientific research, population genetics, and kinship identification of sect. Chrysantha plants.}, } @article {pmid39395498, year = {2024}, author = {Hou, H and Zou, D and Shi, W and Wang, Y and Ma, D and Wang, Y and Li, Q and Gao, Y and Gao, B}, title = {Localized heating coupling with radical oxidation eliminating antibiotic resistance genes (ARGs) in interfacial photothermal Fenton-like disinfection process.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {176779}, doi = {10.1016/j.scitotenv.2024.176779}, pmid = {39395498}, issn = {1879-1026}, abstract = {Conventional oxidative disinfection processes are inefficient in eliminating intracellular antibiotic resistance genes (iARGs) due to the barrier of the cell membrane and the competitive reaction of cellular constituents within antibiotic-resistant bacteria (ARB), resulting in the widespread prevalence of ARGs in recycled water. This study presented the first application of localized heating coupling with advanced oxidation to destroy the resistant Escherichia coli cells and improved subsequent iARGs (blaTEM-1) degradation in a novel photothermal Fenton-like disinfection process. The Fe-Mn@CNT microfiltration membrane, comprising carbon nanotubes wrapped with Fe and Mn nanoparticles (Fe-Mn@CNT), was employed as a nanomaterial for photothermal conversion and H2O2 activation. The highly efficient absorption of full-spectrum photons by CNTs enabled the Fe-Mn@CNT membrane to concentrate light to generate localized intense heat, resulting in the destruction of ARB nearby, and the subsequent release of iARGs. Interfacial heat favored Fe-Mn-induced H2O2 activation, leading to the production of more ·OH, which in turn promoted the oxidation for ARG degradation and ARB cell damage. The results of the acetylcysteine quenching experiments indicated that interfacial heating and radical oxidation-induced accumulation of intracellular reactive oxygen species contributed to the elimination of about 1-log iARGs through direct attack. The integrity of the cell membrane, the morphology of ARB and the variation of i/e ARG copy numbers were observed to reveal that the introduction of interfacial heating aggravated the cell lysis and accelerated the iARGs release, resulting in the inactivation of 7.27-log ARB and the elimination of 4.64-log iARGs and 2.23-log eARGs. Localized heating coupling with ·OH oxidation achieved a 143 % increase in iARGs removal compared to the conventional Fenton-like oxidation. The interfacial photothermal Fenton-like disinfection process exhibited remarkable material stability, robust disinfection performance, and effective suppression of horizontal gene transfer, underscoring its immense potential to mitigate the risk of ARG dissemination in reclaimed water systems.}, } @article {pmid39394251, year = {2024}, author = {Hossain, M and Aslan, B and Hatoum-Aslan, A}, title = {Tandem mobilization of anti-phage defenses alongside SCCmec elements in staphylococci.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8820}, pmid = {39394251}, issn = {2041-1723}, support = {R01 AI173022/AI/NIAID NIH HHS/United States ; R01AI 173022-01//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1020298//Burroughs Wellcome Fund (BWF)/ ; }, mesh = {*Genomic Islands/genetics ; Staphylococcus/genetics ; Recombinases/metabolism/genetics ; Methicillin Resistance/genetics ; Staphylococcus Phages/genetics ; Gene Transfer, Horizontal ; Methicillin-Resistant Staphylococcus aureus/genetics ; Bacteriophages/genetics/physiology ; Chromosomes, Bacterial/genetics ; }, abstract = {Recent research has identified multiple immune systems that bacteria use to protect themselves from viral infections. However, little is known about the mechanisms by which these systems horizontally spread, especially among bacterial pathogens. Here, we investigate antiviral defenses in staphylococci, opportunistic pathogens that constitute leading causes of antibiotic-resistant infections. We show that these organisms harbor a variety of anti-phage defenses encoded within or near SCC (staphylococcal cassette chromosome) mec cassettes, mobile genomic islands that confer methicillin resistance. Importantly, we demonstrate that SCCmec-encoded recombinases mobilize not only SCCmec, but also tandem SCC-like cassettes enriched in genes coding for diverse defense systems. Further, we show that phage infection stimulates cassette mobilization (i.e. excision and circularization). Thus, our findings indicate that SCC/SCCmec cassettes not only spread antibiotic resistance but can also play a role in mobilizing anti-phage defenses.}, } @article {pmid39394195, year = {2024}, author = {Chu, J and Choi, J and Ji, SK and Park, C and Jung, SH and Park, SH and Lee, DG}, title = {An outbreak of blaKPC-4- and blaVIM-1-producing Klebsiella pneumoniae and Klebsiella variicola at a single hospital in South Korea.}, journal = {Antimicrobial resistance and infection control}, volume = {13}, number = {1}, pages = {123}, pmid = {39394195}, issn = {2047-2994}, support = {HI22C0226//Korea Health Industry Development Institute/Republic of Korea ; 2021R1A2C1009867//National Research Foundation of Korea/ ; }, mesh = {Humans ; *beta-Lactamases/genetics/metabolism ; *Disease Outbreaks ; *Klebsiella pneumoniae/genetics/isolation & purification ; Republic of Korea/epidemiology ; *Klebsiella Infections/epidemiology/microbiology/transmission ; *Klebsiella/genetics ; *Plasmids/genetics ; Cross Infection/microbiology/epidemiology ; Bacterial Proteins/genetics/metabolism ; Hospitals ; Whole Genome Sequencing ; Gene Transfer, Horizontal ; Female ; Anti-Bacterial Agents/pharmacology ; Male ; }, abstract = {BACKGROUND: The dissemination of Klebsiella spp. producing multiple carbapenemases has been increasingly recognized. Between July 2019 and August 2021, ten patients were found to carry Klebsiella spp. co-harboring blaKPC-4 and blaVIM-1 across multiple wards at a Korean hospital, and one isolate was recovered from a hand-washing sink, more than a year after the outbreak. This study aimed to investigate the outbreak and conduct a genomic study of these isolates.

METHODS: Whole-genome sequencing, including long-read sequencing, was performed to analyze plasmid structures and mobile genetic elements (MGEs). Bioinformatics analyses were performed to trace clonal transmission chains and horizontal gene transfer.

RESULTS: The findings suggested that the inter-ward spread of Klebsiella spp. seemed to be facilitated by healthcare worker contact or patient movement. Of the nine isolates collected (eight clinical and one environmental), seven (including the environmental isolate) were identified as K. pneumoniae (ST3680) and two were K. variicola (single-locus variant of ST5252). These isolates showed high genetic relatedness within their species and harbored the IncHI5B plasmid carrying both blaKPC-4 and blaVIM-1 (pKPCVIM.1). On this plasmid, blaVIM-1 was located in the Class 1 integron associated with IS1326::IS1353 (In2), and Tn4401b carrying blaKPC-4 was inserted into IS1326::IS1353, creating a novel MGE construct (In2_blaVIM-1-Tn4401b_blaKPC-4).

CONCLUSION: The hospital-wide spread of blaKPC-4 and blaVIM-1 was facilitated by clonal spread and horizontal plasmid transfer. The persistence of this strain in the hospital sink suggests a potential reservoir of the strain. Understanding the transmission mechanisms of persistent pathogens is important for improving infection control strategies in hospitals.}, } @article {pmid39387591, year = {2024}, author = {Zhang, M and Yin, Z and Chen, B and Yu, Z and Liang, J and Tian, X and Li, D and Deng, X and Peng, L}, title = {Investigation of Citrobacter freundii clinical isolates in a Chinese hospital during 2020-2022 revealed genomic characterization of an extremely drug-resistant C. freundii ST257 clinical strain GMU8049 co-carrying blaNDM-1 and a novel blaCMY variant.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0425423}, doi = {10.1128/spectrum.04254-23}, pmid = {39387591}, issn = {2165-0497}, abstract = {The emergence of multidrug-resistant Citrobacter freundii poses a significant threat to public health. C. freundii isolates were collected from clinical patients in a Chinese hospital during 2020-2022. An unusual strain, GMU8049, was not susceptible to any of the antibiotics tested, including the novel β-lactam/β-lactamase inhibitor combination ceftazidime-avibactam. Whole-genome sequencing (WGS) revealed that GMU8049 harbors a circular chromosome belonging to the rare ST257 and an IncX3 resistance plasmid. Genomic analysis revealed the coexistence of two β-lactamase genes, including plasmid-mediated blaNDM-1 and chromosomal blaCMY encoding a novel CMY variant, combined with an outer membrane porin deficiency, which may account for the extreme resistance to β-lactams. Conjugation experiment confirmed that the blaNDM-1 resistance gene located on pGMU8049 could be successfully transferred to Escherichia coli EC600. The novel CMY variant had an amino acid substitution at position 106 (N106S) compared to the closely related CMY-51. Additionally, a GMU8049-specific truncation in an OmpK37 variant that produces a premature stop codon. Moreover, a variety of chromosome-located efflux pump coding genes and virulence-related genes were also identified. Analysis of strain GMU8049 in the context of other C. freundii strains reveals an open pan-genome and the presence of mobile genetic elements that can mediate horizontal gene transfer of antimicrobial resistance and virulence genes. Our work provides comprehensive insights into the genetic mechanisms of highly resistant C. freundii, highlighting the importance of genomic surveillance of this opportunistic pathogen as a high-risk population for emerging resistance and pathogenicity.IMPORTANCEEmerging pathogens exhibiting multi-, extremely, and pan-drug resistance are a major concern for hospitalized patients and the healthcare community due to limited antimicrobial treatment options and the potential for spread. Genomic technologies have enabled clinical surveillance of emerging pathogens and modeling of the evolution and transmission of antimicrobial resistance and virulence. Here, we report the genomic characterization of an extremely drug-resistant ST257 Citrobacter freundii clinical isolate. Genomic analysis of GMU8049 with a rare ST type and unusual phenotypes can provide information on how this extremely resistant clinical isolate has evolved, including the acquisition of blaNDM-1 via the IncX3 plasmid and accumulation through chromosomal mutations leading to a novel CMY variant and deficiency of the outer membrane porin OmpK37. Our work highlights that the emergence of extremely resistant C. freundii poses a significant challenge to the treatment of clinical infections. Therefore, great efforts must be made to specifically monitor this opportunistic pathogen.}, } @article {pmid39393940, year = {2024}, author = {Hall, JPJ}, title = {Loading and unloading plasmid cargoes.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2024.09.012}, pmid = {39393940}, issn = {1878-4380}, abstract = {Plasmids are vehicles for horizontal gene transfer between cells, but they also exchange genes with associated chromosomes in a process termed 'intracellular mobility'. I discuss a recent article by Kadibalban et al. mapping such plasmid-chromosomal sequence similarities across diverse bacteria.}, } @article {pmid39389705, year = {2024}, author = {Zhen, Q and Wang, X and Cheng, X and Fang, W}, title = {Remediation of toxic metal and metalloid pollution with plant symbiotic fungi.}, journal = {Advances in applied microbiology}, volume = {129}, number = {}, pages = {171-187}, doi = {10.1016/bs.aambs.2024.04.001}, pmid = {39389705}, issn = {0065-2164}, mesh = {*Plants/microbiology ; *Symbiosis ; *Biodegradation, Environmental ; *Metalloids/metabolism/toxicity ; *Soil Pollutants/metabolism/toxicity ; *Fungi/metabolism/genetics ; *Mycorrhizae/metabolism/physiology ; Endophytes/metabolism/physiology/isolation & purification/genetics ; Metals/metabolism/toxicity ; Soil Microbiology ; }, abstract = {Anthropogenic activities have dramatically accelerated the release of toxic metal(loid)s into soil and water, which can be subsequently accumulated in plants and animals, threatening biodiversity, human health, and food security. Compared to physical and chemical remediation, bioremediation of metal(loid)-polluted soil using plants and/or plant symbiotic fungi is usually low-cost and environmentally friendly. Mycorrhizal fungi and endophytic fungi are two major plant fungal symbionts. Mycorrhizal fungi can immobilize metal(loid)s via constitutive mechanisms, including intracellular sequestration with vacuoles and vesicles and extracellular immobilization by cell wall components and extracellular polymeric substances such as glomalin. Mycorrhizal fungi can improve the efficacy of phytoremediation by promoting plant symplast and apoplast pathways. Endophytic fungi also use constitutive cellular components to immobilize metal(loid)s and to reduce the accumulation of metal(loid)s in plants by modifying plant physiological status. However, a specific mechanism for the removal of methylmercury pollution was recently discovered in the endophytic fungi Metarhizium, which could be acquired from bacteria via horizontal gene transfer. In contrast to mycorrhizal fungi that are obligate biotrophs, some endophytic fungi, such as Metarhizium and Trichoderma, can be massively and cost-effectively produced, so they seem to be well-placed for remediation of metal(loid)-polluted soil on a large scale.}, } @article {pmid39389327, year = {2024}, author = {Narain Singh, D and Pandey, P and Shankar Singh, V and Kumar Tripathi, A}, title = {Evidence for high-risk pollutants and emerging microbial contaminants at two major bathing ghats of the river Ganga using high-resolution mass spectrometry and metagenomics.}, journal = {Gene}, volume = {}, number = {}, pages = {148991}, doi = {10.1016/j.gene.2024.148991}, pmid = {39389327}, issn = {1879-0038}, abstract = {An efficient wastewater treatment plant is imperative to limit the entry of emerging pollutants (EPs) and emerging microbial contaminants (EMCs) in the river ecosystem. The detection of emerging EPs in aquatic environments is challenging due to complex sample preparation methods, and the need for sophisticated accurate analytical tools. In Varanasi (India), the river Ganga holds immense significance as a holy river but is consistently polluted with municipal (MWW) and hospital wastewater (HWW). We developed an efficient method for untargeted detection of EPs in the water samples using High-resolution mass spectrometry (HRMS), and identified 577 and 670 chemicals (or chemical components) in the water samples from two major bathing ghats, Assi Ghat (AG) and Dashashwamedh Ghat (DG), respectively. The presence of EPs of different categories viz chemicals from research labs, diagnostic labs, lifestyle and industrial chemicals, toxins, flavor and food additives indicated the unsafe disposal of MWW and HWW or inefficient wastewater treatment plants (WWTPs). Besides, shotgun metagenomic analysis depicted the presence of bacteria associated with MWW viz Cloacibacterium normanse, Sphaerotilus natans (sewage fungi), E. coli, and Prevotella. Also, the presence of human pathogens Arcobacter, Polynucleobacter, Pseudomonas, Klebsiella, Aeromonas, Acinetobacter, Vibrio, and Campylobacter suggests the discharge of HWW. EPs are linked to the development, and transmission of antimicrobial resistance (AMR). Occurrence of antibiotic resistance genes (ARGs), plasmid-borne β-lactamases, aminoglycoside transferases, and ARGs associated with integrons, transposons and plasmids viz mcr-3 gene that confer resistance to colistin, the last resort of antibiotics confirmed the presence of emerging microbial contaminants. Subsequent genome reconstruction studies showed the presence of uncultivable ARB and transmission of ARGs through horizontal gene transfer. This study can be used to monitor the health of aquatic bodies as well as the efficiency of WWTPs and raise an urgent need for efficient WWTPs to safeguard the river, Ganga.}, } @article {pmid39386473, year = {2024}, author = {Dalia, TN and Dalia, AB}, title = {SbcB facilitates natural transformation in Vibrio cholerae in an exonuclease-independent manner.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.25.615017}, pmid = {39386473}, issn = {2692-8205}, abstract = {UNLABELLED: Natural transformation (NT) is a conserved mechanism of horizontal gene transfer in bacterial species. During this process, DNA is taken up into the cytoplasm where it can be integrated into the host genome by homologous recombination. We have previously shown that some cytoplasmic exonucleases can inhibit NT by degrading ingested DNA prior to its successful recombination. Here, however, we demonstrate that the exonuclease SbcB counterintuitively promotes NT in Vibrio cholerae . Through a systematic analysis of the distinct steps of NT, we show that SbcB acts downstream of DNA uptake into the cytoplasm, but upstream of recombinational branch migration. Through mutational analysis, we show that the SbcB promotes NT in a manner that does not rely on its exonuclease activity. Finally, we provide genetic evidence that SbcB directly interacts with the primary bacterial recombinase, RecA. Together, these data advance our molecular understanding of horizontal gene transfer in V. cholerae , and reveal that SbcB promotes homologous recombination during NT in a manner that does not rely on its canonical exonuclease activity.

IMPORTANCE: Horizontal gene transfer by natural transformation contributes to the spread of antibiotic resistance and virulence factors in bacterial species. Here, we study how one protein, SbcB, helps facilitate this process in the facultative bacterial pathogen Vibrio cholerae . SbcB is a well-known for its exonuclease activity (i.e ., the ability to degrade the ends of linear DNA). Through this study we uncover that while SbcB is important for natural transformation, it does not facilitate this process using its exonuclease activity. Thus, this work helps further our understanding of the molecular events required for this conserved evolutionary process, and uncovers a function for SbcB beyond its canonical exonuclease activity.}, } @article {pmid39385022, year = {2024}, author = {Samuel, B and Mittelman, K and Croitoru, SY and Ben Haim, M and Burstein, D}, title = {Diverse anti-defence systems are encoded in the leading region of plasmids.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39385022}, issn = {1476-4687}, abstract = {Plasmids are major drivers of gene mobilization by means of horizontal gene transfer and play a key role in spreading antimicrobial resistance among pathogens[1,2]. Despite various bacterial defence mechanisms such as CRISPR-Cas, restriction-modification systems and SOS-response genes that prevent the invasion of mobile genetic elements[3], plasmids robustly transfer within bacterial populations through conjugation[4,5]. Here we show that the leading region of plasmids, the first to enter recipient cells, is a hotspot for an extensive repertoire of anti-defence systems, encoding anti-CRISPR, anti-restriction, anti-SOS and other counter-defence proteins. We further identified in the leading region a prevalence of promoters known to allow expression from single-stranded DNA[6], potentially facilitating rapid protection against bacterial immunity during the early stages of plasmid establishment. We demonstrated experimentally the importance of anti-defence gene localization in the leading region for efficient conjugation. These results indicate that focusing on the leading region of plasmids could lead to the discovery of diverse anti-defence genes. Combined, our findings show a new facet of plasmid dissemination and provide theoretical foundations for developing efficient conjugative delivery systems for natural microbial communities.}, } @article {pmid39384008, year = {2024}, author = {Gentile, A and Di Stasio, L and Oliva, G and Vigliotta, G and Cicatelli, A and Guarino, F and Nissim, WG and Labra, M and Castiglione, S}, title = {Antibiotic Resistance in Urban Soils: Dynamics and Mitigation Strategies.}, journal = {Environmental research}, volume = {}, number = {}, pages = {120120}, doi = {10.1016/j.envres.2024.120120}, pmid = {39384008}, issn = {1096-0953}, abstract = {Antibiotic resistance (AR) is a critical global health issue with significant clinical and economic implications. AR occurs when microorganisms develop mechanisms to withstand the effects of antibiotics, reducing treatment efficacy and increasing the risk of mortality and healthcare costs. While the connection between antibiotic use in clinical and agricultural settings and the emergence of AR is well-established, the role of urban soils as reservoirs and spreaders of AR is underexplored. This review examines the complex dynamics of AR in urban soils, highlighting the various sources of antibiotics, including domestic wastewater, industrial effluents, urban agricultural practices, but also microplastics and domestic animal excrements. The selective pressure exerted by these anthropogenic sources promotes the proliferation of antibiotic-resistant bacteria, particularly through horizontal gene transfer, which facilitates the transmission of resistance genes among soil microorganisms in urban environments. About that, the presence of antibiotics in urban soils poses a significant threat to public health by potentially transferring resistance genes to human pathogens through multiple pathways, including direct contact, food consumption, and water ingestion. Furthermore, AR in urban soils disrupts microbial community dynamics, impacting soil fertility, plant growth, and overall environmental quality. Therefore, this review aims to address gaps in understanding AR in urban soils, offering insights into its implications for human health and ecosystem integrity. By identifying these gaps and suggesting evidence-based strategies, this review proposes valid and sustainable solutions to mitigate and counteract the spread of AR in urban environments.}, } @article {pmid39383948, year = {2024}, author = {Rao, M and Teixeira, JS and Flint, A and Tamber, S}, title = {Hazard characterization of antibiotic-resistant Aeromonas spp. isolated from mussel and oyster shellstock available for retail purchase in Canada.}, journal = {Journal of food protection}, volume = {}, number = {}, pages = {100374}, doi = {10.1016/j.jfp.2024.100374}, pmid = {39383948}, issn = {1944-9097}, abstract = {Surveillance and monitoring of foods for the presence of antimicrobial-resistant (AMR) bacteria is required to assess the risks these bacteria pose to human health. Frequently consumed raw or lightly cooked, live bivalve shellfish such as mussels and oysters can be a source of exposure to AMR bacteria. This study sought to determine the prevalence of third generation cephalosporin (3GC) and carbapenem resistant bacteria in live mussel and oyster shellstock available for retail purchase through the course of one calendar year. Just over half of the 180 samples (52%) tested positive for the presence 3GC-resistant bacteria belonging to thirty distinct bacterial species. Speciation of the isolates was carried out using the Bruker MALDI Biotyper. Serratia spp., Aeromonas spp., and Rahnella spp. were the most frequently isolated groups of bacteria. Antibiotic resistance testing confirmed reduced susceptibility for 3GCs and/or carbapenems in 15 of the 29 Aeromonas isolates. Based on AMR patterns, and species identity, a sub-set of ten Aeromonas strains was chosen for further characterization by whole genome sequence analysis. Genomic analysis revealed the presence of multiple antibiotic resistance and virulence genes. A number of mobile genetic elements were also identified indicating the potential for horizontal gene transfer. Differences in gene detection by the bioinformatic tools and databases used (ResFinder. CARD RGI, PlasmidFinder, and MobSuite) are discussed. This study highlights the strengths and limitations of using genomics tools to perform hazard characterization of diverse foodborne bacterial species.}, } @article {pmid39383803, year = {2024}, author = {Xiang, Y and Song, X and Yang, Y and Deng, S and Fu, L and Yang, C and Chen, M and Pu, J and Zhang, H and Chai, H}, title = {Comammox rather than AOB dominated the efficient autotrophic nitrification-denitrification process in an extremely oxygen-limited environment.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122572}, doi = {10.1016/j.watres.2024.122572}, pmid = {39383803}, issn = {1879-2448}, abstract = {The discovery of complete ammonia oxidizer (comammox) has challenged the traditional understanding of the two-step nitrification process. However, their functions in the oxygen-limited autotrophic nitrification-denitrification (OLAND) process remain unclear. In this study, OLAND was achieved using comammox-dominated nitrifying bacteria in an extremely oxygen-limited environment with a dissolved oxygen concentrations of 0.05 mg/L. The ammonia removal efficiency exceeded 97 %, and the total nitrogen removal efficiency reached 71 % when sodium bicarbonate was used as the carbon source. The pseudo-first- and second-order models were found to best fit the ammonia removal processes under low and high loads, respectively, suggesting distinct ammonia removal pathways. Full-length 16S rRNA gene sequencing and metagenomic results revealed that comammox-dominated under different oxygen levels, in conjunction with anammox and heterotrophic denitrifiers. The abundance of enzymes involved in energy metabolism indicates the coexistence of anammox and autotrophic nitrification-heterotrophic denitrification pathways. The binning results showed that comammox bacteria engaged in horizontal gene transfer with nitrifiers, anammox bacteria, and denitrifiers to adapt to an obligate environments. Therefore, this study demonstrated that comammox, anammox, and heterotrophic denitrifiers play important roles in the OLAND process and provide a reference for further reducing aeration energy in the autotrophic nitrogen removal process.}, } @article {pmid39376581, year = {2024}, author = {Du, Y and Qian, C and Li, X and Zheng, X and Huang, S and Yin, Z and Chen, T and Pan, L}, title = {Unveiling intraspecific diversity and evolutionary dynamics of the foodborne pathogen Bacillus paranthracis through high-quality pan-genome analysis.}, journal = {Current research in food science}, volume = {9}, number = {}, pages = {100867}, pmid = {39376581}, issn = {2665-9271}, abstract = {Understanding the evolutionary dynamics of foodborne pathogens throughout host-associated habitats is of utmost importance. Bacterial pan-genomes, as dynamic entities, are strongly influenced by ecological lifestyles. As a phenotypically diverse species in the Bacillus cereus group, Bacillus paranthracis is recognized as an emerging foodborne pathogen and a probiotic simultaneously. This poorly understood species is a suitable study model for adaptive pan-genome evolution. In this study, we determined the biogeographic distribution, abundance, genetic diversity, and genotypic profiles of key genetic elements of B. paranthracis. Metagenomic read recruitment analyses demonstrated that B. paranthracis members are globally distributed and abundant in host-associated habitats. A high-quality pan-genome of B. paranthracis was subsequently constructed to analyze the evolutionary dynamics involved in ecological adaptation comprehensively. The open pan-genome indicated a flexible gene repertoire with extensive genetic diversity. Significant divergences in the phylogenetic relationships, functional enrichment, and degree of selective pressure between the different components demonstrated different evolutionary dynamics between the core and accessory genomes driven by ecological forces. Purifying selection and gene loss are the main signatures of evolutionary dynamics in B. paranthracis pan-genome. The plasticity of the accessory genome is characterized by horizontal gene transfer (HGT), massive gene losses, and weak purifying or positive selection, which might contribute to niche-specific adaptation. In contrast, although the core genome dominantly undergoes purifying selection, its association with HGT and positively selected mutations indicates its potential role in ecological diversification. Furthermore, host fitness-related dynamics are characterized by the loss of secondary metabolite biosynthesis gene clusters (BGCs) and CAZyme-encoding genes and the acquisition of antimicrobial resistance (AMR) and virulence genes via HGT. This study offers a case study of pan-genome evolution to investigate the ecological adaptations reflected by biogeographical characteristics, thereby advancing the understanding of intraspecific diversity and evolutionary dynamics of foodborne pathogens.}, } @article {pmid39375624, year = {2024}, author = {Männer, L and Schell, T and Spies, J and Galià-Camps, C and Baranski, D and Ben Hamadou, A and Gerheim, C and Neveling, K and Helfrich, EJN and Greve, C}, title = {Chromosome-level genome assembly of the sacoglossan sea slug Elysia timida (Risso, 1818).}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {941}, pmid = {39375624}, issn = {1471-2164}, mesh = {Animals ; *Gastropoda/genetics ; *Molecular Sequence Annotation ; *Genome ; *Chromosomes/genetics ; Genomics/methods ; }, abstract = {BACKGROUND: Sequencing and annotating genomes of non-model organisms helps to understand genome architecture, the genetic processes underlying species traits, and how these genes have evolved in closely-related taxa, among many other biological processes. However, many metazoan groups, such as the extremely diverse molluscs, are still underrepresented in the number of sequenced and annotated genomes. Although sequencing techniques have recently improved in quality and quantity, molluscs are still neglected due to difficulties in applying standardized protocols for obtaining genomic data.

RESULTS: In this study, we present the chromosome-level genome assembly and annotation of the sacoglossan sea slug species Elysia timida, known for its ability to store the chloroplasts of its food algae. In particular, by optimizing the long-read and chromosome conformation capture library preparations, the genome assembly was performed using PacBio HiFi and Arima HiC data. The scaffold and contig N50s, at 41.8 Mb and 1.92 Mb, respectively, are approximately 30-fold and fourfold higher compared to other published sacoglossan genome assemblies. Structural annotation resulted in 19,904 protein-coding genes, which are more contiguous and complete compared to publicly available annotations of Sacoglossa with respect to metazoan BUSCOs. We found no evidence for horizontal gene transfer (HGT), i.e. no photosynthetic genes encoded in the sacoglossan nucleus genome. However, we detected genes encoding polyketide synthases in E. timida, indicating that polypropionates are produced. HPLC-MS/MS analysis confirmed the presence of a large number of polypropionates, including known and yet uncharacterised compounds.

CONCLUSIONS: We can show that our methodological approach helps to obtain a high-quality genome assembly even for a "difficult-to-sequence" organism, which may facilitate genome sequencing in molluscs. This will enable a better understanding of complex biological processes in molluscs, such as functional kleptoplasty in Sacoglossa, by significantly improving the quality of genome assemblies and annotations.}, } @article {pmid39368562, year = {2024}, author = {Hu, JC and Han, M and Yan, RY and Hua, MM and Li, J and Shen, H and Cao, XL}, title = {Mobile Genetic Elements Contributing to Horizontal Gene Transfer of blaNDM among Escherichia coli in the community setting.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {106996}, doi = {10.1016/j.micpath.2024.106996}, pmid = {39368562}, issn = {1096-1208}, abstract = {OBJECTIVE: To investigate the distribution of carbapenem-resistant Enterobacterales (CRE) in the community and to describe the genomic characteristics.

METHODS: CRE screened from fecal samples in healthy people at the health examination center of a tertiary hospital in China underwent Whole genome sequencing (WGS) to analyze genotypic characteristics of CRE. The flanking DNA sequence of blaNDM-5 and mcr1.1 genes were analyzed by Gcluster software.

RESULTS: A total of 7187 fecal samples were screened, and CRE carriage was detected in 0.4% of the sampled population. In total, 30 Escherichia coli, one Citrobacter freundii and one Klebsiella aerogene were screened. The 30 carbapenem-resistant Escherichia coli (CREC) isolates displayed slight resistance to amikacin (13.3%) and aztreonam (20.0%). All the CRE isolates contained blaNDM, and blaNDM-5 (84.4%) was the most common one. B1 (n=11) and A (n=7) were predominant phylogroups. Furthermore, 34 distinct plasmid replicons, 67 different VFs, 22 distinct STs, 17 different FimH types, 26 O:H serotypes as well as 74 MGEs including 61 insertion sequences and 13 transposons were identified. The flanking DNA sequence analysis of blaNDM-5 and mcr1.1 genes indicates the key role of horizontal transfer of blaNDM-5 in the CRE development evidenced by diverse STs and phylogenetic tree.

CONCLUSION: E. coli was the most predominant CRE isolates in community setting, and blaNDM (blaNDM-5) was the main CHßL encoding genes. The high prevalence of ARGs was associated with high resistance to commonly used antimicrobials. Besides, the genetic diversity of these isolates suggested the key role of blaNDM horizontal transfer in the CRE development. Thus, active screening of blaNDM in communities is particularly important for the prevention and control of CRE.}, } @article {pmid39368190, year = {2024}, author = {Jiao, P and Zhou, Y and Zhang, X and Jian, H and Zhang, XX and Ma, L}, title = {Mechanisms of horizontal gene transfer and viral contribution to the fate of intracellular and extracellular antibiotic resistance genes in anaerobic digestion supplemented with conductive materials under ammonia stress.}, journal = {Water research}, volume = {267}, number = {}, pages = {122549}, doi = {10.1016/j.watres.2024.122549}, pmid = {39368190}, issn = {1879-2448}, abstract = {The addition of conductive materials (CMs) is an effective strategy for mitigating ammonia inhibition during anaerobic digestion (AD). However, the introduction of CMs can result in increased antibiotic resistance genes (ARGs) pollution, potentially facilitated by enhanced horizontal gene transfer (HGT). The complex dynamics of intracellular and extracellular ARGs (iARGs/eARGs) and the mechanisms underlying their transfer, mediated by CMs, in ammonia-stressed AD systems remain unclear. In this study, we investigated the effects of three commonly used CMs-nano magnetite (Mag), nano zero-valent iron (nZVI), and granular activated carbon (GAC)-on the fate of iARGs and eARGs during the AD of waste activated sludge under ammonia stress. The results revealed an unexpected enrichment of iARGs by 1.5 %-10.9 % and a reduction of eARGs by 14.1 %-25.2 % in CM-supplemented AD. This discrepancy in the dynamics of iARGs and eARGs may be attributed to changes in microbial hosts and the horizontal transfer of ARGs. Notably, CMs activated prophages within antibiotic-resistant bacteria (ARB) and their symbiotic partners involved in vitamin B12 provision, leading to the lysis of ARB and the subsequent release of eARGs for transformation. Additionally, the abundance of potentially mobile ARGs, which co-occurred with mobile genetic elements, increased by 56.6 %-134.5 % with CM addition, highlighting an enhanced potential for the HGT of ARGs. Specifically, Mag appeared to promote both transformation and conjugation processes, while nZVI only promoted conjugation. Moreover, none of the three CMs had any discernible impact on transduction. GAC proved superior to both nano Mag and nZVI in controlling the enrichment of iARGs, reducing eARGs, and limiting HGTs simultaneously. Overall, these findings provide novel insights into the role of viruses and the mechanisms of ARG spread in CM-assisted AD, offering valuable information for developing strategies to mitigate ARG pollution in practical applications.}, } @article {pmid39368156, year = {2024}, author = {Zhou, Y and Zhang, G and Zhang, D and Zhu, N and Bo, J and Meng, X and Chen, Y and Qin, Y and Liu, H and Li, W}, title = {Microplastic biofilms promote the horizontal transfer of antibiotic resistance genes in estuarine environments.}, journal = {Marine environmental research}, volume = {202}, number = {}, pages = {106777}, doi = {10.1016/j.marenvres.2024.106777}, pmid = {39368156}, issn = {1879-0291}, abstract = {As emerging pollutants, microplastics can aggregate microorganisms on their surfaces and form biofilms, enriching antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Consequently, microplastic biofilms have become a focal point of research. Horizontal gene transfer is one of the primary mechanisms by which bacteria acquire antibiotic resistance, with much of the research focusing on suspended bacteria. However, microplastic biofilms, as hotspots for horizontal gene transfer, also merit significant investigation. This study primarily explored and compared the frequency of ARG conjugative transfer between suspended bacteria and microplastic biofilms. The results demonstrated that, compared to suspended bacteria, microplastic biofilms enhanced the frequency of ARG conjugative transfer by 7.2-19.6 times. Among them, biofilms on polyethylene microplastics showed the strongest promotion of conjugation. After the formation of microplastic biofilms, there was a significant increase in bacterial density within the biofilms, which raised the collision frequency of donor and recipient bacteria. Then microplastic biofilms facilitated the gene expression levels of outer membrane proteins, enhanced bacterial gene transfer capabilities, promoted the synthesis of conjugative pili, accelerated the formation of conjugative pairing systems, and elevated the expression levels of genes related to DNA replication and transfer systems, thereby enhancing the conjugative transfer of ARGs within microplastic biofilms. Among different types of microplastic biofilms, polyethylene biofilms exhibited the highest bacterial density, thus showing the highest frequency of ARG conjugation. This study highlights the risks associated with ARG conjugative transfer following the formation of microplastic biofilms and provides insights into the risks of microplastic and antibiotic resistance propagation in estuarine environments.}, } @article {pmid39194203, year = {2024}, author = {Allain, M and Morel-Journel, T and Condamine, B and Gibeaux, B and Gachet, B and Gschwind, R and Denamur, E and Landraud, L}, title = {IncC plasmid genome rearrangements influence the vertical and horizontal transmission tradeoff in Escherichia coli.}, journal = {Antimicrobial agents and chemotherapy}, volume = {68}, number = {10}, pages = {e0055424}, doi = {10.1128/aac.00554-24}, pmid = {39194203}, issn = {1098-6596}, support = {DEQ20161136698//Fondation pour la Recherche Médicale (FRM)/ ; }, mesh = {*Plasmids/genetics ; *Escherichia coli/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Escherichia coli Infections/microbiology/transmission ; }, abstract = {It has been shown that an evolutionary tradeoff between vertical (host growth rate) and horizontal (plasmid conjugation) transmissions contributes to global plasmid fitness. As conjugative IncC plasmids are important for the spread of multidrug resistance (MDR), in a broad range of bacterial hosts, we investigated vertical and horizontal transmissions of two multidrug-resistant IncC plasmids according to their backbones and MDR-region rearrangements, upon plasmid entry into a new host. We observed plasmid genome deletions after conjugation in three diverse natural Escherichia coli clinical strains, varying from null to high number depending on the plasmid, all occurring in the MDR region. The plasmid burden on bacterial fitness depended more on the strain background than on the structure of the MDR region, with deletions appearing to have no impact. Besides, we observed an increase in plasmid transfer rate, from ancestral host to new clinical recipient strains, when the IncC plasmid was rearranged. Finally, using a second set of conjugation experiments, we investigated the evolutionary tradeoff of the IncC plasmid during the critical period of plasmid establishment in E. coli K-12, by correlating the transfer rates of deleted or non-deleted IncC plasmids and their costs on the recipient strain. Plasmid deletions strongly improved conjugation efficiency with no negative growth effect. Our findings indicate that the flexibility of the MDR-region of the IncC plasmids can promote their dissemination, and provide diverse opportunities to capture new resistance genes. In a broader view, they suggest that the vertical-horizontal transmission tradeoff can be manipulated by the plasmid to improve its fitness.}, } @article {pmid39367299, year = {2024}, author = {Wang, J and Liu, X and Zhang, M and Liu, R}, title = {The mitochondrial genome of Lavandula angustifolia Mill. (Lamiaceae) sheds light on its genome structure and gene transfer between organelles.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {929}, pmid = {39367299}, issn = {1471-2164}, support = {No. 2022BCA022//Hubei Province key research and development project/ ; }, mesh = {*Genome, Mitochondrial ; *Lavandula/genetics ; *Phylogeny ; RNA, Transfer/genetics ; Organelles/genetics ; Gene Transfer, Horizontal ; RNA Editing ; Molecular Sequence Annotation ; Genome, Plant ; Evolution, Molecular ; }, abstract = {BACKGROUND: Lavandula angustifolia holds importance as an aromatic plant with extensive applications spanning the fragrance, perfume, cosmetics, aromatherapy, and spa sectors. Beyond its aesthetic and sensory applications, this plant offers medicinal benefits as a natural herbal remedy and finds use in household cleaning products. While extensive genomic data, inclusive of plastid and nuclear genomes, are available for this species, researchers have yet to characterize its mitochondrial genome. This gap in knowledge hampers deeper understanding of the genome organization and its evolutionary significance.

RESULTS: Through the course of this study, we successfully assembled and annotated the mitochondrial genome of L. angustifolia, marking a first in this domain. This assembled genome encompasses 61 genes, which comprise 34 protein-coding genes, 24 transfer RNA genes, and three ribosomal RNA genes. We identified a chloroplast sequence insertion into the mitogenome, which spans a length of 10,645 bp, accounting for 2.94% of the mitogenome size. Within these inserted sequences, there are seven intact tRNA genes (trnH-GUG, trnW-CCA, trnD-GUC, trnS-GGA, trnN-GUU, trnT-GGU, trnP-UGG) and four complete protein-coding genes (psbA, rps15, petL, petG) of chloroplast derivation. Additional discoveries include 88 microsatellites, 15 tandem repeats, 74 palindromic repeats, and 87 forward long repeats. An RNA editing analysis highlighted an elevated count of editing sites in the cytochrome c oxidase genes, notably ccmB with 34 editing sites, ccmFN with 32, and ccmC with 29. All protein-coding genes showed evidence of cytidine-to-uracil conversion. A phylogenetic analysis, utilizing common protein-coding genes from 23 Lamiales species, yielded a tree with consistent topology, supported by high confidence values.

CONCLUSIONS: Analysis of the current mitogenome resource revealed its typical circular genome structure. Notably, sequences originally from the chloroplast genome were found within the mitogenome, pointing to the occurrence of horizontal gene transfer between organelles. This assembled mitogenome stands as a valuable resource for subsequent studies on mitogenome structures, their evolution, and molecular biology.}, } @article {pmid39366749, year = {2024}, author = {Leclerc, L and Mattick, J and Burns, BP and Sassera, D and Hottop, JD and Lo, N}, title = {Metatranscriptomics provide insights into the role of the symbiont midichloria mitochondrii in Ixodes ticks.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiae133}, pmid = {39366749}, issn = {1574-6941}, abstract = {Ticks are important vectors of bacterial, viral and protozoan pathogens of humans and animals worldwide. Candidatus Midichloria mitochondrii (hereafter M. mitochondrii) is a highly abundant bacterial endosymbiont found in many tick species, including two medically important ticks respectively found in Europe and Australia, Ixodes ricinus and Ixodes holocyclus. The present study aimed to determine the symbiont's biological role by identifying lateral gene transfer (LGT) events, characterising the transcriptome, and performing differential expression analyses. Metatranscriptomic data revealed that M. mitochondrii species in I. ricinus and I. holocyclus were equipped with the metabolic potential and were actively transcribing the genes for several important roles including heme, biotin and folate synthesis, oxidative stress response, osmotic regulation, and ATP production in microaerobic conditions. Differential expression analyses additionally showed an upregulation in stringent response and DNA repair genes in M. mitochondrii of I. holocyclus nymphs compared to adults. Low rates of differential expression suggest the symbiont may lack global gene regulation, as observed in other endosymbionts. Moreover, the identification of an LGT event and the proposed specialisation of the M. mitochondrii strains, mIxholo1 and mIxholo2, for different I. holocyclus life stages highlight the complex interactions between M. mitochondrii and their tick hosts.}, } @article {pmid39366964, year = {2024}, author = {Kawaichi, S and Kotoky, R and Fiutowski, J and Rotaru, AE}, title = {Adaptation of a methanogen to Fe[0] corrosion via direct contact.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {100}, pmid = {39366964}, issn = {2055-5008}, support = {ERC CoG 101045149//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; UFM 5229-00010B//Uddannelses- og Forskningsministeriet (Ministry of Higher Education and Science)/ ; }, mesh = {*Methanococcus/genetics/metabolism ; Corrosion ; *Adaptation, Physiological ; *Hydrogenase/genetics/metabolism ; Gene Transfer, Horizontal ; Methane/metabolism ; Iron/metabolism ; }, abstract = {Due to unique genomic adaptations, Methanococcus maripaludis Mic1c10 is highly corrosive when in direct contact with Fe[0]. A critical adaptation involves increased glycosylation of an extracellular [NiFe]-hydrogenase, facilitating its anchoring to cell surface proteins. Corrosive strains adapt to the constructed environment via horizontal gene transfer while retaining ancestral genes important for intraspecies competition and surface attachment. This calls for a reevaluation of how the built environment impacts methane cycling.}, } @article {pmid39365569, year = {2024}, author = {Gniewosz, M and Andrzejczak-Grządko, S}, title = {[Characterization of KPC-type drug resistance in bacteria].}, journal = {Postepy biochemii}, volume = {70}, number = {3}, pages = {315-324}, doi = {10.18388/pb.2021_555}, pmid = {39365569}, issn = {0032-5422}, mesh = {*beta-Lactamases/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Humans ; Carbapenems/pharmacology ; Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; }, abstract = {One of the main problems of modern medicine is the phenomenon of drug resistance. Inappropriate use of antibiotics is considered to be the most important reason for the emergence of new resistance mechanisms in microorganisms. Carbapenems, which belong to the β-lactams, are considered the most effective group of antimicrobial agents. Unfortunately, as a result of prolonged exposure to the aforementioned drugs, bacteria have developed several mechanisms for survival. The most important of these is the production of hydrolytic enzymes (carbapenemases), which cleave the β-lactam ring and inactivate the antibiotics. The mentioned enzymes are encoded by blaKPC genes, which are located in so-called mobile genetic elements (i.e. plasmids and transposons). Such localization is associated with their ease of transfer between different bacterial species in the process of horizontal gene transfer.}, } @article {pmid39364782, year = {2024}, author = {Bellinazzo, F and Nadal Bigas, J and Hogers, RAH and Kodde, J and van der Wal, F and Kokkinopoulou, P and Duijts, KTM and Angenent, GC and van Dijk, ADJ and van Velzen, R and Immink, RGH}, title = {Evolutionary origin and functional investigation of the widely conserved plant PEBP gene STEPMOTHER OF FT AND TFL1 (SMFT).}, journal = {The Plant journal : for cell and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/tpj.17057}, pmid = {39364782}, issn = {1365-313X}, support = {//KAVB Productgroep Tulp/ ; //Stimuflori/ ; VICI16129//NWO/ ; ALWGR.2017.008//NWO/ ; VICI192033//NWO/ ; }, abstract = {Genes of the family PHOSPHATIDYLETHANOLAMINE-BINDING PROTEINS (PEBP) have been intensely studied in plants for their role in cell (re)programming and meristem differentiation. Recently, sporadic reports of the presence of a new type of PEBP in plants became available, highly similar to the YY-PEBPs of prokaryotes. A comprehensive investigation of their spread, origin, and function revealed conservation across the plant kingdom. The YY-PEBP clade in plants seems to have resulted from a single Horizontal Gene Transfer (HGT) episode from a prokaryotic organism to an ancestral streptophyte. YY-PEBPs are also present in other eukaryotes, such as certain fungi, diatoms, and rotifers, and these cases derive from independent HGT events. Reciprocally, the occurrence of the eukaryotic CETS/RKIP type PEBPs (CR-PEBPs) was noticed in bacteria of the genus Nocardia, showing that HGT has occurred as well from eukaryotes to prokaryotes. Based on these observations, we propose that the current model of the PEBP family in plants needs to be updated with the clade STEPMOTHER OF FT AND TFL1 (SMFT). SMFT genes not only share high sequence conservation but also show specific expression in homologous plant structures that serve as propagules. Functional analysis of Arabidopsis smft mutant lines pointed to a function for this gene in regulating seed germination, both concerning primary dormancy release and in response to adverse high-temperature conditions. Overall, our study reveals an increasing complexity in the evolutionary history of the PEBP gene family, unlocking new potential in understanding the evolution and functional spectrum of these important key regulatory genes.}, } @article {pmid39360841, year = {2024}, author = {Smith, AC and Shrivastava, A and Cartee, JC and Bélanger, M and Sharpe, S and Lewis, J and Budionno, S and Gomez, R and Khubbar, MK and , and Pham, CD and Gernert, KM and Schmerer, MW and Raphael, BH and Learner, ER and Kersh, EN and Joseph, SJ}, title = {Whole-genome sequencing resolves biochemical misidentification of Neisseria species from urogenital specimens.}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {e0070424}, doi = {10.1128/jcm.00704-24}, pmid = {39360841}, issn = {1098-660X}, abstract = {Neisseria meningitidis (Nm) and Neisseria gonorrhoeae (Ng) are human pathogens that sometimes occupy the same anatomical niche. Ng, the causative agent of gonorrhea, infects 87 million individuals annually worldwide and is an urgent threat due to increasing drug resistance. Ng is a pathogen of the urogenital tract and may infect the oropharyngeal or rectal site, often asymptomatically. Conversely, Nm is an opportunistic pathogen. While often a commensal in the oropharyngeal tract, it is also the leading cause of bacterial meningitis with 1.2 million cases globally, causing significant morbidity and mortality. Horizontal gene transfer (HGT) is likely to occur between Ng and Nm due to their shared anatomical niches and genetic similarity, which poses challenges for accurate detection and treatment. Routine surveillance through the Gonococcal Isolate Surveillance Project and Strengthening the U.S. Response to Resistant Gonorrhea detected six concerning urogenital Neisseria isolates with contradicting species identification in Milwaukee (MIL). While all six isolates were positive for Ng using nucleic acid amplification testing (NAAT) and matrix-assisted laser desorption/ionization time of flight identified the isolates as Ng, two biochemical tests, Gonochek-II and API NH, classified them as Nm. To address this discrepancy, we performed whole-genome sequencing (WGS) using Illumina MiSeq on all isolates and employed various bioinformatics tools. Species detection analysis using BMScan, which uses WGS data, identified all isolates as Ng. Furthermore, Kraken revealed over 98% of WGS reads mapped to the Ng genome and <1% to Nm. Recombination analysis identified putative HGT in all MIL isolates within the γ-glutamyl transpeptidase (ggt) gene, a key component in the biochemical tests used to differentiate between Nm and Ng. Further analysis identified Nm as the source of HGT event. Specifically, the active Nm ggt gene replaced the Ng pseudogenes, ggt1 and ggt2. Together, this study demonstrates that closely related Neisseria species sharing a niche underwent HGT, which led to the misidentification of species following biochemical testing. Importantly, NAAT accurately detected Ng. The misidentification highlights the importance of using WGS to continually evaluate diagnostic or bacterial identification tests.}, } @article {pmid39360838, year = {2024}, author = {Ott, L and Smith, C and Mellata, M}, title = {Dietary zinc supplementation inhibits bacterial plasmid conjugation in vitro by regulating plasmid replication (rep) and transfer (tra) genes.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0148024}, doi = {10.1128/aem.01480-24}, pmid = {39360838}, issn = {1098-5336}, abstract = {Humans use dietary supplements for several intended effects, such as supplementing malnutrition. While these compounds have been developed for host end benefits, their ancillary impact on the gut microbiota remains unclear. The human gut has been proposed as a reservoir for the prevalent lateral transfer of antimicrobial resistance and virulence genes in bacteria through plasmid conjugation. Here, we studied the effect of dietary zinc supplements on the incidence of plasmid conjugation in vitro. Supplement effects were analyzed through standardized broth conjugation assays. The avian pathogenic Escherichia coli (APEC) strain APEC-O2-211 was a donor of the multidrug resistance plasmid pAPEC-O2-211A-ColV, and the human commensal isolate E. coli HS-4 was the plasmid-free recipient. Bacterial strains were standardized and mixed 1:1 and supplemented 1:10 with water, or zinc derived from either commercial zinc supplements or zinc gluconate reagent at varying concentrations. We observed a significant reduction in donors, recipients, and transconjugant populations in conjugations supplemented with zinc, with a dose-dependent relationship. Additionally, we observed a significant reduction (P < 0.05) in log conjugation efficiency in zinc-treated reactions. Upregulation of the mRNA for the plasmid replication initiation gene repA and the subset of transfer genes M, J, E, K, B, P, C, W, U, N, F, Q, D, I, and X was observed. Furthermore, we observed a downregulation of the conjugal propilin gene traA and the entry exclusion gene traS. This study demonstrates the effect of dietary zinc supplements on the conjugal transfer of a multidrug resistance plasmid between pathogenic and commensal bacteria during in vitro conditions.IMPORTANCEThis study identifies dietary zinc supplementation as a potential novel intervention for mitigating the emergence of multidrug resistance in bacteria, thus preventing antibiotic treatment failure and death in patients and animals. Further studies are required to determine the applicability of this approach in an in vivo model.}, } @article {pmid39231787, year = {2024}, author = {Baqar, Z and Sinwat, N and Prathan, R and Chuanchuen, R}, title = {Meat ducks as carriers of antimicrobial-resistant Escherichia coli harboring transferable R plasmids.}, journal = {Journal of veterinary science}, volume = {25}, number = {5}, pages = {e62}, pmid = {39231787}, issn = {1976-555X}, support = {N42A660897/NRCT/National Research Council of Thailand/Thailand ; }, mesh = {Animals ; *Ducks ; *Escherichia coli/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Drug Resistance, Bacterial/genetics ; Escherichia coli Infections/veterinary/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Poultry Diseases/microbiology ; Microbial Sensitivity Tests ; R Factors/genetics ; Gene Transfer, Horizontal ; }, abstract = {IMPORTANCE: Antimicrobial resistance (AMR) is a serious public health threat. AMR bacteria and their resistance determinants in food can be transmitted to humans through the food chain and by direct contact and disseminate directly to the environment.

OBJECTIVE: This study examined the AMR characteristics and transferable R plasmids in Escherichia coli isolated from meat ducks raised in an open-house system.

METHODS: One hundred seventy-seven (n = 177) commensal E. coli were examined for their antimicrobial susceptibilities and horizontal resistance transfer. The plasmids were examined by PCR-based plasmid replicon typing (PBRT) and plasmid multi-locus sequence typing (pMLST).

RESULTS: The highest resistance rate was found against ampicillin (AMP, 83.0%) and tetracycline (TET, 81.9%), and most isolates exhibited multidrug resistance (MDR) (86.4%). The R plasmids were conjugally transferred when TET (n = 4), AMP (n = 3), and chloramphenicol (n = 3) were used as a selective pressure. The three isolates transferred resistance genes either in AMP or TET. The blaCTX-M1 gene resided on conjugative plasmids. Five replicon types were identified, of which Inc FrepB was most common in the donors (n = 13, 38.4%) and transconjugants (n = 16, 31.2%). Subtyping F plasmids revealed five distinct replicons combinations, including F47:A-:B- (n = 2), F29:A-:B23 (n = 1), F29:A-:B- (n = 1), F18:A-B:- (n = 1), and F4:A-:B- (n = 1). The chloramphenicol resistance was significantly correlated with the other AMR phenotypes (p < 0.05).

CONCLUSIONS AND RELEVANCE: The meat ducks harbored MDR E. coli and played an important role in the environmental dissemination of AMR bacteria and its determinants. This confirms AMR as a health issue, highlighting the need for routine AMR monitoring and surveillance of meat ducks.}, } @article {pmid39359630, year = {2024}, author = {Wang, Y and Chen, P and Lin, Q and Zuo, L and Li, L}, title = {Endophytic bacteria with allelopathic potential regulate gene expression and metabolite production in host Casuarina equisetifolia.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1435440}, pmid = {39359630}, issn = {1664-462X}, abstract = {INTRODUCTION: Casuarina equisetifolia is a common protective forest in coastal areas. However, artificial C. equisetifolia forests cannot self-renew, mainly due to the accumulation of allelochemicals. Endophytic bacteria may alleviate the root growth inhibition caused by allelochemicals in C. equisetifolia seedlings. B. amyloliquefaciens and B. aryabhattai were endophytic bacteria with strong allelopathy in C. equisetifolia root. The allelopathy mechanism of these two endophytes and their interaction with C. equisetifolia remains to be studied.

METHODS: Whole-genome sequencing of B. amyloliquefaciens and B. aryabhattai isolated from the roots of allelochemical-accumulating C. equisetifolia was performed using Illumina Hiseq and PacBio single-molecule sequencing platforms. Sterile seedlings of C. equisetifolia were treated with either individual or mixed bacterial cultures through root drenching. Transcriptional and metabolomics analyses were conducted after 3 days of infection.

RESULTS AND DISCUSSION: Whole-genome sequencing of Bacillus aryabhattai and Bacillus amyloliquefaciens showed that the two strains contained various horizontal gene transfer elements such as insertion sequence, prophage and transposon. In addition, these two strains also contain numerous genes related to the synthesis and catabolism of allelochemicals. After these two strains of bacteria were individually or mixed infected with C. equisetifolia, metabolomics and transcriptomic analysis of C. equisetifolia showed the 11 important secondary metabolite biosynthesis among them alkaloids biosynthesis, phenylpropanoid and terpenes biosynthesis and related genes were putatively regulated. Correlation analysis revealed that 48 differentially expressed genes had strong positive correlations with 42 differential metabolites, and 48 differentially expressed genes had strong negative correlations with 36 differential metabolites. For example, CMBL gene showed positive correlations with the allelochemical (-)-Catechin gallate, while Bp10 gene showed negative correlations with (-)-Catechin gallate.

CONCLUSION: The intergenerational accumulation of allelochemicals may induce horizontal gene transfer in endogenic bacteria of Casuarina equisetifolia root. Endophytic Bacillus plays an allelopathic role by assisting the host in regulating gene expression and the production and/or variety of allelochemicals. This comprehensive study sheds light on the intricate genetic and metabolic interactions between Bacillus endophytes and C. equisetifolia. These findings provide insights into endophyte-mediated allelopathy and its potential uses in plant biology and forest sustainability.}, } @article {pmid39357349, year = {2024}, author = {Zhang, K and Gao, J and Lu, T and Wang, Y and Zhang, J and An, J and Xu, H}, title = {Evolution of microbial community and resistance genes in denitrification system under single and combined exposure to benzethonium chloride and methylparaben.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136010}, doi = {10.1016/j.jhazmat.2024.136010}, pmid = {39357349}, issn = {1873-3336}, abstract = {Benzethonium chloride (BZC) and methylparaben (MeP) are commonly added into cosmetics as preservatives, which are frequently detected in wastewater treatment plants. Different response patterns of denitrification system were proposed under single and combined exposure to BZC and MeP (0, 0.5, 5 mg/L) by evaluating system performance, functional genes, extracellular polymeric substance (EPS), cytotoxicity, microbial community structure and resistance genes (RGs). The inhibition effect of BZC on denitrification system was stronger than MeP, and the co-exposure of BZC and MeP showed synergistic effect, enhancing the inhibition effect of BZC single exposure. BZC and/or MeP could promote the diffusion of RGs in sludge, including intracellular RGs (si-RGs) and extracellular RGs (se-RGs). Moreover, the single exposure of BZC and co-exposure of BZC and MeP increased the dissemination risks of RGs in water (w-RGs). IntI1 and tnpA-04, mobile genetic elements (MGEs), correlated positively with diverse RGs from different fractions. Notably, the spread of RGs through horizontal gene transfer mediated by MGEs and the flow of si-RGs into extracellular and water were observed in this study.}, } @article {pmid39264161, year = {2024}, author = {Matsumoto, S and Kishida, K and Nonoyama, S and Sakai, K and Tsuda, M and Nagata, Y and Ohtsubo, Y}, title = {Evolution of the Tn4371 ICE family: traR-mediated coordination of cargo gene upregulation and horizontal transfer.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0060724}, pmid = {39264161}, issn = {2165-0497}, support = {K-2016-004//Institute for Fermentation, Osaka (IFO)/ ; 19H02865//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22H02233//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22K19124//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 19K15725//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {*Gene Transfer, Horizontal ; *DNA Transposable Elements/genetics ; *Gene Expression Regulation, Bacterial ; Bacterial Proteins/genetics/metabolism ; Evolution, Molecular ; Operon ; Up-Regulation ; Conjugation, Genetic ; }, abstract = {ICEKKS102Tn4677 carries a bph operon for the mineralization of polychlorinated biphenyls (PCBs)/biphenyl and belongs to the Tn4371 ICE (integrative and conjugative element) family. In this study, we investigated the role of the traR gene in ICE transfer. The traR gene encodes a LysR-type transcriptional regulator, which is conserved in sequence, positioning, and directional orientation among Tn4371 family ICEs. The traR belongs to the bph operon, and its overexpression on solid medium resulted in modest upregulation of traG (threefold), marked upregulation of xis (80-fold), enhanced ICE excision and, most notably, ICE transfer frequency. We propose the evolutional roles of traR, which upon insertion to its current position, might have connected the cargo gene activation and ICE transfer. This property of ICE, i.e., undergoing transfer under environmental conditions that lead to cargo gene activation, would instantly confer fitness advantages to bacteria newly acquiring this ICE, thereby resulting in efficient dissemination of the Tn4371 family ICEs.IMPORTANCEOnly ICEKKS102Tn4677 is proven to transfer among the widely disseminating Tn4371 family integrative and conjugative elements (ICEs) from β and γ-proteobacteria. We showed that the traR gene in ICEKKS102Tn4677, which is conserved in the ICE family with fixed location and direction, is co-transcribed with the cargo gene and activates ICE transfer. We propose that capturing of traR by an ancestral ICE to the current position established the Tn4371 family of ICEs. Our findings provide insights into the evolutionary processes that led to the widespread distribution of the Tn4371 family of ICEs across bacterial species.}, } @article {pmid39352766, year = {2024}, author = {Ling, X and Gu, X and Shen, Y and Fu, C and Zhou, Y and Yin, Y and Gao, Y and Zhu, Y and Lou, Y and Zheng, M}, title = {Comparative genomic analysis of Acanthamoeba from different sources and horizontal transfer events of antimicrobial resistance genes.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0054824}, doi = {10.1128/msphere.00548-24}, pmid = {39352766}, issn = {2379-5042}, abstract = {UNLABELLED: Acanthamoeba species are among the most common free-living amoeba and ubiquitous protozoa, mainly distributed in water and soil, and cause Acanthamoeba keratitis (AK) and severe visual impairment in patients. Although several studies have reported genomic characteristics of Acanthamoeba, limited sample sizes and sources have resulted in an incomplete understanding of the genetic diversity of Acanthamoeba from different sources. While endosymbionts exert a significant influence on the phenotypes of Acanthamoeba, including pathogenicity, virulence, and drug resistance, the species diversity and functional characterization remain largely unexplored. Herein, our study sequenced and analyzed the whole genomes of 19 Acanthamoeba pathogenic strains that cause AK, and by integrating publicly available genomes, we sampled 29 Acanthamoeba strains from ocular, environmental, and other sources. Combined pan-genomic and comparative functional analyses revealed genetic differences and evolutionary relationships among the different sources of Acanthamoeba, as well as classification into multiple functional groups, with ocular isolates in particular showing significant differences that may account for differences in pathogenicity. Phylogenetic and rhizome gene mosaic analyses of ocular Acanthamoeba strains suggested that genomic exchanges between Acanthamoeba and endosymbionts, particularly potential antimicrobial resistance genes trafficking including the adeF, amrA, and amrB genes exchange events, potentially contribute to Acanthamoeba drug resistance. In conclusion, this study elucidated the adaptation of Acanthamoeba to different ecological niches and the influence of gene exchange on the evolution of ocular Acanthamoeba genome, guiding the clinical diagnosis and treatment of AK and laying a theoretical groundwork for developing novel therapeutic approaches.

IMPORTANCE: Acanthamoeba causes a serious blinding keratopathy, Acanthamoeba keratitis, which is currently under-recognized by clinicians. In this study, we analyzed 48 strains of Acanthamoeba using a whole-genome approach, revealing differences in pathogenicity and function between strains of different origins. Horizontal transfer events of antimicrobial resistance genes can help provide guidance as potential biomarkers for the treatment of specific Acanthamoeba keratitis cases.}, } @article {pmid39350642, year = {2024}, author = {Saha, S and Kanaujia, SP}, title = {Decoding Substrate Selectivity of an Archaeal RlmCD-like Methyltransferase Through Its Salient Traits.}, journal = {Biochemistry}, volume = {63}, number = {19}, pages = {2477-2492}, doi = {10.1021/acs.biochem.4c00401}, pmid = {39350642}, issn = {1520-4995}, mesh = {Substrate Specificity ; *Archaeal Proteins/metabolism/genetics/chemistry ; *Methyltransferases/metabolism/chemistry/genetics ; Pyrococcus horikoshii/enzymology/genetics ; Models, Molecular ; Crystallography, X-Ray ; S-Adenosylmethionine/metabolism ; Amino Acid Sequence ; }, abstract = {5-Methyluridine (m[5]U) rRNA modifications frequently occur at U747 and U1939 (Escherichia coli numbering) in domains II and IV of the 23S rRNA in Gram-negative bacteria, with the help of S-adenosyl-l-methionine (SAM)-dependent rRNA methyltransferases (MTases), RlmC and RlmD, respectively. In contrast, Gram-positive bacteria utilize a single SAM-dependent rRNA MTase, RlmCD, to modify both corresponding sites. Notably, certain archaea, specifically within the Thermococcales group, have been found to possess two genes encoding SAM-dependent archaeal (tRNA and rRNA) m[5]U (Arm[5]U) MTases. Among these, a tRNA-specific Arm[5]U MTase (PabTrmU54) has already been characterized. This study focused on the structural and functional characterization of the rRNA-specific Arm[5]U MTase from the hyperthermophilic archaeon Pyrococcus horikoshii (PhRlmCD). An in-depth structural examination revealed a dynamic hinge movement induced by the replacement of the iron-sulfur cluster with disulfide bonds, obstructing the substrate-binding site. It revealed distinctive characteristics of PhRlmCD, including elongated positively charged loops in the central domain and rotational variations in the TRAM domain, which influence substrate selectivity. Additionally, the results suggested that two potential mini-rRNA fragments interact in a similar manner with PhRlmCD at a positively charged cleft at the interface of domains and facilitate dual MTase activities akin to the protein RlmCD. Altogether, these observations showed that Arm[5]U MTases originated from horizontal gene transfer events, most likely from Gram-positive bacteria.}, } @article {pmid39348487, year = {2024}, author = {Ishida, JK and Costa, EC}, title = {What we know so far and what we can expect next: A molecular investigation of plant parasitism.}, journal = {Genetics and molecular biology}, volume = {47Suppl 1}, number = {Suppl 1}, pages = {e20240051}, pmid = {39348487}, issn = {1415-4757}, abstract = {The review explores parasitic plants' evolutionary success and adaptability, highlighting their widespread occurrence and emphasizing the role of an invasive organ called haustorium in nutrient acquisition from hosts. It discusses the genetic and physiological adaptations that facilitate parasitism, including horizontal gene transfer, and the impact of environmental factors like climate change on these relationships. It addresses the need for further research into parasitic plants' genomes and interactions with their hosts to better predict environmental changes' impacts.}, } @article {pmid39348416, year = {2024}, author = {Mayfield, JA and Raman, S and Ramnarine, AK and Mishra, VK and Huang, AD and Dudoit, S and Buter, J and Cheng, TY and Young, DC and Nair, YM and Ouellet, IG and Griebel, BT and Ma, S and Sherman, DR and Mallet, L and Rhee, KY and Minnaard, AJ and Branch Moody, D}, title = {Mycobacteria that cause tuberculosis have retained ancestrally acquired genes for the biosynthesis of chemically diverse terpene nucleosides.}, journal = {PLoS biology}, volume = {22}, number = {9}, pages = {e3002813}, doi = {10.1371/journal.pbio.3002813}, pmid = {39348416}, issn = {1545-7885}, abstract = {Mycobacterium tuberculosis (Mtb) releases the unusual terpene nucleoside 1-tuberculosinyladenosine (1-TbAd) to block lysosomal function and promote survival in human macrophages. Using conventional approaches, we found that genes Rv3377c and Rv3378c, but not Rv3376, were necessary for 1-TbAd biosynthesis. Here, we introduce linear models for mass spectrometry (limms) software as a next-generation lipidomics tool to study the essential functions of lipid biosynthetic enzymes on a whole-cell basis. Using limms, whole-cell lipid profiles deepened the phenotypic landscape of comparative mass spectrometry experiments and identified a large family of approximately 100 terpene nucleoside metabolites downstream of Rv3378c. We validated the identity of previously unknown adenine-, adenosine-, and lipid-modified tuberculosinol-containing molecules using synthetic chemistry and collisional mass spectrometry, including comprehensive profiling of bacterial lipids that fragment to adenine. We tracked terpene nucleoside genotypes and lipid phenotypes among Mycobacterium tuberculosis complex (MTC) species that did or did not evolve to productively infect either human or nonhuman mammals. Although 1-TbAd biosynthesis genes were thought to be restricted to the MTC, we identified the locus in unexpected species outside the MTC. Sequence analysis of the locus showed nucleotide usage characteristic of plasmids from plant-associated bacteria, clarifying the origin and timing of horizontal gene transfer to a pre-MTC progenitor. The data demonstrated correlation between high level terpene nucleoside biosynthesis and mycobacterial competence for human infection, and 2 mechanisms of 1-TbAd biosynthesis loss. Overall, the selective gain and evolutionary retention of tuberculosinyl metabolites in modern species that cause human TB suggest a role in human TB disease, and the newly discovered molecules represent candidate disease-specific biomarkers.}, } @article {pmid39343406, year = {2024}, author = {Lin, L and Sun, M and Pan, X and Zhang, W and Yang, Y and Yang, Y}, title = {Absence of synergistic effects between microplastics and copper ions on the spread of antibiotic resistance genes within aquatic bacteria at the community level.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {176591}, doi = {10.1016/j.scitotenv.2024.176591}, pmid = {39343406}, issn = {1879-1026}, abstract = {Microplastics and copper ions (Cu[2+]) are favorable in accelerating the propagation of antibiotic resistance genes (ARGs) in the plastisphere, however, their combined effects on the ARG spread within the bacterial community of the natural environment were less understood. The influence of microplastic types and Cu[2+] concentrations on the horizontal gene transfer (HGT) of ARGs mediated by RP4 plasmid within natural bacterial communities in aquatic environments was investigated. Both biodegradable polybutylene succinate (PBS) and non-biodegradable polyvinyl chloride (PVC) microplastics significantly enhanced the transfer of ARGs, with PBS showing a significant higher effect compared to PVC. Cu[2+] also increased transconjugation rates at environmentally relevant concentrations (5 μg L[-1]), but higher levels (50 μg L[-1]) lead to decreased rates due to severe bacterial cell membrane damage. The transconjugation rates in the presence of both microplastics and Cu[2+] were lower than the sum of their individual effects, indicating no synergistic effects between them on transconjugation. Proteobacteria dominated the composition of transconjugates for all the treatment. Transmission electron microscope images and reactive oxygen species production in bacterial cells indicated that the increased contact frequency due to extracellular polymeric substances, combined with enhanced membrane permeability induced by microplastics and Cu[2+], accounted for the increasing transconjugation rates. The study provides valuable insight into the potential effects of microplastics and heavy metals on the spread of ARGs from donors to bacterial communities in natural environments.}, } @article {pmid39343112, year = {2024}, author = {Tao, Y and Zeng, Z and Deng, Y and Zhang, M and Wang, F and Wang, Y}, title = {Phylogeny and evolution of dissimilatory sulfite reduction in prokaryotes.}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {108208}, doi = {10.1016/j.ympev.2024.108208}, pmid = {39343112}, issn = {1095-9513}, abstract = {Sulfate is the second most common nonmetallic ion in modern oceans, as its concentration dramatically increased alongside tectonic activity and atmospheric oxidation in the Proterozoic. Microbial sulfate/sulfite metabolism, involving organic carbon or hydrogen oxidation, is linked to sulfur and carbon biogeochemical cycles. However, the coevolution of microbial sulfate/sulfite metabolism and Earth's history remains unclear. Here, we conducted a comprehensive phylogenetic analysis to explore the evolutionary history of the dissimilatory sulfite reduction (Dsr) pathway. The phylogenies of the Dsr-related genes presented similar branching patterns but also some incongruencies, indicating the complex origin and evolution of Dsr. Among these genes, dsrAB is the hallmark of sulfur-metabolizing prokaryotes. Our detailed analyses suggested that the evolution of dsrAB was shaped by vertical inheritance and multiple horizontal gene transfer events and that selection pressure varied across distinct lineages. Dated phylogenetic trees indicated that key evolutionary events of dissimilatory sulfur-metabolizing prokaryotes were related to the Great Oxygenation Event (2.4-2.0 Ga) and several geological events in the "Boring Billion" (1.8-0.8 Ga), including the fragmentation of the Columbia supercontinent (approximately 1.6 Ga), the rapid increase in marine sulfate (1.3-1.2 Ga), and the Neoproterozoic glaciation event (approximately 1.0 Ga). We also proposed that the voluminous iron formations (approximately 1.88 Ga) might have induced the metabolic innovation of iron reduction. In summary, our study provides new insights into Dsr evolution and a systematic view of the coevolution of dissimilatory sulfur-metabolizing prokaryotes and the Earth's environment.}, } @article {pmid39343029, year = {2024}, author = {Fernie, AR and de Vries, S and de Vries, J}, title = {Evolution of plant metabolism: the state-of-the-art.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1914}, pages = {20230347}, doi = {10.1098/rstb.2023.0347}, pmid = {39343029}, issn = {1471-2970}, mesh = {*Plants/metabolism/genetics ; Biological Evolution ; Metabolic Networks and Pathways/genetics ; Evolution, Molecular ; }, abstract = {Immense chemical diversity is one of the hallmark features of plants. This chemo-diversity is mainly underpinned by a highly complex and biodiverse biochemical machinery. Plant metabolic enzymes originated and were inherited from their eukaryotic and prokaryotic ancestors and further diversified by the unprecedentedly high rates of gene duplication and functionalization experienced in land plants. Unlike prokaryotic microbes, which display frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced relatively few gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner using existing networks as a starting point and under various evolutionary constraints. That said, until recently, the evolution of only a handful of metabolic traits had been extensively investigated and as such, the evolution of metabolism has received a fraction of the attention of, the evolution of development, for example. Advances in metabolomics and next-generation sequencing have, however, recently led to a deeper understanding of how a wide range of plant primary and specialized (secondary) metabolic pathways have evolved both as a consequence of natural selection and of domestication and crop improvement processes. This article is part of the theme issue 'The evolution of plant metabolism'.}, } @article {pmid39339889, year = {2024}, author = {Arhab, Y and Pestova, TV and Hellen, CUT}, title = {Translation of Overlapping Open Reading Frames Promoted by Type 2 IRESs in Avian Calicivirus Genomes.}, journal = {Viruses}, volume = {16}, number = {9}, pages = {}, pmid = {39339889}, issn = {1999-4915}, support = {5 R01 GM097014//NIH (NIGMS)/ ; 5 R35 GM122602//NIH (NIGMS)/ ; }, mesh = {*Open Reading Frames ; *Genome, Viral ; Animals ; *Internal Ribosome Entry Sites/genetics ; *Caliciviridae/genetics ; *Protein Biosynthesis ; RNA, Viral/genetics ; 5' Untranslated Regions/genetics ; Ribosomes/metabolism/genetics ; }, abstract = {Caliciviruses have positive-sense RNA genomes, typically with short 5'-untranslated regions (5'UTRs) that precede the long open reading frame 1 (ORF1). Exceptionally, some avian caliciviruses have long 5'UTRs containing a picornavirus-like internal ribosomal entry site (IRES), which was likely acquired by horizontal gene transfer. Here, we identified numerous additional avian calicivirus genomes with IRESs, predominantly type 2, and determined that many of these genomes contain a ~200-300 codon-long ORF (designated ORF1*) that overlaps the 5'-terminal region of ORF1. The activity of representative type 2 IRESs from grey teal calicivirus (GTCV) and Caliciviridae sp. isolate yc-13 (RaCV1) was confirmed by in vitro translation. Toeprinting showed that in cell-free extracts and in vitro reconstituted reactions, ribosomal initiation complexes assembled on the ORF1* initiation codon and at one or two AUG codons in ORF1 at the 3'-border and/or downstream of the IRES. Initiation at all three sites required eIF4A and eIF4G, which bound to a conserved region of the IRES; initiation on the ORF1* and principal ORF1 initiation codons involved eIF1/eIF1A-dependent scanning from the IRES's 3'-border. Initiation on these IRESs was enhanced by the IRES trans-acting factors (ITAFs) Ebp1/ITAF45, which bound to the apical subdomain Id of the IRES, and PTB (GTCV) or PCBP2 (RaCV1).}, } @article {pmid39086116, year = {2024}, author = {Yang, Q and Li, L and Zhao, G and Cui, Q and Gong, X and Ying, L and Yang, T and Fu, M and Shen, Z}, title = {Characterization of a multiresistance optrA- and lsa(E)-harbouring unconventional circularizable structure in Streptococcus suis.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {79}, number = {10}, pages = {2528-2533}, doi = {10.1093/jac/dkae250}, pmid = {39086116}, issn = {1460-2091}, support = {2022YFC2303900//National Key Research and Development Program of China/ ; 32141001//National Natural Science Foundation of China/ ; }, mesh = {*Streptococcus suis/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Microbial Sensitivity Tests ; *Multigene Family ; *Conjugation, Genetic/genetics ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genomic Islands/genetics ; Lincosamides/pharmacology ; Pleuromutilins ; Diterpenes/pharmacology ; Polycyclic Compounds ; Streptococcal Infections/microbiology ; Genes, Bacterial ; Streptogramin A/pharmacology ; }, abstract = {OBJECTIVES: To identify novel genetic elements facilitating the horizontal transfer of the oxazolidinone/phenicol resistance gene optrA and the pleuromutilin-lincosamide-streptogramin A resistance gene lsa(E) in Streptococcus suis.

METHODS: The complete genomes of S. suis HB18 and two transconjugants were obtained using both the Illumina and Nanopore platforms. MICs were determined by broth microdilution. Inverse PCR was performed to identify circular forms of the novel unconventional circularizable structure (UCS), genomic island (GI) and integrative and conjugative element (ICE). Conjugation experiments assessed the transferability of optrA and lsa(E) genes in S. suis.

RESULTS: S. suis HB18 carried a multiresistance gene cluster optrA-lsa(E)-lnu(B)-aphA-aadE-spw. This gene cluster, flanked by intact and truncated erm(B) in the same orientation, resided on a novel ICESsuHB18. Inverse PCR revealed the existence of a novel UCS, named UCS-optrA + lsa(E), which could excise the gene cluster optrA-lsa(E)-lnu(B)-aphA-aadE-spw and one copy of erm(B) from ICESsuHB18. Two transconjugants with different characteristics were obtained. In transconjugant T-JH-GI, UCS-optrA + lsa(E) excised from ICESsuHB18 inserted into the erm(B)-positive GI, designated GISsuHB18, generating the novel GISsuHB18-1. Meanwhile, in T-JH-ICE, genetic rearrangement events occurred in ICESsuHB18 and GISsuHB18, forming the novel ICESsuHB18-1.

CONCLUSIONS: This is the first report demonstrating the functionally active UCS-optrA + lsa(E) excising from ICESsuHB18 and inserting into the erm(B)-positive GISsuHB18 during the conjugation process. The location of optrA and lsa(E) on a multiresistance UCS enhances its persistence and dissemination.}, } @article {pmid39073766, year = {2024}, author = {González-Pinto, L and Alonso-García, I and Blanco-Martín, T and Camacho-Zamora, P and Fraile-Ribot, PA and Outeda-García, M and Lasarte-Monterrubio, C and Guijarro-Sánchez, P and Maceiras, R and Moya, B and Juan, C and Vázquez-Ucha, JC and Beceiro, A and Oliver, A and Bou, G and Arca-Suárez, J}, title = {Impact of chromosomally encoded resistance mechanisms and transferable β-lactamases on the activity of cefiderocol and innovative β-lactam/β-lactamase inhibitor combinations against Pseudomonas aeruginosa.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {79}, number = {10}, pages = {2591-2597}, doi = {10.1093/jac/dkae263}, pmid = {39073766}, issn = {1460-2091}, support = {//European Union/ ; //Merck Sharp & Dohme/ ; //Investigator Initiated Studies Program/ ; CB21/13/00055//Centro de Investigación Biomédica en Red de Enfermedades Infecciosas/ ; //Spanish Network of Research in Infectious Diseases/ ; //National Plan for Scientific Research, Development and Technological Innovation 2013-2016/ ; //ISCIII-General Subdirection of Assessment and Promotion of the Research-European Regional Development Fund/ ; //Axencia Galega de Innovación/ ; IN607D2021/12//Consellería de Innovación, Consellería de Economía, Emprego e Industria/ ; PI21/00704//ISCIII/ ; CM21/00076//Río Hortega program/ ; IN606B-2022/009//Xunta de Galicia/ ; JR21/00026//Juan Rodés program/ ; }, mesh = {*Pseudomonas aeruginosa/drug effects/genetics/enzymology ; *Cephalosporins/pharmacology ; *Microbial Sensitivity Tests ; *beta-Lactamase Inhibitors/pharmacology ; *beta-Lactamases/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Azabicyclo Compounds/pharmacology ; *Drug Combinations ; *Cefiderocol ; Cyclooctanes/pharmacology ; Tazobactam/pharmacology ; beta-Lactams/pharmacology ; Humans ; beta-Lactam Resistance/genetics ; Ceftazidime/pharmacology ; Pseudomonas Infections/microbiology/drug therapy ; Gene Transfer, Horizontal ; Chromosomes, Bacterial/genetics ; }, abstract = {OBJECTIVES: We aimed to compare the stability of the newly developed β-lactams (cefiderocol) and β-lactam/β-lactamase inhibitor combinations (ceftazidime/avibactam, ceftolozane/tazobactam, aztreonam/avibactam, cefepime/taniborbactam, cefepime/zidebactam, imipenem/relebactam, meropenem/vaborbactam, meropenem/nacubactam and meropenem/xeruborbactam) against the most clinically relevant mechanisms of mutational and transferable β-lactam resistance in Pseudomonas aeruginosa.

METHODS: We screened a collection of 61 P. aeruginosa PAO1 derivatives. Eighteen isolates displayed the most relevant mechanisms of mutational resistance to β-lactams. The other 43 constructs expressed transferable β-lactamases from genes cloned in pUCP-24. MICs were determined by reference broth microdilution.

RESULTS: Cefiderocol and imipenem/relebactam exhibited excellent in vitro activity against all of the mutational resistance mechanisms studied. Aztreonam/avibactam, cefepime/taniborbactam, cefepime/zidebactam, meropenem/vaborbactam, meropenem/nacubactam and meropenem/xeruborbactam proved to be more vulnerable to mutational events, especially to overexpression of efflux operons. The agents exhibiting the widest spectrum of activity against transferable β-lactamases were aztreonam/avibactam and cefepime/zidebactam, followed by cefepime/taniborbactam, cefiderocol, meropenem/xeruborbactam and meropenem/nacubactam. However, some MBLs, particularly NDM enzymes, may affect their activity. Combined production of certain enzymes (e.g. NDM-1) with increased MexAB-OprM-mediated efflux and OprD deficiency results in resistance to almost all agents tested, including last options such as aztreonam/avibactam and cefiderocol.

CONCLUSIONS: Cefiderocol and new β-lactam/β-lactamase inhibitor combinations show promising and complementary in vitro activity against mutational and transferable P. aeruginosa β-lactam resistance. However, the combined effects of efflux pumps, OprD deficiency and efficient β-lactamases could still result in the loss of all therapeutic options. Resistance surveillance, judicious use of new agents and continued drug development efforts are encouraged.}, } @article {pmid38867468, year = {2024}, author = {Qi, L and Wang, W and Fang, L and Li, J and Qi, L and Wang, D and Liu, J and Xiao, Y and Zhou, W and Fang, X}, title = {DNA Molecular Glue Assisted Bacterial Conjugative Transfer.}, journal = {Chemistry (Weinheim an der Bergstrasse, Germany)}, volume = {30}, number = {52}, pages = {e202401399}, doi = {10.1002/chem.202401399}, pmid = {38867468}, issn = {1521-3765}, support = {2022YFA1304500,2022YFC3401003//the National Key Scientific Program of China/ ; Nos. 21735006//National Natural Science Foundation of China/ ; Nos.21890742//National Natural Science Foundation of China/ ; }, mesh = {*Escherichia coli/genetics ; *Conjugation, Genetic ; *DNA, Single-Stranded/chemistry ; Click Chemistry ; Gene Transfer, Horizontal ; Oligonucleotides/chemistry ; }, abstract = {Bacterial conjugation, a commonly used method to horizontally transfer functional genes from donor to recipient strains, plays an important role in the genetic manipulation of bacteria for basic research and industrial production. Successful conjugation depends on the donor-recipient cell recognition and a tight mating junction formation. However, the efficiency of conjugative transfer is usually very low. In this work, we developed a new technique that employed DNA molecule "glue" to increase the match frequency and the interaction stability between the donor and recipient cells. We used two E. coli strains, ETZ and BL21, as a model system, and modified them with the complementary ssDNA oligonucleotides by click chemistry. The conjugation efficiency of the modified bacteria was improved more than 4 times from 10 %-46 %. This technique is simple and generalizable as it only relies on the active amino groups on the bacterial surface. It is expected to have broad applications in constructing engineered bacteria.}, } @article {pmid39338985, year = {2024}, author = {Sung, K and Nawaz, M and Park, M and Chon, J and Khan, SA and Alotaibi, K and Khan, AA}, title = {Comprehensive Genomic Analysis of Uropathogenic E. coli: Virulence Factors, Antimicrobial Resistance, and Mobile Genetic Elements.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, pmid = {39338985}, issn = {2076-0817}, support = {E0770601//United States Food and Drug Administration/ ; }, abstract = {Our whole-genome sequencing analysis of sixteen uropathogenic E. coli isolates revealed a concerning picture of multidrug resistance and potentially virulent bacteria. All isolates belonged to four distinct clonal groups, with the highly prevalent ST131 lineage being associated with extensive antibiotic resistance and virulence factors. Notably, all isolates exhibited multidrug resistance, with some resistant to as many as 12 antibiotics. Fluoroquinolone resistance stemmed primarily from efflux pumps and mutations in gyrase and topoisomerase genes. Additionally, we identified genes encoding resistance to extended-spectrum cephalosporins, trimethoprim/sulfamethoxazole, and various heavy metals. The presence of diverse plasmids and phages suggests the potential for horizontal gene transfer and the dissemination of virulence factors. All isolates harbored genomic islands containing virulence factors associated with adhesion, biofilm formation, and invasion. Genes essential for iron acquisition, flagella biosynthesis, secretion systems, and toxin production were also prevalent. Adding further complexity to understanding the isolates' genetic makeup, we identified CRISPR-Cas systems. This study underscores the need for continued genomic surveillance in understanding the pathogenic mechanisms and resistance profiles of uropathogenic E. coli to aid in developing targeted therapeutic strategies.}, } @article {pmid39338594, year = {2024}, author = {Oliveira, M and Antunes, W and Mota, S and Madureira-Carvalho, Á and Dinis-Oliveira, RJ and Dias da Silva, D}, title = {An Overview of the Recent Advances in Antimicrobial Resistance.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338594}, issn = {2076-2607}, support = {UIDP/04378/2020, UIDB/04378/2020, LA/P/0140/2020, UIDB/50006//Fundação para a Ciência e Tecnologia/ ; }, abstract = {Antimicrobial resistance (AMR), frequently considered a major global public health threat, requires a comprehensive understanding of its emergence, mechanisms, advances, and implications. AMR's epidemiological landscape is characterized by its widespread prevalence and constantly evolving patterns, with multidrug-resistant organisms (MDROs) creating new challenges every day. The most common mechanisms underlying AMR (i.e., genetic mutations, horizontal gene transfer, and selective pressure) contribute to the emergence and dissemination of new resistant strains. Therefore, mitigation strategies (e.g., antibiotic stewardship programs-ASPs-and infection prevention and control strategies-IPCs) emphasize the importance of responsible antimicrobial use and surveillance. A One Health approach (i.e., the interconnectedness of human, animal, and environmental health) highlights the necessity for interdisciplinary collaboration and holistic strategies in combating AMR. Advancements in novel therapeutics (e.g., alternative antimicrobial agents and vaccines) offer promising avenues in addressing AMR challenges. Policy interventions at the international and national levels also promote ASPs aiming to regulate antimicrobial use. Despite all of the observed progress, AMR remains a pressing concern, demanding sustained efforts to address emerging threats and promote antimicrobial sustainability. Future research must prioritize innovative approaches and address the complex socioecological dynamics underlying AMR. This manuscript is a comprehensive resource for researchers, policymakers, and healthcare professionals seeking to navigate the complex AMR landscape and develop effective strategies for its mitigation.}, } @article {pmid39338472, year = {2024}, author = {Gonzalez, V and Abarca-Hurtado, J and Arancibia, A and Claverías, F and Guevara, MR and Orellana, R}, title = {Novel Insights on Extracellular Electron Transfer Networks in the Desulfovibrionaceae Family: Unveiling the Potential Significance of Horizontal Gene Transfer.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338472}, issn = {2076-2607}, support = {11190863//ANID/Fondecyt/ ; 1211977//ANID/Fondecyt/ ; PAI79170091//ANID/ ; FOVI 230154//ANID/ ; Milenio-NCN2023_054//ANID/ ; Scholarship 21231799/2023//ANID/ ; }, abstract = {Some sulfate-reducing bacteria (SRB), mainly belonging to the Desulfovibrionaceae family, have evolved the capability to conserve energy through microbial extracellular electron transfer (EET), suggesting that this process may be more widespread than previously believed. While previous evidence has shown that mobile genetic elements drive the plasticity and evolution of SRB and iron-reducing bacteria (FeRB), few have investigated the shared molecular mechanisms related to EET. To address this, we analyzed the prevalence and abundance of EET elements and how they contributed to their differentiation among 42 members of the Desulfovibrionaceae family and 23 and 59 members of Geobacteraceae and Shewanellaceae, respectively. Proteins involved in EET, such as the cytochromes PpcA and CymA, the outer membrane protein OmpJ, and the iron-sulfur cluster-binding CbcT, exhibited widespread distribution within Desulfovibrionaceae. Some of these showed modular diversification. Additional evidence revealed that horizontal gene transfer was involved in the acquiring and losing of critical genes, increasing the diversification and plasticity between the three families. The results suggest that specific EET genes were widely disseminated through horizontal transfer, where some changes reflected environmental adaptations. These findings enhance our comprehension of the evolution and distribution of proteins involved in EET processes, shedding light on their role in iron and sulfur biogeochemical cycling.}, } @article {pmid39337307, year = {2024}, author = {Zhang, J and Zhu, S and Sun, J and Liu, Y}, title = {Bisphenol S Promotes the Transfer of Antibiotic Resistance Genes via Transformation.}, journal = {International journal of molecular sciences}, volume = {25}, number = {18}, pages = {}, doi = {10.3390/ijms25189819}, pmid = {39337307}, issn = {1422-0067}, support = {BE2023332//Key R&D Program of Jiangsu Province (Modern Agriculture)/ ; ZDYF2024SHFZ050//Science and Technology special fund of Hainan Province/ ; }, mesh = {*Phenols ; *Escherichia coli/genetics/drug effects ; *Sulfones/pharmacology ; *Plasmids/genetics ; Reactive Oxygen Species/metabolism ; Transformation, Bacterial ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Benzhydryl Compounds ; Citric Acid Cycle/drug effects/genetics ; }, abstract = {The antibiotic resistance crisis has seriously jeopardized public health and human safety. As one of the ways of horizontal transfer, transformation enables bacteria to acquire exogenous genes naturally. Bisphenol compounds are now widely used in plastics, food, and beverage packaging, and have become a new environmental pollutant. However, their potential relationship with the spread of antibiotic resistance genes (ARGs) in the environment remains largely unexplored. In this study, we aimed to assess whether the ubiquitous bisphenol S (BPS) could promote the transformation of plasmid-borne ARGs. Using plasmid pUC19 carrying the ampicillin resistance gene as an extracellular ARG and model microorganism E. coli DH5α as the recipient, we established a transformation system. Transformation assays revealed that environmentally relevant concentrations of BPS (0.1-10 μg/mL) markedly enhanced the transformation frequency of plasmid-borne ARGs into E. coli DH5α up to 2.02-fold. Fluorescent probes and transcript-level analyses suggest that BPS stimulated increased reactive oxygen species (ROS) production, activated the SOS response, induced membrane damage, and increased membrane fluidity, which weakened the barrier for plasmid transfer, allowing foreign DNA to be more easily absorbed. Moreover, BPS stimulates ATP supply by activating the tricarboxylic acid (TCA) cycle, which promotes flagellar motility and expands the search for foreign DNA. Overall, these findings provide important insight into the role of bisphenol compounds in facilitating the horizontal spread of ARGs and emphasize the need to monitor the residues of these environmental contaminants.}, } @article {pmid39336804, year = {2024}, author = {Opazo-Capurro, A and Xanthopoulou, K and Arazo Del Pino, R and González-Muñoz, P and Matus-Köhler, M and Amsteins-Romero, L and Jerez-Olate, C and Hormazábal, JC and Vera, R and Aguilera, F and Fuller, S and Higgins, PG and González-Rocha, G}, title = {Co-Occurrence of Two Plasmids Encoding Transferable blaNDM-1 and tet(Y) Genes in Carbapenem-Resistant Acinetobacter bereziniae.}, journal = {Genes}, volume = {15}, number = {9}, pages = {}, doi = {10.3390/genes15091213}, pmid = {39336804}, issn = {2073-4425}, support = {FONDECYT 1220708//Agencia Nacional de Investigación y Desarrollo/ ; FONDECYT Iniciacion 11190602//Agencia Nacional de Investigación y Desarrollo/ ; FONDEQUIP EQM200056//Agencia Nacional de Investigación y Desarrollo/ ; }, mesh = {*Plasmids/genetics ; *Acinetobacter/genetics/drug effects ; *beta-Lactamases/genetics ; Humans ; *Carbapenems/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Acinetobacter Infections/microbiology/drug therapy/epidemiology ; Bacterial Proteins/genetics ; Whole Genome Sequencing ; COVID-19 ; }, abstract = {Acinetobacter bereziniae has emerged as a significant human pathogen, acquiring multiple antibiotic resistance genes, including carbapenemases. This study focuses on characterizing the plasmids harboring the blaNDM-1 and tet(Y) genes in two carbapenem-resistant A. bereziniae isolates (UCO-553 and UCO-554) obtained in Chile during the COVID-19 pandemic. Methods: Antibiotic susceptibility testing was conducted on UCO-553 and UCO-554. Both isolates underwent whole-genome sequencing to ascertain their sequence type (ST), core genome multilocus sequence-typing (cgMLST) profile, antibiotic resistance genes, plasmids, and mobile genetic elements. Conjugation experiments were performed for both isolates. Results: Both isolates exhibited broad resistance, including resistance to carbapenems, third-generation cephalosporins, fluoroquinolones, tetracycline, cotrimoxazole, and aminoglycosides. Both isolates belong to sequence type ST[PAS]1761, with a difference of 17 out of 2984 alleles. Each isolate carried a 47,274 bp plasmid with blaNDM-1 and aph(3')-VI genes and two highly similar plasmids: a 35,184 bp plasmid with tet(Y), sul2, aph(6)-Id, and aph(3″)-Ib genes, and a 6078 bp plasmid containing the ant(2″)-Ia gene. Quinolone-resistance mutations were identified in the gyrA and parC genes of both isolates. Importantly, blaNDM-1 was located within a Tn125 transposon, and tet(Y) was embedded in a Tn5393 transposon. Conjugation experiments successfully transferred blaNDM-1 and tet(Y) into the A. baumannii ATCC 19606 strain, indicating the potential for horizontal gene transfer. Conclusions: This study highlights the critical role of plasmids in disseminating resistance genes in A. bereziniae and underscores the need for the continued genomic surveillance of this emerging pathogen. The findings emphasize the importance of monitoring A. bereziniae for its potential to cause difficult-to-treat infections and its capacity to spread resistance determinants against clinically significant antibiotics.}, } @article {pmid39335078, year = {2024}, author = {Tarrah, A and Zhang, D and Darvishzadeh, P and LaPointe, G}, title = {The Contribution of Dairy Bedding and Silage to the Dissemination of Genes Coding for Antimicrobial Resistance: A Narrative Review.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/antibiotics13090905}, pmid = {39335078}, issn = {2079-6382}, abstract = {Antimicrobial resistance (AMR) is a concern in the dairy industry. Recent studies have indicated that bedding serves as a reservoir for antimicrobial-resistant bacteria and antimicrobial-resistance genes (ARGs), while silage has been proposed as another possible source. The impact of AMR in dairy farming can be significant, resulting in decreased productivity and economic losses for farmers. Several studies have highlighted the safety implications of AMR bacteria and genes in bedding and silage, emphasizing the need for further research on how housing, bedding, and silage management affect AMR in farm environments. Exposure to sub-lethal concentrations of antibiotics, such as those from contaminated bedding and silage, can prompt bacteria to develop resistance mechanisms. Thus, even if antimicrobial usage is diminished, ARGs may be maintained in the dairy farm environment. By implementing proactive measures to tackle AMR in dairy farming, we can take steps to preserve the health and productivity of dairy cattle while also protecting public health. This involves addressing the prudent use of antibiotics during production and promoting animal welfare, hygiene, and management practices in bedding and farm environments to minimize the risk of AMR development and spread. This narrative review compiles the growing research, positioning the contribution of bedding and silage to the prevalence and dissemination of AMR, which can elicit insights for researchers and policymakers.}, } @article {pmid39334999, year = {2024}, author = {Mitchell, TM and Ho, T and Salinas, L and VanderYacht, T and Walas, N and Trueba, G and Graham, JP}, title = {Analysis of Antibiotic Resistance Genes (ARGs) across Diverse Bacterial Species in Shrimp Aquaculture.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/antibiotics13090825}, pmid = {39334999}, issn = {2079-6382}, abstract = {There is little information available on antibiotic resistance (ABR) within shrimp aquaculture environments. The aim of this study was to investigate the presence of antibiotic resistance genes (ARGs) in shrimp farming operations in Atacames, Ecuador. Water samples (n = 162) and shrimp samples (n = 54) were collected from three shrimp farming operations. Samples were cultured and a subset of isolates that grew in the presence of ceftriaxone, a third-generation cephalosporin, were analyzed using whole-genome sequencing (WGS). Among the sequenced isolates (n = 44), 73% of the isolates contained at least one ARG and the average number of ARGs per isolate was two, with a median of 3.5 ARGs. Antibiotic resistance genes that confer resistance to the β-lactam class of antibiotics were observed in 65% of the sequenced isolates from water (20/31) and 54% of the isolates from shrimp (7/13). We identified 61 different ARGs across the 44 sequenced isolates, which conferred resistance to nine antibiotic classes. Over half of all sequenced isolates (59%, n = 26) carried ARGs that confer resistance to more than one class of antibiotics. ARGs for certain antibiotic classes were more common, including beta-lactams (26 ARGs); aminoglycosides (11 ARGs); chloramphenicol (three ARGs); and trimethoprim (four ARGs). Sequenced isolates consisted of a diverse array of bacterial orders and species, including Escherichia coli (48%), Klebsiella pneumoniae (7%), Aeromonadales (7%), Pseudomonadales (16%), Enterobacter cloacae (2%), and Citrobacter freundii (2%). Many ARGs were shared across diverse species, underscoring the risk of horizontal gene transfer in these environments. This study indicated the widespread presence of extended-spectrum β-lactamase (ESBL) genes in shrimp aquaculture, including blaCTX-M, blaSHV, and blaTEM genes. Increased antibiotic resistance surveillance of shrimp farms and identification of aquaculture operation-level risk factors, such as antibiotic use, will likely be important for mitigating the spread of ARGs of clinical significance.}, } @article {pmid39334992, year = {2024}, author = {Liu, L and Zou, X and Cheng, Y and Li, H and Zhang, X and Yuan, Q}, title = {Contrasting Dynamics of Intracellular and Extracellular Antibiotic Resistance Genes in Response to Nutrient Variations in Aquatic Environments.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/antibiotics13090817}, pmid = {39334992}, issn = {2079-6382}, support = {No. 42377436 and 42177348//National Natural Science Foundation of China/ ; 2022YFC3205400//China National Key R&D Program/ ; }, abstract = {The propagation of antibiotic resistance in environments, particularly aquatic environments that serve as primary pathways for antibiotic resistance genes (ARGs), poses significant health risks. The impact of nutrients, as key determinants of bacterial growth and metabolism, on the propagation of ARGs, particularly extracellular ARGs (eARGs), remains poorly understood. In this study, we collected microorganisms from the Yangtze River and established a series of microcosms to investigate how variations in nutrient levels and delivery frequency affect the relative abundance of intracellular ARGs (iARGs) and eARGs in bacterial communities. Our results show that the relative abundance of 7 out of 11 representative eARGs in water exceeds that of iARGs, while 8 iARGs dominate in biofilms. Notably, iARGs and eARGs consistently exhibited opposite responses to nutrient variation. When nutrient levels increased, iARGs in the water also increased, with the polluted group (COD = 333.3 mg/L, COD:N:P = 100:3:0.6, m/m) and the eutrophic group (COD = 100 mg/L, COD:N:P = 100:25:5, m/m) showing 1.2 and 3.2 times higher levels than the normal group (COD = 100 mg/L, COD:N:P = 100:10:2, m/m), respectively. In contrast, eARGs decreased by 6.7% and 8.4% in these groups. On the other hand, in biofilms, higher nutrient levels led to an increase in eARGs by 1.5 and 1.7 times, while iARGs decreased by 17.5% and 50.1% in the polluted and eutrophic groups compared to the normal group. Moreover, while increasing the frequency of nutrient delivery (from 1 time/10 d to 20 times/10 d) generally did not favor iARGs in either water or biofilm, it selectively enhanced eARGs in both. To further understand these dynamics, we developed an ARGs-nutrient model by integrating the Lotka-Volterra and Monod equations. The results highlight the complex interplay of bacterial growth, nutrient availability, and mechanisms such as horizontal gene transfer and secretion influencing ARGs' propagation, driving the opposite trend between these two forms of ARGs. This contrasting response between iARGs and eARGs contributes to a dynamic balance that stabilizes bacterial resistance levels amid nutrient fluctuations. This study offers helpful implications regarding the persistence of bacterial resistance in the environment.}, } @article {pmid39329926, year = {2024}, author = {Syed, K}, title = {Ferredoxins: Functions, Evolution, Potential Applications, and Challenges of Subtype Classification.}, journal = {Current issues in molecular biology}, volume = {46}, number = {9}, pages = {9659-9673}, pmid = {39329926}, issn = {1467-3045}, abstract = {Ferredoxins are proteins found in all biological kingdoms and are involved in essential biological processes including photosynthesis, lipid metabolism, and biogeochemical cycles. Ferredoxins are classified into different groups based on the iron-sulfur (Fe-S) clusters that they contain. A new subtype classification and nomenclature system, based on the spacing between amino acids in the Fe-S binding motif, has been proposed in order to better understand ferredoxins' biological diversity and evolutionary linkage across different organisms. This new classification system has revealed an unparalleled diversity between ferredoxins and has helped identify evolutionarily linked ferredoxins between species. The current review provides the latest insights into ferredoxin functions and evolution, and the new subtype classification, outlining their potential biotechnological applications and the future challenges in streamlining the process.}, } @article {pmid39328914, year = {2024}, author = {Yan, J and Doublet, B and Wiedemann, A}, title = {Trends in horizontal gene transfer research in Salmonella antimicrobial resistance: a bibliometric analysis.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1439664}, pmid = {39328914}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) favors the acquisition and spread of antimicrobial resistance (AMR) genes in Salmonella, making it a major public health concern. We performed a bibliometric analysis to provide the current landscape of HGT in research on Salmonella AMR and identify emerging trends and potential research directions for the future. Data were collected from the Web of Science Core Collection and limited to articles and reviews published between 1999 and 2024 in English. VOSviewer 1.6.19 and CiteSpace 6.2.R1 software were used to conduct bibliometric analysis and visualize co-occurring keywords. A total of 1,467 publications were retrieved for analysis. American researchers contributed the most articles (n = 310). In the meantime, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement have the highest citation/publication rate of 85.6. Recent studies have focused on the application of whole genome sequencing (WGS), Salmonella quinolone and colistin resistance, and the biocontrol of Salmonella AMR. These findings provide new insights into the role of HGT and help identify new targets for controlling the spread of AMR in Salmonella populations.}, } @article {pmid39327210, year = {2024}, author = {García-Lozano, M and Salem, H}, title = {Microbial bases of herbivory in beetles.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2024.08.004}, pmid = {39327210}, issn = {1878-4380}, abstract = {The ecological radiation of herbivorous beetles is among the most successful in the animal kingdom. It coincided with the rise and diversification of flowering plants, requiring beetles to adapt to a nutritionally imbalanced diet enriched in complex polysaccharides and toxic secondary metabolites. In this review, we explore how beetles overcame these challenges by coopting microbial genes, enzymes, and metabolites, through both horizontal gene transfer (HGT) and symbiosis. Recent efforts revealed the functional convergence governing both processes and the unique ways in which microbes continue to shape beetle digestion, development, and defense. The development of genetic and experimental tools across a diverse set of study systems has provided valuable mechanistic insights into how microbes spurred metabolic innovation and facilitated an herbivorous transition in beetles.}, } @article {pmid39326418, year = {2024}, author = {Liu, Y and Miao, B and Li, W and Hu, X and Bai, F and Abuduresule, Y and Liu, Y and Zheng, Z and Wang, W and Chen, Z and Zhu, S and Feng, X and Cao, P and Ping, W and Yang, R and Dai, Q and Liu, F and Tian, C and Yang, Y and Fu, Q}, title = {Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2024.08.008}, pmid = {39326418}, issn = {1097-4172}, abstract = {Despite the long history of consumption of fermented dairy, little is known about how the fermented microbes were utilized and evolved over human history. Here, by retrieving ancient DNA of Bronze Age kefir cheese (∼3,500 years ago) from the Xiaohe cemetery, we explored past human-microbial interactions. Although it was previously suggested that kefir was spread from the Northern Caucasus to Europe and other regions, we found an additional spreading route of kefir from Xinjiang to inland East Asia. Over evolutionary history, the East Asian strains gained multiple gene clusters with defensive roles against environmental stressors, which can be a result of the adaptation of Lactobacillus strains to various environmental niches and human selection. Overall, our results highlight the role of past human activities in shaping the evolution of human-related microbes, and such insights can, in turn, provide a better understanding of past human behaviors.}, } @article {pmid39324609, year = {2024}, author = {Liu, QH and Yuan, L and Li, ZH and Leung, KMY and Sheng, GP}, title = {Natural Organic Matter Enhances Natural Transformation of Extracellular Antibiotic Resistance Genes in Sunlit Water.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c08211}, pmid = {39324609}, issn = {1520-5851}, abstract = {Antibiotic resistance genes (ARGs) as emerging environmental contaminants exacerbate the risk of spreading antibiotic resistance. Natural organic matter (NOM) is ubiquitous in aquatic environments and plays a crucial role in biogeochemical cycles. However, its impact on the dissemination of extracellular antibiotic resistance genes (eARGs) under sunlight exposure remains elusive. This study reveals that environmentally relevant levels of NOM (0.1-20 mg/L) can significantly enhance the natural transformation frequency of the model bacterium Acinetobacter baylyi ADP1 by up to 7.6-fold under simulated sunlight. Similarly, this enhancement was consistently observed in natural water and wastewater systems. Further mechanism analysis revealed that reactive oxygen species (ROS) generated by NOM under sunlight irradiation, primarily singlet oxygen and hydroxyl radicals, play a crucial role in this process. These ROS induce intracellular oxidative stress and elevated cellular membrane permeability, thereby indirectly boosting ATP production and enhancing cell competence of extracellular DNA uptake and integration. Our findings highlight a previously underestimated role of natural factors in the dissemination of eARGs within aquatic ecosystems and deepen our understanding of the complex interplay between NOM, sunlight, and microbes in environmental water bodies. This underscores the importance of developing comprehensive strategies to mitigate the spread of antibiotic resistance in aquatic environments.}, } @article {pmid39322056, year = {2024}, author = {Chen, J and Lin, Y and Zhu, Y and Zhang, Y and Qian, Q and Chen, C and Xie, S}, title = {Spatiotemporal profiles and underlying mechanisms of the antibiotic resistome in two water-diversion lakes.}, journal = {Environmental research}, volume = {263}, number = {Pt 1}, pages = {120051}, doi = {10.1016/j.envres.2024.120051}, pmid = {39322056}, issn = {1096-0953}, abstract = {Human-induced interventions have altered the local characteristics of the lake ecosystems through changes in hydraulic exchange, which in turn impacts the ecological processes of antibiotic resistance genes (ARGs) in the lakes. However, the current understanding of the spatiotemporal patterns and driving factors of ARGs in water-diversion lakes is still seriously insufficient. In the present study, we investigated antibiotic resistome in the main regulation and storage hubs, namely Nansi Lake and Dongping Lake, of the eastern part of the South-to-North Water Diversion project in Shandong Province (China) using a metagenomic-based approach. A total of 653 ARG subtypes belonging to 25 ARG types were detected with a total abundance of 0.125-0.390 copies/cell, with the dominance of bacitracin, multidrug, and macrolide-lincosamide streptogramin resistance genes. The ARG compositions were sensitive to seasonal variation and also interfered by artificial regulation structures along the way. Human pathogenic bacteria such as Acinetobacter calcoaceticus, Acinetobacter lwoffii, Klebsiella pneumoniae, along with the multidrug resistance genes they carried, were the focus of risk control in the two studied lakes, especially in summer. Plasmids were the key mobile genetic elements (MGEs) driving the horizontal gene transfer of ARGs, especially multidrug and sulfonamide resistance genes. The null model revealed that stochastic process was the main driver of ecological drift for ARGs in the lakes. The partial least squares structural equation model further determined that seasonal changes of pH and temperature drove a shift in the bacterial community, which in turn shaped the profile of ARGs by altering the composition of MGEs, antibacterial biocide- and metal-resistance genes (BMGs), and virulence factor genes (VFGs). Our results highlighted the importance of seasonal factors in determining the water transfer period. These findings can aid in a deeper understanding of the spatiotemporal variations of ARGs in lakes and their driving factors, offering a scientific basis for antibiotic resistance management.}, } @article {pmid39321479, year = {2024}, author = {Rong, L and Wu, L and Zong, L and Wang, W and Xiao, Y and Yang, C and Pan, H and Zou, X}, title = {Evolution of the Black solider fly larvae gut antibiotic resistome during kitchen waste disposal.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135878}, doi = {10.1016/j.jhazmat.2024.135878}, pmid = {39321479}, issn = {1873-3336}, abstract = {Kitchen waste (KW) is an important reservoir of antibiotic resistance genes (ARGs). Black solider fly larvae (BSFL) are extensively employed in KW disposal, closely linking to their robust gut microbes. However, antibiotic resistome in BSFL gut during the KW disposal processes and the mechanism remain unclear. In the present study, the antibiotic resistome in BSFL gut within the 12 days KW disposal processes were investigated. Results showed that, ARGs abundance initially increased and subsequently decreased, the five most prevalent core ARG classes were tetracycline, aminoglycoside, cephalosporin, lincosamide and multidrug. A total of 7 MGE types were observed and the horizontal gene transfer (HGT) of ARGs was predominantly mediated by plasmids. Host microbes were mainly categorized into Proteobacteria (98.12 %) and their assemblies were mainly classified into the deterministic processes. To elucidate the driving mechanisms, the mantel test and the structural equation model (SEM) were developed. Results indicated that microbial functions (0.912, p < 0.0001) and microbial community (1.014, p = 0.036), consistently showed very significant relationships with the patterns of ARGs, which presented higher direct effects than indirect effects. Overall, this study makes an initial contribution to a more deepgoing comprehension of the gut antibiotic resistome of BSFL during KW disposal.}, } @article {pmid39319368, year = {2024}, author = {Pierpont, CL and Baroch, JJ and Church, MJ and Miller, SR}, title = {Idiosyncratic genome evolution of the thermophilic cyanobacterium Synechococcus at the limits of phototrophy.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae184}, pmid = {39319368}, issn = {1751-7370}, abstract = {Thermophilic microorganisms are expected to have smaller cells and genomes compared with mesophiles, a higher proportion of horizontally acquired genes, and distinct nucleotide and amino acid composition signatures. Here, we took an integrative approach to investigate these apparent correlates of thermophily for Synechococcus A/B cyanobacteria, which include the most heat-tolerant phototrophs on the planet. Phylogenomics confirmed a unique origin of different thermotolerance ecotypes, with low levels of continued gene flow between ecologically divergent but overlapping populations, which has shaped the distribution of phenotypic traits along these geothermal gradients. More thermotolerant strains do have smaller genomes, but genome reduction is associated with a decrease in community richness and metabolic diversity, rather than with cell size. Horizontal gene transfer played only a limited role during Synechococcus evolution, but, the most thermotolerant strains have acquired a Thermus tRNA modification enzyme that may stabilize translation at high temperatures. Although nucleotide base composition was not associated with thermotolerance, we found a general replacement of aspartate with glutamate, as well as a dramatic remodeling of amino acid composition at the highest temperatures that substantially differed from previous predictions. We conclude that Synechococcus A/B genome diversification largely does not conform to the standard view of temperature adaptation. In addition, carbon fixation was more thermolabile than photosynthetic oxygen evolution for the most thermotolerant strains compared with less tolerant lineages. This suggests that increased flow of reducing power generated during the light reactions to an electron sink(s) beyond carbon dioxide has emerged during temperature adaptation of these bacteria.}, } @article {pmid39316921, year = {2024}, author = {Liu, Z and Feng, L and Li, B and Lü, C and Sun, J and Giannakis, S}, title = {Crouching bacteria, hidden tetA genes in natural waters: Intracellular damage via double persulfate activation (UVA/Fe[2+]/PDS) effectively alleviates the spread of antibiotic resistance.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135854}, doi = {10.1016/j.jhazmat.2024.135854}, pmid = {39316921}, issn = {1873-3336}, abstract = {In this study, we elucidated the chemical and biological inactivation mechanisms of peroxydisulfate (PDS) activated by UVA and Fe[2+] (UVA/Fe[2+]/PDS) in wild-type antibiotic-resistant bacteria (ARB) isolated from a river in Inner Mongolia. Among the screened wild-type ARB, the relative abundance of unidentified Enterobacteriaceae, Stenotrophomonas, and Ralstonia was high. A ratio of 1:1 for Fe[2+] and PDS under 18 W·m[-2] UVA radiation (sunny days) completely inactivated the environmental ARB isolates. In the macro view of the inactivation process, Fe[2+] first activates PDS rapidly, and later the UVA energy accumulated starts to activate PDS; HO• then becomes the main active species at a rate-limiting step. From a micro perspective, damage to the cell wall, intracellular proteins, inactivation of antioxidant enzymes, and genetic material degradation are the inactivation series of events by UVA/Fe[2+]/PDS, contributing to the 97.8 % inactivation of ARB at the initial stage. No regrowth of sublethal ARBs was observed. The transfer of tetracycline resistance genes from ARB to lab E. coli was evaluated by horizontal gene transfer (HGT), in which no HGT occurred when ARB was eliminated by UVA/Fe[2+]/PDS. Moreover, the sulfate and iron residuals in the effluents of treated water were lower than the drinking water standards. In summary, PDS, UVA, and Fe[2+] activation effectively inactivated wild ARB with a low concentration of reagents, while inhibiting their regrowth and spread of resistance due to the contribution of intracellular inactivation pathways.}, } @article {pmid39213152, year = {2024}, author = {Cordero, M and Jauffred, L}, title = {Following plasmid propagation in complex bacterial communities.}, journal = {Cell reports}, volume = {43}, number = {9}, pages = {114675}, doi = {10.1016/j.celrep.2024.114675}, pmid = {39213152}, issn = {2211-1247}, mesh = {*Plasmids/genetics/metabolism ; *Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; Conjugation, Genetic ; }, abstract = {In this issue of Cell Reports, Ma et al.[1] identify causative regulatory links between self-organization in surface-attached bacterial colonies and the rate of horizontal gene transfers (conjugations) and subsequent selection of the newly arising population of recipient bacteria (transconjugants).}, } @article {pmid39316269, year = {2024}, author = {Wang, L and Yu, L and Cai, B}, title = {Characteristics of tetracycline antibiotic resistance gene enrichment and migration in soil-plant system.}, journal = {Environmental geochemistry and health}, volume = {46}, number = {11}, pages = {427}, pmid = {39316269}, issn = {1573-2983}, support = {LH2023C088//the Natural Science Foundation of Heilongjiang Province of China/ ; LH2023C088//the Natural Science Foundation of Heilongjiang Province of China/ ; LH2023C088//the Natural Science Foundation of Heilongjiang Province of China/ ; HST2022TR002//the Scientific Research Project on Ecological Environmental Protection in Heilongjiang Province/ ; HST2022TR002//the Scientific Research Project on Ecological Environmental Protection in Heilongjiang Province/ ; HST2022TR002//the Scientific Research Project on Ecological Environmental Protection in Heilongjiang Province/ ; 2023SYSJJ15//2023 Open Fund Subjects of the Key Laboratory of Agro-ecological Safety in Hebei Province Project/ ; 2023SYSJJ15//2023 Open Fund Subjects of the Key Laboratory of Agro-ecological Safety in Hebei Province Project/ ; 2023SYSJJ15//2023 Open Fund Subjects of the Key Laboratory of Agro-ecological Safety in Hebei Province Project/ ; }, mesh = {*Soil Microbiology ; *Soil Pollutants ; *Tetracycline Resistance/genetics ; *Gene Transfer, Horizontal ; Plants/microbiology ; Humans ; Bacteria/genetics/drug effects ; Soil/chemistry ; Tetracycline/pharmacology ; }, abstract = {Tetracycline Resistance Genes (TRGs) have received widespread attention in recent years, as they are a novel environmental pollutant that can rapidly accumulate and migrate in soil plant systems through horizontal gene transfer (HGT), posing a potential threat to food safety and public health. This article systematically reviews the pollution sources, enrichment, and migration characteristics of TRGs in soil. The main sources of TRGs include livestock manure and contaminated wastewater, especially in intensive farming environments where TRGs pollution is more severe. In soil, TRGs diffuse horizontally between bacteria and migrate to plant tissues through mechanisms such as plasmid conjugation, integron mediation, and phage transduction. The migration of TRGs is not limited to the soil interior, and increasing evidence suggests that they can also enter the plant system through plant root absorption and the HGT pathway of endophytic bacteria, ultimately accumulating in plant roots, stems, leaves, fruits, and other parts. This process has a direct impact on human health, especially when TRGs are found in crops such as vegetables, which may be transmitted to the human body through the food chain. In addition, this article also deeply analyzed various factors that affect the migration of TRGs, including the residual level of tetracycline in soil, the type and concentration of microorganisms, heavy metal pollution, and the presence of new pollutants such as microplastics. These factors significantly affect the enrichment rate and migration mode of TRGs in soil. In addition, two technologies that can effectively eliminate TRGs in livestock breeding environments were introduced, providing reference for healthy agricultural production. The article concludes by summarizing the shortcomings of current research on TRGs, particularly the limited understanding of TRG migration pathways and their impact mechanisms. Future research should focus on revealing the migration mechanisms of TRGs in soil plant systems and developing effective control and governance measures to reduce the environmental transmission risks of TRGs and ensure the safety of ecosystems and human health.}, } @article {pmid39312572, year = {2024}, author = {Gonçalves, C and Harrison, MC and Steenwyk, JL and Opulente, DA and LaBella, AL and Wolters, JF and Zhou, X and Shen, XX and Groenewald, M and Hittinger, CT and Rokas, A}, title = {Diverse signatures of convergent evolution in cactus-associated yeasts.}, journal = {PLoS biology}, volume = {22}, number = {9}, pages = {e3002832}, doi = {10.1371/journal.pbio.3002832}, pmid = {39312572}, issn = {1545-7885}, abstract = {Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently approximately 17 times. Using a machine learning-based approach, we further found that cactophily can be predicted with 76% accuracy from both functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which we found to be likely associated with altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall-degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved independently through disparate molecular mechanisms. Notably, we found that multiple cactophilic species and their close relatives have been reported as emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle-and perhaps more generally lifestyles favoring thermotolerance-might preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high-throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.}, } @article {pmid39309771, year = {2024}, author = {Westerström, P and Gabrielsen Ås, C and Bak Dragsted, U}, title = {Characterising virulence in a nontoxigenic non-O1/non-O139 Vibrio cholerae isolate imported from Vietnam.}, journal = {Heliyon}, volume = {10}, number = {18}, pages = {e37205}, pmid = {39309771}, issn = {2405-8440}, abstract = {Vibrio cholerae is a major human pathogen that can cause life-threatening acute diarrhea. V. cholerae are classified according to O-antigen polysaccharide outer membrane properties, where the serotypes O1 and O139 are strains that cause pandemics and epidemics while non-O1/non-O139 usually cause mild disease. The dynamic evolution of V. cholerae involves acquisition of new virulence factors through horizontal gene transfer and formerly nontoxigenic serogroups are increasingly being reported to cause severe forms of human disease. In this study we have serotyped one isolate (ST588-CPH) of imported V. cholerae from Vietnam to Denmark and performed whole genome sequencing to identify known virulence genes and furthermore studied the pattern of virulence in closely related pathogenic strains of V. cholerae. ST558-CPH was found to be a non-O1/non-O139 strain. Initial analysis from the whole genome sequencing gave a 96,6 % match to the O139-specific wbfZ gene, but in a second analysis with a higher identification threshold, the wbfZ gene was absent. We suggest a "de novo" display of a database misannotation, which explains the conflicting results. The MLST analysis revealed that the isolate belongs to the nontoxigenic non-O1/non-O139 sequence type ST558. ST558 has recently been reported as a sequence type forming a cluster of ST's that should be monitored, as it has shown to have virulence causing moderate to severe illness. Our analysis of virulence genes identified MakA, a recently discovered toxin, which seems to be generally present in both toxigenic and nontoxigenic strains.}, } @article {pmid39236811, year = {2024}, author = {Sun, Z and Hong, W and Xue, C and Dong, N}, title = {A comprehensive review of antibiotic resistance gene contamination in agriculture: Challenges and AI-driven solutions.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {175971}, doi = {10.1016/j.scitotenv.2024.175971}, pmid = {39236811}, issn = {1879-1026}, mesh = {*Agriculture/methods ; *Drug Resistance, Microbial/genetics ; Artificial Intelligence ; Anti-Bacterial Agents ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Wastewater/microbiology ; Animals ; }, abstract = {Since their discovery, the prolonged and widespread use of antibiotics in veterinary and agricultural production has led to numerous problems, particularly the emergence and spread of antibiotic-resistant bacteria (ARB). In addition, other anthropogenic factors accelerate the horizontal transfer of antibiotic resistance genes (ARGs) and amplify their impact. In agricultural environments, animals, manure, and wastewater are the vectors of ARGs that facilitate their spread to the environment and humans via animal products, water, and other environmental pathways. Therefore, this review comprehensively analyzed the current status, removal methods, and future directions of ARGs on farms. This article 1) investigates the origins of ARGs on farms, the pathways and mechanisms of their spread to surrounding environments, and various strategies to mitigate their spread; 2) determines the multiple factors influencing the abundance of ARGs on farms, the pathways through which ARGs spread from farms to the environment, and the effects and mechanisms of non-antibiotic factors on the spread of ARGs; 3) explores methods for controlling ARGs in farm wastes; and 4) provides a comprehensive summary and integration of research across various fields, proposing that in modern smart farms, emerging technologies can be integrated through artificial intelligence to control or even eliminate ARGs. Moreover, challenges and future research directions for controlling ARGs on farms are suggested.}, } @article {pmid39308980, year = {2024}, author = {Mendoza, H and Lamb, EA and Thomas, J and Tavares, DG and Schroeder, LA and Müller, C and Agrawal, N and Schirawski, J and Perlin, MH}, title = {Comparative mitogenomic analysis of Sporisorium reilianum f. sp. zeae suggests recombination events during its evolutionary history.}, journal = {Frontiers in physiology}, volume = {15}, number = {}, pages = {1264359}, pmid = {39308980}, issn = {1664-042X}, abstract = {INTRODUCTION: Modern understanding of the concept of genetic diversity must include the study of both nuclear and organellar DNA, which differ greatly in terms of their structure, organization, gene content and distribution. This study comprises an analysis of the genetic diversity of the smut fungus Sporisorium reilianum f. sp. zeae from a mitochondrial perspective.

METHODS: Whole-genome sequencing data was generated from biological samples of S. reilianum collected from different geographical regions. Multiple sequence alignment and gene synteny analysis were performed to further characterize genetic diversity in the context of mitogenomic polymorphisms.

RESULTS: Mitochondria of strains collected in China contained unique sequences. The largest unique sequence stretch encompassed a portion of cox1, a mitochondrial gene encoding one of the subunits that make up complex IV of the mitochondrial electron transport chain. This unique sequence had high percent identity to the mitogenome of the related species Sporisorium scitamineum and Ustilago bromivora.

DISCUSSION: The results of this study hint at potential horizontal gene transfer or mitochondrial genome recombination events during the evolutionary history of basidiomycetes. Additionally, the distinct polymorphic region detected in the Chinese mitogenome provides the ideal foundation to develop a diagnostic method to discern between mitotypes and enhance knowledge on the genetic diversity of this organism.}, } @article {pmid39305601, year = {2024}, author = {Wang, F and Hu, Z and Wang, W and Wang, J and Xiao, Y and Shi, J and Wang, C and Mai, W and Li, G and An, T}, title = {Selective enrichment of high-risk antibiotic resistance genes and priority pathogens in freshwater plastisphere: Unique role of biodegradable microplastics.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135901}, doi = {10.1016/j.jhazmat.2024.135901}, pmid = {39305601}, issn = {1873-3336}, abstract = {Microplastics (MPs) has been concerned as emerging vectors for spreading antibiotic resistance and pathogenicity in aquatic environments, but the role of biodegradable MPs remains largely unknown. Herein, field in-situ incubation method combined with metagenomic sequencing were employed to reveal the dispersal characteristics of microbial community, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factors (VFs) enriched by MPs biofilms. Results showed that planktonic microbes were more prone to enrich on biodegradable MPs (i.e., polyhydroxyalkanoate and polylactic acid) than non-biodegradable MPs (i.e., polystyrene, polypropylene and polyethylene). Distinctive microbial communities were assembled on biodegradable MPs, and the abundances of ARGs, MGEs, and VFs on biofilms of biodegradable MPs were much higher than that of non-biodegradable MPs. Notably, network analysis showed that the biodegradable MPs selectively enriched pathogens carrying ARGs, VFs and MGEs concurrently, suggesting a strong potential risks of co-spreading antibiotic resistance and pathogenicity through horizontal gene transfer. According to WHO priority list of Antibiotic Resistant Pathogens (ARPs) and ARGs health risk assessment framework, the highest abundances of Priority 1 ARPs and Rank I risk ARGs were found on polylactic acid and polyhydroxyalkanoate, respectively. These findings elucidate the unique and critical role of biodegradable MPs for selective enrichment of high-risk ARGs and priority pathogens in freshwater environments.}, } @article {pmid39304531, year = {2024}, author = {Umar, M and Merlin, TS and Puthiyedathu, ST}, title = {Genomic insights into symbiosis and host adaptation of sponge-associated novel bacterium, Rossellomorea orangium sp. nov.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnae074}, pmid = {39304531}, issn = {1574-6968}, abstract = {Sponge-associated microorganisms play vital roles in marine sponge ecology. This study presents a genomic investigation of Rossellomorea sp. MCCB 382, isolated from Stelletta sp., reveals insights into its adaptations and symbiotic roles. Phylogenomic study and Overall Genomic Relatedness Index (OGRI) classify MCCB 382 as a novel species, Rossellomorea orangium sp. nov. The genome encodes numerous carbohydrate metabolism enzymes (CAZymes), likely aiding nutrient cycling in the sponge host. Unique eukaryotic-like protein domains hint at potential mechanisms of symbiosis. Defense mechanisms include CRISPR, restriction modification systems, DNA phosphorothioation, toxin-antitoxin systems, and heavy metal and multidrug resistance genes, indicating adaptation to challenging marine environments. Unlike obligate mutualists, MCCB 382 shows no genome reduction. Furthermore, the presence of mobile genetic elements, horizontal gene transfer, and prophages suggest genetic versatility, implying flexible metabolic potential and capacity for rapid adaptation and symbiosis shifts. MCCB 382 possesses six biosynthetic gene clusters for secondary metabolites, including both type II and III polyketide synthases (PKS), terpenes, (NRPS), NRPS-independent-siderophore, and lassopeptide. Further genome mining using BiGScape revealed four distinct gene cluster families, T2PKS, NRPS-independent-siderophore, lasso peptide, and terpene, presenting opportunities for novel compound elucidation. Our study reveals a symbiotic lifestyle of MCCB 382 with the host sponge, highlighting symbiont factors that aid in establishing and sustaining this relationship. This is the pioneering genomic characterisation of a novel Rossellomorea sp. within the sponge Stelletta sp. holobiont.}, } @article {pmid39304387, year = {2024}, author = {Vos, M and Buckling, A and Kuijper, B and Eyre-Walker, A and Bontemps, C and Leblond, P and Dimitriu, T}, title = {Why do mobile genetic elements transfer DNA of their hosts?.}, journal = {Trends in genetics : TIG}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tig.2024.07.008}, pmid = {39304387}, issn = {0168-9525}, abstract = {The prokaryote world is replete with mobile genetic elements (MGEs) - self-replicating entities that can move within and between their hosts. Many MGEs not only transfer their own DNA to new hosts but also transfer host DNA located elsewhere on the chromosome in the process. This could potentially lead to indirect benefits to the host when the resulting increase in chromosomal variation results in more efficient natural selection. We review the diverse ways in which MGEs promote the transfer of host DNA and explore the benefits and costs to MGEs and hosts. In many cases, MGE-mediated transfer of host DNA might not be selected for because of a sex function, but evidence of MGE domestication suggests that there may be host benefits of MGE-mediated sex.}, } @article {pmid39304140, year = {2024}, author = {Qi, Q and Ghaly, TM and Rajabal, V and Russell, DH and Gillings, MR and Tetu, SG}, title = {Vegetable phylloplane microbiomes harbour class 1 integrons in novel bacterial hosts and drive the spread of chlorite resistance.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {176348}, doi = {10.1016/j.scitotenv.2024.176348}, pmid = {39304140}, issn = {1879-1026}, abstract = {Bacterial hosts in vegetable phylloplanes carry mobile genetic elements such as plasmids and transposons that are associated with integrons. These mobile genetic elements and their cargo genes can enter human microbiomes via consumption of fresh agricultural produce, including uncooked vegetables. This presents a risk of acquiring antimicrobial resistance genes from uncooked vegetables. To better understand horizontal gene transfer of class 1 integrons in these compartments, we applied epicPCR, a single-cell fusion-PCR surveillance technique, to link the class 1 integron integrase (intI1) gene with phylogenetic markers of their bacterial hosts. Ready-to-eat salads carried class 1 integrons from the phyla Bacteroidota and Pseudomonadota, including four novel genera that were previously not known to be associated with intI1. We whole-genome sequenced Pseudomonas and Erwinia hosts of pre-clinical class 1 integrons that are embedded in Tn402-like transposons. The proximal gene cassette in these integrons was identified as a chlorite dismutase gene cassette, which we showed experimentally to confer chlorite resistance. Chlorine-derived compounds such as acidified sodium chlorite and chloride dioxide are used to disinfectant raw vegetables in food processing facilities, suggesting selection for chlorite resistance in phylloplane integrons. The spread of integrons conferring chlorite resistance has the potential to exacerbate integron-mediated antimicrobial resistance (AMR) via co-selection of chlorite resistance and AMR, thus highlighting the importance of monitoring chlorite residues in agricultural produce. These results demonstrate the strength of combining epicPCR and culture-based isolation approaches for identifying hosts and dissecting the molecular ecology of class 1 integrons.}, } @article {pmid39303860, year = {2024}, author = {Yong, Y and Hu, S and Zhong, M and Wen, Y and Zhou, Y and Ma, R and Jiang, X and Zhang, Q}, title = {Horizontal gene transfer from chloroplast to mitochondria of seagrasses in the yellow-Bohai seas.}, journal = {Genomics}, volume = {116}, number = {5}, pages = {110940}, doi = {10.1016/j.ygeno.2024.110940}, pmid = {39303860}, issn = {1089-8646}, abstract = {Seagrasses are ideal for studying plant adaptation to marine environments. In this study, the mitochondrial (mt) and chloroplast (cp) genomes of Ruppia sinensis were sequenced. The results showed an extensive gene loss in seagrasses, including a complete loss of cp-rpl19 genes in Zosteraceae, most cp-ndh genes in Hydrocharitaceae, and mt-rpl and mt-rps genes in all seagrasses, except for the mt-rpl16 gene in Phyllospadix iwatensis. Notably, most ribosomal protein genes were lost in the mt and cp genomes. The deleted cp genes were not transferred to the mt genomes through horizontal gene transfer. Additionally, a significant DNA transfer between seagrass organelles was found, with the mt genomes of Zostera containing numerous sequences from the cp genome. Rearrangement analyses revealed an unreported inversion of the cp genome in R. sinensis. Moreover, four positively selected genes (atp8, nad5, atp4, and ccmFn) and five variable regions (matR, atp4, atp8, rps7, and ccmFn) were identified.}, } @article {pmid39303615, year = {2024}, author = {Li, X and Cai, S and Xu, M}, title = {Nanoscale zero-valent iron alleviated horizontal transfer of antibiotic resistance genes in soil: The important role of extracellular polymeric substances.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135902}, doi = {10.1016/j.jhazmat.2024.135902}, pmid = {39303615}, issn = {1873-3336}, abstract = {Extracellular polymeric substances (EPS) are tightly related to the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs), but often neglected in soil. In this study, nanoscale zero-valent iron (nZVI) was utilized for attenuation of ARGs in contaminated soil, with an emphasis on its effects on EPS secretion and HGT. Results showed during soil microbe cultivation exposed to tetracycline, more EPS was secreted and significant increase of tet was observed due to facilitated HGT. Notably, copies of EPS-tet accounted for 71.39 % of the total tet, implying vital effects of EPS on ARGs proliferation. When co-exposed to nZVI, EPS secretion was decreased by 38.36-71.46 %, for that nZVI could alleviate the microbial oxidative stress exerted by tetracycline resulting in downregulation of genes expression related to the c-di-GMP signaling system. Meanwhile, the abundance of EPS-tet was obviously reduced from 7.04 to 5.12-6.47 log unit, directly causing decrease of total tet from 7.19 to 5.68-6.69 log unit. For the reduced tet, it was mainly due to decreased EPS secretion induced by nZVI resulting in inhibition of HGT especially transformation of the EPS-tet. This work gives an inspiration for attenuation of ARGs dissemination in soil through an EPS regulation strategy.}, } @article {pmid39301187, year = {2024}, author = {Xu, M and Ke, H and Zang, Y and Gou, H and Yang, D and Shi, K and Zhang, K and Li, Y and Jiang, Z and Chu, P and Zhai, S and Li, C}, title = {Outer membrane vesicles secreted from Actinobacillus pleuropneumoniae isolate disseminating the floR resistance gene to Enterobacteriaceae.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1467847}, pmid = {39301187}, issn = {1664-302X}, abstract = {Actinobacillus pleuropneumoniae, a significant respiratory pig pathogen, is causing substantial losses in the global swine industry. The resistance spectrum of A. pleuropneumoniae is expanding, and multidrug resistance is a severe issue. Horizontal gene transfer (HGT) plays a crucial role in the development of the bacterial genome by facilitating the dissemination of resistance determinants. However, the horizontal transfer of resistance genes via A. pleuropneumoniae-derived outer membrane vesicles (OMVs) has not been previously reported. In this study, we used Illumina NovaSeq and PacBio SequeI sequencing platforms to determine the whole genome sequence of A. pleuropneumoniae GD2107, a multidrug-resistant (MDR) isolate from China. We detected a plasmid in the isolate named pGD2107-1; the plasmid was 5,027 bp in size with 7 putative open reading frames (ORF) and included the floR resistance genes. The carriage of resistance genes in A. pleuropneumoniae OMVs was identified using a polymerase chain reaction (PCR) assay, and then we thoroughly evaluated the influence of OMVs on the horizontal transfer of drug-resistant plasmids. The transfer of the plasmid to recipient bacteria via OMVs was confirmed by PCR. In growth competition experiments, all recipients carrying the pGD2107-1 plasmid exhibited a fitness cost compared to the corresponding original recipients. This study revealed that OMVs could mediate interspecific horizontal transfer of the resistance plasmid pGD2107-1 into Escherichia coli recipient strains and significantly enhance the resistance of the transformants. In summary, A. pleuropneumoniae-OMVs play the pivotal role of vectors for dissemination of the floR gene spread and may contribute to more antimicrobial resistance gene transfer in other Enterobacteriaceae.}, } @article {pmid39299886, year = {2024}, author = {Urquhart, A and Vogan, AA and Gluck-Thaler, E}, title = {Starships: a new frontier for fungal biology.}, journal = {Trends in genetics : TIG}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tig.2024.08.006}, pmid = {39299886}, issn = {0168-9525}, abstract = {Transposable elements (TEs) are semiautonomous genetic entities that proliferate in genomes. We recently discovered the Starships, a previously hidden superfamily of giant TEs found in a diverse subphylum of filamentous fungi, the Pezizomycotina. Starships are unlike other eukaryotic TEs because they have evolved mechanisms for both mobilizing entire genes, including those encoding conditionally beneficial phenotypes, and for horizontally transferring between individuals. We argue that Starships have unrivaled capacity to engage their fungal hosts as genetic parasites and mutualists, revealing unexplored terrain for investigating the ecoevolutionary dynamics of TE-eukaryote interactions. We build on existing models of fungal genome evolution by conceptualizing Starships as a distinct genomic compartment whose dynamics profoundly shape fungal biology.}, } @article {pmid39296779, year = {2024}, author = {Thomy, J and Sanchez, F and Prioux, C and Yau, S and Xu, Y and Mak, J and Sun, R and Piganeau, G and Yung, CCM}, title = {Unveiling Prasinovirus diversity and host specificity through targeted enrichment in the South China Sea.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae109}, pmid = {39296779}, issn = {2730-6151}, abstract = {Unicellular green picophytoplankton from the Mamiellales order are pervasive in marine ecosystems and susceptible to infections by prasinoviruses, large double-stranded DNA viruses within the Nucleocytoviricota phylum. We developed a double-stranded DNA virus enrichment and shotgun sequencing method, and successfully assembled 80 prasinovirus genomes from 43 samples in the South China Sea. Our research delivered the first direct estimation of 94% accuracy in correlating genome similarity to host range. Stirkingly, our analyses uncovered unexpected host-switching across diverse algal lineages, challenging the existing paradigms of host-virus co-speciation and revealing the dynamic nature of viral evolution. We also detected six instances of horizontal gene transfer between prasinoviruses and their hosts, including a novel alternative oxidase. Additionally, diversifying selection on a major capsid protein suggests an ongoing co-evolutionary arms race. These insights not only expand our understanding of prasinovirus genomic diversity but also highlight the intricate evolutionary mechanisms driving their ecological success and shaping broader virus-host interactions in marine environments.}, } @article {pmid39255666, year = {2024}, author = {Li, Y and Zheng, Q and Lu, Y and Qiao, Y and Guo, H and Ma, Q and Zhou, J and Li, H and Wang, T}, title = {Water temperature disturbance alters the conjugate transfer of antibiotic resistance genes via affecting ROS content and intercellular aggregation.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135762}, doi = {10.1016/j.jhazmat.2024.135762}, pmid = {39255666}, issn = {1873-3336}, mesh = {*Reactive Oxygen Species/metabolism ; *Temperature ; *Plasmids/genetics ; Drug Resistance, Microbial/genetics ; Water/chemistry ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Gene Transfer, Horizontal ; Escherichia coli/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Cell Membrane Permeability/drug effects ; Water Microbiology ; }, abstract = {Spread of antibiotic resistance genes (ARGs) in aquatic ecosystems poses a significant global challenge to public health. The potential effects of water temperature perturbation induced by specific water environment changes on ARGs transmission are still unclear. The conjugate transfer of plasmid-mediated ARGs under water temperature perturbation was investigated in this study. The conjugate transfer frequency (CTF) was only 7.16 × 10[-7] at a constant water temperature of 5 °C, and it reached 2.18 × 10[-5] at 30 °C. Interestingly, compared to the constant 5 °C, the water temperature perturbations (cooling and warming models between 5-30 °C) significantly promoted the CTF. Intracellular reactive oxygen species was a dominant factor, which not only directly affected the CTF of ARGs, but also functioned indirectly via influencing the cell membrane permeability and cell adhesion. Compared to the constant 5 °C, water temperature perturbations significantly elevated the gene expression associated with intercellular contact, cell membrane permeability, oxidative stress responses, and energy driven force for CTF. Furthermore, based on the mathematical model predictions, the stabilization times of acquiring plasmid maintenance were shortened to 184 h and 190 h under cooling and warming model, respectively, thus the water temperature perturbations promoted the ARGs transmission in natural conditions compared with the constant low temperature conditions.}, } @article {pmid39191006, year = {2024}, author = {Zhao, H and Sun, Y and Cao, X and Waigi, MG and Liu, J}, title = {Effects and mechanisms of chlormequat on horizontal transfer of antibiotic resistance genes through plasmid-mediated conjugation in agro-ecosystems.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135639}, doi = {10.1016/j.jhazmat.2024.135639}, pmid = {39191006}, issn = {1873-3336}, mesh = {*Plasmids/genetics ; *Oryza/microbiology/growth & development/drug effects/genetics ; *Gene Transfer, Horizontal ; *Conjugation, Genetic ; *Escherichia coli/genetics/drug effects ; *Pseudomonas/genetics/drug effects/metabolism ; Pseudomonas putida/genetics/drug effects/metabolism ; Genes, Bacterial/drug effects ; Anti-Bacterial Agents/pharmacology ; Agriculture ; Drug Resistance, Bacterial/genetics/drug effects ; Drug Resistance, Microbial/genetics ; }, abstract = {Chlormequat (CCC) is widely used in agricultural production to increase the crop yield. However, the effects of CCC on transfer of ARGs in agricultural system are still unclear. In this study, using E.coli DH5α (carrying RP4 plasmid with Amp[R], Tet[R], Kan[R]) as the donor bacterium, E.coli HB101, endophytic Pseudomonas sp. Ph6 or rhizosphere Pseudomonas putida KT2440 as the recipient strain, three conjugative systems were designed to investigate the effects of CCC on ARG transfer. Meanwhile, hydroponics experiments were designed to study the ARG spread in the rice-nutrient solution system after CCC application. The results showed that CCC significantly promoted the RP4 conjugation by expanding cell membrane permeability and improving the relative transcription levels of trfAp, trbBp, traA and traL genes in RP4. Furthermore, the conjugation frequency between E. coli and Pseudomonas was much higher than that between E. coli cells. Compared with spraying foliage with 2500 mg·L[-1] of CCC, soaking seeds with 250 mg·L[-1] of CCC was more beneficial to the colonization of ARB in rice, and also increased the abundance of ARGs in rice cultivation system. These results remind that the use of CCC in agricultural production might promote the ARG transmission in agro-ecosystems; however, foliage spraying with 2500 mg·L[-1] of CCC could control its spread.}, } @article {pmid39295911, year = {2023}, author = {Panwar, S and Kumari, S and Verma, J and Bakshi, S and Narendrakumar, L and Paul, D and Das, B}, title = {Toxin-linked mobile genetic elements in major enteric bacterial pathogens.}, journal = {Gut microbiome (Cambridge, England)}, volume = {4}, number = {}, pages = {e5}, pmid = {39295911}, issn = {2632-2897}, abstract = {One of the fascinating outcomes of human microbiome studies adopting multi-omics technology is its ability to decipher millions of microbial encoded functions in the most complex and crowded microbial ecosystem, including the human gastrointestinal (GI) tract without cultivating the microbes. It is well established that several functions that modulate the human metabolism, nutrient assimilation, immunity, infections, disease severity and therapeutic efficacy of drugs are mostly of microbial origins. In addition, these microbial functions are dynamic and can disseminate between microbial taxa residing in the same ecosystem or other microbial ecosystems through horizontal gene transfer. For clinicians and researchers alike, understanding the toxins, virulence factors and drug resistance traits encoded by the microbes associated with the human body is of utmost importance. Nevertheless, when such traits are genetically linked with mobile genetic elements (MGEs) that make them transmissible, it creates an additional burden to public health. This review mainly focuses on the functions of gut commensals and the dynamics and crosstalk between commensal and pathogenic bacteria in the gut. Also, the review summarises the plethora of MGEs linked with virulence genes present in the genomes of various enteric bacterial pathogens, which are transmissible among other pathogens and commensals.}, } @article {pmid39294579, year = {2024}, author = {Shabbir, MAB and Shamim, M and Tahir, AH and Sattar, A and Qin, W and Ahmad, W and Ahmad, W and Khan, FA and Ashraf, MA}, title = {Potential of ZnO nanoparticles for multi-drug resistant Escherichia coli having CRISPR-Cas from poultry market in Lahore.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {355}, pmid = {39294579}, issn = {1471-2180}, mesh = {*Zinc Oxide/pharmacology ; Animals ; *Escherichia coli/genetics/drug effects ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *CRISPR-Cas Systems ; *Microbial Sensitivity Tests ; *Poultry/microbiology ; *Escherichia coli Infections/microbiology/veterinary ; *Poultry Diseases/microbiology ; Nanoparticles ; }, abstract = {BACKGROUND AND OBJECTIVES: Apart from known factors such as irrational use of antibiotics and horizontal gene transfer, it is now reported that clustered regularly interspaced short palindromic repeats (CRISPR) are also associated with increased antimicrobial resistance. Hence, it is critical to explore alternatives to antibiotics to control economic losses. Therefore, the present study aimed to determine not only the association of CRISPR-Cas system with antibiotic resistance but also the potential of Zinc Oxide nanoparticles (ZnO-NPs) for avian pathogenic Escherichia coli (APEC) isolated from poultry market Lahore.

MATERIALS AND METHODS: Samples (n = 100) were collected from live bird markets of Lahore, and isolates were confirmed as Escherichia coli (E. coli) using the Remel One fast kit, and APEC was identified using PCR. The antibiotic resistance pattern in APEC was determined using the minimum inhibitory concentration (MIC), followed by genotypic confirmation of antibiotic-resistant genes using the PCR. The CRISPR-Cas system was also identified in multidrug-resistant (MDR) isolates, and its association with antibiotics was determined using qRT-PCR. The potential of ZnO-NPs was evaluated for multidrug-resistant (MDR) isolates by MIC.

RESULTS: All isolates of APEC were resistant to nalidixic acid, whereas 95% were resistant to chloramphenicol and 89% were resistant to streptomycin. Nineteen MDR APEC were found in the present study and the CRISPR-Cas system was detected in all of these MDR isolates. In addition, an increased expression of CRISPR-related genes was observed in the standard strain and MDR isolates of APEC. ZnO-NPs inhibited the growth of resistant isolates.

CONCLUSIONS: The findings showed the presence of the CRISPR-Cas system in MDR strains of APEC, along with the potential of ZnO-NPs for a possible solution to proceed. This highlights the importance of regulating antimicrobial resistance in poultry to reduce potential health consequences.}, } @article {pmid39293438, year = {2024}, author = {Zhang, ZJ and Cole, CG and Coyne, MJ and Lin, H and Dylla, N and Smith, RC and Pappas, TE and Townson, SA and Laliwala, N and Waligurski, E and Ramaswamy, R and Woodson, C and Burgo, V and Little, JC and Moran, D and Rose, A and McMillin, M and McSpadden, E and Sundararajan, A and Sidebottom, AM and Pamer, EG and Comstock, LE}, title = {Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species- and strain-level diversity and evolution.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2024.08.016}, pmid = {39293438}, issn = {1934-6069}, abstract = {Species of the Bacteroidales order are among the most abundant and stable bacterial members of the human gut microbiome, with diverse impacts on human health. We cultured and sequenced the genomes of 408 Bacteroidales isolates from healthy human donors representing nine genera and 35 species and performed comparative genomic, gene-specific, metabolomic, and horizontal gene transfer analyses. Families, genera, and species could be grouped based on many distinctive features. We also observed extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-species diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses represents a valuable resource to facilitate informed selection of strains for microbiome reconstitution.}, } @article {pmid39288183, year = {2024}, author = {Tuffet, R and Carvalho, G and Godeux, AS and Mazzamurro, F and Rocha, EPC and Laaberki, MH and Venner, S and Charpentier, X}, title = {Manipulation of natural transformation by AbaR-type islands promotes fixation of antibiotic resistance in Acinetobacter baumannii.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {39}, pages = {e2409843121}, doi = {10.1073/pnas.2409843121}, pmid = {39288183}, issn = {1091-6490}, support = {ANR-20-CE12-0004//Agence Nationale de la Recherche (ANR)/ ; ANR-11-LABX-0048//Agence Nationale de la Recherche (ANR)/ ; PhD grant//VetAgro Sup (VetAgro-Sup)/ ; 80|PRIME//Centre National de la Recherche Scientifique (CNRS)/ ; }, mesh = {*Acinetobacter baumannii/genetics/drug effects ; *Genomic Islands ; Drug Resistance, Multiple, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Transformation, Bacterial ; Polymorphism, Single Nucleotide ; Bacterial Proteins/genetics/metabolism ; }, abstract = {The opportunistic pathogen Acinetobacter baumannii, carries variants of A. baumannii resistance islands (AbaR)-type genomic islands conferring multidrug resistance. Their pervasiveness in the species has remained enigmatic. The dissemination of AbaRs is intricately linked to their horizontal transfer via natural transformation, a process through which bacteria can import and recombine exogenous DNA, effecting allelic recombination, genetic acquisition, and deletion. In experimental populations of the closely related pathogenic Acinetobacter nosocomialis, we quantified the rates at which these natural transformation events occur between individuals. When integrated into a model of population dynamics, they lead to the swift removal of AbaRs from the population, contrasting with the high prevalence of AbaRs in genomes. Yet, genomic analyses show that nearly all AbaRs specifically disrupt comM, a gene encoding a helicase critical for natural transformation. We found that such disruption impedes gene acquisition, and deletion, while moderately impacting acquisition of single nucleotide polymorphism. A mathematical evolutionary model demonstrates that AbaRs inserted into comM gain a selective advantage over AbaRs inserted in sites that do not inhibit or completely inhibit transformation, in line with the genomic observations. The persistence of AbaRs can be ascribed to their integration into a specific gene, diminishing the likelihood of their removal from the bacterial genome. This integration preserves the acquisition and elimination of alleles, enabling the host bacterium-and thus its AbaR-to adapt to unpredictable environments and persist over the long term. This work underscores how manipulation of natural transformation by mobile genetic elements can drive the prevalence of multidrug resistance.}, } @article {pmid39287446, year = {2024}, author = {Contarin, R and Drapeau, A and François, P and Madec, J-Y and Haenni, M and Dordet-Frisoni, E}, title = {The interplay between mobilome and resistome in Staphylococcus aureus.}, journal = {mBio}, volume = {}, number = {}, pages = {e0242824}, doi = {10.1128/mbio.02428-24}, pmid = {39287446}, issn = {2150-7511}, abstract = {Antibiotic resistance genes (ARGs) in Staphylococcus aureus can disseminate vertically through successful clones, but also horizontally through the transfer of genes conveyed by mobile genetic elements (MGEs). Even though underexplored, MGE/ARG associations in S. aureus favor the emergence of multidrug-resistant clones, which are challenging therapeutic success in both human and animal health. This study investigated the interplay between the mobilome and the resistome of more than 10,000 S. aureus genomes from human and animal origin. The analysis revealed a remarkable diversity of MGEs and ARGs, with plasmids and transposons being the main carriers of ARGs. Numerous MGE/ARG associations were identified, suggesting that MGEs play a critical role in the dissemination of resistance. A high degree of similarity was observed in MGE/ARG associations between human and animal isolates, highlighting the potential for unrestricted spread of ARGs between hosts. Our results showed that in parallel to clonal expansion, MGEs and their associated ARGs can spread across different strain types sequence types (STs), favoring the evolution of these clones and their adaptation in selective environments. The high variability of MGE/ARG associations within individual STs and their spread across several STs highlight the crucial role of MGEs in shaping the S. aureus resistome. Overall, this study provides valuable insights into the complex interplay between MGEs and ARGs in S. aureus, emphasizing the need to elucidate the mechanisms governing the epidemic success of MGEs, particularly those implicated in ARG transfer.IMPORTANCEThe research presented in this article highlights the importance of understanding the interactions between mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs) carried by Staphylococcus aureus, a versatile bacterium that can be both a harmless commensal and a dangerous pathogen for humans and animals. S. aureus has a great capacity to acquire and disseminate ARGs, enabling efficient adaption to various environmental or clinical conditions. By analyzing a large data set of S. aureus genomes, we highlighted the substantial role of MGEs, particularly plasmids and transposons, in disseminating ARGs within and between S. aureus populations, bypassing host barriers. Given that multidrug-resistant S. aureus strains are classified as a high-priority pathogen by global health organizations, this knowledge is crucial for understanding the complex dynamics of transmission of antibiotic resistance in this species.}, } @article {pmid39287432, year = {2024}, author = {Nwokocha, GC and Ghosh, A and Grove, A}, title = {Regulation of bacterial virulence genes by PecS family transcription factors.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0030224}, doi = {10.1128/jb.00302-24}, pmid = {39287432}, issn = {1098-5530}, abstract = {Bacterial plant pathogens adjust their gene expression programs in response to environmental signals and host-derived compounds. This ensures that virulence genes or genes encoding proteins, which promote bacterial fitness in a host environment, are expressed only when needed. Such regulation is in the purview of transcription factors, many of which belong to the ubiquitous multiple antibiotic resistance regulator (MarR) protein family. PecS proteins constitute a subset of this large protein family. PecS has likely been distributed by horizontal gene transfer, along with the divergently encoded efflux pump PecM, suggesting its integration into existing gene regulatory networks. Here, we discuss the roles of PecS in the regulation of genes associated with virulence and fitness of bacterial plant pathogens. A comparison of phenotypes and differential gene expression associated with the disruption of pecS shows that functional consequences of PecS integration into existing transcriptional networks are highly variable, resulting in distinct PecS regulons. Although PecS universally binds to the pecS-pecM intergenic region to repress the expression of both genes, binding modes differ. A particularly relaxed sequence preference appears to apply for Dickeya dadantii PecS, perhaps to optimize its integration as a global regulator and regulate genes ancestral to the acquisition of pecS-pecM. Even inducing ligands for PecS are not universally conserved. It appears that PecS function has been optimized to match the unique regulatory needs of individual bacterial species and that its roles must be appreciated in the context of the regulatory networks into which it was recruited.}, } @article {pmid39287139, year = {2024}, author = {Pu, L and Shamir, R}, title = {4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkae799}, pmid = {39287139}, issn = {1362-4962}, support = {1339/18//Israel Science Foundation/ ; //Edmond J. Safra Center for Bioinformatics at Tel-Aviv University/ ; //Planning & Budgeting Committee/ ; //Council for Higher Education/ ; }, abstract = {Microbial communities usually harbor a mix of bacteria, archaea, plasmids, viruses and microeukaryotes. Within these communities, viruses, plasmids, and microeukaryotes coexist in relatively low abundance, yet they engage in intricate interactions with bacteria. Moreover, viruses and plasmids, as mobile genetic elements, play important roles in horizontal gene transfer and the development of antibiotic resistance within microbial populations. However, due to the difficulty of identifying viruses, plasmids, and microeukaryotes in microbial communities, our understanding of these minor classes lags behind that of bacteria and archaea. Recently, several classifiers have been developed to separate one or more minor classes from bacteria and archaea in metagenome assemblies. However, these classifiers often overlook the issue of class imbalance, leading to low precision in identifying the minor classes. Here, we developed a classifier called 4CAC that is able to identify viruses, plasmids, microeukaryotes, and prokaryotes simultaneously from metagenome assemblies. 4CAC generates an initial four-way classification using several sequence length-adjusted XGBoost models and further improves the classification using the assembly graph. Evaluation on simulated and real metagenome datasets demonstrates that 4CAC substantially outperforms existing classifiers and combinations thereof on short reads. On long reads, it also shows an advantage unless the abundance of the minor classes is very low. 4CAC runs 1-2 orders of magnitude faster than the other classifiers. The 4CAC software is available at https://github.com/Shamir-Lab/4CAC.}, } @article {pmid39189727, year = {2024}, author = {Xu, Y and Liu, B and Jiao, N and Liu, J and Chen, F}, title = {New evidence supports the prophage origin of RcGTA.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0043424}, doi = {10.1128/aem.00434-24}, pmid = {39189727}, issn = {1098-5336}, support = {2020ZLYS04//Department of Science and Technology of Shandong Province ()/ ; 2018YFA0605800//Ministry of Science and Technology of the People's Republic of China (MOST)/ ; }, mesh = {*Prophages/genetics ; Rhodobacter capsulatus/virology/genetics ; Gene Transfer, Horizontal ; Genome, Viral ; Phylogeny ; Evolution, Molecular ; Methylobacterium/virology/genetics ; }, abstract = {Gene transfer agents (GTAs) are phage-like entities that package and transfer random host genome fragments between prokaryotes. RcGTA, produced by Rhodobacter capsulatus, is hypothesized to originate from a prophage ancestor. Most of the evidence supporting this hypothesis came from the finding of RcGTA-like genes in phages. More than 75% of the RcGTA genes have a phage homolog. However, only a few RcGTA homologs have been identified in a (pro)phage genome, leaving the hypothesis that GTAs evolved from prophages through gene loss with only weak evidence. We herein report the discovery of an inducible prophage (vB_MseS-P1) from a Mesorhizobium sediminum strain that contains the largest number (12) of RcGTA homologs found in a phage genome to date. We also identified three putative prophages and two prophage remnants harboring 12-14 RcGTA homologs in a Methylobacterium nodulans strain. The protein remote homology detection also revealed more RcGTA homologs from other phages than we previously thought. Moreover, the head-tail gene architecture of these newly discovered prophage-related elements closely resembles that of RcGTA. Furthermore, vB_MseS-P1 virions have structural proteins similar to RcGTA particles. Close phylogenetic relationships between certain prophage genes and RcGTA-like genes in Alphaproteobacteria further support the shared ancestry between RcGTA and prophages. Our findings provide new relatively direct evidence of the origin of RcGTA from a prophage progenitor.IMPORTANCEGTAs are important genetic elements in certain groups of bacteria and contribute to the genetic diversification, evolution, and ecological adaptation of bacteria. RcGTA, a common type of GTA, is known to package and transfer random fragments of the bacterial genome to recipient cells. However, the origin of RcGTA is still elusive. It has been hypothesized that RcGTA evolved from a prophage ancestor through gene loss. However, the few RcGTA homologs identified in a (pro)phage genome leave the hypothesis lacking direct evidence. This study uncovers the presence of a large number of RcGTA homologs in an inducible prophage and several putative prophages. The similar head-tail gene architecture and structural protein compositions of these newly discovered prophage-related elements and RcGTA further demonstrate an unprecedentedly observed close evolutionary relationship between prophages and RcGTA. Together, our findings provide more direct evidence supporting the origin of RcGTA from prophage.}, } @article {pmid39158311, year = {2024}, author = {Liu, H and Zheng, L and Fan, H and Pang, J}, title = {Genomic analysis of antibiotic resistance genes and mobile genetic elements in eight strains of nontyphoid Salmonella.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0058624}, pmid = {39158311}, issn = {2379-5077}, support = {2022-JSYZ-13//The Second Phase of Jinshan Medical Personnel Training Program/ ; KFQM-27//Rehabilitation Medicine Talent Leading Program/ ; }, mesh = {Humans ; *Salmonella/genetics/drug effects/isolation & purification ; *Interspersed Repetitive Sequences/genetics ; *Salmonella Infections/microbiology/epidemiology ; Anti-Bacterial Agents/pharmacology ; China/epidemiology ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Plasmids/genetics ; Genomics ; Feces/microbiology ; }, abstract = {UNLABELLED: Nontyphoidal Salmonella (NTS) is the main etiological agent of human nontyphoidal salmonellosis. The aim of this study was to analyze the epidemiological characteristics and horizontal transfer mechanisms of antimicrobial resistance (AMR) genes from eight strains of NTS detected in Zhenjiang City, Jiangsu Province, China. Fecal samples from outpatients with food-borne diarrhea were collected in 2022. The NTS isolates were identified, and their susceptibility was tested with the Vitek 2 Compact system. The genomes of the NTS isolates were sequenced with the Illumina NovaSeq platform and Oxford Nanopore Technologies platform. The AMR genes and mobile genetic elements (MGEs) were predicted with the relevant open access resources. Eight strains of NTS were isolated from 153 specimens, and Salmonella Typhimurium ST19 was the most prevalent serotype. The AMR gene with the highest detection rate was AAC(6')-Iaa (10.5%) followed by TEM-1 (7.9%), sul2 (6.6%), and tet(A) (5.3%). Eleven MGEs carrying 34 AMR genes were identified on the chromosomes of 3 of the 8 NTS, including 3 resistance islands, 6 composite transposons (Tns), and 2 integrons. Eighteen plasmids carrying 40 AMR genes were detected in the 8 NTS strains, including 6 mobilizable plasmids, 3 conjugative plasmids, and 9 nontransferable plasmids, 7 of which carried 10 composite Tns and 3 integrons. This study provided a theoretical basis, from a genetic perspective, for the prevention and control of NTS resistance in Zhenjiang City.

IMPORTANCE: Human nontyphoidal salmonellosis is one of the common causes of bacterial food-borne illnesses, with significant social and economic impacts, especially those caused by invasive multidrug-resistant nontyphoidal Salmonella, which entails high morbidity and mortality. Antimicrobial resistance is mainly mediated by drug resistance genes, and mobile genetic elements play key roles in the capture, accumulation, and dissemination of antimicrobial resistance genes. Therefore, it is necessary to study the epidemiological characteristics and horizontal transfer mechanisms of antimicrobial resistance genes of nontyphoidal Salmonella to prevent the spread of multidrug-resistant nontyphoidal Salmonella.}, } @article {pmid39282498, year = {2024}, author = {Jiang, C and Yang, J and Xiao, G and Xiao, N and Hu, J and Yang, Y and Sun, Z and Li, Y}, title = {The ISVsa3-ORF2-abh-tet(X4) circular intermediate-mediated transmission of tigecycline resistance in Escherichia coli isolates from duck farms.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1444031}, pmid = {39282498}, issn = {2235-2988}, mesh = {*Ducks/microbiology ; *Tigecycline/pharmacology ; Animals ; *Escherichia coli/genetics/drug effects/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; China ; *Plasmids/genetics ; *Farms ; *Escherichia coli Infections/veterinary/microbiology ; *Whole Genome Sequencing ; Feces/microbiology ; Multilocus Sequence Typing ; Drug Resistance, Multiple, Bacterial/genetics ; Genotype ; Poultry Diseases/microbiology ; Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; }, abstract = {Tigecycline is a last-resort drug used to treat serious infections caused by multidrug-resistant bacteria. tet(X4) is a recently discovered plasmid-mediated tigecycline resistance gene that confers high-level resistance to tigecycline and other tetracyclines. Since the first discovery of tet(X4) in 2019, it has spread rapidly worldwide, and as a consequence, tigecycline has become increasingly ineffective in the clinical treatment of multidrug-resistant infections. In this study, we identified and analyzed tet(X4)-positive Escherichia coli isolates from duck farms in Hunan Province, China. In total, 976 samples were collected from nine duck farms. Antimicrobial susceptibility testing and whole-genome sequencing (WGS) were performed to establish the phenotypes and genotypes of tet(X4)-positive isolates. In addition, the genomic characteristics and transferability of tet(X4) were determined based on bioinformatics analysis and conjugation. We accordingly detected an E. coli strain harboring tet(X4) and seven other resistance genes in duck feces. Multi-locus sequence typing analysis revealed that this isolate belonged to a new clone, and subsequent genetic analysis indicated that tet(X4) was carried in a 4608-bp circular intermediate, flanked by ISVsa3-ORF2-abh elements. Moreover, it exhibited transferability to E. coli C600 with a frequency of 10[-5]. The detection of tet(X4)-harboring E, coli strains on duck farms enhances our understanding of tigecycline resistance dynamics. The transferable nature of the circular intermediate of tet(X4) contributing to the spread of tigecycline resistance genes poses a substantial threat to healthcare. Consequently, vigilant monitoring and proactive measures are necessary to prevent their spread.}, } @article {pmid39278585, year = {2024}, author = {Yang, B and Sun, J and Zhu, S and Wang, Z and Liu, Y}, title = {Exposure to bisphenol compounds accelerates the conjugative transfer of antibiotic resistance plasmid.}, journal = {Environmental research}, volume = {}, number = {}, pages = {120002}, doi = {10.1016/j.envres.2024.120002}, pmid = {39278585}, issn = {1096-0953}, abstract = {Antimicrobial resistance poses the most formidable challenge to public health, with plasmid-mediated horizontal gene transfer playing a pivotal role in its global spread. Bisphenol compounds (BPs), a group of environmental contaminants with endocrine-disrupting properties, are extensively used in various plastic products and can be transmitted to food. However, the impact of BPs on the plasmid-mediated horizontal transfer of antibiotic resistance genes (ARGs) has not yet been elucidated. Herein, we demonstrate that BPs could promote the conjugative transfer frequency of RP4-7 and clinically multidrug-resistant plasmids. Furthermore, the promoting effect of BPs on the plasmid transfer was also confirmed in a murine model. Microbial diversity analysis of transconjugants indicated an increase in α diversity in the BPAF-treated group, along with the declined richness of some beneficial bacteria and elevated richness of Faecalibaculum rodentium, which might serve as an intermediate repository for resistance plasmids. The underlying mechanisms driving the enhanced conjugative transfer upon BPAF treatment include exacerbated oxidative stress, disrupted membrane homeostasis, augmented energy metabolism, and the increased expression of conjugation-related genes. Collectively, our findings highlight the potential risk associated with the exacerbated dissemination of AMR both in vitro and in vivo caused by BPs exposure.}, } @article {pmid39277355, year = {2024}, author = {Gao, Y and Guo, Y and Wang, L and Guo, L and Shi, B and Zhu, L and Wang, J and Kim, YM and Wang, J}, title = {Tebuconazole exacerbates co-occurrence and horizontal transfer of antibiotic resistance genes.}, journal = {Pesticide biochemistry and physiology}, volume = {204}, number = {}, pages = {106026}, doi = {10.1016/j.pestbp.2024.106026}, pmid = {39277355}, issn = {1095-9939}, mesh = {*Triazoles/toxicity/pharmacology ; *Gene Transfer, Horizontal ; *Fungicides, Industrial/toxicity/pharmacology ; *Biofilms/drug effects ; Drug Resistance, Microbial/genetics ; Plasmids/genetics ; Genes, Bacterial ; }, abstract = {As one of the most widely used pesticides in the global fungicide market, tebuconazole has become heavily embedded in soil along with antibiotic resistance genes (ARGs). However, it remains unclear whether the selective pressure produced by tebuconazole affects ARGs and their horizontal transfer. In this experiment, we simulated a tebuconazole-contaminated soil ecosystem and observed changes in the abundance of ARGs and mobile genetic element (MGEs) due to tebuconazole exposure. We also established a plasmid RP4-mediated conjugative transfer system to investigate in depth the impact of tebuconazole on the horizontal transfer of ARGs and its mechanism of action. The results showed that under tebuconazole treatment at concentrations ranging from 0 to 10 mg/L, there was a gradual increase in the frequency of plasmid conjugative transfer, peaking at 10 mg/L which was 7.93 times higher than that of the control group, significantly promoting horizontal transfer of ARGs. Further analysis revealed that the conjugative transfer system under tebuconazole stress exhibited strong ability to form biofilm, and the conjugative transfer frequency ratio of biofilm to planktonic bacteria varied with the growth cycle of biofilm. Additionally, scanning electron microscopy and flow cytometry demonstrated increased cell membrane permeability in both donor and recipient bacteria under tebuconazole stress, accompanied by upregulation of ompA gene expression controlling cell membrane permeability. Furthermore, enzyme activity assays indicated significant increases in CAT, SOD activity, and GSH content in recipient bacteria under tebuconazole stress. Moreover, expression levels of transmembrane transporter gene trfAp as well as genes involved in oxidative stress and SOS response were found to be correlated with the frequency of plasmid conjugative transfer.}, } @article {pmid39276831, year = {2024}, author = {Li, C and Zhang, Y and Shi, W and Peng, Y and Han, Y and Jiang, S and Dong, X and Zhang, R}, title = {Viral diversity within marine biofilms and interactions with corrosive microbes.}, journal = {Environmental research}, volume = {}, number = {}, pages = {119991}, doi = {10.1016/j.envres.2024.119991}, pmid = {39276831}, issn = {1096-0953}, abstract = {In marine environments, a wide variety of microbes like bacteria, and archaea influence on the corrosion of materials. Viruses are widely distributed in biofilms among these microbes and may affect the corrosion process through interactions with key corrosive prokaryotes. However, understanding of the viral communities within biofilms and their interactions with corrosive microbes remains is limited. To improve this knowledge gap, 53 metagenomes were utilized to investigate the diversity of viruses within biofilms on 8 different materials and their interactions with corrosive microbes. Notably, the viruses within biofilms predominantly belonged to Caudoviricetes, and phylogenetic analysis of Caudoviricetes and protein-sharing networks with other environments revealed the presence of numerous novel viral clades in biofilms. The virus‒host linkages revealed a close association between viruses and corrosive microbes in biofilms. This mean that viruses may modulate host corrosion-related metabolism through auxiliary metabolic genes. It was observed that the virus could enhance host resistance to metals and antibiotics via horizontal gene transfer. Interestingly, viruses could protect themselves from host antiviral systems through anti-defense systems. This study illustrates the diversity of viruses within biofilms formed on materials and the intricate interactions between viruses and corrosive microbes, showing the potential roles of viruses in corrosive biofilms.}, } @article {pmid39270765, year = {2024}, author = {Bjornson, S and Verbruggen, H and Upham, NS and Steenwyk, JL}, title = {Reticulate evolution: Detection and utility in the phylogenomics era.}, journal = {Molecular phylogenetics and evolution}, volume = {201}, number = {}, pages = {108197}, doi = {10.1016/j.ympev.2024.108197}, pmid = {39270765}, issn = {1095-9513}, abstract = {Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Two non-vertical modes of evolution - hybridization/introgression and horizontal gene transfer - deviate from a strictly bifurcating tree model, causing non-treelike patterns. However, these reticulate processes can produce similar patterns to incomplete lineage sorting or recombination, potentially leading to ambiguity. Here, we present a brief overview of a phylogenomic workflow for inferring organismal histories and compare methods for distinguishing modes of reticulate evolution. We discuss how the timing of coalescent events can help disentangle introgression from incomplete lineage sorting and how horizontal gene transfer events can help determine the relative timing of speciation events. In doing so, we identify pitfalls of certain methods and discuss how to extend their utility across the Tree of Life. Workflows, methods, and future directions discussed herein underscore the need to embrace reticulate evolutionary patterns for understanding the timing and rates of evolutionary events, providing a clearer view of life's history.}, } @article {pmid39270668, year = {2024}, author = {Aserse, AA and Nimusiima, J and Tumuhairwe, JB and Yli-Halla, M and Lindström, K}, title = {Phylogenetic diversity of Rhizobium species recovered from nodules of common beans (Phaseolus vulgaris L.) in fields in Uganda: R. phaseoli, R. etli, and R. hidalgonense.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiae120}, pmid = {39270668}, issn = {1574-6941}, abstract = {A total of 75 bacterial isolates were obtained from nodules of beans cultivated across 10 sites in six agro-ecological zones in Uganda. Using recA gene sequence analysis, 66 isolates were identified as members of the genus Rhizobium, while nine were related to Agrobacterium species. In the recA gene tree, most Rhizobium strains were classified into five recognized species. Phylogenetic analysis based on six concatenated sequences (recA-rpoB-dnaK-glnII-gyrB-atpD) placed 32 representative strains into five distinct Rhizobium species, consistent with the species groups observed in the recA gene tree: R. phaseoli, R. etli, R. hidalgonense, R. ecuadorense, and R. sophoriradicis, with the first three being the predominant. The rhizobial strains grouped into three nodC subclades within the symbiovar phaseoli clade, encompassing strains from distinct phylogenetic groups. This pattern reflects the conservation of symbiotic genes, likely acquired through horizontal gene transfer among diverse rhizobial species. The 32 representative strains formed symbiotic relationships with host beans, while the Agrobacterium strains did not form nodules and lacked symbiotic genes. Multivariate analysis revealed that species distribution was influenced by the environmental factors of the sampling sites, emphasizing the need to consider these factors in future effectiveness studies to identify effective nitrogen-fixing strains for specific locations.}, } @article {pmid39269515, year = {2024}, author = {Amara, Y and Mahjoubi, M and Souissi, Y and Cherif, H and Naili, I and ElHidri, D and Kadidi, I and Mosbah, A and Masmoudi, AS and Cherif, A}, title = {Tapping into haloalkaliphilic bacteria for sustainable agriculture in treated wastewater: insights into genomic fitness and environmental adaptation.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {1}, pages = {1}, pmid = {39269515}, issn = {1572-9699}, support = {No 688320//European Union's Horizon 2020, MADFORWATER/ ; No 688320//European Union's Horizon 2020, MADFORWATER/ ; No 688320//European Union's Horizon 2020, MADFORWATER/ ; No 688320//European Union's Horizon 2020, MADFORWATER/ ; }, mesh = {*Wastewater/microbiology ; *Phylogeny ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; Salinity ; Rhizosphere ; Bacteria/genetics/classification/isolation & purification/metabolism ; Agriculture/methods ; Tunisia ; Adaptation, Physiological ; Olea/microbiology ; Genome, Bacterial ; }, abstract = {The increasing salinity and alkalinity of soils pose a global challenge, particularly in arid regions such as Tunisia, where about 50% of lands are sensitive to soil salinization. Anthropogenic activities, including the use of treated wastewater (TWW) for irrigation, exacerbate these issues. Haloalkaliphilic bacteria, adapted to TWW conditions and exhibiting plant-growth promotion (PGP) and biocontrol traits, could offer solutions. In this study, 24 haloalkaliphilic bacterial strains were isolated from rhizosphere sample of olive tree irrigated with TWW for more than 20 years. The bacterial identification using 16S rRNA gene sequencing showed that the haloalkaliphilic isolates, capable of thriving in high salinity and alkaline pH, were primarily affiliated to Bacillota (Oceanobacillus and Staphylococcus). Notably, these strains exhibited biofertilization and enzyme production under both normal and saline conditions. Traits such as phosphate solubilization, and the production of exopolysaccharide, siderophore, ammonia, and hydrogen cyanide were observed. The strains also demonstrated enzymatic activities, including protease, amylase, and esterase. Four selected haloalkaliphilic PGPR strains displayed antifungal activity against Alternaria terricola, with three showing tolerances to heavy metals and pesticides. The strain Oceanobacillus picturea M4W.A2 was selected for genome sequencing. Phylogenomic analyses indicated that the extreme environmental conditions probably influenced the development of specific adaptations in M4W.A2 strain, differentiating it from other Oceanobacillus picturae strains. The presence of the key genes associated with plant growth promotion, osmotic and oxidative stress tolerance, antibiotic and heavy metals resistance hinted the functional capabilities might help the strain M4W.A2 to thrive in TWW-irrigated soils. By demonstrating this connection, we aim to improve our understanding of genomic fitness to stressed environments. Moreover, the identification of gene duplication and horizontal gene transfer events through mobile genetic elements allow the comprehension of these adaptation dynamics. This study reveals that haloalkaliphilc bacteria from TWW-irrigated rhizosphere exhibit plant-growth promotion and biocontrol traits, with genomic adaptations enabling their survival in high salinity and alkaline conditions, offering potential solutions for soil salinization issues.}, } @article {pmid39268957, year = {2024}, author = {Yang, P and Li, J and Lv, M and He, P and Song, G and Shan, B and Yang, X}, title = {Molecular Epidemiology and Horizontal Transfer Mechanism of optrA-Carrying Linezolid-Resistant Enterococcus faecalis.}, journal = {Polish journal of microbiology}, volume = {73}, number = {3}, pages = {349-362}, pmid = {39268957}, issn = {2544-4646}, mesh = {*Enterococcus faecalis/genetics/drug effects ; *Linezolid/pharmacology ; *Gene Transfer, Horizontal ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Gram-Positive Bacterial Infections/microbiology/epidemiology ; China/epidemiology ; Bacterial Proteins/genetics/metabolism ; Molecular Epidemiology ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Drug Resistance, Multiple, Bacterial/genetics ; Whole Genome Sequencing ; Conjugation, Genetic ; }, abstract = {The aim of this work was to provide a theoretical and scientific basis for the treatment, prevention, and control of clinical drug-resistant bacterial infections by studying the molecular epidemiology and horizontal transfer mechanism of optrA-carrying linezolid-resistant Enterococcus faecalis strains (LREfs) that were clinically isolated in a tertiary hospital in Kunming, China. Non-repetitive LREfs retained in a tertiary A hospital in Kunming, China. The strains were identified by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The transferability and horizontal transfer mechanism of optrA gene were analyzed using polymerase chain reaction (PCR), whole-genome sequencing (WGS), and conjugation experiments. A total of 39 LREfs strains were collected, and all of them were multi-drug resistant. There were 30 LREfs strains (76.9%) carrying the optrA gene, The cfr, poxtA genes and mutations in the 23S rRNA gene were not detected. The conjugation experiments showed that only three of 10 randomly selected optrA-carrying LREfs were successfully conjugated with JH2-2. Further analysis of one successfully conjugated strain revealed that the optrA gene, located in the donor bacterium, formed the IS1216E-erm(A)-optrA-fexA-IS1216E transferable fragment under the mediation of the mobile genetic element (MGE) IS1216E, which was then transferred to the recipient bacterium via horizontal plasmid transfer. Carrying the optrA gene is the primary resistance mechanism of LREfs strains. The optrA gene could carry the erm(A) and fexA genes to co-transfer among E. faecalis. MGEs such as insertion sequence IS1216E play an important role in the horizontal transfer of the optrA gene.}, } @article {pmid39268528, year = {2024}, author = {Riva, F and Dechesne, A and Eckert, EM and Riva, V and Borin, S and Mapelli, F and Smets, BF and Crotti, E}, title = {Conjugal plasmid transfer in the plant rhizosphere in the One Health context.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1457854}, pmid = {39268528}, issn = {1664-302X}, abstract = {INTRODUCTION: Horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) is one of the primary routes of antimicrobial resistance (AMR) dissemination. In the One Health context, tracking the spread of mobile genetic elements (MGEs) carrying ARGs in agri-food ecosystems is pivotal in understanding AMR diffusion and estimating potential risks for human health. So far, little attention has been devoted to plant niches; hence, this study aimed to evaluate the conjugal transfer of ARGs to the bacterial community associated with the plant rhizosphere, a hotspot for microbial abundance and activity in the soil. We simulated a source of AMR determinants that could enter the food chain via plants through irrigation.

METHODS: Among the bacterial strains isolated from treated wastewater, the strain Klebsiella variicola EEF15 was selected as an ARG donor because of the relevance of Enterobacteriaceae in the AMR context and the One Health framework. The strain ability to recolonize lettuce, chosen as a model for vegetables that were consumed raw, was assessed by a rifampicin resistant mutant. K. variicola EEF15 was genetically manipulated to track the conjugal transfer of the broad host range plasmid pKJK5 containing a fluorescent marker gene to the natural rhizosphere microbiome obtained from lettuce plants. Transconjugants were sorted by fluorescent protein expression and identified through 16S rRNA gene amplicon sequencing.

RESULTS AND DISCUSSION: K. variicola EEF15 was able to colonize the lettuce rhizosphere and inhabit its leaf endosphere 7 days past bacterial administration. Fluorescence stereomicroscopy revealed plasmid transfer at a frequency of 10[-3]; cell sorting allowed the selection of the transconjugants. The conjugation rates and the strain's ability to colonize the plant rhizosphere and leaf endosphere make strain EEF15::lacI[q]-pLpp-mCherry-gm[R] with pKJK5::Plac::gfp an interesting candidate to study ARG spread in the agri-food ecosystem. Future studies taking advantage of additional environmental donor strains could provide a comprehensive snapshot of AMR spread in the One Health context.}, } @article {pmid39266980, year = {2024}, author = {Wu, H and Dongchen, W and Li, Y and Brown, SE and Wei, S and Lin, C and Mao, Z and Liu, Z}, title = {Mitogenomes comparison of 3 species of Asparagus L shedding light on their functions due to domestication and adaptative evolution.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {857}, pmid = {39266980}, issn = {1471-2164}, support = {202305A0350012//Yunnan Basic Research Program/ ; 202305A0350012//Yunnan Basic Research Program/ ; 202305A0350012//Yunnan Basic Research Program/ ; 202305A0350012//Yunnan Basic Research Program/ ; 202305A0350012//Yunnan Basic Research Program/ ; 32360089//National Natural Science Foundation of China/ ; 32360089//National Natural Science Foundation of China/ ; 202101BD070001-027//Yunnan Agricultural joint Fund-key project/ ; }, mesh = {*Asparagus Plant/genetics ; *Genome, Mitochondrial ; *Phylogeny ; *Domestication ; *Evolution, Molecular ; RNA Editing ; Gene Transfer, Horizontal ; Genome, Chloroplast ; }, abstract = {BACKGROUND: Asparagus L., widely distributed in the old world is a genus under Asparagaceae, Asparagales. The species of the genus were mainly used as vegetables, traditional medicines as well as ornamental plants. However, the evolution and functions of mitochondrial (Mt) genomes (mitogenomes) remains largely unknown. In this study, the typical herbal medicine A. taliensis and ornamental plant A. setaceus were used to assemble and annotate the mitogenomes, and the resulting mitogenomes were further compared with published mitogenome of A. officinalis for the analysis of their functions in the context of domestication and adaptative evolution.

RESULTS: The mitochondrial genomes of both A. taliensis and A. setaceus were assembled as complete circular ones. The phylogenetic trees based on conserved protein-coding genes of Mt genomes and whole chloroplast (Cp) genomes showed that, the phylogenetic relationship of the sampled 13 species of Asparagus L. were not exactly consistent. The collinear analyses between the nuclear (Nu) and Mt genomes confirmed the existence of mutual horizontal genes transfers (HGTs) between Nu and Mt genomes within these species. Based on RNAseq data, the Mt RNA editing were predicted and atp1 and ccmB RNA editing of A. taliensis were further confirmed by DNA sequencing. Simultaneously homologous search found 5 Nu coding gene families including pentatricopeptide-repeats (PPRs) involved in Mt RNA editing. Finally, the Mt genome variations, gene expressions and mutual HGTs between Nu and Mt were detected with correlation to the growth and developmental phenotypes respectively. The results suggest that, both Mt and Nu genomes co-evolved and maintained the Mt organella replication and energy production through TCA and oxidative phosphorylation .

CONCLUSION: The assembled and annotated complete mitogenomes of both A. taliensis and A. setaceus provide valuable information for their phylogeny and concerted action of Nu and Mt genomes to maintain the energy production system of Asparagus L. in the context of domestication and adaptation to environmental niches.}, } @article {pmid39266188, year = {2024}, author = {Ali, N and Vora, C and Mathuria, A and Kataria, N and Mani, I}, title = {Advances in CRISPR-Cas systems for gut microbiome.}, journal = {Progress in molecular biology and translational science}, volume = {208}, number = {}, pages = {59-81}, doi = {10.1016/bs.pmbts.2024.07.008}, pmid = {39266188}, issn = {1878-0814}, mesh = {*CRISPR-Cas Systems/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; Animals ; Gene Editing ; Probiotics/therapeutic use ; }, abstract = {CRISPR-Cas technology has revolutionized microbiome research by enabling precise genetic manipulation of microbial communities. This review explores its diverse applications in gut microbiome studies, probiotic development, microbiome diagnostics, pathogen targeting, and microbial community engineering. Engineered bacteriophages and conjugative probiotics exemplify CRISPR-Cas's capability for targeted bacterial manipulation, offering promising strategies against antibiotic-resistant infections and other gut-related disorders. CRISPR-Cas systems also enhance probiotic efficacy by improving stress tolerance and colonization in the gastrointestinal tract. CRISPR-based techniques in diagnostics enable early intervention by enabling fast and sensitive pathogen identification. Furthermore, CRISPR-mediated gene editing allows tailored modification of microbial populations, mitigating risks associated with horizontal gene transfer and enhancing environmental and health outcomes. Despite its transformative potential, ethical and regulatory challenges loom large, demanding robust frameworks to guide its responsible application. This chapter highlights CRISPR-Cas's pivotal role in advancing microbiome research toward personalized medicine and microbial therapeutics while emphasizing the imperative of balanced ethical deliberations and comprehensive regulatory oversight.}, } @article {pmid39138294, year = {2024}, author = {York, A}, title = {Targeting the spread of antimicrobial resistance plasmids.}, journal = {Nature reviews. Microbiology}, volume = {22}, number = {10}, pages = {595}, pmid = {39138294}, issn = {1740-1534}, mesh = {*Plasmids/genetics ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Bacteria/drug effects/genetics ; Gene Transfer, Horizontal ; }, } @article {pmid39103039, year = {2024}, author = {Zhang, H and Xu, L and Hou, X and Li, Y and Niu, L and Zhang, J and Wang, X}, title = {Ketoprofen promotes the conjugative transfer of antibiotic resistance among antibiotic resistant bacteria in natural aqueous environments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {360}, number = {}, pages = {124676}, doi = {10.1016/j.envpol.2024.124676}, pmid = {39103039}, issn = {1873-6424}, mesh = {*Ketoprofen/pharmacology ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; Escherichia coli/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Water Pollutants, Chemical/toxicity ; Anti-Inflammatory Agents, Non-Steroidal/pharmacology ; }, abstract = {The emergence and spread of antibiotic resistance in the environment pose a serious threat to global public health. It is acknowledged that non-antibiotic stresses, including disinfectants, pharmaceuticals and organic pollutants, play a crucial role in horizontal transmission of antibiotic resistance genes (ARGs). Despite the widespread presence of non-steroidal anti-inflammatory drugs (NSAIDs), notably in surface water, their contributions to the transfer of ARGs have not been systematically explored. Furthermore, previous studies have primarily concentrated on model strains to investigate whether contaminants promote the conjugative transfer of ARGs, leaving the mechanisms of ARG transmission among antibiotic resistant bacteria in natural aqueous environments under the selective pressures of non-antibiotic contaminants remains unclear. In this study, the Escherichia coli (E. coli) K12 carrying RP4 plasmid was used as the donor strain, indigenous strain Aeromonas veronii containing rifampicin resistance genes in Taihu Lake, and E. coli HB101 were used as receptor strains to establish inter-genus and intra-genus conjugative transfer systems, examining the conjugative transfer frequency under the stress of ketoprofen. The results indicated that ketoprofen accelerated the environmental spread of ARGs through several mechanisms. Ketoprofen promoted cell-to-cell contact by increasing cell surface hydrophobicity and reducing cell surface charge, thereby mitigating cell-to-cell repulsion. Furthermore, ketoprofen induced increased levels of reactive oxygen species (ROS) production, activated the DNA damage-induced response (SOS), and enhanced cell membrane permeability, facilitating ARG transmission in intra-genus and inter-genus systems. The upregulation of outer membrane proteins, oxidative stress, SOS response, mating pair formation (Mpf) system, and DNA transfer and replication (Dtr) system related genes, as well as the inhibition of global regulatory genes, all contributed to higher transfer efficiency under ketoprofen treatment. These findings served as an early warning for a comprehensive assessment of the roles of NSAIDs in the spread of antibiotic resistance in natural aqueous environments.}, } @article {pmid39266183, year = {2024}, author = {Mathuria, A and Vora, C and Ali, N and Mani, I}, title = {Advances in CRISPR-Cas systems for human bacterial disease.}, journal = {Progress in molecular biology and translational science}, volume = {208}, number = {}, pages = {19-41}, doi = {10.1016/bs.pmbts.2024.07.013}, pmid = {39266183}, issn = {1878-0814}, mesh = {*CRISPR-Cas Systems/genetics ; Humans ; *Bacterial Infections/microbiology/genetics ; Gene Editing ; Bacteria/genetics ; }, abstract = {Prokaryotic adaptive immune systems called CRISPR-Cas systems have transformed genome editing by allowing for precise genetic alterations through targeted DNA cleavage. This system comprises CRISPR-associated genes and repeat-spacer arrays, which generate RNA molecules that guide the cleavage of invading genetic material. CRISPR-Cas is classified into Class 1 (multi-subunit effectors) and Class 2 (single multi-domain effectors). Its applications span combating antimicrobial resistance (AMR), targeting antibiotic resistance genes (ARGs), resensitizing bacteria to antibiotics, and preventing horizontal gene transfer (HGT). CRISPR-Cas3, for example, effectively degrades plasmids carrying resistance genes, providing a precise method to disarm bacteria. In the context of ESKAPE pathogens, CRISPR technology can resensitize bacteria to antibiotics by targeting specific resistance genes. Furthermore, in tuberculosis (TB) research, CRISPR-based tools enhance diagnostic accuracy and facilitate precise genetic modifications for studying Mycobacterium tuberculosis. CRISPR-based diagnostics, leveraging Cas endonucleases' collateral cleavage activity, offer highly sensitive pathogen detection. These advancements underscore CRISPR's transformative potential in addressing AMR and enhancing infectious disease management.}, } @article {pmid39264185, year = {2024}, author = {Magar, S and Kolte, V and Sharma, G and Govindarajan, S}, title = {Exploring pangenomic diversity and CRISPR-Cas evasion potential in jumbo phages: a comparative genomics study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0420023}, doi = {10.1128/spectrum.04200-23}, pmid = {39264185}, issn = {2165-0497}, abstract = {UNLABELLED: Jumbo phages are characterized by their remarkably large-sized genome and unique life cycles. Jumbo phages belonging to Chimalliviridae family protect the replicating phage DNA from host immune systems like CRISPR-Cas and restriction-modification system through a phage nucleus structure. Several recent studies have provided new insights into jumbo phage infection biology, but the pan-genome diversity of jumbo phages and their relationship with CRISPR-Cas targeting beyond Chimalliviridae are not well understood. In this study, we used pan-genome analysis to identify orthologous gene families shared among 331 jumbo phages with complete genomes. We show that jumbo phages lack a universally conserved set of core genes but identified seven "soft-core genes" conserved in over 50% of these phages. These genes primarily govern DNA-related activities, such as replication, repair, or nucleotide synthesis. Jumbo phages exhibit a wide array of accessory and unique genes, underscoring their genetic diversity. Phylogenetic analyses of the soft-core genes revealed frequent horizontal gene transfer events between jumbo phages, non-jumbo phages, and occasionally even giant eukaryotic viruses, indicating a polyphyletic evolutionary nature. We categorized jumbo phages into 11 major viral clusters (VCs) spanning 130 sub-clusters, with the majority being multi-genus jumbo phage clusters. Moreover, through the analysis of hallmark genes related to CRISPR-Cas targeting, we predict that many jumbo phages can evade host immune systems using both known and yet-to-be-identified mechanisms. In summary, our study enhances our understanding of jumbo phages, shedding light on their pan-genome diversity and remarkable genome protection capabilities.

IMPORTANCE: Jumbo phages are large bacterial viruses known for more than 50 years. However, only in recent years, a significant number of complete genome sequences of jumbo phages have become available. In this study, we employed comparative genomic approaches to investigate the genomic diversity and genome protection capabilities of the 331 jumbo phages. Our findings revealed that jumbo phages exhibit high genetic diversity, with only a few genes being relatively conserved across jumbo phages. Interestingly, our data suggest that jumbo phages employ yet-to-be-identified strategies to protect their DNA from the host immune system, such as CRISPR-Cas.}, } @article {pmid39258299, year = {2024}, author = {Song, W and Li, C and Lu, Y and Shen, D and Jia, Y and Huo, Y and Piao, W and Jin, H}, title = {Chlomito: a novel tool for precise elimination of organelle genome contamination from nuclear genome assembly.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1430443}, pmid = {39258299}, issn = {1664-462X}, abstract = {INTRODUCTION: Accurate reference genomes are fundamental to understanding biological evolution, biodiversity, hereditary phenomena and diseases. However, many assembled nuclear chromosomes are often contaminated by organelle genomes, which will mislead bioinformatic analysis, and genomic and transcriptomic data interpretation.

METHODS: To address this issue, we developed a tool named Chlomito, aiming at precise identification and elimination of organelle genome contamination from nuclear genome assembly. Compared to conventional approaches, Chlomito utilized new metrics, alignment length coverage ratio (ALCR) and sequencing depth ratio (SDR), thereby effectively distinguishing true organelle genome sequences from those transferred into nuclear genomes via horizontal gene transfer (HGT).

RESULTS: The accuracy of Chlomito was tested using sequencing data from Plum, Mango and Arabidopsis. The results confirmed that Chlomito can accurately detect contigs originating from the organelle genomes, and the identified contigs covered most regions of the organelle reference genomes, demonstrating efficiency and precision of Chlomito. Considering user convenience, we further packaged this method into a Docker image, simplified the data processing workflow.

DISCUSSION: Overall, Chlomito provides an efficient, accurate and convenient method for identifying and removing contigs derived from organelle genomes in genomic assembly data, contributing to the improvement of genome assembly quality.}, } @article {pmid39253440, year = {2024}, author = {Frail, S and Steele-Ogus, M and Doenier, J and Moulin, SLY and Braukmann, T and Xu, S and Yeh, E}, title = {Genomes of nitrogen-fixing eukaryotes reveal a non-canonical model of organellogenesis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39253440}, issn = {2692-8205}, support = {S10 OD030441/OD/NIH HHS/United States ; T32 AI007328/AI/NIAID NIH HHS/United States ; T32 GM007276/GM/NIGMS NIH HHS/United States ; }, abstract = {Endosymbiont gene transfer and import of host-encoded proteins are considered hallmarks of organelles necessary for stable integration of two cells. However, newer endosymbiotic models have challenged the origin and timing of such genetic integration during organellogenesis. Epithemia diatoms contain diazoplasts, closely related to recently-described nitrogen-fixing organelles, that are also stably integrated and co-speciating with their host algae. We report genomic analyses of two species, freshwater E.clementina and marine E.pelagica, which are highly divergent but share a common endosymbiotic origin. We found minimal evidence of genetic integration: nonfunctional diazoplast-to-nuclear DNA transfers in the E.clementina genome and 6 host-encoded proteins of unknown function in the E.clementina diazoplast proteome, far fewer than in other recently-acquired organelles. Epithemia diazoplasts are a valuable counterpoint to existing organellogenesis models, demonstrating that endosymbionts can be stably integrated and inherited absent significant genetic integration. The minimal genetic integration makes diazoplasts valuable blueprints for bioengineering endosymbiotic compartments de novo.}, } @article {pmid39254330, year = {2024}, author = {Lee, E and Priutt, E and Woods, S and Quick, A and King, S and McLellan, LK and Shields, RC}, title = {Genomic analysis of conjugative and chromosomally integrated mobile genetic elements in oral streptococci.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0136024}, doi = {10.1128/aem.01360-24}, pmid = {39254330}, issn = {1098-5336}, abstract = {This study aimed to investigate the diversity of conjugative and chromosomally integrated mobile genetic elements (cciMGEs) within six oral streptococci species. cciMGEs, including integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs), are stably maintained on the host cell chromosome; however, under certain conditions, they are able to excise, form extrachromosomal circles, and transfer via a conjugation apparatus. Many cciMGEs encode "cargo" functions that aid survival in new niches and evolve new antimicrobial resistance or virulence properties, whereas others have been shown to influence host bacterial physiology. Here, using a workflow employing preexisting bioinformatics tools, we analyzed 551 genomes for the presence of cciMGEs across six common health- and disease-associated oral streptococci. We identified 486 cciMGEs, 173 of which were ICEs and 233 of which were IMEs. The cciMGEs were diverse in size, cargo genes, and relaxase types. We identified several novel relaxase proteins and a widespread IME carrying a small multidrug resistance transporter. Additionally, we provide evidence that several of the bioinformatically predicted cciMGEs encoded within various Streptococcus mutans strains are capable of excision and circularization, a critical step for cciMGE conjugative transfer. These findings highlight the significance and potential impact of MGEs in shaping the genetic landscape, pathogenicity, and antimicrobial resistance profiles of the oral microbiota.IMPORTANCEOral streptococci are important players in the oral microbiome, influencing both health and disease states within dental bacterial communities. Evolutionary adaptation, shaped in a major part by the horizontal transfer of genes, is essential for their survival in the oral cavity and within new environments. Conjugation is a significant driver of horizontal gene transfer; however, there is limited information regarding this process in oral bacteria. This study utilizes publicly available genome sequences to identify conjugative and chromosomally integrated mobile genetic elements (cciMGEs) across several species of oral streptococci and presents the preliminary characterization of these elements. Our findings significantly enhance our understanding of the mobile genomic landscape of oral streptococci critical for human health, with valuable insights into how cciMGEs might influence the survival and pathogenesis of these bacteria in the oral microbiome.}, } @article {pmid39249569, year = {2024}, author = {Ruhal, R and Sahu, A and Koujalagi, T and Das, A and Prasanth, H and Kataria, R}, title = {Biofilm-specific determinants of enterococci pathogen.}, journal = {Archives of microbiology}, volume = {206}, number = {10}, pages = {397}, pmid = {39249569}, issn = {1432-072X}, support = {NA//VIT University/ ; NA//VIT University/ ; NA//VIT University/ ; NA//VIT University/ ; NA//VIT University/ ; NA//VIT University/ ; }, mesh = {*Enterococcus/genetics/metabolism ; *Biofilms ; Gene Expression Regulation, Bacterial ; *Gram-Positive Bacterial Infections/epidemiology/microbiology/physiopathology ; Bacterial Adhesion/genetics ; Adhesins, Bacterial/genetics/metabolism ; Polysaccharides, Bacterial/metabolism ; Gene Transfer, Horizontal ; }, abstract = {Amongst all Enterococcus spp., E. faecalis and E. faecium are most known notorious pathogen and their biofilm formation has been associated with endocarditis, oral, urinary tract, and wound infections. Biofilm formation involves a pattern of initial adhesion, microcolony formation, and mature biofilms. The initial adhesion and microcolony formation involve numerous surface adhesins e.g. pili Ebp and polysaccharide Epa. The mature biofilms are maintained by eDNA, It's worth noting that phage-mediated dispersal plays a prominent role. Further, the involvement of peptide pheromones in regulating biofilm maintenance sets it apart from other pathogens and facilitating the horizontal transfer of resistance genes. The role of fsr based regulation by regulating gelE expression is also discussed. Thus, we provide a concise overview of the significant determinants at each stage of Enterococcus spp. biofilm formation. These elements could serve as promising targets for antibiofilm strategies.}, } @article {pmid39248479, year = {2024}, author = {Glen, KA and Lamont, IL}, title = {Characterization of acquired β-lactamases in Pseudomonas aeruginosa and quantification of their contributions to resistance.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0069424}, doi = {10.1128/spectrum.00694-24}, pmid = {39248479}, issn = {2165-0497}, abstract = {Pseudomonas aeruginosa is a highly problematic opportunistic pathogen that causes a range of different infections. Infections are commonly treated with β-lactam antibiotics, including cephalosporins, monobactams, penicillins, and carbapenems, with carbapenems regarded as antibiotics of last resort. Isolates of P. aeruginosa can contain horizontally acquired bla genes encoding β-lactamase enzymes, but the extent to which these contribute to β-lactam resistance in this species has not been systematically quantified. The overall aim of this research was to address this knowledge gap by quantifying the frequency of β-lactamase-encoding genes in P. aeruginosa and by determining the effects of β-lactamases on susceptibility of P. aeruginosa to β-lactams. Genome analysis showed that β-lactamase-encoding genes are present in 3% of P. aeruginosa but are enriched in carbapenem-resistant isolates (35%). To determine the substrate antibiotics, 10 β-lactamases were expressed from an integrative plasmid in the chromosome of P. aeruginosa reference strain PAO1. The β-lactamases reduced susceptibility to a variety of clinically used antibiotics, including carbapenems (meropenem, imipenem), penicillins (ticarcillin, piperacillin), cephalosporins (ceftazidime, cefepime), and a monobactam (aztreonam). Different enzymes acted on different β-lactams. β-lactamases encoded by the genomes of P. aeruginosa clinical isolates had similar effects to the enzymes expressed in strain PAO1. Genome engineering was used to delete β-lactamase-encoding genes from three carbapenem-resistant clinical isolates and increased susceptibility to substrate β-lactams. Our findings demonstrate that acquired β-lactamases play an important role in β-lactam resistance in P. aeruginosa, identifying substrate antibiotics for a range of enzymes and quantifying their contributions to resistance.IMPORTANCEPseudomonas aeruginosa is an extremely problematic pathogen, with isolates that are resistant to the carbapenem class of β-lactam antibiotics being in critical need of new therapies. Genes encoding β-lactamase enzymes that degrade β-lactam antibiotics can be present in P. aeruginosa, including carbapenem-resistant isolates. Here, we show that β-lactamase genes are over-represented in carbapenem-resistant isolates, indicating their key role in resistance. We also show that different β-lactamases alter susceptibility of P. aeruginosa to different β-lactam antibiotics and quantify the effects of selected enzymes on β-lactam susceptibility. This research significantly advances the understanding of the contributions of acquired β-lactamases to antibiotic resistance, including carbapenem resistance, in P. aeruginosa and by implication in other species. It has potential to expedite development of methods that use whole genome sequencing of infecting bacteria to inform antibiotic treatment, allowing more effective use of antibiotics, and facilitate the development of new antibiotics.}, } @article {pmid38723713, year = {2024}, author = {Na, IY and Seo, J and Jin, Y and Ko, KS}, title = {Whole-plasmid analysis of NDM-1-producing Acinetobacter seifertii isolate and its fitness in several Acinetobacter species.}, journal = {Journal of global antimicrobial resistance}, volume = {38}, number = {}, pages = {223-226}, doi = {10.1016/j.jgar.2024.05.003}, pmid = {38723713}, issn = {2213-7173}, mesh = {*Acinetobacter/genetics/drug effects/isolation & purification/enzymology ; *beta-Lactamases/genetics ; *Plasmids/genetics ; Humans ; *Microbial Sensitivity Tests ; Republic of Korea ; *Anti-Bacterial Agents/pharmacology ; *Acinetobacter Infections/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Genotype ; Carbapenems/pharmacology ; Conjugation, Genetic ; }, abstract = {OBJECTIVES: The aim of this study was to characterize an NDM-1-producing Acinetobacter seifertii isolates from a patient in South Korea.

METHODS: Antibiotic susceptibility testing and genotyping using multigene sequencing were performed and whole plasmid sequences were determined.

RESULTS: The genotype of A. seifertii was ST1899 and was resistant to ceftazidime, trimethoprim-sulfamethoxazole, and piperacillin-tazobactam, in addition to carbapenem. blaNDM-1 was surrounded by the ISAba125 insertion sequence within the structure of Tn125 in the 47 kb-sized plasmid. The plasmid exhibited a structure similar to that of other plasmids of diverse Acinetobacter sp. found worldwide. Transconjugation and the growth curve indicated that the plasmid was adapted to A. seifertii rather than other closely related Acinetobacter sp.

CONCLUSIONS: Acquisition of carbapenem resistance by horizontal transfer of the blaNDM-1-carrying plasmid from another Acinetobacter species was found with no growth defect.}, } @article {pmid39243547, year = {2024}, author = {Hu, RG and Yang, L and Wang, LY and Yang, YL and Li, HJ and Yang, BT and Kang, YH and Liang, ZL and Cong, W}, title = {Unveiling the pathogenic and multidrug-resistant profiles of Vibrio alfacsensis: A potential identified threat in turbot (Scophthalmus maximus) aquaculture.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135729}, doi = {10.1016/j.jhazmat.2024.135729}, pmid = {39243547}, issn = {1873-3336}, abstract = {Vibrio alfacsensis is traditionally seen as an environmental symbiont within its genus, with no detailedly documented pathogenicity in marine aquaculture to date. This study delves into the largely unexplored pathogenic potential and emerging antibiotic resistance of V. alfacsensis. The VA-1 strain, isolated from recirculating aquaculture system (RAS) effluent of cultured turbot (Scophthalmus maximus), underwent comprehensive analysis including biochemical identification, antibiotic susceptibility testing and reinfection trials. The results confirmed VA-1's pathogenicity and significant multiple antibiotic resistance. VA-1 could induce systemic infection in turbot, with symptoms like kidney enlargement, exhibiting virulence comparable to known Vibrio pathogens, with an LD50 around 2.36 × 10[6] CFU/fish. VA-1's remarkable resistance phenotype (14/22) suggested potential for genetic exchange and resistance factor acquisition in aquaculture environments. Phylogenetic analysis based on 16S rDNA sequences and whole-genome sequencing has firmly placed VA-1 within the V. alfacsensis clade, while genome-wide analysis highlights its similarity and diversity in relation to strains from across the globe. VA-1 contained numerous replicons, indicating the possibility for the spread of resistance and virulence genes. This study suggests V. alfacsensis may acquire and transfer pathogenic and resistant traits through horizontal gene transfer, a likelihood intensified by changing environmental and aquaculture conditions, highlighting the need for vigilant pathogen monitoring and new non-antibiotic treatments.}, } @article {pmid39243538, year = {2024}, author = {Lin, L and Li, L and Yang, X and Hou, L and Wu, D and Wang, B and Ma, B and Liao, X and Yan, X and Gad, M and Su, J and Liu, Y and Liu, K and Hu, A}, title = {Unnoticed antimicrobial resistance risk in Tibetan cities unveiled by sewage metagenomic surveillance: Compared to the eastern Chinese cities.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135730}, doi = {10.1016/j.jhazmat.2024.135730}, pmid = {39243538}, issn = {1873-3336}, abstract = {Sewage surveillance is a cost-effective tool for assessing antimicrobial resistance (AMR) in urban populations. However, research on sewage AMR in remote areas is still limited. Here, we used shotgun metagenomic sequencing to profile antibiotic resistance genes (ARGs) and ARG-carrying pathogens (APs) across 15 cities in Tibetan Plateau (TP) and the major cities in eastern China. Notable regional disparities in sewage ARG composition were found, with a significantly higher ARG abundance in TP (2.97 copies/cell). A total of 542 and 545 APs were identified in sewage from TP and the East, respectively, while more than 40 % carried mobile genetic elements (MGEs). Moreover, 65 MGEs-carrying APs were identified as World Health Organization (WHO) priority-like bacterial and fungal pathogens. Notably, a fungal zoonotic pathogen, Enterocytozoon bieneusi, was found for the first time to carry a nitroimidazole resistance gene (nimJ). Although distinct in AP compositions, the relative abundances of APs were comparable in these two regions. Furthermore, sewage in TP was found to be comparable to the cities in eastern China in terms of ARG mobility and AMR risks. These findings provide insights into ARGs and APs distribution in Chinese sewage and stress the importance of AMR surveillance and management strategies in remote regions.}, } @article {pmid39208359, year = {2024}, author = {Ares-Arroyo, M and Coluzzi, C and Moura de Sousa, JA and Rocha, EPC}, title = {Hijackers, hitchhikers, or co-drivers? The mysteries of mobilizable genetic elements.}, journal = {PLoS biology}, volume = {22}, number = {8}, pages = {e3002796}, doi = {10.1371/journal.pbio.3002796}, pmid = {39208359}, issn = {1545-7885}, mesh = {*Gene Transfer, Horizontal ; Interspersed Repetitive Sequences/genetics ; Bacteria/genetics ; Evolution, Molecular ; Genomic Islands ; Symbiosis/genetics ; Genome, Bacterial ; }, abstract = {Mobile genetic elements shape microbial gene repertoires and populations. Recent results reveal that many, possibly most, microbial mobile genetic elements require helpers to transfer between genomes, which we refer to as Hitcher Genetic Elements (hitchers or HGEs). They may be a large fraction of pathogenicity and resistance genomic islands, whose mechanisms of transfer have remained enigmatic for decades. Together with their helper elements and their bacterial hosts, hitchers form tripartite networks of interactions that evolve rapidly within a parasitism-mutualism continuum. In this emerging view of microbial genomes as communities of mobile genetic elements many questions arise. Which elements are being moved, by whom, and how? How often are hitchers costly hyper-parasites or beneficial mutualists? What is the evolutionary origin of hitchers? Are there key advantages associated with hitchers' lifestyle that justify their unexpected abundance? And why are hitchers systematically smaller than their helpers? In this essay, we start answering these questions and point ways ahead for understanding the principles, origin, mechanisms, and impact of hitchers in bacterial ecology and evolution.}, } @article {pmid39242818, year = {2024}, author = {Porras, MÁG and Assié, A and Tietjen, M and Violette, M and Kleiner, M and Gruber-Vodicka, H and Dubilier, N and Leisch, N}, title = {An intranuclear bacterial parasite of deep-sea mussels expresses apoptosis inhibitors acquired from its host.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {39242818}, issn = {2058-5276}, support = {340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; 340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; 340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; 340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; Gottfried Wilhelm Leibniz Prize//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Heisenberggrant GR 5028/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; OIA 1934844//National Science Foundation (NSF)/ ; IOS 2003107//National Science Foundation (NSF)/ ; }, abstract = {A limited number of bacteria are able to colonize the nuclei of eukaryotes. 'Candidatus Endonucleobacter' infects the nuclei of deep-sea mussels, where it replicates to ≥80,000 bacteria per nucleus and causes nuclei to swell to 50 times their original size. How these parasites are able to replicate and avoid apoptosis is not known. Dual RNA-sequencing transcriptomes of infected nuclei isolated using laser-capture microdissection revealed that 'Candidatus Endonucleobacter' does not obtain most of its nutrition from nuclear DNA or RNA. Instead, 'Candidatus Endonucleobacter' upregulates genes for importing and digesting sugars, lipids, amino acids and possibly mucin from its host. It likely prevents apoptosis of host cells by upregulating 7-13 inhibitors of apoptosis, proteins not previously seen in bacteria. Comparative phylogenetic analyses revealed that 'Ca. Endonucleobacter' acquired inhibitors of apoptosis through horizontal gene transfer from their hosts. Horizontal gene transfer from eukaryotes to bacteria is assumed to be rare, but may be more common than currently recognized.}, } @article {pmid39236533, year = {2024}, author = {Yuan, Q and Li, W and Goh, SG and Chen, SL and Ng, OT and He, Y and Gin, KY}, title = {Genetic traits and transmission of antimicrobial resistance characteristics of cephalosporin resistant Escherichia coli in tropical aquatic environments.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135707}, doi = {10.1016/j.jhazmat.2024.135707}, pmid = {39236533}, issn = {1873-3336}, abstract = {This study investigates the genetic traits and transmission mechanisms of cephalosporin-resistant Escherichia coli in tropical aquatic environments in Singapore. From 2016 to 2020, monthly samples were collected from wastewater treatment plants, marine niches, community sewage, beaches, reservoirs, aquaculture farms, and hospitals, yielding 557 isolates that were analyzed for antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) using genomic methods. Findings reveal significant genotypic similarities between environmental and hospital-derived strains, particularly the pandemic E. coli ST131. Environmental strains exhibited high levels of intrinsic resistance mechanisms, including mutations in porins and efflux pumps, with key ARGs such as CMY-2 and NDM-9 predominantly carried by MGEs, which facilitate horizontal gene transfer. Notably, pathogenic EPEC and EHEC strains were detected in community sewage and aquaculture farms, posing substantial public health risks. This underscores the critical role of these environments as reservoirs for multidrug-resistant pathogens and emphasizes the interconnectedness of human activities and environmental health.}, } @article {pmid39236354, year = {2024}, author = {Brdová, D and Ruml, T and Viktorová, J}, title = {Mechanism of staphylococcal resistance to clinically relevant antibiotics.}, journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy}, volume = {77}, number = {}, pages = {101147}, doi = {10.1016/j.drup.2024.101147}, pmid = {39236354}, issn = {1532-2084}, abstract = {Staphylococcus aureus, a notorious pathogen with versatile virulence, poses a significant challenge to current antibiotic treatments due to its ability to develop resistance mechanisms against a variety of clinically relevant antibiotics. In this comprehensive review, we carefully dissect the resistance mechanisms employed by S. aureus against various antibiotics commonly used in clinical settings. The article navigates through intricate molecular pathways, elucidating the mechanisms by which S. aureus evades the therapeutic efficacy of antibiotics, such as β-lactams, vancomycin, daptomycin, linezolid, etc. Each antibiotic is scrutinised for its mechanism of action, impact on bacterial physiology, and the corresponding resistance strategies adopted by S. aureus. By synthesising the knowledge surrounding these resistance mechanisms, this review aims to serve as a comprehensive resource that provides a foundation for the development of innovative therapeutic strategies and alternative treatments for S. aureus infections. Understanding the evolving landscape of antibiotic resistance is imperative for devising effective countermeasures in the battle against this formidable pathogen.}, } @article {pmid39235659, year = {2024}, author = {Fu, Y and Fu, Z and Yu, J and Wang, H and Zhang, Y and Liu, M and Wang, X and Yu, W and Han, F}, title = {Biochemical Characterization of Hyaluronate Lyase CpHly8 from an Intestinal Microorganism Clostridium perfringens G1121.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39235659}, issn = {1559-0291}, support = {2022QNLM030003-1//Qingdao Marine Science and Technology Center/ ; ZR2019ZD18//Natural Science Foundation of Shandong Province/ ; 2018YFC0311105//Shandong Province Technology Innovation Guidance Program/ ; 22-3-6-gjxm-5-gx//Science & Technology Development Project of Qingdao/ ; 21-1-6-gjxm-27-gx//Science & Technology Development Project of Qingdao/ ; 20-11-6-64-gx//Science & Technology Development Project of Qingdao/ ; }, abstract = {Hyaluronic acid (HA) is an important component of extracellular matrices (ECM) and a linear polysaccharide involved in various physiological and pathological processes within the biological system. Several pathogens exploit HA degradation within the extracellular matrix to facilitate infection. While many intestinal microorganisms play significant roles in HA utilization in the human body, there remains a scarcity of related studies. This paper addressed this gap by screening intestinal microorganisms capable of degrading HA, resulting in the isolation of Clostridium perfringens G1121, which had been demonstrated the ability to degrade HA. Subsequent genome sequencing and analysis of C. perfringens G1121 revealed its utilization of the polysaccharide utilization loci of HA (PULHA), which was obtained by horizontal gene transfer. The PULHA contains a sequence encoding a hyaluronic acid-specific degradation enzyme designated CpHly8, belonging to polysaccharide lyase family 8. The specific activity of CpHly8 towards HA was 142.98 U/mg, with the optimum reaction temperature and pH observed at 50℃ and 6.0, respectively. The final product of HA degradation by CpHly8 was unsaturated hyaluronic acid disaccharide. Moreover, subcutaneous diffusion experiments with trypan blue in mice revealed that CpHly8 effectively promoted subcutaneous diffusion and sustained its effects long-term, suggesting its potential application as an adjunct in drug delivery. Overall, our study enriches our understanding of intestinal microbial degradation of HA, provides new evidence for horizontal gene transfer among intestinal microorganisms, and confirms that CpHly8 is a promising candidate for intestinal microbial hyaluronidase.}, } @article {pmid39235644, year = {2024}, author = {Jaswal, R and Dubey, H and Kiran, K and Rawal, H and Kumar, G and Rajarammohan, S and Deshmukh, R and Sonah, H and Prasad, P and Bhardwaj, SC and Gupta, N and Sharma, TR}, title = {Identification and functional characterization of the npc-2-like domain containing rust effector protein that suppresses cell death in plants.}, journal = {Molecular biology reports}, volume = {51}, number = {1}, pages = {962}, pmid = {39235644}, issn = {1573-4978}, mesh = {*Plant Diseases/microbiology ; *Phylogeny ; *Cell Death ; *Fungal Proteins/metabolism/genetics ; Nicotiana/microbiology/metabolism/genetics ; Basidiomycota/pathogenicity/metabolism/genetics ; Puccinia/pathogenicity/metabolism ; Protein Domains ; Molecular Docking Simulation ; Onions/microbiology/metabolism/genetics ; }, abstract = {The MD-2-related lipid-recognition (ML/Md-2) domain is a lipid/sterol-binding domain that are involved in sterol transfer and innate immunity in eukaryotes. Here we report a genome-wide survey of this family, identifying 84 genes in 30 fungi including plant pathogens. All the studied species were found to have varied ML numbers, and expansion of the family was observed in Rhizophagus irregularis (RI) with 33 genes. The molecular docking studies of these proteins with cholesterol derivatives indicate lipid-binding functional conservation across the animal and fungi kingdom. The phylogenetic studies among eukaryotic ML proteins showed that Puccinia ML members are more closely associated with animal (insect) npc2 proteins than other fungal ML members. One of the candidates from leaf rust fungus Puccinia triticina, Pt5643 was PCR amplified and further characterized using various studies such as qRT-PCR, subcellular localization studies, yeast functional complementation, signal peptide validation, and expression studies. The Pt5643 exhibits the highest expression on the 5th day post-infection (dpi). The confocal microscopy of Pt5643 in onion epidermal cells and N. benthamiana shows its location in the cytoplasm and nucleus. The functional complementation studies of Pt5643 in npc2 mutant yeast showed its functional similarity to the eukaryotic/yeast npc2 gene. Furthermore, the overexpression of Pt5643 also suppressed the BAX, NEP1, and H2O2-induced program cell death in Nicotiana species and yeast. Altogether the present study reports the novel function of ML domain proteins in plant fungal pathogens and their possible role as effector molecules in host defense manipulation.}, } @article {pmid39235595, year = {2024}, author = {Xu, R and Huang, C and Yang, B and Wang, S and Zhong, T and Ma, L and Shang, Q and Zhang, M and Chu, Z and Liu, X}, title = {Influence of Two-Dimensional Black Phosphorus on the Horizontal Transfer of Plasmid-Mediated Antibiotic Resistance Genes: Promotion or Inhibition?.}, journal = {Current microbiology}, volume = {81}, number = {10}, pages = {344}, pmid = {39235595}, issn = {1432-0991}, support = {52070063//National Natural Science Foundation of China/ ; 2308085Y38//Science Fund for Distinguished Young Scholars of Anhui Province/ ; 21-22RC30//Hefei University/ ; }, mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Phosphorus/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Conjugation, Genetic ; Escherichia coli/genetics/drug effects ; Nanostructures ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial/drug effects ; Bacteria/genetics/drug effects ; }, abstract = {The problem of bacterial resistance caused by antibiotic abuse is seriously detrimental to global human health and ecosystem security. The two-dimensional nanomaterial (2D) such as black phosphorus (BP) is recently expected to become a new bacterial inhibitor and has been widely used in the antibacterial field due to its specific physicochemical properties. Nevertheless, the effects of 2D-BP on the propagation of antibiotic resistance genes (ARGs) in environments and the relevant mechanisms are not clear. Herein, we observed that the sub-inhibitory concentrations of 2D-BP dramatically increased the conjugative transfer of ARGs mediated by the RP4 plasmid up to 2.6-fold at the 125 mg/L exposure level compared with the untreated bacterial cells. Nevertheless, 2D-BP with the inhibitory concentration caused a dramatic decrease in the conjugative frequency. The phenotypic changes revealed that the increase of the conjugative transfer caused by 2D-BP exposure were attributed to the excessive reactive oxygen species and oxidative stress, and increased bacterial cell membrane permeability. The genotypic evidence demonstrated that 2D-BP affecting the horizontal gene transfer of ARGs was probably through the upregulation of mating pair formation genes (trbBp and traF) and DNA transfer and replication genes (trfAp and traJ), as well as the downregulation of global regulatory gene expression (korA, korB, and trbA). In summary, the changes in the functional and regulatory genes in the conjugative transfer contributed to the stimulation of conjugative transfer. This research aims to broaden our comprehension of how nanomaterials influence the dissemination of ARGs by elucidating their effects and mechanisms.}, } @article {pmid39233522, year = {2024}, author = {Lee, JH and Tareen, AR and Kim, NH and Jeong, C and Kang, B and Lee, G and Kim, DW and Zahra, R and Lee, SH}, title = {Comparative Genomic Analyses of E. coli ST2178 Strains Originated from Wild Birds in Pakistan.}, journal = {Journal of microbiology and biotechnology}, volume = {34}, number = {10}, pages = {1-8}, doi = {10.4014/jmb.2407.07026}, pmid = {39233522}, issn = {1738-8872}, abstract = {The emergence and spread of multidrug-resistance (MDR) pathogenic Escherichia coli due to horizontal gene transfer of antibiotic resistance genes (ARGs) and virulence factors (VFs) is a global health concern, particularly in developing countries. While numerous studies have focused on major sequence types (STs), the implication of minor STs in ARG dissemination and their pathogenicity remains crucial. In this study, two E. coli strains (PEC1011 and PEC1012) were isolated from wild bird feces in Pakistan and identified as ST2178 based on their complete genome sequences. To understand this minor ST, 204 genome assemblies of ST2178 were comparatively analyzed with the isolates' genomes. The phylogenetic analyses revealed five subclades of ST2178. Subclade E strains were predominantly isolated from human specimens, whereas subclades A and B strains including strains PEC1011 and PEC1012, respectively, were frequently isolated from animal. Mobile genetic elements (MGEs) exhibited the positive correlation with ARGs but not with VFs in this ST. Plasmid-borne ARGs exhibited higher correlation with plasmid-borne MGEs, indicating the role of diverse mobile plasmid structures in ARG transmission. Subclade E exhibited diverse plasmid-borne ARG repertoires correlated with MGEs, marking it as a critical surveillance target. In the case of VFs, they exhibited phylogeny-dependent profiles. Strain PEC1012 harbored various plasmid-borne ARGs, which are similar with conserved ARG repertoires in subclade A. The presence of unique ARG insertion in pPEC1012 highlights the importance of subclade A in ARG dissemination. This study comprehensively elucidates the landscape of ST2178, identifying critical phylogenetic subclades and their characteristics in ARG and VF occurrence.}, } @article {pmid39233087, year = {2024}, author = {Kong, F and Qi, Z and Tong, H and Ren, N and You, S}, title = {Case study on the relationship between transmission of antibiotic resistance genes and microbial community under freeze-thaw cycle on cold-region dairy farm.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {175989}, doi = {10.1016/j.scitotenv.2024.175989}, pmid = {39233087}, issn = {1879-1026}, abstract = {Freeze-thaw cycle (FTC) is a naturally occurring phenomenon in high-latitude terrestrial ecosystems, which may exert influence on distribution and evolution of microbial community in the soil. The relationship between transmission of antibiotic resistance genes (ARGs) and microbial community was investigated upon the case study on the soil of cold-region dairy farm under seasonal FTC. The results demonstrated that 37 ARGs underwent decrease in the abundance of blaTEM from 80.4 % for frozen soil to 71.7 % for thawed soil, and that sul2 from 8.8 % for frozen soil to 6.5 % for thawed soil, respectively. Antibiotic deactivation was identified to be closely related to the highest relative abundance of blaTEM, and the spread of sulfonamide resistance genes (SRGs) occurred mainly via target modification. Firmicutes in frozen soil were responsible for dominating the abundance of ARGs by suppressing the native bacteria under starvation effect in cold regions, and then underwent horizontal gene transfer (HGT) among native bacteria through mobile genetic elements (MGEs). The TRB-C (32.6-49.1 %) and tnpA-06 (0.27-7.5 %) were significantly increased in frozen soil, while Int3 (0.67-10.6 %) and tnpA-04 (11.1-19.4 %) were up-regulated in thawed soil. Moreover, the ARGs in frozen soil primarily underwent HGT through MGEs, i.e. TRB-C and tnpA-06, with increased number of Firmicutes serving as carrier. The case study not only demonstrated relationship between transmission of ARGs and microbial community in the soil under practically relevant FTC condition, but also emphasized the importance for formulating better strategies for preventing FTC-induced ARGs in dairy farm in cold regions.}, } @article {pmid39226958, year = {2024}, author = {Muñoz, JSC and Aransiola, SA and Reddy, KV and Ranjit, P and Victor-Ekwebelem, MO and Oyedele, OJ and Pérez-Almeida, IB and Maddela, NR and Díaz, JMR}, title = {Antibiotic resistant bacteria and antibiotic resistance genes as contaminants of emerging concern: Occurrences, impacts, mitigations and future guidelines.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {175906}, doi = {10.1016/j.scitotenv.2024.175906}, pmid = {39226958}, issn = {1879-1026}, abstract = {Antibiotic resistance, driven by the proliferation of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARBs), has emerged as a pressing global health concern. Antimicrobial resistance is exacerbated by the widespread use of antibiotics in agriculture, aquaculture, and human medicine, leading to their accumulation in various environmental compartments such as soil, water, and sediments. The presence of ARGs in the environment, particularly in municipal water, animal husbandry, and hospital environments, poses significant risks to human health, as they can be transferred to potential human pathogens. Current remediation strategies, including the use of pyroligneous acid, coagulants, advanced oxidation, and bioelectrochemical systems, have shown promising results in reducing ARGs and ARBs from soil and water. However, these methods come with their own set of challenges, such as the need for elevated base levels in UV-activated persulfate and the long residence period required for photocatalysts. The future of combating antibiotic resistance lies in the development of standardized monitoring techniques, global collaboration, and the exploration of innovative remediation methods. Emphasis on combination therapies, advanced oxidation processes, and monitoring horizontal gene transfer can pave the way for a comprehensive approach to mitigate the spread of antibiotic resistance in the environment.}, } @article {pmid39224035, year = {2024}, author = {Chopra, A and Bhuvanagiri, G and Natu, K and Chopra, A}, title = {Role of CRISPR-Cas systems in periodontal disease pathogenesis and potential for periodontal therapy: A review.}, journal = {Molecular oral microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/omi.12483}, pmid = {39224035}, issn = {2041-1014}, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences capable of editing a host genome sequence. CRISPR and its specific CRISPR-associated (Cas) protein complexes have been adapted for various applications. These include activating or inhibiting specific genetic sequences or acting as molecular scissors to cut and modify the host DNA precisely. CRISPR-Cas systems are also naturally present in many oral bacteria, where they aid in nutrition, biofilm formation, inter- and intraspecies communication (quorum sensing), horizontal gene transfer, virulence, inflammation modulation, coinfection, and immune response evasion. It even functions as an adaptive immune system, defending microbes against invading viruses and foreign genetic elements from other bacteria by targeting and degrading their DNA. Recently, CRISPR-Cas systems have been tested as molecular editing tools to manipulate specific genes linked with periodontal disease (such as periodontitis) and as novel methods of delivering antimicrobial agents to overcome antimicrobial resistance. With the rapidly increasing role of CRISPR in treating inflammatory diseases, its application in periodontal disease is also becoming popular. Therefore, this review aims to discuss the different types of CRISPR-Cas in oral microbes and their role in periodontal disease pathogenesis and precision periodontal therapy.}, } @article {pmid39223450, year = {2024}, author = {Valerio, F and Martel, C and Stefanescu, C and van Nouhuys, S and Kankare, M and Duplouy, A}, title = {Wolbachia strain diversity in a complex group of sympatric cryptic parasitoid wasp species.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {319}, pmid = {39223450}, issn = {1471-2180}, mesh = {Animals ; *Wolbachia/genetics/classification/isolation & purification ; *Wasps/microbiology ; *Symbiosis ; *Phylogeny ; Sympatry ; Gene Transfer, Horizontal ; Genetic Variation ; Lepidoptera/microbiology/parasitology ; }, abstract = {BACKGROUND: Maternally-inherited symbionts can induce pre-mating and/or post-mating reproductive isolation between sympatric host lineages, and speciation, by modifying host reproductive phenotypes. The large parasitoid wasp genus Cotesia (Braconidae) includes a diversity of cryptic species, each specialized in parasitizing one to few related Lepidoptera host species. Here, we characterized the infection status of an assemblage of 21 Cotesia species from 15 countries by several microbial symbionts, as a first step toward investigating whether symbionts may provide a barrier to gene flow between these parasitoid host lineages.

RESULTS: The symbiotic microbes Arsenophonus, Cardinium, Microsporidium and Spiroplasma were not detected in the Cotesia wasps. However, the endosymbiotic bacterium Wolbachia was present in at least eight Cotesia species, and hence we concentrated on it upon screening additional DNA extracts and SRAs from NCBI. Some of the closely related Cotesia species carry similar Wolbachia strains, but most Wolbachia strains showed patterns of horizontal transfer between phylogenetically distant host lineages.

CONCLUSIONS: The lack of co-phylogenetic signal between Wolbachia and Cotesia suggests that the symbiont and hosts have not coevolved to an extent that would drive species divergence between the Cotesia host lineages. However, as the most common facultative symbiont of Cotesia species, Wolbachia may still function as a key-player in the biology of the parasitoid wasps. Its precise role in the evolution of this complex clade of cryptic species remains to be experimentally investigated.}, } @article {pmid39222343, year = {2024}, author = {Lyulina, AS and Liu, Z and Good, BH}, title = {Linkage equilibrium between rare mutations.}, journal = {Genetics}, volume = {}, number = {}, pages = {}, doi = {10.1093/genetics/iyae145}, pmid = {39222343}, issn = {1943-2631}, abstract = {Recombination breaks down genetic linkage by reshuffling existing variants onto new genetic backgrounds. These dynamics are traditionally quantified by examining the correlations between alleles, and how they decay as a function of the recombination rate. However, the magnitudes of these correlations are strongly influenced by other evolutionary forces like natural selection and genetic drift, making it difficult to tease out the effects of recombination. Here we introduce a theoretical framework for analyzing an alternative family of statistics that measure the homoplasy produced by recombination. We derive analytical expressions that predict how these statistics depend on the rates of recombination and recurrent mutation, the strength of negative selection and genetic drift, and the present-day frequencies of the mutant alleles. We find that the degree of homoplasy can strongly depend on this frequency scale, which reflects the underlying timescales over which these mutations occurred. We show how these scaling properties can be used to isolate the effects of recombination, and discuss their implications for the rates of horizontal gene transfer in bacteria.}, } @article {pmid39221153, year = {2024}, author = {Belay, WY and Getachew, M and Tegegne, BA and Teffera, ZH and Dagne, A and Zeleke, TK and Abebe, RB and Gedif, AA and Fenta, A and Yirdaw, G and Tilahun, A and Aschale, Y}, title = {Mechanism of antibacterial resistance, strategies and next-generation antimicrobials to contain antimicrobial resistance: a review.}, journal = {Frontiers in pharmacology}, volume = {15}, number = {}, pages = {1444781}, pmid = {39221153}, issn = {1663-9812}, abstract = {Antibacterial drug resistance poses a significant challenge to modern healthcare systems, threatening our ability to effectively treat bacterial infections. This review aims to provide a comprehensive overview of the types and mechanisms of antibacterial drug resistance. To achieve this aim, a thorough literature search was conducted to identify key studies and reviews on antibacterial resistance mechanisms, strategies and next-generation antimicrobials to contain antimicrobial resistance. In this review, types of resistance and major mechanisms of antibacterial resistance with examples including target site modifications, decreased influx, increased efflux pumps, and enzymatic inactivation of antibacterials has been discussed. Moreover, biofilm formation, and horizontal gene transfer methods has also been included. Furthermore, measures (interventions) taken to control antimicrobial resistance and next-generation antimicrobials have been discussed in detail. Overall, this review provides valuable insights into the diverse mechanisms employed by bacteria to resist the effects of antibacterial drugs, with the aim of informing future research and guiding antimicrobial stewardship efforts.}, } @article {pmid39221073, year = {2024}, author = {Xie, X and Deng, X and Chen, L and Yuan, J and Chen, H and Wei, C and Liu, X and Wuertz, S and Qiu, G}, title = {Integrated genomics provides insights into the evolution of the polyphosphate accumulation trait of Ca. Accumulibacter.}, journal = {Environmental science and ecotechnology}, volume = {20}, number = {}, pages = {100353}, pmid = {39221073}, issn = {2666-4984}, abstract = {Candidatus Accumulibacter, a prominent polyphosphate-accumulating organism (PAO) in wastewater treatment, plays a crucial role in enhanced biological phosphorus removal (EBPR). The genetic underpinnings of its polyphosphate accumulation capabilities, however, remain largely unknown. Here, we conducted a comprehensive genomic analysis of Ca. Accumulibacter-PAOs and their relatives within the Rhodocyclaceae family, identifying 124 core genes acquired via horizontal gene transfer (HGT) at its least common ancestor. Metatranscriptomic analysis of an enrichment culture of Ca. Accumulibacter revealed active transcription of 44 of these genes during an EBPR cycle, notably including the polyphosphate kinase 2 (PPK2) gene instead of the commonly recognized polyphosphate kinase 1 (PPK1) gene. Intriguingly, the phosphate regulon (Pho) genes showed minimal transcriptions, pointing to a distinctive fact of Pho dysregulation, where PhoU, the phosphate signaling complex protein, was not regulating the high-affinity phosphate transport (Pst) system, resulting in continuous phosphate uptake. To prevent phosphate toxicity, Ca. Accumulibacter utilized the laterally acquired PPK2 to condense phosphate into polyphosphate, resulting in the polyphosphate-accumulating feature. This study provides novel insights into the evolutionary emergence of the polyphosphate-accumulating trait in Ca. Accumulibacter, offering potential advancements in understanding the PAO phenotype in the EBPR process.}, } @article {pmid39219575, year = {2024}, author = {He, XY and Chen, JM and Li, ZZ}, title = {Complete organelle genomes of the threatened aquatic species Scheuchzeria palustris (Scheuchzeriaceae): Insights into adaptation and phylogenomic placement.}, journal = {Ecology and evolution}, volume = {14}, number = {9}, pages = {e70248}, pmid = {39219575}, issn = {2045-7758}, abstract = {Scheuchzeria palustris, the only species in the Scheuchzeriaceae family, plays a crucial role in methane production and transportation, influencing the global carbon cycle and maintaining ecosystem stability. However, it is now threatened by human activities and global warming. In this study, we generated new organelle genomes for S. palustris, with the plastome (pt) measuring 158,573 bp and the mitogenome (mt) measuring 420,724 bp. We predicted 296 RNA editing sites in mt protein-coding genes (PCGs) and 142 in pt-PCGs. Notably, abundant RNA editing sites in pt-PCGs likely originated from horizontal gene transfer between the plastome and mitogenome. Additionally, we identified positive selection signals in four mt-PCGs (atp4, ccmB, nad3, and sdh4) and one pt-PCG (rps7), which may contribute to the adaptation of S. palustris to low-temperature and high-altitude environments. Furthermore, we identified 35 mitochondrial plastid DNA (MTPT) segments totaling 58,479 bp, attributed to dispersed repeats near most MTPT. Phylogenetic trees reconstructed from mt- and pt-PCGs showed topologies consistent with the APG IV system. However, the conflicting position of S. palustris can be explained by significant differences in the substitution rates of its mt- and pt-PCGs (p < .001). In conclusion, our study provides vital genomic resources to support future conservation efforts and explores the adaptation mechanisms of S. palustris.}, } @article {pmid39216666, year = {2024}, author = {Qiu, T and Shen, L and Guo, Y and Gao, M and Gao, H and Li, Y and Zhao, G and Wang, X}, title = {Impact of aeration rate on the transfer range of antibiotic-resistant plasmids during manure composting.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {124851}, doi = {10.1016/j.envpol.2024.124851}, pmid = {39216666}, issn = {1873-6424}, abstract = {Conjugative plasmids are important vectors of mobile antibiotic resvistance genes (ARGs), facilitating their horizontal transfer within the environment. While composting is recognized as an effective method to reduce antibiotics and ARGs in animal manure, its impact on the bacterial host communities containing antibiotic-resistant plasmids remains unclear. In this study, we investigated the permissiveness of bacterial community during composting when challenged with multidrug-resistant conjugative RP4 plasmids, employing Pseudomonas putida as the donor strain. Ultimately, this represents the first exploration of the effects of aeration rates on the range of RP4 plasmid transfer hosts. Transconjugants were analyzed through fluorescent reporter gene-based fluorescence-activated cell sorting and Illumina sequencing. Overall, aeration rates were found to influence various physicochemical parameters of compost, including temperature, pH, total organic matter, total nitrogen, and potassium. Regarding RP4 plasmid host bacteria, the dominant phylum was determined to shift from Bacteroidetes in the raw material to Proteobacteria in the compost. Notably, a moderate-intensity aeration rate (0.05 L/min/L) was found to be more effective in reducing the diversity and richness of the RP4 plasmid host bacterial community. Following composting, the total percentage of dominant transconjugant-related genera decreased by 66.15-76.62%. Ultimately, this study determined that the aeration rate negatively impacts RP4 plasmid host abundance primarily through alterations to the environmental factors during composting. In summary, these findings enhance our understanding of plasmid host bacterial communities under varying composting aeration rates and offer novel insights into preventing the dissemination of ARGs from animal manure to farmland.}, } @article {pmid39216410, year = {2024}, author = {Vissapragada, M and Addala, S and Aggunna, M and Sodasani, M and Grandhi, AVKS and Yedidi, RS}, title = {Leveraging the potential of bacterial lateral gene transfer in boosting the efficacy of an edible probiotic prototype yogurt vaccine for COVID-19.}, journal = {Biochemical and biophysical research communications}, volume = {734}, number = {}, pages = {150622}, doi = {10.1016/j.bbrc.2024.150622}, pmid = {39216410}, issn = {1090-2104}, abstract = {Administration of coronavirus disease-2019 (COVID-19) vaccines with appropriate booster doses through painful injections under clinical supervision was challenging during the recent COVID-19 pandemic. As an alternative solution, we designed a safer, edible probiotic yogurt vaccine prototype (YoVac) that can be orally consumed by circumventing painful injections and clinical supervision. We hypothesized that YoVac prepared using Lactobacillus carrying an antigen coding gene (donor) can transfer the same to other bacteria (recipients) in the human gut microbiome (hgMb) through lateral gene transfer (LGT) for boosted antigen levels potentially triggering a robust immune response. In this study we confirmed the in vitro LGT efficiency of a plasmid (pRBD-Amp[r]) containing severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) spike protein-receptor binding domain (RBD) coding gene along with an ampicillin-resistance gene (selection marker) from the probiotic Lactobacillus (donor) cultured from homemade yogurt to E. coli and Helicobacter pylori (recipients). Both the donor and recipient bacteria not only exhibited ampicillin-resistance from pRBD-Amp[r] but also expressed RBD protein. Furthermore, Lactobacillus isolated from YoVac consistently showed the expression of RBD protein over a period of one month confirming the shelf life of our prototype stored at 4 °C. Taken together, our in vitro results provide a preliminary basis for the potential in vivo transfer of RBD coding gene from YoVac to other bacterial species in the hgMb through LGT and may potentially boost the vaccine dosage by delegating them.}, } @article {pmid39216330, year = {2024}, author = {Fernández-Arévalo, U and Fuchs, J and Boll, M and Díaz, E}, title = {Transcriptional regulation of the anaerobic 3-hydroxybenzoate degradation pathway in Aromatoleum sp. CIB.}, journal = {Microbiological research}, volume = {288}, number = {}, pages = {127882}, doi = {10.1016/j.micres.2024.127882}, pmid = {39216330}, issn = {1618-0623}, abstract = {Phenolic compounds are commonly found in anoxic environments, where they serve as both carbon and energy sources for certain anaerobic bacteria. The anaerobic breakdown of m-cresol, catechol, and certain lignin-derived compounds yields the central intermediate 3-hydroxybenzoate/3-hydroxybenzoyl-CoA. In this study, we have characterized the transcription and regulation of the hbd genes responsible for the anaerobic degradation of 3-hydroxybenzoate in the β-proteobacterium Aromatoleum sp. CIB. The hbd cluster is organized in three catabolic operons and a regulatory hbdR gene that encodes a dimeric transcriptional regulator belonging to the TetR family. HbdR suppresses the activity of the three catabolic promoters (PhbdN, PhbdE and PhbdH) by binding to a conserved palindromic operator box (ATGAATGAN4TCATTCAT). 3-Hydroxybenzoyl-CoA, the initial intermediate of the 3-hydroxybenzoate degradation pathway, along with benzoyl-CoA, serve as effector molecules that bind to HbdR inducing the expression of the hbd genes. Moreover, the hbd genes are subject to additional regulation influenced by the presence of non-aromatic carbon sources (carbon catabolite repression), and their expression is induced in oxygen-deprived conditions by the AcpR transcriptional activator. The prevalence of the hbd cluster among members of the Aromatoleum/Thauera bacterial group, coupled with its association with mobile genetic elements, suggests acquisition through horizontal gene transfer. These findings significantly enhance our understanding of the regulatory mechanisms governing the hbd gene cluster in bacteria, paving the way for further exploration into the anaerobic utilization/valorization of phenolic compounds derived from lignin.}, } @article {pmid39214976, year = {2024}, author = {Yi, X and Liang, JL and Wen, P and Jia, P and Feng, SW and Liu, SY and Zhuang, YY and Guo, YQ and Lu, JL and Zhong, SJ and Liao, B and Wang, Z and Shu, WS and Li, JT}, title = {Giant viruses as reservoirs of antibiotic resistance genes.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7536}, pmid = {39214976}, issn = {2041-1723}, mesh = {*Phylogeny ; *Giant Viruses/genetics ; *Genome, Viral/genetics ; Drug Resistance, Microbial/genetics ; Bacteriophages/genetics/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Metagenome/genetics ; Gene Transfer, Horizontal ; Trimethoprim/pharmacology ; Drug Resistance, Bacterial/genetics ; }, abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs; also called giant viruses), constituting the phylum Nucleocytoviricota, can infect a wide range of eukaryotes and exchange genetic material with not only their hosts but also prokaryotes and phages. A few NCLDVs were reported to encode genes conferring resistance to beta‑lactam, trimethoprim, or pyrimethamine, suggesting that they are potential vehicles for the transmission of antibiotic resistance genes (ARGs) in the biome. However, the incidence of ARGs across the phylum Nucleocytoviricota, their evolutionary characteristics, their dissemination potential, and their association with virulence factors remain unexplored. Here, we systematically investigated ARGs of 1416 NCLDV genomes including those of almost all currently available cultured isolates and high-quality metagenome-assembled genomes from diverse habitats across the globe. We reveal that 39.5% of them carry ARGs, which is approximately 37 times higher than that for phage genomes. A total of 12 ARG types are encoded by NCLDVs. Phylogenies of the three most abundant NCLDV-encoded ARGs hint that NCLDVs acquire ARGs from not only eukaryotes but also prokaryotes and phages. Two NCLDV-encoded trimethoprim resistance genes are demonstrated to confer trimethoprim resistance in Escherichia coli. The presence of ARGs in NCLDV genomes is significantly correlated with mobile genetic elements and virulence factors.}, } @article {pmid39047887, year = {2024}, author = {Wu, X and Jia, W and Fang, Z and Sun, H and Wang, G and Liu, L and Zheng, M and Chen, G}, title = {Cyanobacteria mediate the dissemination of bacterial antibiotic resistance through conjugal transfer.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {359}, number = {}, pages = {124592}, doi = {10.1016/j.envpol.2024.124592}, pmid = {39047887}, issn = {1873-6424}, mesh = {*Drug Resistance, Bacterial/genetics ; *Microcystis/genetics ; *Gene Transfer, Horizontal ; *Cyanobacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Genes, Bacterial ; Bacteria/genetics/drug effects ; }, abstract = {Cyanobacterial blooms are expanding world-wide in freshwater and marine environments, and can cause serious ecological and environmental issues, which also contribute to the spread of antibiotic resistance genes (ARGs). However, the mechanistic understanding of cyanobacteria-mediated resistance dynamics is not fully elucidated yet. We selected Microcystis aeruginosa as a model cyanobacteria to illustrate how cyanobacteria mediate the evolution and transfer processes of bacterial antibiotic resistance. The results show that the presence of cyanobacteria significantly decreased the abundance of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) by 3%-99% and 2%-18%, respectively. In addition, it clearly altered bacterial community structure, with the dominant genera evolving from Acinetobacter (27%) and Enterobacter (42%) to Porphyrobacter (59%). The abundance of ARGs positively correlated with Proteobacteria and Firmicutes, rather than Cyanobacteria, and Bacteroidetes. In the presence of cyanobacteria, the transfer events of bacterial resistance genes via conjugation were found to decrease by 10%-89% (p < 0.05). Surprisingly, we found an extradentary high transfer frequency (about 0.1) for the ARGs via plasmid conjugation from the bacteria into M. aeruginosa population. It confirmed the role of cyanobacterial population as the competent hosts to facilitate ARGs spreading. Our findings provide valuable information on the risk evaluation of ARGs caused by cyanobacterial blooms in aquatic environments, key for the protection and assessment of aquatic environmental quality.}, } @article {pmid39214865, year = {2024}, author = {Fonseca, DR and Day, LA and Crone, KK and Costa, KC}, title = {An Extracellular, Ca[2+]-Activated Nuclease (EcnA) Mediates Transformation in a Naturally Competent Archaeon.}, journal = {Molecular microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mmi.15311}, pmid = {39214865}, issn = {1365-2958}, support = {MCB-2148165//National Science Foundation/ ; }, abstract = {Transformation, the uptake of DNA directly from the environment, is a major driver of gene flow in microbial populations. In bacteria, DNA uptake requires a nuclease that processes dsDNA to ssDNA, which is subsequently transferred into the cell and incorporated into the genome. However, the process of DNA uptake in archaea is still unknown. Previously, we cataloged genes essential to natural transformation in Methanococcus maripaludis, but few homologs of bacterial transformation-associated genes were identified. Here, we characterize one gene, MMJJ_16440 (named here as ecnA), to be an extracellular nuclease. We show that EcnA is Ca[2+]-activated, present on the cell surface, and essential for transformation. While EcnA can degrade several forms of DNA, the highest activity was observed with ssDNA as a substrate. Activity was also observed with circular dsDNA, suggesting that EcnA is an endonuclease. This is the first biochemical characterization of a transformation-associated protein in a member of the archaeal domain and suggests that both archaeal and bacterial transformation initiate in an analogous fashion.}, } @article {pmid39214042, year = {2024}, author = {Li, G and Long, TF and Zhou, SY and Xia, LJ and Gao, A and Wan, L and Diao, XY and He, YZ and Sun, RY and Yang, JT and Tang, SQ and Ren, H and Fang, LX and Liao, XP and Liu, YH and Chen, L and Sun, J}, title = {CRISPR-AMRtracker: A novel toolkit to monitor the antimicrobial resistance gene transfer in fecal microbiota.}, journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy}, volume = {77}, number = {}, pages = {101142}, doi = {10.1016/j.drup.2024.101142}, pmid = {39214042}, issn = {1532-2084}, abstract = {The spread of antibiotic resistance genes (ARGs), particularly those carried on plasmids, poses a major risk to global health. However, the extent and frequency of ARGs transfer in microbial communities among human, animal, and environmental sectors is not well understood due to a lack of effective tracking tools. We have developed a novel fluorescent tracing tool, CRISPR-AMRtracker, to study ARG transfer. It combines CRISPR/Cas9 fluorescence tagging, fluorescence-activated cell sorting, 16S rRNA gene sequencing, and microbial community analysis. CRISPR-AMRtracker integrates a fluorescent tag immediately downstream of ARGs, enabling the tracking of ARG transfer without compromising the host cell's antibiotic susceptibility, fitness, conjugation, and transposition. Notably, our experiments demonstrate that sfGFP-tagged plasmid-borne mcr-1 can transfer across diverse bacterial species within fecal samples. This innovative approach holds the potential to illuminate the dynamics of ARG dissemination and provide valuable insights to shape effective strategies in mitigating the escalating threat of antibiotic resistance.}, } @article {pmid39213533, year = {2024}, author = {Zeng, Q and Wu, X and Song, M and Jiang, L and Zeng, Q and Qiu, R and Luo, C}, title = {Opposite Effects of Planting on Antibiotic Resistomes in Rhizosphere Soil with Different Sulfamethoxazole Levels.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c04258}, pmid = {39213533}, issn = {1520-5118}, abstract = {Achieving consensus about the rhizosphere effect on soil antibiotic resistomes is challenging due to the variability in antibiotic concentrations, sources, and the elusory underlying mechanisms. Here, we characterized the antibiotic resistomes in both the rhizosphere and bulk soils of soybean plants grown in environments with varying levels of antibiotic contamination, using sulfamethoxazole (SMX) as a model compound. We also investigated the factors influencing resistome profiles. Soybean cultivation altered the structure of antibiotic-resistant genes (ARGs) and increased their absolute abundance. However, the rhizosphere effect on the relative abundance of ARGs was dependent on SMX concentrations. At low SMX levels, the rhizosphere effect was characterized by the inhibition of antibiotic-resistant bacteria (ARBs) and the promotion of sensitive bacteria. In contrast, at high SMX levels, the rhizosphere promoted the growth of ARBs and facilitated horizontal gene transfer of ARGs. This novel mechanism provides new insights into accurately assessing the rhizosphere effect on soil antibiotic resistomes.}, } @article {pmid39213158, year = {2024}, author = {Ma, Y and Kan, A and Johnson, DR}, title = {Metabolic interactions control the transfer and spread of plasmid-encoded antibiotic resistance during surface-associated microbial growth.}, journal = {Cell reports}, volume = {43}, number = {9}, pages = {114653}, doi = {10.1016/j.celrep.2024.114653}, pmid = {39213158}, issn = {2211-1247}, abstract = {Surface-associated microbial systems are hotspots for the spread of plasmid-encoded antibiotic resistance, but how surface association affects plasmid transfer and proliferation remains unclear. Surface association enables prolonged spatial proximities between different populations, which promotes plasmid transfer between them. However, surface association also fosters strong metabolic interactions between different populations, which can direct their spatial self-organization with consequences for plasmid transfer and proliferation. Here, we hypothesize that metabolic interactions direct the spatial self-organization of different populations and, in turn, regulate the spread of plasmid-encoded antibiotic resistance. We show that resource competition causes populations to spatially segregate, which represses plasmid transfer. In contrast, resource cross-feeding causes populations to spatially intermix, which promotes plasmid transfer. We further show that the spatial positionings that emerge from metabolic interactions determine the proliferation of plasmid recipients. Our results demonstrate that metabolic interactions are important regulators of both the transfer and proliferation of plasmid-encoded antibiotic resistance.}, } @article {pmid39211246, year = {2024}, author = {Hughes Lago, C and Blackburn, D and Kinder Pavlicek, M and Threadgill, DS}, title = {Comparative Genomic Analysis of Campylobacter rectus and Closely Related Species.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.07.26.605372}, pmid = {39211246}, issn = {2692-8205}, abstract = {Campylobacter rectus is a gram-negative, anaerobic bacterium strongly associated with periodontitis. It also causes various extraoral infections and is linked to adverse pregnancy outcomes in humans and murine models. C. rectus and related oral Campylobacters have been termed "emerging Campylobacter species" because infections by these organisms are likely underreported. Previously, no comparative methods have been used to analyze more than single C. rectus strains and until recently, very few C. rectus genomes have been publicly available. More sequenced genomes and comparative analyses are needed to study the genomic features and pathogenicity of this species. We sequenced eight new C. rectus strains and used comparative methods to identify regions of interest. An emphasis was put on the type III flagellar secretion system (T3SS), type IV secretion system (T4SS), and type VI secretion system (T6SS) because these protein complexes are important for pathogenesis in other Campylobacter species. RAST, BV-BRC, and other bioinformatics tools were used to assemble, annotate, and compare these regions in the genomes. The pan-genome of C. rectus consists of 2670 genes with core and accessory genomes of 1429 and 1241 genes, respectively. All isolates analyzed in this study have T3SS and T6SS hallmark proteins, while five of the isolates are missing a T4SS system. Twenty-one prophage clusters were identified across the panel of isolates, including four that appear intact. Overall, significant genomic islands were found, suggesting regions in the genomes that underwent horizontal gene transfer. Additionally, the high frequency of CRISPR arrays and other repetitive elements has led to genome rearrangements across the strains, including in areas adjacent to secretion system gene clusters. This study describes the substantial diversity present among C. rectus isolates and highlights tools/assays that have been developed to permit functional genomic studies. Additionally, we have expanded the studies on C. showae T4SS since we have two new C. showae genomes to report. We also demonstrate that unlike C. rectus , C showae does not demonstrate evidence of intact T6SS except for the strain CAM. The only strain of sequenced C. massilensis has neither T4SS or T6SS.}, } @article {pmid39211212, year = {2024}, author = {Marcarian, HQ and Sivakoses, A and Arias, AM and Ihedioha, OC and Lee, BR and Bishop, MC and Bothwell, ALM}, title = {Renal cancer cells acquire immune surface protein through trogocytosis and horizontal gene transfer.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.08.07.607036}, pmid = {39211212}, issn = {2692-8205}, abstract = {UNLABELLED: Trogocytosis is an underappreciated phenomenon that shapes the immune microenvironment surrounding many types of solid tumors. The consequences of membrane-bound proteins being deposited from a donor immune cell to a recipient cancer cell via trogocytosis are still unclear. Here, we report that human clear cell renal carcinoma tumors stably express the lymphoid markers CD45, CD56, CD14, and CD16. Flow cytometry performed on fresh kidney tumors revealed consistent CD45 expression on tumor cells, as well as varying levels of the other markers mentioned previously. These results were consistent with our immunofluorescent analysis, which also revealed colocalization of lymphoid markers with carbonic anhydrase 9 (CAIX), a standard kidney tumor marker. RNA analysis showed a significant upregulation of genes typically associated with immune cells in tumor cells following trogocytosis. Finally, we show evidence of chromosomal DNA being transferred from immune cells to tumor cells during trogocytosis. This horizontal gene transfer has transcriptional consequences in the recipient tumor cell, resulting in a fusion phenotype that expressed both immune and cancer specific proteins. This work demonstrates a novel mechanism by which tumor cell protein expression is altered through the acquisition of surface membrane fragments and genomic DNA from infiltrating lymphocytes. These results alter the way in which we understand tumor-immune cell interactions and may reveal new insights into the mechanisms by which tumors develop. Additionally, further studies into trogocytosis will help push the field towards the next generation of immunotherapies and biomarkers for treating renal cell carcinoma and other types of cancers.

SIGNIFICANCE STATEMENT: We have identified trogocytosis as a mechanism by which human clear cell renal carcinoma tumors acquire lymphocyte surface protein expression from tumor infiltrating immune cells. In addition to the transfer of membrane fragments, we have provided evidence to show that genomic DNA is transferred from a normal immune cell to a tumor cell during trogocytosis. This process alters the transcriptome of cancer cells such that they express significantly more mRNA for immune proteins such as the lymphocyte marker CD45 compared to tumor cells that have not undergone trogocytosis. This study provides an in-depth analysis of the interactions between cancer cells and tumor infiltrating lymphocytes, and how these interactions alter the development of human tumors.}, } @article {pmid39210455, year = {2024}, author = {Abdellati, S and Gestels, Z and Laumen, JGE and Van Dijck, C and De Baetselier, I and de Block, T and Van den Bossche, D and Vanbaelen, T and Kanesaka, I and Manoharan-Basil, SS and Kenyon, C}, title = {Antimicrobial susceptibility of commensal Neisseria spp. In parents and their children in Belgium: a cross-sectional survey.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnae069}, pmid = {39210455}, issn = {1574-6968}, abstract = {BACKGROUND: Commensal Neisseria species are part of the oropharyngeal microbiome and play an important role in nitrate reduction and protecting against colonization by pathogenic bacteria. They do, however, also serve as a reservoir of antimicrobial resistance. Little is known about the prevalence of these species in the general population, how this varies by age and how antimicrobial susceptibility varies between species.

METHODS: We assessed the prevalence and antimicrobial susceptibility of commensal Neisseria species in the parents (n = 38) and children (n = 50) of 35 families in Belgium.

RESULTS: Various commensal Neisseria (n = 5) could be isolated from the participants. Most abundant were N. subflava and N. mucosa. N. subflava was detected in 77 of 88 (87.5%) individuals and N. mucosa in 64 of 88 (72.7%). N. mucosa was more prevalent in children (41/50 [82%]) than parents (23/38 [60.5%]; P < 0.05), while N. bacilliformis was more prevalent in parents (7/36 [19.4%]) than children (2/50 [4%]; P < 0.05). N. bacilliformis had high ceftriaxone minimum inhibitory concentrations (MICs; median MIC 0.5 mg/L; IQR 0.38-0.75). The ceftriaxone MICs of all Neisseria isolates were higher in the parents than in the children. This could be explained by a higher prevalence of N. bacilliformis in the parents.

INTERPRETATION: The N. bacilliformis isolates had uniformly high ceftriaxone MICs which warrant further investigation.}, } @article {pmid39207571, year = {2024}, author = {Smiatek, J}, title = {Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning.}, journal = {Journal of molecular evolution}, volume = {}, number = {}, pages = {}, pmid = {39207571}, issn = {1432-1432}, abstract = {We present a non-equilibrium thermodynamics approach to the multilevel theory of learning for the study of molecular evolution. This approach allows us to study the explicit time dependence of molecular evolutionary processes and their impact on entropy production. Interpreting the mathematical expressions, we can show that two main contributions affect entropy production of molecular evolution processes which can be identified as mutation and gene transfer effects. Accordingly, our results show that the optimal adaptation of organisms to external conditions in the context of evolutionary processes is driven by principles of minimum entropy production. Such results can also be interpreted as the basis of some previous postulates of the theory of learning. Although our macroscopic approach requires certain simplifications, it allows us to interpret molecular evolutionary processes using thermodynamic descriptions with reference to well-known biological processes.}, } @article {pmid39207102, year = {2024}, author = {Zhang, W and Fan, Y and Deng, W and Chen, Y and Wang, S and Kang, S and Steenwyk, JL and Xiang, M and Liu, X}, title = {Characterization of genome-wide phylogenetic conflict uncovers evolutionary modes of carnivorous fungi.}, journal = {mBio}, volume = {}, number = {}, pages = {e0213324}, doi = {10.1128/mbio.02133-24}, pmid = {39207102}, issn = {2150-7511}, abstract = {Mass extinction has often paved the way for rapid evolutionary radiation, resulting in the emergence of diverse taxa within specific lineages. The emergence and diversification of carnivorous nematode-trapping fungi (NTF) in Ascomycota have been linked to the Permian-Triassic (PT) extinction, but the processes underlying NTF radiation remain unclear. We conducted phylogenomic analyses using 23 genomes that represent three NTF lineages, each employing distinct nematode traps-mechanical traps (Drechslerella spp.), three-dimensional (3D) adhesive traps (Arthrobotrys spp.), and two-dimensional (2D) adhesive traps (Dactylellina spp.), and the genome of one non-NTF species as the outgroup. These analyses revealed multiple mechanisms that likely contributed to the tempo of the NTF evolution and rapid radiation. The species tree of NTFs based on 2,944 single-copy orthologous genes suggested that Drechslerella emerged earlier than Arthrobotrys and Dactylellina. Extensive genome-wide phylogenetic discordance was observed, mainly due to incomplete lineage sorting (ILS) between lineages. Two modes of non-vertical evolution (introgression and horizontal gene transfer) also contributed to phylogenetic discordance. The ILS genes that are associated with hyphal growth and trap morphogenesis (e.g., those associated with the cell membrane system and polarized cell division) exhibited signs of positive selection.IMPORTANCEBy conducting a comprehensive phylogenomic analysis of 23 genomes across three NTF lineages, the research reveals how diverse evolutionary mechanisms, including ILS and non-vertical evolution (introgression and horizontal gene transfer), contribute to the swift diversification of NTFs. These findings highlight the complex evolutionary dynamics that drive the rapid radiation of NTFs, providing valuable insights into the processes underlying their diversity and adaptation.}, } @article {pmid39206372, year = {2024}, author = {Kirk, A and Stavrinides, J}, title = {Distribution and comparative genomic analysis of antimicrobial gene clusters found in Pantoea.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1416674}, doi = {10.3389/fmicb.2024.1416674}, pmid = {39206372}, issn = {1664-302X}, abstract = {Members of the bacterial genus Pantoea produce a variety of antimicrobial products that are effective against plant, animal, and human pathogens. To date, little is known about the distribution and evolutionary history of these clusters. We surveyed the public databases for the 12 currently known antibiotic biosynthetic gene clusters found across Pantoea strains to determine their distribution. We show that some clusters, namely pantocin B, PNP-3, and PNP-4 are found strictly in Pantoea, while agglomerin, andrimid, AGA, dapdiamide, herbicolin, PNP-1, PNP-2, PNP-5, and pantocin A, are more broadly distributed in distantly related genera within Vibrionaceae, Pectobacteriaceae, Yersiniaceae, Morganellaceae, and Hafniaceae. We evaluated the evolutionary history of these gene clusters relative to a cpn60-based species tree, considering the flanking regions of each cluster, %GC, and presence of mobile genetic elements, and identified potential occurrences of horizontal gene transfer. Lastly, we also describe the biosynthetic gene cluster of pantocin B in the strain Pantoea agglomerans Eh318 more than 20 years after this antibiotic was first described.}, } @article {pmid39203510, year = {2024}, author = {Lv, N and Ni, J and Fang, S and Liu, Y and Wan, S and Sun, C and Li, J and Zhou, A}, title = {Potential Convergence to Accommodate Pathogenicity Determinants and Antibiotic Resistance Revealed in Salmonella Mbandaka.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, doi = {10.3390/microorganisms12081667}, pmid = {39203510}, issn = {2076-2607}, support = {32260032//National Natural Science Foundation of China/ ; 32370143//National Natural Science Foundation of China/ ; 31800118//National Natural Science Foundation of China/ ; jxsq2019101054//Double Thousand Talents Plan of Jiangxi/ ; }, abstract = {Salmonella species are causal pathogens instrumental in human food-borne diseases. The pandemic survey related to multidrug resistant (MDR) Salmonella genomics enables the prevention and control of their dissemination. Currently, serotype Mbandaka is notorious as a multiple host-adapted non-typhoid Salmonella. However, its epidemic and MDR properties are still obscure, especially its genetic determinants accounting for virulence and MD resistance. Here, we aim to characterize the genetic features of a strain SMEH pertaining to Salmonella Mbandaka (S. Mbandaka), isolated from the patient's hydropericardium, using cell infections, a mouse model, antibiotic susceptibility test and comparative genomics. The antibiotic susceptibility testing showed that it could tolerate four antibiotics, including chloramphenicol, tetracycline, fisiopen and doxycycline by Kirby-Bauer (K-B) testing interpreted according to the Clinical and Laboratory Standards Institute (CLSI). Both the reproducibility in RAW 264.7 macrophages and invasion ability to infect HeLa cells with strain SMEH were higher than those of S. Typhimurium strain 14028S. In contrast, its attenuated virulence was determined in the survival assay using a mouse model. As a result, the candidate genetic determinants responsible for antimicrobial resistance, colonization/adaptability and their transferability were comparatively investigated, such as bacterial secretion systems and pathogenicity islands (SPI-1, SPI-2 and SPI-6). Moreover, collective efforts were made to reveal a potential role of the plasmid architectures in S. Mbandaka as the genetic reservoir to transfer or accommodate drug-resistance genes. Our findings highlight the essentiality of antibiotic resistance and risk assessment in S. Mbandaka. In addition, genomic surveillance is an efficient method to detect pathogens and monitor drug resistance. The genetic determinants accounting for virulence and antimicrobial resistance underscore the increasing clinical challenge of emerging MDR Mbandaka isolates, and provide insights into their prevention and treatment.}, } @article {pmid39201699, year = {2024}, author = {Li, H and Liang, T and Liu, Y and Wang, P and Wang, S and Zhao, M and Zhang, Y}, title = {Exploring Mitochondrial Heterogeneity and Evolutionary Dynamics in Thelephora ganbajun through Population Genomics.}, journal = {International journal of molecular sciences}, volume = {25}, number = {16}, pages = {}, doi = {10.3390/ijms25169013}, pmid = {39201699}, issn = {1422-0067}, support = {31870009//National Natural Science Foundation of China/ ; YNWR-QNBJ-2018-355//Top Young Talents Program of the Ten Thousand Talents Plan in Yunnan Province/ ; 2021KF009//YNCUB/ ; }, mesh = {*Genome, Mitochondrial ; *Evolution, Molecular ; Phylogeny ; Introns/genetics ; Mitochondria/genetics ; Basidiomycota/genetics ; DNA, Mitochondrial/genetics ; Genomics/methods ; Gene Transfer, Horizontal ; }, abstract = {Limited exploration in fungal mitochondrial genetics has uncovered diverse inheritance modes. The mitochondrial genomes are inherited uniparentally in the majority of sexual eukaryotes, our discovery of persistent mitochondrial heterogeneity within the natural population of the basidiomycete fungus Thelephora ganbajun represents a significant advance in understanding mitochondrial inheritance and evolution in eukaryotes. Here, we present a comprehensive analysis by sequencing and assembling the complete mitogenomes of 40 samples exhibiting diverse cox1 heterogeneity patterns from various geographical origins. Additionally, we identified heterogeneous variants in the nad5 gene, which, similar to cox1, displayed variability across multiple copies. Notably, our study reveals a distinct prevalence of introns and homing endonucleases in these heterogeneous genes. Furthermore, we detected potential instances of horizontal gene transfer involving homing endonucleases. Population genomic analyses underscore regional variations in mitochondrial genome composition among natural samples exhibiting heterogeneity. Thus, polymorphisms in heterogeneous genes, introns, and homing endonucleases significantly influence mitochondrial structure, structural variation, and evolutionary dynamics in this species. This study contributes valuable insights into mitochondrial genome architecture, population dynamics, and the evolutionary implications of mitochondrial heterogeneity in sexual eukaryotes.}, } @article {pmid39200594, year = {2024}, author = {Habibi, N and Uddin, S and Behbehani, M and Mustafa, AS and Al-Fouzan, W and Al-Sarawi, HA and Safar, H and Alatar, F and Al Sawan, RMZ}, title = {Aerosol-Mediated Spread of Antibiotic Resistance Genes: Biomonitoring Indoor and Outdoor Environments.}, journal = {International journal of environmental research and public health}, volume = {21}, number = {8}, pages = {}, doi = {10.3390/ijerph21080983}, pmid = {39200594}, issn = {1660-4601}, mesh = {*Aerosols/analysis ; *Gene Transfer, Horizontal ; Humans ; Biological Monitoring ; Drug Resistance, Microbial/genetics ; Air Microbiology ; Air Pollution, Indoor/analysis ; Environmental Monitoring ; Anti-Bacterial Agents/analysis ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antimicrobial resistance (AMR) has emerged as a conspicuous global public health threat. The World Health Organization (WHO) has launched the "One-Health" approach, which encourages the assessment of antibiotic resistance genes (ARGs) within an environment to constrain and alleviate the development of AMR. The prolonged use and overuse of antibiotics in treating human and veterinary illnesses, and the inability of wastewater treatment plants to remove them have resulted in elevated concentrations of these metabolites in the surroundings. Microbes residing within these settings acquire resistance under selective pressure and circulate between the air-land interface. Initial evidence on the indoor environments of wastewater treatment plants, hospitals, and livestock-rearing facilities as channels of AMR has been documented. Long- and short-range transport in a downwind direction disseminate aerosols within urban communities. Inhalation of such aerosols poses a considerable occupational and public health risk. The horizontal gene transfer (HGT) is another plausible route of AMR spread. The characterization of ARGs in the atmosphere therefore calls for cutting-edge research. In the present review, we provide a succinct summary of the studies that demonstrated aerosols as a media of AMR transport in the atmosphere, strengthening the need to biomonitor these pernicious pollutants. This review will be a useful resource for environmental researchers, healthcare practitioners, and policymakers to issue related health advisories.}, } @article {pmid39200027, year = {2024}, author = {Milani, G and Cortimiglia, C and Belloso Daza, MV and Greco, E and Bassi, D and Cocconcelli, PS}, title = {Microplastic-Mediated Transfer of Tetracycline Resistance: Unveiling the Role of Mussels in Marine Ecosystems.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/antibiotics13080727}, pmid = {39200027}, issn = {2079-6382}, support = {PE00000003//Italian Ministry of University and Research funded by the European Union - NextGenerationEU/ ; }, abstract = {The global threat of antimicrobial resistance (AMR) is exacerbated by the mobilization of antimicrobial resistance genes (ARGs) occurring in different environmental niches, including seawater. Marine environments serve as reservoirs for resistant bacteria and ARGs, further complicated by the ubiquity of microplastics (MPs). MPs can adsorb pollutants and promote bacterial biofilm formation, creating conditions favorable to the dissemination of ARGs. This study explores the dynamics of ARG transfer in the marine bivalve Mytilus galloprovincialis within a seawater model, focusing on the influence of polyethylene MPs on the mobilization of the Tn916-carrying tetM gene and plasmid-encoded ermB. Experiments revealed that biofilm formation on MPs by Enterococcus faecium and Listeria monocytogenes facilitated the transfer of the tetM resistance gene, but not the ermB gene. Furthermore, the presence of MPs significantly increased the conjugation frequency of tetM within mussels, indicating that MPs enhance the potential for ARG mobilization in marine environments. These findings highlight the role of MPs and marine organisms in ARG spread, underscoring the ecological and public health implications.}, } @article {pmid39199982, year = {2024}, author = {Yao, Y and Imirzalioglu, C and Falgenhauer, L and Falgenhauer, J and Heinmüller, P and , and Domann, E and Chakraborty, T}, title = {Plasmid-Mediated Spread of Carbapenem Resistance in Enterobacterales: A Three-Year Genome-Based Survey.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/antibiotics13080682}, pmid = {39199982}, issn = {2079-6382}, abstract = {The worldwide emergence and dissemination of carbapenem-resistant Gram-negative bacteria (CRGNB) is a challenging problem of antimicrobial resistance today. Outbreaks with CRGNB have severe consequences for both the affected healthcare settings as well as the patients with infection. Thus, bloodstream infections caused by metallo-ß-lactamase-producing Enterobacterales can often have clinical implications, resulting in high mortality rates due to delays in administering effective treatment and the limited availability of treatment options. The overall threat of CRGNB is substantial because carbapenems are used to treat infections caused by ESBL-producing Enterobacterales which also exist with high frequency within the same geographical regions. A genome-based surveillance of 589 CRGNB from 61 hospitals across the federal state Hesse in Germany was implemented using next-generation sequencing (NGS) technology to obtain a high-resolution landscape of carbapenem-resistant isolates over a three-year period (2017-2019). The study examined all reportable CRGNB isolates submitted by participating hospitals. This included isolates carrying known carbapenemases (435) together with carbapenem-resistant non-carbapenemase producers (154). Predominant carbapenemase producers included Klebsiella pneumoniae, Escherichia coli, Citrobacter freundii and Acinetobacter baumannii. Over 80% of 375 carbapenem-resistant determinants including KPC-, NDM-, VIM- and OXA-48-like ones detected in 520 Enterobacterales were plasmid-encoded, and half of these were dominated by a few incompatibility (Inc) types, viz., IncN, IncL/M, IncFII and IncF(K). Our results revealed that plasmids play an extraordinary role in the dissemination of carbapenem resistance in the heterogeneous CRGNB population. The plasmids were also associated with several multispecies dissemination events and local outbreaks throughout the study period, indicating the substantial role of horizontal gene transfer in carbapenemase spread. Furthermore, due to vertical and horizontal plasmid transfer, this can have an impact on implant-associated infections and is therefore important for antibiotic-loaded bone cement and drug-containing devices in orthopedic surgery. Future genomic surveillance projects should increase their focus on plasmid characterization.}, } @article {pmid39198891, year = {2024}, author = {Tian, F and Wainaina, JM and Howard-Varona, C and Domínguez-Huerta, G and Bolduc, B and Gazitúa, MC and Smith, G and Gittrich, MR and Zablocki, O and Cronin, DR and Eveillard, D and Hallam, SJ and Sullivan, MB}, title = {Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {159}, pmid = {39198891}, issn = {2049-2618}, support = {ABI#1759874, ABI#2149505, OCE#1536989, OCE#1829831, and OCE#2019589//National Science Foundation/ ; #3790//Gordon and Betty Moore Foundation Investigator Award/ ; }, mesh = {*Oceans and Seas ; *Seawater/virology/microbiology ; Metagenomics ; Bacteria/genetics/classification/metabolism ; Viruses/genetics/classification/isolation & purification ; Prokaryotic Cells/metabolism/virology ; Metagenome ; Metabolic Networks and Pathways/genetics ; Gene Transfer, Horizontal ; Phosphatidylethanolamines/metabolism ; }, abstract = {BACKGROUND: Prokaryotic microbes have impacted marine biogeochemical cycles for billions of years. Viruses also impact these cycles, through lysis, horizontal gene transfer, and encoding and expressing genes that contribute to metabolic reprogramming of prokaryotic cells. While this impact is difficult to quantify in nature, we hypothesized that it can be examined by surveying virus-encoded auxiliary metabolic genes (AMGs) and assessing their ecological context.

RESULTS: We systematically developed a global ocean AMG catalog by integrating previously described and newly identified AMGs and then placed this catalog into ecological and metabolic contexts relevant to ocean biogeochemistry. From 7.6 terabases of Tara Oceans paired prokaryote- and virus-enriched metagenomic sequence data, we increased known ocean virus populations to 579,904 (up 16%). From these virus populations, we then conservatively identified 86,913 AMGs that grouped into 22,779 sequence-based gene clusters, 7248 (~ 32%) of which were not previously reported. Using our catalog and modeled data from mock communities, we estimate that ~ 19% of ocean virus populations carry at least one AMG. To understand AMGs in their metabolic context, we identified 340 metabolic pathways encoded by ocean microbes and showed that AMGs map to 128 of them. Furthermore, we identified metabolic "hot spots" targeted by virus AMGs, including nine pathways where most steps (≥ 0.75) were AMG-targeted (involved in carbohydrate, amino acid, fatty acid, and nucleotide metabolism), as well as other pathways where virus-encoded AMGs outnumbered cellular homologs (involved in lipid A phosphates, phosphatidylethanolamine, creatine biosynthesis, phosphoribosylamine-glycine ligase, and carbamoyl-phosphate synthase pathways).

CONCLUSIONS: Together, this systematically curated, global ocean AMG catalog and analyses provide a valuable resource and foundational observations to understand the role of viruses in modulating global ocean metabolisms and their biogeochemical implications. Video Abstract.}, } @article {pmid39198572, year = {2024}, author = {Sastre-Dominguez, J and DelaFuente, J and Toribio-Celestino, L and Herencias, C and Herrador-Gómez, P and Costas, C and Hernández-García, M and Cantón, R and Rodríguez-Beltrán, J and Santos-Lopez, A and San Millan, A}, title = {Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria.}, journal = {Nature ecology & evolution}, volume = {}, number = {}, pages = {}, pmid = {39198572}, issn = {2397-334X}, support = {757440-PLASREVOLUTION//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 895671-REPLAY//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101077809-HorizonGT//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PI19/00749//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; CD21/00115//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PI23/01945//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; CP20/00154//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PI21/01363//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; LCF/BQ/PR22/11920001//"la Caixa" Foundation (Caixa Foundation)/ ; Research Grant 2022//European Society of Clinical Microbiology and Infectious Diseases (ESCMID)/ ; }, abstract = {Plasmids are extrachromosomal genetic elements commonly found in bacteria. They are known to fuel bacterial evolution through horizontal gene transfer, and recent analyses indicate that they can also promote intragenomic adaptations. However, the role of plasmids as catalysts of bacterial evolution beyond horizontal gene transfer is poorly explored. In this study, we investigated the impact of a widespread conjugative plasmid, pOXA-48, on the evolution of several multidrug-resistant clinical enterobacteria. Combining experimental and within-patient evolution analyses, we unveiled that plasmid pOXA-48 promotes bacterial evolution through the transposition of plasmid-encoded insertion sequence 1 (IS1) elements. Specifically, IS1-mediated gene inactivation expedites the adaptation rate of clinical strains in vitro and fosters within-patient adaptation in the gut microbiota. We deciphered the mechanism underlying the plasmid-mediated surge in IS1 transposition, revealing a negative feedback loop regulated by the genomic copy number of IS1. Given the overrepresentation of IS elements in bacterial plasmids, our findings suggest that plasmid-mediated IS1 transposition represents a crucial mechanism for swift bacterial adaptation.}, } @article {pmid39198281, year = {2024}, author = {He, Z and Smets, BF and Dechesne, A}, title = {Mating Assay: Plating Below a Cell Density Threshold is Required for Unbiased Estimation of Plasmid Conjugation Frequency of RP4 Transfer Between E. coli Strains.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {109}, pmid = {39198281}, issn = {1432-184X}, support = {0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; PhD Scholarship//Sino-Danish Center/ ; PhD Scholarship//Sino-Danish Center/ ; }, mesh = {*Escherichia coli/genetics ; *Conjugation, Genetic ; *Plasmids/genetics ; Gene Transfer, Horizontal ; }, abstract = {Mating assays are common laboratory experiments for measuring the conjugation frequency, i.e. efficiency at which a plasmid transfers from a population of donor cells to a population of recipient cells. Selective plating remains a widely used quantification method to enumerate transconjugants at the end of such assays. However, conjugation frequencies may be inaccurately estimated because plasmid transfer can occur on transconjugant-selective plates rather than only during the intended mating duration. We investigated the influence of cell density on this phenomenon. We conducted mating experiments with IncPα plasmid RP4 harbored in Escherichia coli at a fixed cell density and mating conditions, inoculated a serial dilution of the mating mixture on transconjugant-selective plates or in transconjugant-selective broth, and compared the results to a model of cell-to-cell distance distribution. Our findings suggest that irrespective of the mating mode (liquid vs solid), the enumeration of transconjugants becomes significantly biased if the plated cell density exceeds 28 Colony Forming Unit (CFU)/mm[2] (or 1.68•10[5] CFU/standard 9 cm Petri dish). This threshold is determined with a 95% confidence interval of ± 4 CFU/mm[2] (± 2.46•10[4] CFU/standard 9 cm Petri dish). Liquid mating assays were more sensitive to this bias because the conjugation frequency of RP4 is several orders of magnitude lower in suspension compared to surface mating. Therefore, if selective plating is used, we recommend to plate at this density threshold and that negative controls are performed where donors and recipients are briefly mixed before plating at the same dilutions as for the actual mating assay. As an alternative, a liquid enumeration method can be utilized to increase the signal-to-noise ratio and allow for more accurate enumeration of transconjugants.}, } @article {pmid39194517, year = {2024}, author = {Yang, X and Liu, Z and Zhang, Y and Shi, X and Wu, Z}, title = {Dinoflagellate-Bacteria Interactions: Physiology, Ecology, and Evolution.}, journal = {Biology}, volume = {13}, number = {8}, pages = {}, pmid = {39194517}, issn = {2079-7737}, support = {42106093 and 41976130//National Natural Science Foundation of China/ ; 2022T150706//China Postdoctoral Science Foundation/ ; GPCGD223103FG015F//Comprehensive Protection and Utilization Program for the Coastal Zone of Guangdong 534 Province (Revision)/ ; DD20230460, DD20230107, and DD20242792//Marine Geological Survey 535 Program of China Geological Survey/ ; }, abstract = {Dinoflagellates and heterotrophic bacteria are two major micro-organism groups within marine ecosystems. Their coexistence has led to a co-evolutionary relationship characterized by intricate interactions that not only alter their individual behaviors but also exert a significant influence on the broader biogeochemical cycles. Our review commenced with an analysis of bacterial populations, both free-living and adherent to dinoflagellate surfaces. Members of Alphaproteobacteria, Gammaproteobacteria, and the Cytophaga-Flavobacterium-Bacteroides group are repeatedly found to be associated with dinoflagellates, with representation by relatively few genera, such as Methylophaga, Marinobacter, and Alteromonas. These bacterial taxa engage with dinoflagellates in a limited capacity, involving nutrient exchange, the secretion of pathogenic substances, or participation in chemical production. Furthermore, the genomic evolution of dinoflagellates has been profoundly impacted by the horizontal gene transfer from bacteria. The integration of bacterial genes into dinoflagellates has been instrumental in defining their biological characteristics and nutritional strategies. This review aims to elucidate the nuanced interactions between dinoflagellates and their associated bacteria, offering a detailed perspective on their complex relationship.}, } @article {pmid39193949, year = {2024}, author = {Kim, HJ and Koo, SH and Choi, Q}, title = {Horizontal Gene Transfer of blaNDM-5 Among Three Different Enterobacteriaceae Species Isolated from a Single Patient.}, journal = {Clinical laboratory}, volume = {70}, number = {8}, pages = {}, doi = {10.7754/Clin.Lab.2024.240309}, pmid = {39193949}, issn = {1433-6510}, mesh = {Humans ; *Gene Transfer, Horizontal ; *Microbial Sensitivity Tests ; *beta-Lactamases/genetics ; *Enterobacteriaceae/genetics/drug effects/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; *Plasmids/genetics ; Enterobacteriaceae Infections/microbiology/diagnosis/drug therapy ; Whole Genome Sequencing ; Escherichia coli/genetics/drug effects/isolation & purification ; Klebsiella oxytoca/genetics/isolation & purification/drug effects ; Citrobacter/genetics/isolation & purification/drug effects ; }, abstract = {BACKGROUND: In this study, Escherichia coli, Klebsiella oxytoca, and Citrobacter amalonaticus carrying blaNDM-5 were isolated from a single patient.

METHODS: The antibiotic susceptibility of the isolates was evaluated by using E-test and agar dilution methods, and blaNDM-5 was identified in genomic and plasmid DNA by using polymerase chain reaction and sequencing. Whole genome sequencing and de novo assembly were used for species characterization, resistance gene identification, and plasmid analysis.

RESULTS: All three species had identical plasmids, which were similar to pEC463-NDM5, a plasmid harboring blaNDM-5. Transconjugation experiments confirmed the horizontal gene transfer of blaNDM-5, highlighting the need for a close monitoring of Enterobacteriaceae species harboring this gene.

CONCLUSIONS: This study conclusively demonstrates the propensity for horizontal gene transfer of blaNDM-5 among Enterobacteriaceae species, underlining the importance of vigilant monitoring to combat antibiotic resistance.}, } @article {pmid39191402, year = {2024}, author = {Aoun, N and Georgoulis, SJ and Avalos, JK and Grulla, KJ and Miqueo, K and Tom, C and Lowe-Power, TM}, title = {A pangenomic atlas reveals eco-evolutionary dynamics that shape type VI secretion systems in plant-pathogenic Ralstonia.}, journal = {mBio}, volume = {}, number = {}, pages = {e0032324}, doi = {10.1128/mbio.00323-24}, pmid = {39191402}, issn = {2150-7511}, abstract = {Soilborne Ralstonia solanacearum species complex (RSSC) pathogens disrupt microbial communities as they invade roots and fatally wilt plants. RSSC pathogens secrete antimicrobial toxins using a type VI secretion system (T6SS). To investigate how evolution and ecology have shaped the T6SS of these bacterial pathogens, we analyzed the T6SS gene content and architecture across the RSSC and their evolutionary relatives. Our analysis reveals that two ecologically similar Burkholderiaceae taxa, xylem-pathogenic RSSC and Paracidovorax, have convergently evolved to wield large arsenals of T6SS toxins. To understand the mechanisms underlying genomic enrichment of T6SS toxins, we compiled an atlas of 1,066 auxiliary T6SS toxin clusters ("aux" clusters) across 99 high-quality RSSC genomes. We classified 25 types of aux clusters with toxins that predominantly target lipids, nucleic acids, or unknown cellular substrates. The aux clusters were located in diverse genetic neighborhoods and had complex phylogenetic distributions, suggesting frequent horizontal gene flow. Phages and other mobile genetic elements account for most of the aux cluster acquisition on the chromosome but very little on the megaplasmid. Nevertheless, RSSC genomes were more enriched in aux clusters on the megaplasmid. Although the single, ancestral T6SS was broadly conserved in the RSSC, the T6SS has been convergently lost in atypical, non-soilborne lineages. Overall, our data suggest dynamic interplay between the lifestyle of RSSC lineages and the evolution of T6SSes with robust arsenals of toxins. This pangenomic atlas poises the RSSC as an emerging, tractable model to understand the role of the T6SS in shaping pathogen populations.IMPORTANCEWe explored the eco-evolutionary dynamics that shape the inter-microbial warfare mechanisms of a globally significant plant pathogen, the Ralstonia solanacearum species complex. We discovered that most Ralstonia wilt pathogens have evolved extensive and diverse repertoires of type VI secretion system-associated antimicrobial toxins. These expansive toxin arsenals potentially enhance the ability of Ralstonia pathogens to invade plant microbiomes, enabling them to rapidly colonize and kill their host plants. We devised a classification system to categorize the Ralstonia toxins. Interestingly, many of the toxin gene clusters are encoded on mobile genetic elements, including prophages, which may be mutualistic symbionts that enhance the inter-microbial competitiveness of Ralstonia wilt pathogens. Moreover, our findings suggest that the convergent loss of this multi-gene trait contributes to genome reduction in two vector-transmitted lineages of Ralstonia pathogens. Our findings demonstrate that the interplay between microbial ecology and pathogen lifestyle shapes the evolution of a genetically complex antimicrobial weapon.}, } @article {pmid39191296, year = {2024}, author = {Xiao, Y and Qin, Y and Jiang, X and Gao, P}, title = {Effects of polypropylene microplastics on digestion performance, microbial community, and antibiotic resistance during microbial anaerobic digestion.}, journal = {Bioresource technology}, volume = {411}, number = {}, pages = {131358}, doi = {10.1016/j.biortech.2024.131358}, pmid = {39191296}, issn = {1873-2976}, abstract = {As an emerging pollutant, microplastics (MPs) have attracted increasing attention worldwide. The effects of polypropylene (PP) MPs on digestion performance, behaviors of dominant microbial communities, antibiotic resistance genes (ARGs) and mobile genetic elements in microbial anaerobic digesters were investigated. The results showed that the addition of PP-MPs to digesters led to an increase in methane production of 10.8% when 300 particles/g TSS of PP-MPs was introduced compared with that in digester not treated with PP-MPs. This increase was attributed to the enrichment of acetogens such as Syntrophobacter (42.0%), Syntrophorhabdus (27.0%), and Syntrophomonas (10.6%), and methanogens including Methanobacterium and Methanosaeta. tetX was highly enriched due to PP-MP exposure, whereas parC exhibited the greatest increase (35.5% - 222.7%). Horizontal gene transfer via ISCR1 and intI1 genes might play an important role in the spread of ARGs. Overall, these findings provide comprehensive insight into the ecological dynamics of PP-MPs during microbial anaerobic digestion.}, } @article {pmid39191191, year = {2024}, author = {Middendorf, PS and Zomer, AL and Bergval, IL and Jacobs-Reitsma, WF and den Besten, HMW and Abee, T}, title = {Host associations of Campylobacter jejuni and Campylobacter coli isolates carrying the L-fucose or d-glucose utilization cluster.}, journal = {International journal of food microbiology}, volume = {425}, number = {}, pages = {110855}, doi = {10.1016/j.ijfoodmicro.2024.110855}, pmid = {39191191}, issn = {1879-3460}, abstract = {Campylobacter was considered asaccharolytic, but is now known to carry saccharide metabolization pathways for L-fucose and d-glucose. We hypothesized that these clusters are beneficial for Campylobacter niche adaptation and may help establish human infection. We investigated the distribution of d-glucose and L-fucose clusters among ∼9600 C. jejuni and C. coli genomes of different isolation sources in the Netherlands, the United Kingdom, the United States of America and Finland. The L-fucose utilization cluster was integrated at the same location in all C. jejuni and C. coli genomes, and was flanked by the genes rpoB, rpoC, rspL, repsG and fusA, which are associated with functions in transcription as well as translation and in acquired drug resistance. In contrast, the flanking regions of the d-glucose utilization cluster were variable among the isolates, and integration sites were located within one of the three different 16S23S ribosomal RNA areas of the C. jejuni and C. coli genomes. In addition, we investigated whether acquisition of the L-fucose utilization cluster could be due to horizontal gene transfer between the two species and found three isolates for which this was the case: one C. jejuni isolate carrying a C. coli L-fucose cluster, and two C. coli isolates which carried a C. jejuni L-fucose cluster. Furthermore, L-fucose utilization cluster alignments revealed multiple frameshift mutations, most of which were commonly found in the non-essential genes for L-fucose metabolism, namely, Cj0484 and Cj0489. These findings support our hypothesis that the L-fucose cluster was integrated multiple times across the C. coli/C. jejuni phylogeny. Notably, association analysis using the C. jejuni isolates from the Netherlands showed a significant correlation between human C. jejuni isolates and C. jejuni isolates carrying the L-fucose utilization cluster. This correlation was even stronger when the Dutch isolates were combined with the isolates from the UK, the USA and Finland. No such correlations were observed for C. coli or for the d-glucose cluster for both species. This research provides insight into the spread and host associations of the L-fucose and d-glucose utilization clusters in C. jejuni and C. coli, and the potential benefits in human infection and/or proliferation in humans, conceivably after transmission from any reservoir.}, } @article {pmid39190937, year = {2024}, author = {Wen, AX and Herman, C}, title = {Horizontal gene transfer and beyond: the delivery of biological matter by bacterial membrane vesicles to host and bacterial cells.}, journal = {Current opinion in microbiology}, volume = {81}, number = {}, pages = {102525}, doi = {10.1016/j.mib.2024.102525}, pmid = {39190937}, issn = {1879-0364}, abstract = {Membrane vesicles (MVs) are produced in all domains of life. In eukaryotes, extracellular vesicles have been shown to mediate the horizontal transfer of biological material between cells [1]. Therefore, bacterial MVs are also thought to mediate horizontal material transfer to host cells and other bacteria, especially in the context of cell stress. In this review, we discuss the mechanisms of bacterial MV production, evidence that their contents can be trafficked to host cells and other bacteria, and the biological relevance of horizontal material transfer by bacterial MVs.}, } @article {pmid39190025, year = {2024}, author = {Alav, I and Pordelkhaki, P and Rodriguez-Navarro, J and Neo, O and Kessler, C and Awodipe, RJ and Cliffe, P and Pulavan, N and Marton, HL and Gibbons, S and Buckner, MMC}, title = {Natural products from food sources can alter the spread of antimicrobial resistance plasmids in Enterobacterales.}, journal = {Microbiology (Reading, England)}, volume = {170}, number = {8}, pages = {}, doi = {10.1099/mic.0.001496}, pmid = {39190025}, issn = {1465-2080}, mesh = {*Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; *Klebsiella pneumoniae/drug effects/genetics ; *Escherichia coli/genetics/drug effects ; *beta-Lactamases/genetics/metabolism ; *Biological Products/pharmacology ; Drug Resistance, Bacterial/genetics ; Conjugation, Genetic ; Bacterial Proteins/genetics/metabolism ; Enterobacteriaceae/drug effects/genetics ; Microbial Sensitivity Tests ; Food Microbiology ; Gene Transfer, Horizontal ; }, abstract = {Antimicrobial resistance (AMR) poses a significant threat to global public health. Notably, resistance to carbapenem and extended-spectrum β-lactam antibiotics in Gram-negative bacteria is a major impediment to treating infections. Genes responsible for antibiotic resistance are frequently carried on plasmids, which can transfer between bacteria. Therefore, exploring strategies to prevent this transfer and the prevalence of AMR plasmids is timely and pertinent. Here, we show that certain natural product extracts and associated pure compounds can reduce the conjugation of AMR plasmids into new bacterial hosts. Using our established high-throughput fluorescence-based flow cytometry assay, we found that the natural products were more active in reducing transmission of the IncK extended-spectrum β-lactamase-encoding plasmid pCT in Escherichia coli EC958c, compared to Klebsiella pneumoniae Ecl8 carrying the IncFII carbapenemase-encoding plasmid pKpQIL. The exception was the natural product rottlerin, also active in K. pneumoniae. In classical conjugation assays, rottlerin also reduced the conjugation frequency of the IncFII bla NDM-1 carrying plasmid pCPE16_3 from a clinical K. pneumoniae isolate. Our data indicate that the natural products tested here, in their current molecular structure, reduced conjugation by a small amount, which is unlikely to achieve a large-scale reduction in AMR in bacterial populations. However, certain natural products like rottlerin could provide a foundation for further research into compounds with effective anti-plasmid activity.}, } @article {pmid39189989, year = {2024}, author = {Brewer, TE and Wagner, A}, title = {Horizontal gene transfer of a key translation factor and its role in polyproline proteome evolution.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msae180}, pmid = {39189989}, issn = {1537-1719}, abstract = {Prolines cause ribosomes to stall during translation due to their rigid structure. This phenomenon occurs in all domains of life and is exacerbated at polyproline motifs. Such stalling can be eased by the elongation factor P (EF-P) in bacteria. We discovered a potential connection between the loss of ancestral EF-P, the appearance of horizontally transferred EF-P variants, and genomic signs of EF-P dysfunction. Horizontal transfer of the efp gene has occurred several times among bacteria and is associated with the loss of highly conserved polyproline motifs. In this study, we pinpoint cases of horizontal EF-P transfer among a diverse set of bacteria and examine genomic features associated with these events in the phyla Thermotogota and Planctomycetes. In these phyla, horizontal EF-P transfer is also associated with the loss of entire polyproline motif containing proteins, whose expression is likely dependent on EF-P. In particular, three proteases (Lon, ClpC, and FtsH) and three tRNA synthetases (ValS, IleS1, IleS2) appear highly sensitive to EF-P transfer. The conserved polyproline motifs within these proteins all reside within close proximity to ATP-binding-regions, some of which are crucial for their function. Our work shows that an ancient EF-P dysfunction has left genomic traces that persist to this day, although it remains unclear whether this dysfunction was strictly due to loss of ancestral EF-P or was related to the appearance of an exogenous variant. The latter possibility would imply that the process of 'domesticating' a horizontally transferred efp gene can perturb the overall function of EF-P.}, } @article {pmid39189956, year = {2024}, author = {Zheng, X and Huang, L}, title = {Diverse non-canonical electron bifurcating [FeFe]-hydrogenases of separate evolutionary origins in Hydrogenedentota.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0099924}, doi = {10.1128/msystems.00999-24}, pmid = {39189956}, issn = {2379-5077}, abstract = {UNLABELLED: Hydrogenedentota, a globally distributed bacterial phylum-level lineage, is poorly understood. Here, we established a comprehensive genomic catalog of Hydrogenedentota, including a total of seven clades (or families) with 179 genomes, and explored the metabolic potential and evolutionary history of these organisms. We show that a single genome, especially those belonging to Clade 6, often encodes multiple hydrogenases with genomes in Clade 2, which rarely encode hydrogenases being the exception. Notably, most members of Hydrogenedentota contain a group A3 [FeFe]-hydrogenase (BfuABC) with a non-canonical electron bifurcation mechanism, in addition to substrate-level phosphorylation and electron transport-linked phosphorylation pathways, in energy conservation. Furthermore, we show that BfuABC from Hydrogenedentota fall into five sub-types. Phylogenetic analysis reveals five independent routes for the evolution of BfuABC homologs in Hydrogenedentota. We speculate that the five sub-types of BfuABC might be acquired from Bacillota (synonym Firmicutes) through separate horizontal gene transfer events. These data shed light on the diversity and evolution of bifurcating [FeFe]-hydrogenases and provide insight into the strategy of Hydrogenedentota to adapt to survival in various habitats.

IMPORTANCE: The phylum Hydrogenedentota is widely distributed in various environments. However, their physiology, ecology, and evolutionary history remain unknown, primarily due to the limited availability of the genomes and the lack of cultured representatives of the phylum. Our results have increased the knowledge of the genetic and metabolic diversity of these organisms and shed light on their diverse energy conservation strategies, especially those involving electron bifurcation with a non-canonical mechanism, which are likely responsible for their wide distribution. Besides, the organization and phylogenetic relationships of gene clusters coding for BfuABC in Hydrogenedentota provide valuable clues to the evolutionary history of group A3 electron bifurcating [FeFe]-hydrogenases.}, } @article {pmid39189770, year = {2024}, author = {Kopejtka, K and Tomasch, J and Shivaramu, S and Saini, MK and Kaftan, D and Koblížek, M}, title = {Minimal transcriptional regulation of horizontally transferred photosynthesis genes in phototrophic bacterium Gemmatimonas phototrophica.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0070624}, doi = {10.1128/msystems.00706-24}, pmid = {39189770}, issn = {2379-5077}, abstract = {UNLABELLED: The first phototrophic member of the bacterial phylum Gemmatimonadota, Gemmatimonas phototrophica AP64[T], received all its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Here, we investigated how these acquired genes, which are tightly controlled by oxygen and light in the ancestor, are integrated into the regulatory system of its new host. G. phototrophica grew well under aerobic and semiaerobic conditions, with almost no difference in gene expression. Under aerobic conditions, the growth of G. phototrophica was optimal at 80 µmol photon m[-2] s[-1], while higher light intensities had an inhibitory effect. The transcriptome showed only a minimal response to the dark-light shift at optimal light intensity, while the exposure to a higher light intensity (200 µmol photon m[-2] s[-1]) induced already stronger but still transient changes in gene expression. Interestingly, a singlet oxygen defense was not activated under any conditions tested. Our results indicate that G. phototrophica possesses neither the oxygen-dependent repression of photosynthesis genes known from purple bacteria nor the light-dependent repression described in aerobic anoxygenic phototrophs. Instead, G. phototrophica has evolved as a low-light species preferring reduced oxygen concentrations. Under these conditions, the bacterium can safely employ its photoheterotrophic metabolism without the need for complex regulatory mechanisms.

IMPORTANCE: Horizontal gene transfer is one of the main mechanisms by which bacteria acquire new genes. However, it represents only the first step as the transferred genes have also to be functionally and regulatory integrated into the recipient's cellular machinery. Gemmatimonas phototrophica, a member of bacterial phylum Gemmatimonadota, acquired its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Thus, it represents a unique natural experiment, in which the entire package of photosynthesis genes was transplanted into a distant host. We show that G. phototrophica lacks the regulation of photosynthesis gene expressions in response to oxygen concentration and light intensity that are common in purple bacteria. This restricts its growth to low-light habitats with reduced oxygen. Understanding the regulation of horizontally transferred genes is important not only for microbial evolution but also for synthetic biology and the engineering of novel organisms, as these rely on the successful integration of foreign genes.}, } @article {pmid39189747, year = {2024}, author = {Duchin Rapp, Y and Lipsman, V and Yuda, L and Kublanov, IV and Matsliyah, D and Segev, E}, title = {Algal exudates promote conjugation in marine Roseobacters.}, journal = {mBio}, volume = {}, number = {}, pages = {e0106224}, doi = {10.1128/mbio.01062-24}, pmid = {39189747}, issn = {2150-7511}, abstract = {UNLABELLED: Horizontal gene transfer (HGT) is a pivotal mechanism driving bacterial evolution, conferring adaptability within dynamic marine ecosystems. Among HGT mechanisms, conjugation mediated by type IV secretion systems (T4SSs) plays a central role in the ecological success of marine bacteria. However, the conditions promoting conjugation events in the marine environment are not well-understood. Roseobacters, abundant marine bacteria commonly associated with algae, possess a multitude of T4SSs. Many Roseobacters are heterotrophic bacteria that rely on algal secreted compounds to support their growth. These compounds attract bacteria, facilitating colonization and attachment to algal cells. Algae and their metabolites bring bacteria into close proximity, potentially promoting bacterial HGT. Investigation across various Roseobacters revealed that algal exudates indeed enhance plasmid transfer through conjugation. While algal exudates do not influence the transcription of bacterial conjugative machinery genes, they promote bacterial attachment, potentially stabilizing proximity and facilitating HGT. Notably, under conditions where attachment is less advantageous, the impact of algal exudates on conjugation is reduced. These findings suggest that algae enhance bacterial conjugation primarily by fostering attachment and highlight the importance of studying bacterial HGT within the context of algal-bacterial interactions.

IMPORTANCE: This study explores how algal-bacterial interactions influence horizontal gene transfer (HGT) among marine bacteria. HGT, a key driver of bacterial evolution, is facilitated by conjugation mediated by type IV secretion systems (T4SSs). Through investigating Roseobacters, abundant marine bacteria often found to be associated with algae, the study reveals that algal exudates enhance plasmid transfer via conjugation. This enhancement is attributed to the promotion of bacterial attachment by algal compounds, emphasizing the role of algal-bacterial interactions in shaping genetic exchange within dynamic marine ecosystems. Understanding these mechanisms is crucial for elucidating bacterial adaptability and evolution in the marine environment.}, } @article {pmid39187833, year = {2024}, author = {Yutin, N and Tolstoy, I and Mutz, P and Wolf, YI and Krupovic, M and Koonin, EV}, title = {DNA polymerase swapping in Caudoviricetes bacteriophages.}, journal = {Virology journal}, volume = {21}, number = {1}, pages = {200}, pmid = {39187833}, issn = {1743-422X}, mesh = {*DNA-Directed DNA Polymerase/genetics ; *Phylogeny ; *Viral Proteins/genetics/metabolism ; Evolution, Molecular ; Genome, Viral ; Caudovirales/genetics/classification ; DNA, Viral/genetics ; Bacteriophages/genetics/enzymology/classification ; DNA Replication ; }, abstract = {BACKGROUND: Viruses with double-stranded (ds) DNA genomes in the realm Duplodnaviria share a conserved structural gene module but show a broad range of variation in their repertoires of DNA replication proteins. Some of the duplodnaviruses encode (nearly) complete replication systems whereas others lack (almost) all genes required for replication, relying on the host replication machinery. DNA polymerases (DNAPs) comprise the centerpiece of the DNA replication apparatus. The replicative DNAPs are classified into 4 unrelated or distantly related families (A-D), with the protein structures and sequences within each family being, generally, highly conserved. More than half of the duplodnaviruses encode a DNAP of family A, B or C. We showed previously that multiple pairs of closely related viruses in the order Crassvirales encode DNAPs of different families.

METHODS: Groups of phages in which DNAP swapping likely occurred were identified as subtrees of a defined depth in a comprehensive evolutionary tree of tailed bacteriophages that included phages with DNAPs of different families. The DNAP swaps were validated by constrained tree analysis that was performed on phylogenetic tree of large terminase subunits, and the phage genomes encoding swapped DNAPs were aligned using Mauve. The structures of the discovered unusual DNAPs were predicted using AlphaFold2.

RESULTS: We identified four additional groups of tailed phages in the class Caudoviricetes in which the DNAPs apparently were swapped on multiple occasions, with replacements occurring both between families A and B, or A and C, or between distinct subfamilies within the same family. The DNAP swapping always occurs "in situ", without changes in the organization of the surrounding genes. In several cases, the DNAP gene is the only region of substantial divergence between closely related phage genomes, whereas in others, the swap apparently involved neighboring genes encoding other proteins involved in phage genome replication. In addition, we identified two previously undetected, highly divergent groups of family A DNAPs that are encoded in some phage genomes along with the main DNAP implicated in genome replication.

CONCLUSIONS: Replacement of the DNAP gene by one encoding a DNAP of a different family occurred on many independent occasions during the evolution of different families of tailed phages, in some cases, resulting in very closely related phages encoding unrelated DNAPs. DNAP swapping was likely driven by selection for avoidance of host antiphage mechanisms targeting the phage DNAP that remain to be identified, and/or by selection against replicon incompatibility.}, } @article {pmid39186748, year = {2024}, author = {Pradel, N and Bartoli, M and Koenen, M and Bale, N and Neumann-Schaal, M and Spröer, C and Bunk, B and Rohde, M and Pester, M and Spring, S}, title = {Description and genome analysis of a novel archaeon isolated from a syntrophic pyrite-forming enrichment culture and reclassification of Methanospirillum hungatei strains GP1 and SK as Methanospirillum purgamenti sp. nov.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0308405}, pmid = {39186748}, issn = {1932-6203}, mesh = {*Methanospirillum/genetics/metabolism ; *Phylogeny ; *Genome, Archaeal ; Sulfides/metabolism ; Iron/metabolism ; RNA, Ribosomal, 16S/genetics ; Methane/metabolism ; }, abstract = {The archaeal isolate J.3.6.1-F.2.7.3T was obtained from an anaerobic enrichment culture, where it may play an important role in methane production during pyrite formation. The new isolate formed a species-level clade with Methanospirillum hungatei strains GP1 and SK, which is separate from the type strain JF-1T. Cultivation-independent surveys indicate the occurrence of this phylogenetic group in sediments and anaerobic digesters. The abundance of this clade appears to be negatively affected by high nitrogen loads, indicating a sensitivity to certain nitrogen compounds that is not known in M. hungatei JF-1T. The relatively large core genome of this Methanospirillum clade is indicative of niche specialization and efficient control of horizontal gene transfer. Genes for nitrogenase and F420-dependent secondary alcohol dehydrogenase contribute to the metabolic versatility of this lineage. Characteristics of the new isolate such as the ability to utilize 2-propanol as an electron donor or the requirement for acetate as a carbon source are found also in the strains GP1 and SK, but not in the type strain M. hungatei JF-1T. Based on the genomic differences to related species, a new species within the genus Methanospirillum is proposed with the name M. purgamenti sp. nov. The determined phenotypic characteristics support this proposal and indicate a metabolic adaptation to a separate ecological niche.}, } @article {pmid39184916, year = {2024}, author = {Han, H and He, T and Wu, Y and He, T and Zhou, W}, title = {Multidimensional analysis of tumor stem cells: from biological properties, metabolic adaptations to immune escape mechanisms.}, journal = {Frontiers in cell and developmental biology}, volume = {12}, number = {}, pages = {1441081}, pmid = {39184916}, issn = {2296-634X}, abstract = {As a key factor in tumorigenesis, progression, recurrence and metastasis, the biological properties, metabolic adaptations and immune escape mechanisms of CSCs are the focus of current oncological research. CSCs possess self-renewal, multidirectional differentiation and tumorigenicity, and their mechanisms of action can be elucidated by the clonal evolution, hierarchical model and the dynamic CSCs model, of which the dynamic model is widely recognized due to its better explanation of the function and origin of CSCs. The origin hypothesis of CSCs involves cell-cell fusion, horizontal gene transfer, genomic instability and microenvironmental regulation, which together shape the diversity of CSCs. In terms of classification, CSCs include primary CSCs (pri-CSCs), precancerous stem cells (pre-CSCs), migratory CSCs (mig-CSCs), and chemo-radiotherapy-resistant CSCs (cr-CSCs and rr-CSCs), with each type playing a specific role in tumor progression. Surface markers of CSCs, such as CD24, CD34, CD44, CD90, CD133, CD166, EpCAM, and LGR5, offer the possibility of identifying, isolating, and targeting CSCs, but the instability and heterogeneity of their expression increase the difficulty of treatment. CSCs have adapted to their survival needs through metabolic reprogramming, showing the ability to flexibly switch between glycolysis and oxidative phosphorylation (OXPHOS), as well as adjustments to amino acid and lipid metabolism. The Warburg effect typifies their metabolic profiles, and altered glutamine and fatty acid metabolism further contributes to the rapid proliferation and survival of CSCs. CSCs are able to maintain their stemness by regulating the metabolic networks to maintain their stemness characteristics, enhance antioxidant defences, and adapt to therapeutic stress. Immune escape is another strategy for CSCs to maintain their survival, and CSCs can effectively evade immune surveillance through mechanisms such as up-regulating PD-L1 expression and promoting the formation of an immunosuppressive microenvironment. Together, these properties reveal the multidimensional complexity of CSCs, underscoring the importance of a deeper understanding of the biology of CSCs for the development of more effective tumor therapeutic strategies. In the future, therapies targeting CSCs will focus on precise identification of surface markers, intervention of metabolic pathways, and overcoming immune escape, with the aim of improving the relevance and efficacy of cancer treatments, and ultimately improving patient prognosis.}, } @article {pmid39184814, year = {2024}, author = {Chen, N and Li, Y and Liang, X and Qin, K and Zhang, Y and Wang, J and Wu, Q and Gupta, TB and Ding, Y}, title = {Bacterial extracellular vesicle: A non-negligible component in biofilm life cycle and challenges in biofilm treatments.}, journal = {Biofilm}, volume = {8}, number = {}, pages = {100216}, pmid = {39184814}, issn = {2590-2075}, abstract = {Bacterial biofilms, especially those formed by pathogens, have been increasingly impacting human health. Bacterial extracellular vesicle (bEV), a kind of spherical membranous structure released by bacteria, has not only been reported to be a component of the biofilm matrix but also plays a non-negligible role in the biofilm life cycle. Nevertheless, a comprehensive overview of the bEVs functions in biofilms remains elusive. In this review, we summarize the biogenesis and distinctive features characterizing bEVs, and consolidate the current literature on their functions and proposed mechanisms in the biofilm life cycle. Furthermore, we emphasize the formidable challenges associated with vesicle interference in biofilm treatments. The primary objective of this review is to raise awareness regarding the functions of bEVs in the biofilm life cycle and lay the groundwork for the development of novel therapeutic strategies to control or even eliminate bacterial biofilms.}, } @article {pmid39182428, year = {2024}, author = {Ando, S and Tanaka, R and Ito, H}, title = {Activity examination of plant Mg-dechelatase and its bacterial homolog in plants and in vitro.}, journal = {Plant physiology and biochemistry : PPB}, volume = {215}, number = {}, pages = {109073}, doi = {10.1016/j.plaphy.2024.109073}, pmid = {39182428}, issn = {1873-2690}, abstract = {Chlorophyll a serves as a photosynthetic pigment in plants. Its degradation is initiated by the extraction of the central Mg by the Mg-dechelatase enzyme, which is encoded by Stay-Green (SGR). Plant SGR is believed to be derived from bacterial SGR homolog obtained through horizontal gene transfer into photosynthetic eukaryotes. However, it is not known how the bacterial SGR homolog was modified to function in plants. To assess its adaptation mechanism in plants, a bacterial SGR homolog derived from the Anaerolineae bacterium SM23_63 was introduced into plants. It was found that the bacterial SGR homolog metabolized chlorophyll in plants. However, its chlorophyll catabolic activity was lower than that of plant SGR. Recombinant proteins of the bacterial SGR homolog exhibited higher activity than those of the plant SGR. The reduced chlorophyll catabolic activity of bacterial SGR homologs in plants may be associated with low hydrophobicity of the entrance to the catalytic site compared to that of plant SGR. This hinders the enzyme access to chlorophyll, which is localized in hydrophobic environments. This study offers insights into the molecular changes underlying the optimization of enzyme function.}, } @article {pmid39107250, year = {2024}, author = {Barragan, AC and Latorre, SM and Malmgren, A and Harant, A and Win, J and Sugihara, Y and Burbano, HA and Kamoun, S and Langner, T}, title = {Multiple Horizontal Mini-chromosome Transfers Drive Genome Evolution of Clonal Blast Fungus Lineages.}, journal = {Molecular biology and evolution}, volume = {41}, number = {8}, pages = {}, pmid = {39107250}, issn = {1537-1719}, support = {//Gatsby Charitable Foundation/ ; UKRI-BBSRC//UK Research and Innovation Biotechnology and Biological Sciences Research Council/ ; /ERC_/European Research Council/International ; 743165//BLASTOFF/ ; 101077853//PANDEMIC/ ; RSWF\R1\191011//Royal Society/ ; }, mesh = {*Gene Transfer, Horizontal ; *Evolution, Molecular ; Chromosomes, Fungal/genetics ; Ascomycota/genetics ; Plant Diseases/microbiology ; Genome, Fungal ; }, abstract = {Crop disease pandemics are often driven by asexually reproducing clonal lineages of plant pathogens that reproduce asexually. How these clonal pathogens continuously adapt to their hosts despite harboring limited genetic variation, and in absence of sexual recombination remains elusive. Here, we reveal multiple instances of horizontal chromosome transfer within pandemic clonal lineages of the blast fungus Magnaporthe (Syn. Pyricularia) oryzae. We identified a horizontally transferred 1.2Mb accessory mini-chromosome which is remarkably conserved between M. oryzae isolates from both the rice blast fungus lineage and the lineage infecting Indian goosegrass (Eleusine indica), a wild grass that often grows in the proximity of cultivated cereal crops. Furthermore, we show that this mini-chromosome was horizontally acquired by clonal rice blast isolates through at least nine distinct transfer events over the past three centuries. These findings establish horizontal mini-chromosome transfer as a mechanism facilitating genetic exchange among different host-associated blast fungus lineages. We propose that blast fungus populations infecting wild grasses act as genetic reservoirs that drive genome evolution of pandemic clonal lineages that afflict cereal crops.}, } @article {pmid39089095, year = {2024}, author = {Zhuang, M and Yan, W and Xiong, Y and Wu, Z and Cao, Y and Sanganyado, E and Siame, BA and Chen, L and Kashi, Y and Leung, KY}, title = {Horizontal plasmid transfer promotes antibiotic resistance in selected bacteria in Chinese frog farms.}, journal = {Environment international}, volume = {190}, number = {}, pages = {108905}, doi = {10.1016/j.envint.2024.108905}, pmid = {39089095}, issn = {1873-6750}, mesh = {Animals ; *Plasmids/genetics ; China ; *Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Farms ; Drug Resistance, Bacterial/genetics ; Rana catesbeiana/microbiology/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/genetics ; }, abstract = {The emergence and dissemination of antibiotic resistance genes (ARGs) in the ecosystem are global public health concerns. One Health emphasizes the interconnectivity between different habitats and seeks to optimize animal, human, and environmental health. However, information on the dissemination of antibiotic resistance genes (ARGs) within complex microbiomes in natural habitats is scarce. We investigated the prevalence of antibiotic resistant bacteria (ARB) and the spread of ARGs in intensive bullfrog (Rana catesbeiana) farms in the Shantou area of China. Antibiotic susceptibilities of 361 strains, combined with microbiome analyses, revealed Escherichia coli, Edwardsiella tarda, Citrobacter and Klebsiella sp. as prevalent multidrug resistant bacteria on these farms. Whole genome sequencing of 95 ARB identified 250 large plasmids that harbored a wide range of ARGs. Plasmid sequences and sediment metagenomes revealed an abundance of tetA, sul1, and aph(3″)-Ib ARGs. Notably, antibiotic resistance (against 15 antibiotics) highly correlated with plasmid-borne rather than chromosome-borne ARGs. Based on sequence similarities, most plasmids (62%) fell into 32 distinct groups, indicating a potential for horizontal plasmid transfer (HPT) within the frog farm microbiome. HPT was confirmed in inter- and intra-species conjugation experiments. Furthermore, identical mobile ARGs, flanked by mobile genetic elements (MGEs), were found in different locations on the same plasmid, or on different plasmids residing in the same or different hosts. Our results suggest a synergy between MGEs and HPT to facilitate ARGs dissemination in frog farms. Mining public databases retrieved similar plasmids from different bacterial species found in other environmental niches globally. Our findings underscore the importance of HPT in mediating the spread of ARGs in frog farms and other microbiomes of the ecosystem.}, } @article {pmid39180708, year = {2024}, author = {Witt, ASA and Carvalho, JVRP and Serafim, MSM and Arias, NEC and Rodrigues, RAL and Abrahão, JS}, title = {The GC% landscape of the Nucleocytoviricota.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {39180708}, issn = {1678-4405}, support = {88882.348380/2010-1//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 405249/2022-5//Ministry of Science and Technology/ ; 406441/2022-7//Ministry of Science and Technology/ ; }, abstract = {Genomic studies on sequence composition employ various approaches, such as calculating the proportion of guanine and cytosine within a given sequence (GC% content), which can shed light on various aspects of the organism's biology. In this context, GC% can provide insights into virus-host relationships and evolution. Here, we present a comprehensive gene-by-gene analysis of 61 representatives belonging to the phylum Nucleocytoviricota, which comprises viruses with the largest genomes known in the virosphere. Parameters were evaluated not only based on the average GC% of a given viral species compared to the entire phylum but also considering gene position and phylogenetic history. Our results reveal that while some families exhibit similar GC% among their representatives (e.g., Marseilleviridae), others such as Poxviridae, Phycodnaviridae, and Mimiviridae have members with discrepant GC% values, likely reflecting adaptation to specific biological cycles and hosts. Interestingly, certain genes located at terminal regions or within specific genomic clusters show GC% values distinct from the average, suggesting recent acquisition or unique evolutionary pressures. Horizontal gene transfer and the presence of potential paralogs were also assessed in genes with the most discrepant GC% values, indicating multiple evolutionary histories. Taken together, to the best of our knowledge, this study represents the first global and gene-by-gene analysis of GC% distribution and profiles within genomes of Nucleocytoviricota members, highlighting their diversity and identifying potential new targets for future studies.}, } @article {pmid39179660, year = {2024}, author = {Wang, S and Sun, S and Wang, Q and Chen, H and Guo, Y and Cai, M and Yin, Y and Ma, S and Wang, H}, title = {PathoTracker: an online analytical metagenomic platform for Klebsiella pneumoniae feature identification and outbreak alerting.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1038}, pmid = {39179660}, issn = {2399-3642}, support = {32141001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81991533//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Klebsiella pneumoniae/genetics/isolation & purification ; *Metagenomics/methods ; Humans ; *Disease Outbreaks ; *Klebsiella Infections/microbiology/epidemiology/diagnosis ; *Phylogeny ; China/epidemiology ; Nanopore Sequencing/methods ; Databases, Genetic ; Genome, Bacterial ; }, abstract = {Clinical metagenomics (CMg) Nanopore sequencing can facilitate infectious disease diagnosis. In China, sub-lineages ST11-KL64 and ST11-KL47 Carbapenem-resistant Klebsiella pneumoniae (CRKP) are widely prevalent. We propose PathoTracker, a specially compiled database and arranged method for strain feature identification in CMg samples and CRKP traceability. A database targeting high-prevalence horizontal gene transfer in CRKP strains and a ST11-only database for distinguishing two sub-lineages in China were created. To make the database user-friendly, facilitate immediate downstream strain feature identification from raw Nanopore metagenomic data, and avoid the need for phylogenetic analysis from scratch, we developed data analysis methods. The methods included pre-performed phylogenetic analysis, gene-isolate-cluster index and multilevel pan-genome database and reduced storage space by 10-fold and random-access memory by 52-fold compared with normal methods. PathoTracker can provide accurate and fast strain-level analysis for CMg data after 1 h Nanopore sequencing, allowing early warning of outbreaks. A user-friendly page (http://PathoTracker.pku.edu.cn/) was developed to facilitate online analysis, including strain-level feature, species identifications and phylogenetic analyses. PathoTracker proposed in this study will aid in the downstream analysis of CMg.}, } @article {pmid39176446, year = {2024}, author = {Ahmed, M and Kayal, E and Lavrov, DV}, title = {Mitochondrial DNA of the demosponge Acanthella acuta: Linear Architecture and Other Unique Features.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evae168}, pmid = {39176446}, issn = {1759-6653}, abstract = {While Acanthella acuta (Schmidt 1862), a common demosponge found in the Mediterranean Sea and Atlantic Ocean, is-morphologically-little distinguishable from other sponges, its mitochondrial DNA (mtDNA) is unique within the class. In contrast to all other studied demosponges, mtDNA of A. acuta is inferred to be linear and displays several unusual features: inverted terminal repeats, group II introns in three mt-genes, and two unique ORFs. One of the ORFs (ORF1535) combines a DNA-polymerase domain with a DNA-directed RNA-polymerase domain, while the second bears no discernible similarity to any reported sequences. The group II intron within the cox2 gene is the first such intron reported in an animal. Our phylogenetic analyses indicate that the cox1 intron is related to similar introns found in other demosponges, while the cox2 intron is likely not of animal origin. The two domains found within ORF1535 do not share a common origin and, along with the cox2 intron, were likely acquired by horizontal transfer. The findings of this paper open new avenues of exploration in the understanding of mtDNA linearization within Metazoa.}, } @article {pmid39174812, year = {2024}, author = {Döcker, J and Linz, S and Wicke, K}, title = {Bounding the Softwired Parsimony Score of a Phylogenetic Network.}, journal = {Bulletin of mathematical biology}, volume = {86}, number = {10}, pages = {121}, pmid = {39174812}, issn = {1522-9602}, support = {XXXX//Marsden Fund/ ; }, mesh = {*Phylogeny ; *Models, Genetic ; *Mathematical Concepts ; Algorithms ; Evolution, Molecular ; Sequence Alignment/statistics & numerical data ; }, abstract = {In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction of phylogenetic networks remains challenging and computationally expensive due to their intricate structural properties. For example, the small parsimony problem that is solvable in polynomial time for phylogenetic trees, becomes NP-hard on phylogenetic networks under softwired and parental parsimony, even for a single binary character and structurally constrained networks. To calculate the parsimony score of a phylogenetic network N, these two parsimony notions consider different exponential-size sets of phylogenetic trees that can be extracted from N and infer the minimum parsimony score over all trees in the set. In this paper, we ask: What is the maximum difference between the parsimony score of any phylogenetic tree that is contained in the set of considered trees and a phylogenetic tree whose parsimony score equates to the parsimony score of N? Given a gap-free sequence alignment of multi-state characters and a rooted binary level-k phylogenetic network, we use the novel concept of an informative blob to show that this difference is bounded by k + 1 times the softwired parsimony score of N. In particular, the difference is independent of the alignment length and the number of character states. We show that an analogous bound can be obtained for the softwired parsimony score of semi-directed networks, while under parental parsimony on the other hand, such a bound does not hold.}, } @article {pmid39173632, year = {2024}, author = {Yang, XY and Shen, Z and Wang, C and Nakanishi, K and Fu, TM}, title = {DdmDE eliminates plasmid invasion by DNA-guided DNA targeting.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2024.07.028}, pmid = {39173632}, issn = {1097-4172}, abstract = {Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, bacteria have developed various defense systems, including prokaryotic Argonautes (pAgos) and the DNA defense module DdmDE system. Through biochemical analysis, structural determination, and in vivo plasmid clearance assays, we elucidate the assembly and activation mechanisms of DdmDE, which eliminates small, multicopy plasmids. We demonstrate that DdmE, a pAgo-like protein, acts as a catalytically inactive, DNA-guided, DNA-targeting defense module. In the presence of guide DNA, DdmE targets plasmids and recruits a dimeric DdmD, which contains nuclease and helicase domains. Upon binding to DNA substrates, DdmD transitions from an autoinhibited dimer to an active monomer, which then translocates along and cleaves the plasmids. Together, our findings reveal the intricate mechanisms underlying DdmDE-mediated plasmid clearance, offering fundamental insights into bacterial defense systems against plasmid invasions.}, } @article {pmid39173362, year = {2024}, author = {Zhang, Y and Zuo, S and Zheng, Q and Yu, G and Wang, Y}, title = {Removal of antibiotic resistant bacteria and antibiotic resistance genes by an electrochemically driven UV/chlorine process for decentralized water treatment.}, journal = {Water research}, volume = {265}, number = {}, pages = {122298}, doi = {10.1016/j.watres.2024.122298}, pmid = {39173362}, issn = {1879-2448}, abstract = {The UV/chlorine (UV/Cl2) process is a developing advanced oxidation process and can efficiently remove antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). However, the transportation and storage of chlorine solutions limit the application of the UV/Cl2 process, especially for decentralized water treatment. To overcome the limitation, an electrochemically driven UV/Cl2 process (E-UV/Cl2) where Cl2 can be electrochemically produced in situ from anodic oxidation of chloride (Cl[-]) ubiquitously present in various water matrices was evaluated in this study. >5-log inactivation of the ARB (E. coli) was achieved within 5 s of the E-UV/Cl2 process, and no photoreactivation of the ARB was observed after the treatment. In addition to the ARB, intracellular and extracellular ARGs (tetA, sul1, sul2, and ermB) could be effectively degraded (e.g., log(C0/C) > 4 for i-ARGs) within 5 min of the E-UV/Cl2 process. Atomic force microscopy showed that the most of the i-ARGs were interrupted into short fragments (< 30 nm) during the E-UV/Cl2 process, which can thus effectively prevent the self-repair of i-ARGs and the horizontal gene transfer. Modelling results showed that the abatement efficiencies of i-ARG correlated positively with the exposures of •OH, Cl2[-]•, and ClO• during the E-UV/Cl2 process. Due to the short treatment time (5 min) required for ARB and ARG removal, insignificant concentrations of trihalomethanes (THMs) were generated during of the E-UV/Cl2 process, and the energy consumption (EEO) of ARG removal was ∼0.20‒0.27 kWh/m[3]-log, which is generally comparable to that of the UV/Cl2 process (0.18-0.23 kWh/m[3]-log). These results demonstrate that the E-UV/Cl2 process can provide a feasible and attractive alternative to the UV/Cl2 process for ARB and ARG removal in decentralized water treatment system.}, } @article {pmid39172952, year = {2024}, author = {Zhou, W and Karan, KR and Gu, W and Klein, HU and Sturm, G and De Jager, PL and Bennett, DA and Hirano, M and Picard, M and Mills, RE}, title = {Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts.}, journal = {PLoS biology}, volume = {22}, number = {8}, pages = {e3002723}, doi = {10.1371/journal.pbio.3002723}, pmid = {39172952}, issn = {1545-7885}, mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Fibroblasts/metabolism ; *Brain/metabolism ; Male ; Female ; Cell Nucleus/metabolism ; Middle Aged ; Adult ; Aged ; Longevity/genetics ; Aging/physiology/genetics ; }, abstract = {The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in nonhuman species and recently demonstrated to occur in rare instances from one human generation to the next. Here, we investigated numtogenesis dynamics in humans in 2 ways. First, we quantified Numts in 1,187 postmortem brain and blood samples from different individuals. Compared to circulating immune cells (n = 389), postmitotic brain tissue (n = 798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples, we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex (DLPFC) compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, an increase in the number of brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment (NCI) who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeated-measures whole-genome sequencing design in a human fibroblast model that recapitulates several molecular hallmarks of aging. These longitudinal experiments revealed a gradual accumulation of 1 Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven by cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derived SURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7-fold faster than healthy donors. Combined, our data document spontaneous numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human postmitotic tissues produces functionally relevant human Numts over timescales shorter than previously assumed.}, } @article {pmid39172793, year = {2024}, author = {Chen, X and Wang, M and Luo, L and Liu, X and An, L and Nie, Y and Wu, XL}, title = {The evolution of autonomy from two cooperative specialists in fluctuating environments.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {35}, pages = {e2317182121}, doi = {10.1073/pnas.2317182121}, pmid = {39172793}, issn = {1091-6490}, support = {2018YFA0902100//MOST | National Key Research and Development Program of China (NKPs)/ ; 91951204//Data Center of Management Science, National Natural Science Foundation of China - Peking University (DCMS, NSFC-PKU)/ ; }, mesh = {*Naphthalenes/metabolism ; Gene Transfer, Horizontal ; Biological Evolution ; Symbiosis ; Microbial Consortia/genetics/physiology ; Genotype ; }, abstract = {From microbes to humans, organisms perform numerous tasks for their survival, including food acquisition, migration, and reproduction. A complex biological task can be performed by either an autonomous organism or by cooperation among several specialized organisms. However, it remains unclear how autonomy and cooperation evolutionarily switch. Specifically, it remains unclear whether and how cooperative specialists can repair deleted genes through direct genetic exchange, thereby regaining metabolic autonomy. Here, we address this question by experimentally evolving a mutualistic microbial consortium composed of two specialists that cooperatively degrade naphthalene. We observed that autonomous genotypes capable of performing the entire naphthalene degradation pathway evolved from two cooperative specialists and dominated the community. This evolutionary transition was driven by the horizontal gene transfer (HGT) between the two specialists. However, this evolution was exclusively observed in the fluctuating environment alternately supplied with naphthalene and pyruvate, where mutualism and competition between the two specialists alternated. The naphthalene-supplied environment exerted selective pressure that favors the expansion of autonomous genotypes. The pyruvate-supplied environment promoted the coexistence and cell density of the cooperative specialists, thereby increasing the likelihood of HGT. Using a mathematical model, we quantitatively demonstrate that environmental fluctuations facilitate the evolution of autonomy through HGT when the relative growth rate and carrying capacity of the cooperative specialists allow enhanced coexistence and higher cell density in the competitive environment. Together, our results demonstrate that cooperative specialists can repair deleted genes through a direct genetic exchange under specific conditions, thereby regaining metabolic autonomy.}, } @article {pmid39106433, year = {2024}, author = {Tan, Y and Aravind, L and Zhang, D}, title = {Genomic Underpinnings of Cytoplasmic Incompatibility: CIF Gene-Neighborhood Diversification Through Extensive Lateral Transfers and Recombination in Wolbachia.}, journal = {Genome biology and evolution}, volume = {16}, number = {8}, pages = {}, doi = {10.1093/gbe/evae171}, pmid = {39106433}, issn = {1759-6653}, support = {//Saint Louis University/ ; //Intramural Research Program of the NIH/ ; /LM/NLM NIH HHS/United States ; }, mesh = {*Wolbachia/genetics ; *Gene Transfer, Horizontal ; *Recombination, Genetic ; Evolution, Molecular ; Phylogeny ; Genome, Bacterial ; Cytoplasm/genetics ; Animals ; Bacterial Proteins/genetics ; }, abstract = {Cytoplasmic incompatibility (CI), a non-Mendelian genetic phenomenon, involves the manipulation of host reproduction by Wolbachia, a maternally transmitted alphaproteobacterium. The underlying mechanism is centered around the CI Factor (CIF) system governed by two genes, cifA and cifB, where cifB induces embryonic lethality, and cifA counteracts it. Recent investigations have unveiled intriguing facets of this system, including diverse cifB variants, prophage association in specific strains, copy number variation, and rapid component divergence, hinting at a complex evolutionary history. We utilized comparative genomics to systematically classify CIF systems, analyze their locus structure and domain architectures, and reconstruct their diversification and evolutionary trajectories. Our new classification identifies ten distinct CIF types, featuring not just versions present in Wolbachia, but also other intracellular bacteria, and eukaryotic hosts. Significantly, our analysis of CIF loci reveals remarkable variability in gene composition and organization, encompassing an array of diverse endonucleases, variable toxin domains, deubiquitinating peptidases (DUBs), prophages, and transposons. We present compelling evidence that the components within the loci have been diversifying their sequences and domain architectures through extensive, independent lateral transfers and interlocus recombination involving gene conversion. The association with diverse transposons and prophages, coupled with selective pressures from host immunity, likely underpins the emergence of CIF loci as recombination hotspots. Our investigation also posits the origin of CifB-REase domains from mobile elements akin to CR (Crinkler-RHS-type) effectors and Tribolium Medea1 factor, which is linked to another non-Mendelian genetic phenomenon. This comprehensive genomic analysis offers novel insights into the molecular evolution and genomic foundations of Wolbachia-mediated host reproductive control.}, } @article {pmid39168346, year = {2024}, author = {Li, J and Li, C and Han, Y and Yang, J and Hu, Y and Xu, H and Zhou, Y and Zuo, J and Tang, Y and Lei, C and Li, C and Wang, H}, title = {Bacterial membrane vesicles from swine farm microbial communities harboring and safeguarding diverse functional genes promoting horizontal gene transfer.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {175639}, doi = {10.1016/j.scitotenv.2024.175639}, pmid = {39168346}, issn = {1879-1026}, abstract = {Antibiotic resistance (AMR) poses a significant global health challenge, with swine farms recognized as major reservoirs of antibiotic resistance genes (ARGs). Recently, bacterial membrane vesicles (BMVs) have emerged as novel carriers mediating horizontal gene transfer. However, little is known about the ARGs carried by BMVs in swine farm environments and their transfer potential. This study investigated the distribution, sources, and microbiological origins of BMVs in three key microbial habitats of swine farms (feces, soil, and fecal wastewater), along with the ARGs and mobile genetic elements (MGEs) they harbor. Characterization of BMVs revealed particle sizes ranging from 20 to 500 nm and concentrations from 10[8] to 10[12] particles/g, containing DNA and proteins. Metagenomic sequencing identified BMVs predominantly composed of members of the Proteobacteria phyla, including Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae, carrying diverse functional genes encompassing resistance to 14 common antibiotics and 74,340 virulence genes. Notably, multidrug resistance, tetracycline, and chloramphenicol resistance genes were particularly abundant. Furthermore, BMVs harbored various MGEs, primarily plasmids, and demonstrated the ability to protect their DNA cargo from degradation and facilitate horizontal gene transfer, including the transmission of resistance genes. In conclusion, this study reveals widespread presence of BMVs carrying ARGs and potential virulence genes in swine farm feces, soil, and fecal wastewater. These findings not only provide new insights into the role of extracellular DNA in the environment but also highlight concerns regarding the gene transfer potential mediated by BMVs and associated health risks.}, } @article {pmid39167960, year = {2024}, author = {Nasu, T and Maeda, S}, title = {Escherichia coli persisters in biofilm can perform horizontal gene transfer by transformation.}, journal = {Biochemical and biophysical research communications}, volume = {738}, number = {}, pages = {150549}, doi = {10.1016/j.bbrc.2024.150549}, pmid = {39167960}, issn = {1090-2104}, abstract = {Persisters represent a subset of cells that exhibit transient tolerance to antimicrobials. These persisters can withstand sudden exposure to antimicrobials, even as the majority of normal cells perish. In this study, we have demonstrated the capacity of ampicillin-tolerant and alkali-tolerant persisters to execute horizontal gene transfer via in situ transformation within biofilms. Air-solid biofilms, comprising two Escherichia coli populations each with a distinct plasmid, were formed on agar media. They were treated with lethal doses of ampicillin or NaOH for 24 h, followed by a 1-min glass-ball roll. This process led to a high frequency of horizontal plasmid transfer (10[-7]-10[-6] per cell) from dead cells to surviving persisters within the biofilms. Plasmid transfer was DNase-sensitive and also occurred by adding purified plasmid DNA to plasmid-free biofilms, demonstrating a transformation mechanism. This marks the first evidence of persisters' novel ability for horizontal gene transfer, via transformation.}, } @article {pmid39166873, year = {2024}, author = {Kwan, S-Y and Sabotta, CM and Cruz, LR and Wong, MC and Ajami, NJ and McCormick, JB and Fisher-Hoch, SP and Beretta, L}, title = {Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0043424}, doi = {10.1128/msystems.00434-24}, pmid = {39166873}, issn = {2379-5077}, abstract = {Mexican Americans are disproportionally affected by metabolic dysfunction-associated steatotic liver disease (MASLD), which often co-occurs with diabetes. Despite extensive evidence on the causative role of the gut microbiome in MASLD, studies determining the involvement of the gut phageome are scarce. In this cross-sectional study, we characterized the gut phageome in Mexican Americans of South Texas by stool shotgun metagenomic sequencing of 340 subjects, concurrently screened for liver steatosis by transient elastography. Inter-individual variations in the phageome were associated with gender, country of birth, diabetes, and liver steatosis. The phage signatures for diabetes and liver steatosis were subsequently determined. Enrichment of Inoviridae was associated with both diabetes and liver steatosis. Diabetes was further associated with the enrichment of predominantly temperate Escherichia phages, some of which possessed virulence factors. Liver steatosis was associated with the depletion of Lactococcus phages r1t and BK5-T, and enrichment of the globally prevalent Crassvirales phages, including members of genus cluster IX (Burzaovirus coli, Burzaovirus faecalis) and VI (Kahnovirus oralis). The Lactococcus phages showed strong correlations and co-occurrence with Lactococcus lactis, while the Crassvirales phages, B. coli, B. faecalis, and UAG-readthrough crAss clade correlated and co-occurred with Prevotella copri. In conclusion, we identified the gut phageome signatures for two closely linked metabolic diseases with significant global burden. These phage signatures may have utility in risk modeling and disease prevention in this high-risk population, and identification of potential bacterial targets for phage therapy.IMPORTANCEPhages influence human health and disease by shaping the gut bacterial community. Using stool samples from a high-risk Mexican American population, we provide insights into the gut phageome changes associated with diabetes and liver steatosis, two closely linked metabolic diseases with significant global burden. Common to both diseases was an enrichment of Inoviridae, a group of phages that infect bacterial hosts chronically without lysis, allowing them to significantly influence bacterial growth, virulence, motility, biofilm formation, and horizontal gene transfer. Diabetes was additionally associated with the enrichment of Escherichia coli-infecting phages, some of which contained virulence factors. Liver steatosis was additionally associated with the depletion of Lactococcus lactis-infecting phages, and enrichment of Crassvirales phages, a group of virulent phages with high global prevalence and persistence across generations. These phageome signatures may have utility in risk modeling, as well as identify potential bacterial targets for phage therapy.}, } @article {pmid39166856, year = {2024}, author = {Karpenko, A and Shelenkov, A and Manzeniuk, I and Kulikova, N and Gevorgyan, A and Mikhaylova, Y and Akimkin, V}, title = {Whole genome analysis of multidrug-resistant Escherichia coli isolate collected from drinking water in Armenia revealed the plasmid-borne mcr-1.1-mediated colistin resistance.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0075124}, doi = {10.1128/spectrum.00751-24}, pmid = {39166856}, issn = {2165-0497}, abstract = {UNLABELLED: The rate of polymyxin-resistant Enterobacteriaceae, as well as human and animal infections caused by them, is increasing worldwide, posing a high epidemiological threat since colistin represents a last-resort antibiotic to treat complicated infections. The study of environmental niches, in particular, aquatic ecosystems in terms of genome analysis of inhabiting antimicrobial-resistant (AMR) microorganisms as reservoirs of acquired resistance determinants (AMR genes), represents a specific concern from a One Health approach. Here, we present a phenotypic AMR analysis and molecular characterization of Escherichia coli isolate found in municipal drinking water after an accident in the water supply system of a residential building in Armenia in 2021. CrieF1144 E. coli isolate was resistant to ampicillin, ampicillin/sulbactam, cefuroxime, ciprofloxacin, levofloxacin, trimethoprim/sulfamethoxazole, colistin, and tigecycline, whereas whole genome sequencing (WGS) revealed blaTEM-1B, tet(A), and a combination of dfrA14 with sul1 resistance determinants, which corresponds well with phenotypic resistance above. Moreover, the multidrug-resistant isolate studied harbored mcr-1.1 gene on a conjugative 251 Kb IncHI2 plasmid, whose structure was determined using hybrid short- and long-reads assembly. CrieF1141_p1 plasmid carried all antimicrobial resistance genes revealed in the isolate and did not harbor any virulence determinants, so it could contribute to the spread of AMR genes in the bacterial population. Two copies of ISApl1 transposase-encoding element, which is likely to mediate mcr-1.1 gene mobilization, were revealed surrounding this gene in a plasmid.

IMPORTANCE: Evolutionary patterns of Escherichia coli show that they usually develop into highly pathogenic forms by acquiring fitness advantages such as antimicrobial resistance (AMR) and various virulence factors through horizontal gene transfer mediated by mobile elements. This has led to high prevalence of multidrug-resistant (MDR) strains, which highlights the relevancy of enhanced surveillance to monitor and prevent transmission of the MDR bacteria to human and animal populations. However, the limited number of reports regarding the whole genome sequencing (WGS) investigation of MDR E. coli strains isolated from drinking water and harboring mcr genes hampers the adoption of a comprehensive approach to address the relationship between environmental E. coli populations and human and veterinary infections. Our results highlight the relevance of analyzing the environment, especially water, as a part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance within the One Health concept.}, } @article {pmid39166427, year = {2024}, author = {Wu, JJ and Deng, QW and Qiu, YY and Liu, C and Lin, CF and Ru, YL and Sun, Y and Lai, J and Liu, LX and Shen, XX and Pan, R and Zhao, YP}, title = {Post-transfer adaptation of HGT-acquired genes and contribution to guanine metabolic diversification in land plants.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.20040}, pmid = {39166427}, issn = {1469-8137}, support = {32071484//National Natural Science Foundation of China/ ; 32200231//National Natural Science Foundation of China/ ; 32371691//National Natural Science Foundation of China/ ; LZ21C030003//Natural Science Foundation of Zhejiang Province/ ; LZ23C020002//Natural Science Foundation of Zhejiang Province/ ; LR23C140001//Natural Science Foundation of Zhejiang Province/ ; 2023000CC0010//Beijing Life Science Academy/ ; 226-2023-00021//Fundamental Research Funds for the Central Universities/ ; 2022YFD1401600//National Key Research and Development Program of China/ ; }, abstract = {Horizontal gene transfer (HGT) is a major driving force in the evolution of prokaryotic and eukaryotic genomes. Despite recent advances in distribution and ecological importance, the extensive pattern, especially in seed plants, and post-transfer adaptation of HGT-acquired genes in land plants remain elusive. We systematically identified 1150 foreign genes in 522 land plant genomes that were likely acquired via at least 322 distinct transfers from nonplant donors and confirmed that recent HGT events were unevenly distributed between seedless and seed plants. HGT-acquired genes evolved to be more similar to native genes in terms of average intron length due to intron gains, and HGT-acquired genes containing introns exhibited higher expression levels than those lacking introns, suggesting that intron gains may be involved in the post-transfer adaptation of HGT in land plants. Functional validation of bacteria-derived gene GuaD in mosses and gymnosperms revealed that the invasion of foreign genes introduced a novel bypass of guanine degradation and resulted in the loss of native pathway genes in some gymnosperms, eventually shaping three major types of guanine metabolism in land plants. We conclude that HGT has played a critical role in land plant evolution.}, } @article {pmid39165128, year = {2024}, author = {Trost, K and Knopp, MR and Wimmer, JLE and Tria, FDK and Martin, WF}, title = {A universal and constant rate of gene content change traces pangenome flux to LUCA.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnae068}, pmid = {39165128}, issn = {1574-6968}, abstract = {Prokaryotic genomes constantly undergo gene flux via lateral gene transfer, generating a pangenome structure consisting of a conserved core genome surrounded by a more variable accessory genome shell. Over time, flux generates change in genome content. Here we measure and compare the rate of genome flux for 5 655 prokaryotic genomes as a function of amino acid sequence divergence in 36 universally distributed proteins of the informational core (IC). We find a clock of gene content change. The long-term average rate of gene content flux is remarkably constant across all higher prokaryotic taxa sampled, whereby the size of the accessory genome-the proportion of the genome harboring gene content difference for genome pairs-varies across taxa. The proportion of species-level accessory genes per genome, varies from 0% (Chlamydia) to 30-33% (Alphaproteobacteria, Gammaproteobacteria, Clostridia). A clock-like rate of gene content change across all prokaryotic taxa sampled suggest that pangenome structure is a general feature of prokaryotic genomes and that it has been in existence since the divergence of bacteria and archaea.}, } @article {pmid39163267, year = {2024}, author = {Kloub, L and Gosselin, S and Graf, J and Gogarten, JP and Bansal, MS}, title = {Investigating Additive and Replacing Horizontal Gene Transfers Using Phylogenies and Whole Genomes.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evae180}, pmid = {39163267}, issn = {1759-6653}, abstract = {Horizontal gene transfer (HGT) is fundamental to microbial evolution and adaptation. When a gene is horizontally transferred, it may either add itself as a new gene to the recipient genome (possibly displacing non-homologous genes) or replace an existing homologous gene. Currently, studies do not usually distinguish between "additive" and "replacing" HGTs, and their relative frequencies, integration mechanisms, and specific roles in microbial evolution are poorly understood. In this work, we develop a novel computational framework for large-scale classification of HGTs as either additive or replacing. Our framework leverages recently developed phylogenetic approaches for HGT detection and classifies HGTs inferred between terminal edges based on gene orderings along genomes and phylogenetic relationships between the microbial species under consideration. The resulting 9 method, called DART, is highly customizable and scalable and can classify a large fraction of inferred HGTs with high confidence and statistical support. Our application of DART to a large dataset of thousands of gene families from 103 Aeromonas genomes provides insights into the relative frequencies, functional biases, and integration mechanisms of additive and replacing HGTs. Among other results, we find that (i) the relative frequency of additive HGT increases with increasing phylogenetic distance, (ii) replacing HGT dominates at shorter phylogenetic distances, (iii) additive and replacing HGTs have strikingly different functional profiles, (iv) homologous recombination in flanking regions of a novel gene may be a frequent integration mechanism for additive HGT, and (v) phages and mobile genetic elements likely play an important role in facilitating additive HGT.}, } @article {pmid39162532, year = {2024}, author = {Ito, Y and Hashimoto, Y and Suzuki, M and Kaneko, N and Yoshida, M and Nakayama, H and Tomita, H}, title = {The emergence of metronidazole-resistant Prevotella bivia harboring nimK gene in Japan.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0056224}, doi = {10.1128/spectrum.00562-24}, pmid = {39162532}, issn = {2165-0497}, abstract = {UNLABELLED: We present the identification and characterization of the complete genome of metronidazole (MTZ)-resistant Prevotella bivia strain TOH-2715 [minimum inhibitory concentration (MIC): 8 mg/L], isolated from the urine of an elderly Japanese woman, as well as details of its mobile genetic elements (MGEs) containing antimicrobial resistance (AMR) genes and its relationship with other bacterial species determined using whole-genome sequencing (WGS) data. TOH-2715 possessed two chromosomes with putative MGEs containing AMR genes. Two AMR-related MGE regions were present in chromosome 2. MGE-region 1 (7,821 bp) included Tn6456, where nimK was located, and MGE-region 2 (58.8 Kbp) included the integrative and conjugative element (ICE), where tet(Q) and ermF were located. The genetic structure of the ICE of TOH-2715 was similar to that of CTnDOT-family transposons, where ermF and tet(Q) are located. A search of public databases revealed that nimK was present in Prevotella spp., including P. bivia, and was partially composed of a Tn6456-like element lacking the efflux transporter gene qacE and the Crp/Fnr family transcriptional regulator gene in some cases. Core ICE gene analysis showed that ICEs similar to that of TOH-2715 were present in Prevotella spp. and Bacteroides spp., suggesting horizontal gene transfer among anaerobes. This is the report of WGS analysis of an MTZ-resistant clinical strain of P. bivia (TOH-2715) with Tn6456 encoding nimK. Other submitted genomes have described the presence of nimK, but none of them have described MTZ resistance. Additionally, we described putative MGE regions containing the AMR gene within the genus Prevotella and among anaerobes, raising concerns about the future spread of nimK among anaerobes.

IMPORTANCE: Metronidazole (MTZ) is an important antimicrobial agent in anaerobic infections and is widely used in clinical settings. The rate of MTZ resistance in anaerobic bacteria has been increasing in recent years, and the nim gene (nitro-imidazole reductase) is one of the resistance mechanisms. Prevotella bivia is found in humans in the urinary tract and vagina and is known to cause infections in some cases. One of the nim genes, nimK, has recently been discovered in this species of bacteria, but there are no reports of antimicrobial resistance (AMR)-related regions in its whole genome level. In this study, we analyzed the AMR region of nimK-positive P. bivia derived from clinical specimens based on comparisons with other anaerobic genomes. P. bivia was found to be engaged in horizontal gene transfer with other anaerobic bacteria, and the future spread of the nimK gene is a concern.}, } @article {pmid39162515, year = {2024}, author = {Wang, Z and Hülpüsch, C and Foesel, B and Traidl-Hoffmann, C and Reiger, M and Schloter, M}, title = {Genomic and functional divergence of Staphylococcus aureus strains from atopic dermatitis patients and healthy individuals: insights from global and local scales.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0057124}, doi = {10.1128/spectrum.00571-24}, pmid = {39162515}, issn = {2165-0497}, abstract = {Atopic dermatitis (AD) is the most common chronic inflammatory skin disease worldwide and is characterized by a complex interplay with skin microbiota, with Staphylococcus aureus often abnormally more abundant in AD patients than in healthy individuals (HE). S. aureus harbors diverse strains with varied genetic compositions and functionalities, which exhibit differential connections with the severity of AD. However, the differences in S. aureus strains between AD and HE remain unclear, with most variations seen at a specific geographic level, implying spontaneous adaptations rather than systematic distinctions. This study presents genomic and functional differences between these S. aureus strains from AD and HE on both global and local levels. We observed reduced gene content diversity but increased functional variation in the global AD-associated strains. Two additional AD-dominant clusters emerged, with Cluster 1 enriched in transposases and Cluster 2 showcasing genes linked to adaptability and antibiotic resistance. Particularly, robust evidence illustrates that the lantibiotic operon of S. aureus, involved in the biosynthesis of lantibiotics, was acquired via horizontal gene transfer from environmental bacteria. Comparisons of the gene abundance profiles in functional categories also indicate limited zoonotic potential between human and animal isolates. Local analysis mirrored global gene diversity but showed distinct functional variations between AD and HE strains. Overall, this research provides foundational insights into the genomic evolution, adaptability, and antibiotic resistance of S. aureus, with significant implications for clinical microbiology.IMPORTANCEOur study uncovers significant genomic variations in Staphylococcus aureus strains associated with atopic dermatitis. We observed adaptive evolution tailored to the disease microenvironment, characterized by a smaller pan-genome than strains from healthy skin both on the global and local levels. Key functional categories driving strain diversification include "replication and repair" and "transporters," with transposases being pivotal. Interestingly, the local strains predominantly featured metal-related genes, whereas global ones emphasized antimicrobial resistances, signifying scale-dependent diversification nuances. We also pinpointed horizontal gene transfer events, indicating interactions between human-associated and environmental bacteria. These insights expand our comprehension of S. aureus's genetic adaptation in atopic dermatitis, yielding valuable implications for clinical approaches.}, } @article {pmid39159726, year = {2024}, author = {Zhang, Y and Wang, N and Wan, J and Jousset, A and Jiang, G and Wang, X and Wei, Z and Xu, Y and Shen, Q}, title = {Exploring the antibiotic resistance genes removal dynamics in chicken manure by composting.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {131309}, doi = {10.1016/j.biortech.2024.131309}, pmid = {39159726}, issn = {1873-2976}, abstract = {Prolonged antibiotic usage in livestock farming leads to the accumulation of antibiotic resistance genes in animal manure. Composting has been shown as an effective way of removing antibiotic resistance from manures, but the specific mechanisms remain unclear. This study used time-series sampling and metagenomics to analyse the resistome types and their bacterial host in chicken manures. Composting significantly altered the physicochemical properties and microbiome composition, reduced antibiotic resistance genes by 65.71 %, mobile genetic elements by 68.15 % and horizontal gene transfer frequency. Source tracking revealed that Firmicutes, Actinobacteria, and Proteobacteria are the major bacterial hosts involved in resistome and gene transfer events. Composting reduces the resistome risk by targeting pathogens such as Staphylococcus aureus. Structural equation modelling confirmed that composting reduces resistome risk by changing pH and pathogen abundance. This study demonstrates that composting is an effective strategy for mitigating resistome risk in chicken manure, thereby supporting the "One Health" initiative.}, } @article {pmid39158272, year = {2024}, author = {Upreti, C and Kumar, P and Durso, LM and Palmer, KL}, title = {CRISPR-Cas inhibits plasmid transfer and immunizes bacteria against antibiotic resistance acquisition in manure.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0087624}, doi = {10.1128/aem.00876-24}, pmid = {39158272}, issn = {1098-5336}, abstract = {The horizontal transfer of antibiotic resistance genes among bacteria is a pressing global issue. The bacterial defense system clustered regularly interspaced short palindromic repeats (CRISPR)-Cas acts as a barrier to the spread of antibiotic resistance plasmids, and CRISPR-Cas-based antimicrobials can be effective to selectively deplete antibiotic-resistant bacteria. While significant surveillance efforts monitor the spread of antibiotic-resistant bacteria in the clinical context, a major, often overlooked aspect of the issue is resistance emergence in agriculture. Farm animals are commonly treated with antibiotics, and antibiotic resistance in agriculture is on the rise. Yet, CRISPR-Cas efficacy has not been investigated in this setting. Here, we evaluate the prevalence of CRISPR-Cas in agricultural Enterococcus faecalis strains and its antiplasmid efficacy in an agricultural niche: manure. Analyzing 1,986 E. faecalis genomes from human and animal hosts, we show that the prevalence of CRISPR-Cas subtypes is similar between clinical and agricultural E. faecalis strains. Using plasmid conjugation assays, we found that CRISPR-Cas is a significant barrier against resistance plasmid transfer in manure. Finally, we used a CRISPR-based antimicrobial approach to cure resistant E. faecalis of erythromycin resistance, but this was limited by delivery efficiency of the CRISPR antimicrobial in manure. However, immunization of bacteria against resistance gene acquisition in manure was highly effective. Together, our results show that E. faecalis CRISPR-Cas is prevalent and effective in an agricultural setting and has the potential to be utilized for depleting antibiotic-resistant populations. Our work has broad implications for tackling antibiotic resistance in the increasingly relevant agricultural setting, in line with a One Health approach.IMPORTANCEAntibiotic resistance is a growing global health crisis in human and veterinary medicine. Previous work has shown technologies based on CRISPR-Cas-a bacterial defense system-to be effective in tackling antibiotic resistance. Here we test if CRISPR-Cas is present and effective in agricultural niches, specifically in the ubiquitously present bacterium, Enterococcus faecalis. We show that CRISPR-Cas is both prevalent and functional in manure and has the potential to be used to specifically kill bacteria carrying antibiotic resistance genes. This study demonstrates the utility of CRISPR-Cas-based strategies for control of antibiotic resistance in agricultural settings.}, } @article {pmid39158107, year = {2024}, author = {Ming, Y and Abdullah Al, M and Zhang, D and Zhu, W and Liu, H and Cai, L and Yu, X and Wu, K and Niu, M and Zeng, Q and He, Z and Yan, Q}, title = {Insights into the evolutionary and ecological adaption strategies of nirS- and nirK-type denitrifying communities.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17507}, doi = {10.1111/mec.17507}, pmid = {39158107}, issn = {1365-294X}, support = {SML2020SP004//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2021SP203//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP205//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 42377111//National Natural Science Foundation of China/ ; //Ocean Negative Carbon Emissions (ONCE) Program/ ; }, abstract = {Denitrification is a crucial process in the global nitrogen cycle, in which two functionally equivalent genes, nirS and nirK, catalyse the critical reaction and are usually used as marker genes. The nirK gene can function independently, whereas nirS requires additional genes to encode nitrite reductase and is more sensitive to environmental factors than nirK. However, the ecological differentiation mechanisms of those denitrifying microbial communities and their adaptation strategies to environmental stresses remain unclear. Here, we conducted metagenomic analysis for sediments and bioreactor samples from Lake Donghu, China. We found that nirS-type denitrifying communities had a significantly lower horizontal gene transfer frequency than that of nirK-type denitrifying communities, and nirS gene phylogeny was more congruent with taxonomy than that of nirK gene. Metabolic reconstruction of metagenome-assembled genomes further revealed that nirS-type denitrifying communities have robust metabolic systems for energy conservation, enabling them to survive under environmental stresses. Nevertheless, nirK-type denitrifying communities seemed to adapt to oxygen-limited environments with the ability to utilize various carbon and nitrogen compounds. Thus, this study provides novel insights into the ecological differentiation mechanism of nirS and nirK-type denitrifying communities, as well as the regulation of the global nitrogen cycle and greenhouse gas emissions.}, } @article {pmid39153565, year = {2024}, author = {Yang, C and Yan, S and Zhang, B and Yao, X and Mo, J and Rehman, F and Guo, J}, title = {Spatiotemporal distribution of the planktonic microbiome and antibiotic resistance genes in a typical urban river contaminated by macrolide antibiotics.}, journal = {Environmental research}, volume = {}, number = {}, pages = {119808}, doi = {10.1016/j.envres.2024.119808}, pmid = {39153565}, issn = {1096-0953}, abstract = {The widespread application of macrolide antibiotics has caused antibiotic resistance pollution, threatening the river ecological health. In this study, five macrolide antibiotics (azithromycin, clarithromycin, roxithromycin, erythromycin, and anhydro erythromycin A) were monitored in the Zao River across three hydrological periods (April, July, and December). Simultaneously, the changes in antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and planktonic bacterial communities were determined using metagenomic sequencing. A clear pollution gradient was observed for azithromycin and roxithromycin, with the concentrations in the dry season surpassing those in other seasons. The highest concentration was observed for azithromycin (1.36 μg/L). The abundance of MLS resistance genes increased along the Zao River during the dry season, whereas the opposite trend was obtained during the wet season. A significant correlation between the levels of MLS resistance genes and macrolide antibiotics was identified during the dry season. Notably, compared with the reference site, the abundance of transposase in the effluent from wastewater treatment plants (WWTPs) was significantly elevated in both dry and wet seasons, whereas the abundance of insertion sequences (IS) and plasmids declined during the dry season. The exposure to wastewater containing macrolide antibiotics altered the diversity of planktonic bacterial communities. The bacterial host for ARGs appeared to be Pseudomonas, primarily associated with multidrug subtypes. Moreover, the ARG subtypes were highly correlated with MGEs (transposase and istA). The partial least-squares path model (PLS-PM) demonstrated a positive correlation between the abundance of MGEs and ARGs, indicating the significance of horizontal gene transfer (HGT) in the dissemination of ARGs within the Zao River. Environmental variables, such as TN and NO3[-]-N, were significantly correlated with the abundance of MGEs, ARGs, and bacteria. Collectively, our findings could provide insights into the shift patterns of the microbiome and ARGs across the contamination gradient of AZI and ROX in the river.}, } @article {pmid39153075, year = {2024}, author = {Panickar, A and Manoharan, A and Anbarasu, A and Ramaiah, S}, title = {Respiratory tract infections: an update on the complexity of bacterial diversity, therapeutic interventions and breakthroughs.}, journal = {Archives of microbiology}, volume = {206}, number = {9}, pages = {382}, pmid = {39153075}, issn = {1432-072X}, support = {IRIS ID: 2021-11889//Indian Council of Medical Research/ ; }, mesh = {*Respiratory Tract Infections/microbiology/drug therapy ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics/drug effects/classification ; Drug Resistance, Bacterial ; Bacterial Infections/microbiology/drug therapy ; Virulence ; }, abstract = {Respiratory tract infections (RTIs) have a significant impact on global health, especially among children and the elderly. The key bacterial pathogens Streptococcus pneumoniae, Haemophilus influenzae, Klebsiella pneumoniae, Staphylococcus aureus and non-fermenting Gram Negative bacteria such as Acinetobacter baumannii and Pseudomonas aeruginosa are most commonly associated with RTIs. These bacterial pathogens have evolved a diverse array of resistance mechanisms through horizontal gene transfer, often mediated by mobile genetic elements and environmental acquisition. Treatment failures are primarily due to antimicrobial resistance and inadequate bacterial engagement, which necessitates the development of alternative treatment strategies. To overcome this, our review mainly focuses on different virulence mechanisms and their resulting pathogenicity, highlighting different therapeutic interventions to combat resistance. To prevent the antimicrobial resistance crisis, we also focused on leveraging the application of artificial intelligence and machine learning to manage RTIs. Integrative approaches combining mechanistic insights are crucial for addressing the global challenge of antimicrobial resistance in respiratory infections.}, } @article {pmid39149034, year = {2024}, author = {Kadkhoda, H and Gholizadeh, P and Samadi Kafil, H and Ghotaslou, R and Pirzadeh, T and Ahangarzadeh Rezaee, M and Nabizadeh, E and Feizi, H and Aghazadeh, M}, title = {Role of CRISPR-Cas systems and anti-CRISPR proteins in bacterial antibiotic resistance.}, journal = {Heliyon}, volume = {10}, number = {14}, pages = {e34692}, pmid = {39149034}, issn = {2405-8440}, abstract = {The emergence and development of antibiotic resistance in bacteria is a serious threat to global public health. Antibiotic resistance genes (ARGs) are often located on mobile genetic elements (MGEs). They can be transferred among bacteria by horizontal gene transfer (HGT), leading to the spread of drug-resistant strains and antibiotic treatment failure. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated genes) is one of the many strategies bacteria have developed under long-term selection pressure to restrict the HGT. CRISPR-Cas systems exist in about half of bacterial genomes and play a significant role in limiting the spread of antibiotic resistance. On the other hand, bacteriophages and other MGEs encode a wide range of anti-CRISPR proteins (Acrs) to counteract the immunity of the CRISPR-Cas system. The Acrs could decrease the CRISPR-Cas system's activity against phages and facilitate the acquisition of ARGs and virulence traits for bacteria. This review aimed to assess the relationship between the CRISPR-Cas systems and Acrs with bacterial antibiotic resistance. We also highlighted the CRISPR technology and Acrs to control and prevent antibacterial resistance. The CRISPR-Cas system can target nucleic acid sequences with high accuracy and reliability; therefore, it has become a novel gene editing and gene therapy tool to prevent the spread of antibiotic resistance. CRISPR-based approaches may pave the way for developing smart antibiotics, which could eliminate multidrug-resistant (MDR) bacteria and distinguish between pathogenic and beneficial microorganisms. Additionally, the engineered anti-CRISPR gene-containing phages in combination with antibiotics could be used as a cutting-edge treatment approach to reduce antibiotic resistance.}, } @article {pmid39148687, year = {2024}, author = {Santos, AJDC and Dias, RS and da Silva, CHM and Vidigal, PMP and de Sousa, MP and da Silva, CC and de Paula, SO}, title = {Genomic analysis of Oceanotoga teriensis strain UFV_LIMV02, a multidrug-resistant thermophilic bacterium isolated from an offshore oil reservoir.}, journal = {Access microbiology}, volume = {6}, number = {8}, pages = {}, pmid = {39148687}, issn = {2516-8290}, abstract = {Bacteria of the species Oceanotoga teriensis belong to the family Petrotogaceae, are Gram-negative bacilli, are moderately thermophilic and are included in the group of thiosulfate-reducing bacteria, being capable of significantly accelerating corrosion in metallic structures. However, no in-depth study on the genome, antibiotic resistance and mobile elements has been carried out so far. In this work, the isolation, phenotypic and genotypic characterization of the multi-resistant O. teriensis UFV_LIMV02 strain was carried out, from water samples from an offshore oil extraction platform in Rio de Janeiro (Brazil). We determined that the isolate has a genome of 2 812 778 bp in size, with 26 % GC content, organized into 34 contigs. Genomic annotation using Rapid Annotation using Subsystem Technology revealed the presence of genes related to resistance to antibiotics and heavy metals. By evaluating the antimicrobial resistance of the isolate using the disc diffusion technique, resistance was verified for the classes of antibiotics, beta-lactams, fluoroquinolones, aminoglycosides, sulfonamides, lincosamides and rifamycins, a total of 14 antibiotics. The search for genomic islands, prophages and defence systems against phage infection revealed the presence of five genomic islands in its genome, containing genes related to resistance to heavy metals and antibiotics, most of which are efflux pumps and several transposases. No prophage was found in its genome; however, nine different defence systems against phage infection were detected. When analysing the clustered regularly interspaced short palindromic repeat (CRISPR) systems, four CRISPR arrays, classified as types I-B and III-B, with 272 spacers, can provide the strain with immunity to different mobile genetic elements and bacteriophage infection. The results found in this study show that the isolate UFV_LIVM02 is an environmental bacterium, resistant to different classes of antibiotics, and that the proteins encoded by the predicted genomic islands may be associated with the development of greater resistance to antibiotics and heavy metals. They provide evidence that environmental bacteria found in offshore oil exploration residues may pose a risk for the spread of antibiotic resistance genes. More comprehensive studies on the microbial community present in oil waste are needed to assess the risks of horizontal gene transfer.}, } @article {pmid39147525, year = {2024}, author = {Wu, Q and Li, W and Kwok, LY and Lv, H and Sun, J and Sun, Z}, title = {Regional variation and adaptive evolution in Bifidobacterium pseudocatenulatum: Insights into genomic and functional diversity in human gut.}, journal = {Food research international (Ottawa, Ont.)}, volume = {192}, number = {}, pages = {114840}, doi = {10.1016/j.foodres.2024.114840}, pmid = {39147525}, issn = {1873-7145}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Phylogeny ; *Genome, Bacterial ; *Bifidobacterium pseudocatenulatum/genetics/metabolism ; Genetic Variation ; Genomics ; Diet ; }, abstract = {Bifidobacterium pseudocatenulatum is a prevalent gut microbe in humans of all ages and plays a crucial role in host health. However, its adaptive evolutionary characteristics remain poorly understood. This study analyzed the genome of 247 B. pseudocatenulatum isolates from Chinese, Vietnamese, Japanese and other region populations using population genomics and functional genomics. Our findings revealed high genetic heterogeneity and regional clustering within B. pseudocatenulatum isolates. Significant differences were observed in genome characteristics, phylogeny, and functional genes. Specifically, Chinese and Vietnamese isolates exhibited a higher abundance of genes involved in the metabolism of plant-derived carbohydrates (GH13, GH43, and GH5 enzyme families), aligning with the predominantly vegetable-, wheat- and fruit-based diets of these populations. Additionally, we found widespread transmission of antibiotic resistance genes (tetO and tetW) through mobile genetic elements, such as genomic islands (GIs), resulting in substantial intra-regional differences. Our findings highlight distinct adaptive evolution in B. pseudocatenulatum driven by gene specialization, possibly in response to regional variations in diet and lifestyle. This study sheds light on bifidobacteria colonization mechanisms in the host gut. IMPORTANCE: Gut microbiota, as a key link in the gut-brain axis, helps to maintain the health of the organism, among which, Bifidobacterium pseudocatenulatum (B. pseudocatenulatum) is an important constituent member of the gut microbiota, which plays an important role in maintaining the balance of gut microbiota. The probiotic properties of B. pseudocatenulatum have been widely elaborated, and in order to excavate its evolutionary features at the genomic level, here we focused on the genetic background and evolutionary mechanism of the B. pseudocatenulatum genomes isolated from the intestinal tracts of different populations. Ultimately, based on the phylogenetic tree, we found that B. pseudocatenulatum has high genetic diversity and regional clustering phenomenon, in which plant-derived carbohydrate metabolism genes (GH13, GH43, GH5) showed significant regional differences, and this genetic differentiation drove the adaptive evolution, which likely shaped by diet and lifestyle.}, } @article {pmid39144201, year = {2024}, author = {Pramanik, S and Sil, AK}, title = {Anti-foam cell activity of metabolites of a bacterium isolated from yogurt.}, journal = {Food science and biotechnology}, volume = {33}, number = {11}, pages = {2597-2610}, pmid = {39144201}, issn = {2092-6456}, abstract = {UNLABELLED: Existing literature documents the beneficial effects of probiotics against atherosclerosis, a major cause of human death. However, it suffers from a serious limitation due to horizontal gene transfer. Therefore, currently, efforts are targeted to examine the beneficial effects of metabolites obtained from probiotics. In this context, the current study isolated a bacterium from yogurt and investigated the effect of its metabolites on foam cell formation, a key event for developing atherosclerosis. Results showed that the cell-free conditioned medium (CM) of this isolate and di-chloro methane extract of CM (CME) not only prevented the formation but also reduced the level of preformed foam cells. To understand the mechanism, the GC-MS study revealed the presence of compounds known to exert anti-atherogenic activities like anti-oxidant, anti-NF-κB, and lipolytic activities. Consistently, CME exhibited substantial anti-oxidant and anti-NF-κB activity. In conclusion, metabolites of this bacterium have anti-atherogenic activities and thus have therapeutic potential.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-023-01515-7.}, } @article {pmid39141729, year = {2024}, author = {Lai, S and Wang, H and Bork, P and Chen, WH and Zhao, XM}, title = {Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts.}, journal = {Science advances}, volume = {10}, number = {33}, pages = {eadn3316}, doi = {10.1126/sciadv.adn3316}, pmid = {39141729}, issn = {2375-2548}, mesh = {*Bacteriophages/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/virology/genetics ; *Gene Transfer, Horizontal ; Metagenomics/methods ; Genetic Variation ; Virome/genetics ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; }, abstract = {Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here, we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By using virome-enriched long-read metagenomic sequencing across 91 individuals, we identified a total of 14,438 nonredundant phage SVs and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Notably, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibit a higher frequency of genetic exchange with bacterial chromosomes and then virulent phages. Collectively, our findings provide insights into the genetic landscape of the human gut phageome.}, } @article {pmid39141562, year = {2024}, author = {Karan, J and Mandal, S and Khan, G and Arya, H and Samhita, L}, title = {Enhanced Extraction of Low-Molecular Weight DNA from Wastewater for Comprehensive Assessment of Antimicrobial Resistance.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {209}, pages = {}, doi = {10.3791/66899}, pmid = {39141562}, issn = {1940-087X}, mesh = {*Wastewater/microbiology/chemistry ; Polyethylene Glycols/chemistry ; Molecular Weight ; DNA, Bacterial/genetics/isolation & purification ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Environmental surveillance is recognized as an important tool for assessing public health in the post-pandemic era. Water, in particular wastewater, has emerged as the source of choice to sample pathogen burdens in the environment. Wastewater from open drains and community water treatment plants is a reservoir of both pathogens and antimicrobial resistance (AMR) genes, and frequently comes in contact with humans. While there are many methods of tracking AMR from water, isolating good-quality DNA at high yields from heterogeneous samples remains a challenge. To compensate, sample volumes often need to be high, creating practical constraints. Additionally, environmental DNA is frequently fragmented, and the sources of AMR (plasmids, phages, linear DNA) consist of low-molecular-weight DNA. Yet, few extraction processes have focused on methods for high-yield extraction of linear and low-molecular-weight DNA. Here, a simple method for high-yield linear DNA extraction from small volumes of wastewater using the precipitation properties of polyethylene glycol (PEG) is reported. This study makes a case for increasing overall DNA yields from water samples collected for metagenomic analyses by enriching the proportion of linear DNA. In addition, enhancing low-molecular-weight DNA overcomes the current problem of under-sampling environmental AMR due to a focus on high-molecular-weight and intracellular DNA. This method is expected to be particularly useful when extracellular DNA exists but at low concentrations, such as with effluents from treatment plants. It should also enhance the environmental sampling of AMR gene fragments that spread through horizontal gene transfer.}, } @article {pmid39096644, year = {2024}, author = {Wu, Q and Wu, GG and Pan, KN and Wang, XP and Li, HY and Tian, Z and Jin, RC and Fan, NS}, title = {Beta-blocker drives the conjugative transfer of multidrug resistance genes in pure and complex biological systems.}, journal = {Journal of hazardous materials}, volume = {477}, number = {}, pages = {135403}, doi = {10.1016/j.jhazmat.2024.135403}, pmid = {39096644}, issn = {1873-3336}, mesh = {*Metoprolol ; *Plasmids/genetics ; *Conjugation, Genetic/drug effects ; Drug Resistance, Multiple, Bacterial/genetics/drug effects ; Adrenergic beta-Antagonists/pharmacology ; Gene Transfer, Horizontal ; Bacteria/genetics/drug effects/metabolism ; Anti-Bacterial Agents/pharmacology ; Genes, MDR/genetics ; Microbiota/drug effects ; }, abstract = {Drug resistance poses a high risk to human health. Extensive use of non-antibiotic drugs contributes to antibiotic resistance genes (ARGs) transfer. However, how they affect the spread of broad-host plasmids in complex biological systems remains unknown. This study investigated the effect of metoprolol on the transfer frequency and host range of ARGs in both intrageneric and intergeneric pure culture systems, as well as in anammox microbiome. The results showed that environmental concentrations of metoprolol significantly promoted the intrageneric and intergeneric conjugative transfer. Initially, metoprolol induced excessive oxidative stress, resulting in high cell membrane permeability and bacterial SOS response. Meanwhile, more pili formation increased the adhesion and contact between bacteria, and the abundance of conjugation-related genes also increased significantly. Activation of the electron transport chain provided more ATP for this energy-consuming process. The underlying mechanism was further verified in the complex anammox conjugative system. Metoprolol induced the enrichment of ARGs and mobile genetic elements. The enhanced bacterial interaction and energy generation facilitated the high conjugative transfer frequency of ARGs. In addition, plasmid-borne ARGs tended to transfer to opportunistic pathogens. This work raises public concerns about the health and ecological risks of non-antibiotic drugs.}, } @article {pmid39139006, year = {2024}, author = {Rao, Y and Wang, Y and Zhang, H and Wang, Y and He, Q and Yuan, X and Guo, J and Chen, H}, title = {A Strategy of Killing Two Birds With One Stone for Blocking Drug Resistance Spread With Engineered Bdellovibrio bacteriovorus.}, journal = {Advanced materials (Deerfield Beach, Fla.)}, volume = {}, number = {}, pages = {e2406910}, doi = {10.1002/adma.202406910}, pmid = {39139006}, issn = {1521-4095}, support = {21935008//National Natural Science Foundation of China/ ; SKJY2021042//Livelihood Technology Project of Suzhou/ ; 23KJA150008//Jiangsu Province Higher Education Natural Science Research Major Project/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; }, abstract = {Drug-resistant pathogens significantly threaten human health and life. Simply killing drug-resistant pathogens cannot effectively eliminate their threat since the drug-resistant genes (DRGs) released from dead drug-resistant pathogens are difficult to eliminate and can further spread via horizontal gene transfer, leading to the spread of drug resistance. The development of antibacterial materials with sterilization and DRGs cleavage activities is highly crucial. Herein, a living system, Ce-PEA@Bdello, is fabricated with bacterial killing and DRGs cleavage activities for blocking bacterial drug resistance dissemination by engineered Bdellovibrio bacteriovorus (Bdello). Ce-PEA@Bdello is obtained by engineering Bdello with dopamine and a multinuclear cerium (IV) complex. Ce-PEA@Bdello can penetrate and eliminate kanamycin-resistant P. aeruginosa (Kan[R]) biofilms via the synergistic effect of predatory Bdello and photothermal polydopamine under near-infrared light. Additionally, the DNase-mimicking ability of Ce-PEA@Bdello endows it with genome and plasmid DNA cleavage ability. An in vivo study reveals that Ce-PEA@Bdello can eliminate P. aeruginosa (Kan[R]) and cleave DRGs in scald/burn infected wounds to block the spread of drug resistance and accelerate wound healing. This bioactive system constructed from natural living materials offers a promising means for blocking the spread of drug resistance.}, } @article {pmid39135654, year = {2024}, author = {Winter, M and Vos, M and Buckling, A and Johnsen, PJ and Harms, K}, title = {Effect of chemotherapeutic agents on natural transformation frequency in Acinetobacter baylyi.}, journal = {Access microbiology}, volume = {6}, number = {7}, pages = {}, pmid = {39135654}, issn = {2516-8290}, abstract = {Natural transformation is the ability of a bacterial cell to take up extracellular DNA which is subsequently available for recombination into the chromosome (or maintenance as an extrachromosomal element). Like other mechanisms of horizontal gene transfer, natural transformation is a significant driver for the dissemination of antimicrobial resistance. Recent studies have shown that many pharmaceutical compounds such as antidepressants and anti-inflammatory drugs can upregulate transformation frequency in the model species Acinetobacter baylyi. Chemotherapeutic compounds have been shown to increase the abundance of antimicrobial resistance genes and increase colonization rates of potentially pathogenic bacteria in patient gastrointestinal tracts, indicating an increased risk of infection and providing a pool of pathogenicity or resistance genes for transformable commensal bacteria. We here test for the effect of six cancer chemotherapeutic compounds on A. baylyi natural transformation frequency, finding two compounds, docetaxel and daunorubicin, to significantly decrease transformation frequency, and daunorubicin to also decrease growth rate significantly. Enhancing our understanding of the effect of chemotherapeutic compounds on the frequency of natural transformation could aid in preventing the horizontal spread of antimicrobial resistance genes.}, } @article {pmid39132438, year = {2024}, author = {Liu, H and Fan, S and Zhang, X and Yuan, Y and Zhong, W and Wang, L and Wang, C and Zhou, Z and Zhang, S and Geng, Y and Peng, G and Wang, Y and Zhang, K and Yan, Q and Luo, Y and Shi, K and Zhong, Z}, title = {Antibiotic-resistant characteristics and horizontal gene transfer ability analysis of extended-spectrum β-lactamase-producing Escherichia coli isolated from giant pandas.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1394814}, pmid = {39132438}, issn = {2297-1769}, abstract = {Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) is regarded as one of the most important priority pathogens within the One Health interface. However, few studies have investigated the occurrence of ESBL-EC in giant pandas, along with their antibiotic-resistant characteristics and horizontal gene transfer abilities. In this study, we successfully identified 12 ESBL-EC strains (8.33%, 12/144) out of 144 E. coli strains which isolated from giant pandas. We further detected antibiotic resistance genes (ARGs), virulence-associated genes (VAGs) and mobile genetic elements (MGEs) among the 12 ESBL-EC strains, and the results showed that 13 ARGs and 11 VAGs were detected, of which bla CTX-M (100.00%, 12/12, with 5 variants observed) and papA (83.33%, 10/12) were the most prevalent, respectively. And ISEcp1 (66.67%, 8/12) and IS26 (66.67%, 8/12) were the predominant MGEs. Furthermore, horizontal gene transfer ability analysis of the 12 ESBL-EC showed that all bla CTX-M genes could be transferred by conjugative plasmids, indicating high horizontal gene transfer ability. In addition, ARGs of rmtB and sul2, VAGs of papA, fimC and ompT, MGEs of ISEcp1 and IS26 were all found to be co-transferred with bla CTX-M. Phylogenetic analysis clustered these ESBL-EC strains into group B2 (75.00%, 9/12), D (16.67%, 2/12), and B1 (8.33%, 1/12), and 10 sequence types (STs) were identified among 12 ESBL-EC (including ST48, ST127, ST206, ST354, ST648, ST1706, and four new STs). Our present study showed that ESBL-EC strains from captive giant pandas are reservoirs of ARGs, VAGs and MGEs that can co-transfer with bla CTX-M via plasmids. Transmissible ESBL-EC strains with high diversity of resistance and virulence elements are a potential threat to humans, animals and surrounding environment.}, } @article {pmid39128935, year = {2024}, author = {Wang, W and Ge, Q and Wen, J and Zhang, H and Guo, Y and Li, Z and Xu, Y and Ji, D and Chen, C and Guo, L and Xu, M and Shi, C and Fan, G and Xie, C}, title = {Horizontal gene transfer and symbiotic microorganisms regulate the adaptive evolution of intertidal algae, Porphyra sense lato.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {976}, pmid = {39128935}, issn = {2399-3642}, support = {42176117//National Natural Science Foundation of China (National Science Foundation of China)/ ; U21A20265//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32100514//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Symbiosis/genetics ; *Porphyra/microbiology/genetics ; Adaptation, Physiological/genetics ; Phylogeny ; Biological Evolution ; }, abstract = {Intertidal algae may adapt to environmental challenges by acquiring genes from other organisms and relying on symbiotic microorganisms. Here, we obtained a symbiont-free and chromosome-level genome of Pyropia haitanensis (47.2 Mb), a type of intertidal algae, by using multiple symbiont screening methods. We identified 286 horizontal gene transfer (HGT) genes, 251 of which harbored transposable elements (TEs), reflecting the importance of TEs for facilitating the transfer of genes into P. haitanensis. Notably, the bulked segregant analysis revealed that two HGT genes, sirohydrochlorin ferrochelatase and peptide-methionine (R)-S-oxide reductase, play a significant role in the adaptation of P. haitanensis to heat stress. Besides, we found Pseudomonas, Actinobacteria, and Bacteroidetes are the major taxa among the symbiotic bacteria of P. haitanensis (nearly 50% of the HGT gene donors). Among of them, a heat-tolerant actinobacterial strain (Saccharothrix sp.) was isolated and revealed to be associated with the heat tolerance of P. haitanensis through its regulatory effects on the genes involved in proline synthesis (proC), redox homeostasis (ggt), and protein folding (HSP20). These findings contribute to our understanding of the adaptive evolution of intertidal algae, expanding our knowledge of the HGT genes and symbiotic microorganisms to enhance their resilience and survival in challenging intertidal environments.}, } @article {pmid39127705, year = {2024}, author = {Park, H and Bulzu, PA and Shabarova, T and Kavagutti, VS and Ghai, R and Kasalický, V and Jezberová, J}, title = {Uncovering the genomic basis of symbiotic interactions and niche adaptations in freshwater picocyanobacteria.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {150}, pmid = {39127705}, issn = {2049-2618}, support = {20‑12496X//Grantová Agentura Ceské Republiky (GAČR)/ ; 20‑12496X//Grantová Agentura Ceské Republiky (GAČR)/ ; 23-05081S//Grantová Agentura Ceské Republiky (GAČR)/ ; 19-23261S//Grantová Agentura Ceské Republiky (GAČR)/ ; 20‑12496X//Grantová Agentura Ceské Republiky (GAČR)/ ; 19-23261S//Grantová Agentura Ceské Republiky (GAČR)/ ; 19-23261S//Grantová Agentura Ceské Republiky (GAČR)/ ; }, mesh = {*Symbiosis ; *Fresh Water/microbiology ; *Genome, Bacterial ; *Phylogeny ; *Cyanobacteria/genetics/classification ; Adaptation, Physiological/genetics ; Europe ; Ecosystem ; Gene Transfer, Horizontal ; Genomics ; }, abstract = {BACKGROUND: Picocyanobacteria from the genera Prochlorococcus, Synechococcus, and Cyanobium are the most widespread photosynthetic organisms in aquatic ecosystems. However, their freshwater populations remain poorly explored, due to uneven and insufficient sampling across diverse inland waterbodies.

RESULTS: In this study, we present 170 high-quality genomes of freshwater picocyanobacteria from non-axenic cultures collected across Central Europe. In addition, we recovered 33 genomes of their potential symbiotic partners affiliated with four genera, Pseudomonas, Mesorhizobium, Acidovorax, and Hydrogenophaga. The genomic basis of symbiotic interactions involved heterotrophs benefiting from picocyanobacteria-derived nutrients while providing detoxification of ROS. The global abundance patterns of picocyanobacteria revealed ecologically significant ecotypes, associated with trophic status, temperature, and pH as key environmental factors. The adaptation of picocyanobacteria in (hyper-)eutrophic waterbodies could be attributed to their colonial lifestyles and CRISPR-Cas systems. The prevailing CRISPR-Cas subtypes in picocyanobacteria were I-G and I-E, which appear to have been acquired through horizontal gene transfer from other bacterial phyla.

CONCLUSIONS: Our findings provide novel insights into the population diversity, ecology, and evolutionary strategies of the most widespread photoautotrophs within freshwater ecosystems. Video Abstract.}, } @article {pmid39125965, year = {2024}, author = {Sadowska-Bartosz, I and Bartosz, G}, title = {Antioxidant Defense in the Toughest Animals on the Earth: Its Contribution to the Extreme Resistance of Tardigrades.}, journal = {International journal of molecular sciences}, volume = {25}, number = {15}, pages = {}, pmid = {39125965}, issn = {1422-0067}, mesh = {Animals ; *Tardigrada/metabolism/genetics ; *Antioxidants/metabolism ; Oxidative Stress ; Earth, Planet ; Trehalose/metabolism ; }, abstract = {Tardigrades are unique among animals in their resistance to dehydration, mainly due to anhydrobiosis and tun formation. They are also very resistant to high-energy radiation, low and high temperatures, low and high pressure, and various chemical agents, Interestingly, they are resistant to ionizing radiation both in the hydrated and dehydrated states to a similar extent. They are able to survive in the cosmic space. Apparently, many mechanisms contribute to the resistance of tardigrades to harmful factors, including the presence of trehalose (though not common to all tardigrades), heat shock proteins, late embryogenesis-abundant proteins, tardigrade-unique proteins, DNA repair proteins, proteins directly protecting DNA (Dsup and TDR1), and efficient antioxidant system. Antioxidant enzymes and small-molecular-weight antioxidants are an important element in the tardigrade resistance. The levels and activities of many antioxidant proteins is elevated by anhydrobiosis and UV radiation; one explanation for their induction during dehydration is provided by the theory of "preparation for oxidative stress", which occurs during rehydration. Genes coding for some antioxidant proteins are expanded in tardigrades; some genes (especially those coding for catalases) were hypothesized to be of bacterial origin, acquired by horizontal gene transfer. An interesting antioxidant protein found in tardigrades is the new Mn-dependent peroxidase.}, } @article {pmid39125866, year = {2024}, author = {Cheng, X and Liu, X and Jordan, KW and Yu, J and Whitworth, RJ and Park, Y and Chen, MS}, title = {Frequent Acquisition of Glycoside Hydrolase Family 32 (GH32) Genes from Bacteria via Horizontal Gene Transfer Drives Adaptation of Invertebrates to Diverse Sources of Food and Living Habitats.}, journal = {International journal of molecular sciences}, volume = {25}, number = {15}, pages = {}, pmid = {39125866}, issn = {1422-0067}, mesh = {*Gene Transfer, Horizontal ; *Glycoside Hydrolases/genetics/metabolism ; Animals ; *Bacteria/genetics/enzymology ; *Phylogeny ; Invertebrates/genetics ; Adaptation, Physiological/genetics ; Ecosystem ; Evolution, Molecular ; }, abstract = {Glycoside hydrolases (GHs, also called glycosidases) catalyze the hydrolysis of glycosidic bonds in polysaccharides. Numerous GH genes have been identified from various organisms and are classified into 188 families, abbreviated GH1 to GH188. Enzymes in the GH32 family hydrolyze fructans, which are present in approximately 15% of flowering plants and are widespread across microorganisms. GH32 genes are rarely found in animals, as fructans are not a typical carbohydrate source utilized in animals. Here, we report the discovery of 242 GH32 genes identified in 84 animal species, ranging from nematodes to crabs. Genetic analyses of these genes indicated that the GH32 genes in various animals were derived from different bacteria via multiple, independent horizontal gene transfer events. The GH32 genes in animals appear functional based on the highly conserved catalytic blades and triads in the active center despite the overall low (35-60%) sequence similarities among the predicted proteins. The acquisition of GH32 genes by animals may have a profound impact on sugar metabolism for the recipient organisms. Our results together with previous reports suggest that the acquired GH32 enzymes may not only serve as digestive enzymes, but also may serve as effectors for manipulating host plants, and as metabolic enzymes in the non-digestive tissues of certain animals. Our results provide a foundation for future studies on the significance of horizontally transferred GH32 genes in animals. The information reported here enriches our knowledge of horizontal gene transfer, GH32 functions, and animal-plant interactions, which may result in practical applications. For example, developing crops via targeted engineering that inhibits GH32 enzymes could aid in the plant's resistance to animal pests.}, } @article {pmid39125715, year = {2024}, author = {Bucka-Kolendo, J and Kiousi, DE and Dekowska, A and Mikołajczuk-Szczyrba, A and Karadedos, DM and Michael, P and Galanis, A and Sokołowska, B}, title = {Exploration of Alicyclobacillus spp. Genome in Search of Antibiotic Resistance.}, journal = {International journal of molecular sciences}, volume = {25}, number = {15}, pages = {}, pmid = {39125715}, issn = {1422-0067}, mesh = {*Alicyclobacillus/genetics/drug effects ; *Genome, Bacterial ; *Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Guaiacol/pharmacology/analogs & derivatives ; }, abstract = {The study investigates the antibiotic resistance (AR) profiles and genetic determinants in three strains of guaiacol-producing Alicyclobacillus spp. isolated from orchard soil and pears. Their phenotypic characteristics, such as spore formation; resistance to different factors, including drugs or disinfectants; or production of off-flavor compounds, can affect the taste and aroma of spoiled products. Food and beverages are potential vectors for the transfer of antibiotic resistance genes, which is a growing health concern; thus, microorganisms in food and beverages should not be a potential source of drug resistance to consumers. Whole-genome sequencing (WGS) was utilized to identify antibiotic resistance genes, metabolic pathways, and elements associated with guaiacol and halophenol production. Minimum inhibitory concentration (MIC) testing revealed that all strains were susceptible to eight out of nine tested antibiotics (ampicillin, gentamycin, kanamycin, streptomycin, clindamycin, tetracycline, chloramphenicol, and vancomycin) but exhibited high resistance to erythromycin. Analysis indicated that the erythromycin resistance gene, ribosomal RNA small subunit methyltransferase A (RsmA), was intrinsic and likely acquired through horizontal gene transfer (HGT). The comprehensive genomic analysis provides insights into the molecular mechanisms of antibiotic resistance in Alicyclobacillus spp., highlighting the potential risk of these bacteria as vectors for antibiotic resistance genes in the food chain. This study expands the understanding of the genetic makeup of these spoilage bacteria and their role in antimicrobial resistance dissemination.}, } @article {pmid39122691, year = {2024}, author = {Williams, SK and Jerlström Hultqvist, J and Eglit, Y and Salas-Leiva, DE and Curtis, B and Orr, RJS and Stairs, CW and Atalay, TN and MacMillan, N and Simpson, AGB and Roger, AJ}, title = {Extreme mitochondrial reduction in a novel group of free-living metamonads.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6805}, pmid = {39122691}, issn = {2041-1723}, support = {FRN-142349//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; }, mesh = {*Mitochondria/metabolism/genetics ; *Phylogeny ; *Proteome/metabolism/genetics ; Transcriptome ; Eukaryota/genetics/metabolism/classification ; Gene Transfer, Horizontal ; Iron-Sulfur Proteins/metabolism/genetics ; }, abstract = {Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered 'mitochondrion-related organelles' (MROs) with reduced functions, however the degree of reduction varies. Here, we generate high-quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we name the 'BaSk' (Barthelonids+Skoliomonads) clade, a deeply branching sister group to the Fornicata, a phylum that includes parasitic and free-living flagellates. Bioinformatic analyses of gene models shows that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system Fe/S cluster pathway by lateral gene transfer. One of the isolates, Skoliomonas litria, appears to have lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade demonstrates that mitochondrial functions may be completely lost even in free-living organisms.}, } @article {pmid37754684, year = {2023}, author = {Zhang, Y and Kitazumi, A and Liao, Y-T and de Los Reyes, BG and Wu, VCH}, title = {Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0022623}, pmid = {37754684}, issn = {2165-0497}, support = {2030-42000-0055-000-D//USDA | Agricultural Research Service (ARS)/ ; }, mesh = {*Bacteriophages/genetics ; *Gene Transfer, Horizontal ; *Metagenomics ; *Agriculture ; *Bacteria/genetics/virology/drug effects ; *Microbiota/genetics ; Metagenome ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; Drug Resistance, Bacterial/genetics ; Soil Microbiology ; }, abstract = {Antibiotic resistance has become a serious health concern worldwide. The potential impact of viruses, bacteriophages in particular, on spreading antibiotic resistance genes is still controversial due to the complexity of bacteriophage-bacterial interactions within diverse environments. In this study, we determined the microbiome profiles and the potential antibiotic resistance gene (ARG) transfer between bacterial and viral populations in different agricultural samples using a high-resolution analysis of the metagenomes. The results of this study provide compelling genetic evidence for ARG transfer through bacteriophage-bacteria interactions, revealing the inherent risks associated with bacteriophage-mediated ARG transfer across the agricultural microbiome.}, } @article {pmid39121985, year = {2024}, author = {Yan, Y and Lu, H and Liang, X and Xu, T and Yan, S and Yu, Y and Wang, Y}, title = {The virulence plasmid associated with AHPND in shrimp appears to have originated from Vibrio owensii through a process of homologous recombination of parental plasmids and the transposable insertion of two large fragments.}, journal = {Journal of invertebrate pathology}, volume = {}, number = {}, pages = {108173}, doi = {10.1016/j.jip.2024.108173}, pmid = {39121985}, issn = {1096-0805}, abstract = {Acute hepatopancreatic necrosis disease (AHPND) is a highly contagious and lethal disease of shrimp caused by Vibrio strains carrying the virulence plasmid (pAHPND) containing the pirAB virulence genes. Through analysis of plasmid sequence similarity, clustering, and phylogeny, a horizontal transfer element similar to IS91 was discovered within the pAHPND plasmid. Additionally, two distinct clades of plasmids related to pAHPND (designated as pAHPND-r1 and pAHPND-r2) were identified, which may serve as potential parental plasmids for pAHPND. The available evidence, including the difference in G+C content between the plasmid and its host, codon usage preference, and plasmid recombination event prediction, suggests that the formation of the pAHPND plasmid in the Vibrio owensii strain was likely due to the synergistic effect of the recombinase RecA and the associated proteins RecBCD on the pAHPND-r1 and pAHPND-r2, resulting in the recombination and formation of the precursor plasmid for pAHPND (pre-pAHPND). The emergence of pAHPND was found to be a result of successive insertions of the horizontal transfer elements of pirAB-Tn903 and IS91-like segment, which led to the deletion of one third of the pre-pAHPND. This plasmid was then able to spread horizontally to other Vibrio strains, contributing to the epidemics of AHPND. These findings shed light on previously unknown mechanisms involved in the emergence of pAHPND and improve our understanding of the disease's spread.}, } @article {pmid39119206, year = {2024}, author = {Zaer-Anaqz, Z and Khakvar, R and Mohammadi, SA and Bannazadeh Baghi, H and Koolivand, D}, title = {Physicochemical Characterization of Novel Bacteriophages of Pseudomonas syringe from Northwest Iran.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {5}, number = {2}, pages = {99-106}, pmid = {39119206}, issn = {2641-6549}, abstract = {Bacterial canker, caused by Pseudomonas syringae, is a devastating disease of stone fruit trees worldwide. The bacterium has a broad host range and a high capacity for adaptation and dissemination, owing to its high mutation rate and horizontal gene transfer. Traditional control methods based on copper compounds and antibiotics have resulted in the development of resistance in the bacterial population. Thus, alternative approaches are needed, such as phage therapy. This study aimed to characterize the physicochemical and biological properties of novel Pseudomonas syringae pv. syringae (Pss)-specific phages isolated from the soils of northwestern Iran. Seventy-five phage isolates were obtained, and their host range was determined against various bacterial pathogens. Five phages exhibiting the highest lytic activity against Pss and a narrow host range were selected for subsequent analysis. The stability of the selected phages was assessed under different conditions such as ultraviolet irradiation, temperature, pH, NaCl concentration, and chloroform exposure. The selected phages demonstrated significant effectiveness in vivo, exerting substantial suppression on the population of Pss. This reduction was observed for both individual phages and when the phages were utilized as a mixture. The findings indicate that phages have the potential to be used as biocontrol agents in agriculture.}, } @article {pmid39119203, year = {2024}, author = {Delesalle, VA and Ankeriasniemi, RE and Lewis, CM and Mody, JM and Roy, AM and Sarvis, WA and Vo, DD and Walsh, AE and Zappia, RJ}, title = {Introducing Casbah, Kronus, and MmasiCarm, Members of the Mycobacteriophage Subcluster B3.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {5}, number = {2}, pages = {84-90}, pmid = {39119203}, issn = {2641-6549}, abstract = {BACKGROUND: As part of a large science education effort, bacteriophages that lyse Mycobacterium smegmatis mc[2]155 continue to be discovered.

MATERIALS AND METHODS: Phages were isolated from soil samples from urban sites in the Northeastern United States. Their genomes were sequenced, assembled, and bioinformatically compared.

RESULTS: Three lytic siphoviruses belonging to subcluster B3 with high similarity to each other and other B3 mycobacteriophages were isolated. These phages contain double-stranded DNA genomes (68,754 to 69,495 bp) with high GC content (67.4-67.5%) and 102-104 putative protein coding genes. Notable features include a HicA-like toxin and 33 genes exclusive to subcluster B3. One phage had an intein in its terminase sequence.

CONCLUSIONS: Genomic analyses of these phages provide insights into genome evolution and horizontal gene transfer (HGT). The networks for HGT are apparently vast and gene specific. Interestingly, a number of genes are found in both B3 and Gordonia DR phages.}, } @article {pmid39117207, year = {2024}, author = {Erler, T and Droop, F and Lübbert, C and Knobloch, JK and Carlsen, L and Papan, C and Schwanz, T and Zweigner, J and Dengler, J and Hoffmann, M and Mutters, NT and Savin, M}, title = {Analysing carbapenemases in hospital wastewater: Insights from intracellular and extracellular DNA using qPCR and digital PCR.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {175344}, doi = {10.1016/j.scitotenv.2024.175344}, pmid = {39117207}, issn = {1879-1026}, abstract = {The widespread dissemination of carbapenem-resistant bacteria in wastewater systems, particularly from clinical sources, poses a significant public health risk. This study assessed the concentrations and distributions of extracellular DNA (exDNA) and intracellular DNA (iDNA) harboring carbapenemase genes in wastewater from six tertiary care hospitals in Germany. We collected a total of 36 samples, comprising six biological replicates from each hospital, and analysed them using quantitative real-time PCR (qPCR) and digital PCR (dPCR). The analysis targeted seven carbapenemase genes: blaNDM, blaKPC, blaIMP, blaVIM, blaOXA-23-like, blaOXA-48-like, and blaOXA-58-like across both DNA fractions. Our results revealed significant variability in the concentrations of exDNA and iDNA across the sampling sites, with iDNA typically present at higher concentrations. Using NanoDrop One spectrophotometry and the Qubit dsDNA kit, exDNA concentrations ranged from 2.7 to 7.7 ng/mL, while Qubit recorded lower values between 1.1 and 4.0 ng/mL. Conversely, iDNA concentrations were markedly higher, spanning from 42.3 to 191.7 ng/mL with NanoDrop and 12.0 to 46.5 ng/mL with Qubit, highlighting the variability between DNA types and quantification methods. Despite its lower concentrations, exDNA comprised up to 18.2 % of total DNA, highlighting its potential role in the horizontal transfer of antimicrobial resistance genes (ARGs). The study detected target ARGs in both DNA fractions at all sites, with notable differences in their concentrations; iDNA consistently exhibited higher levels of ARGs, with the highest concentrations reaching 10.57 ± 0.20 log gene copies per liter (GC/L) for blaVIM in iDNA and 6.96 ± 0.72 log GC/L for blaIMP in exDNA. dPCR demonstrated greater sensitivity than qPCR, especially effective for detecting low-abundance targets like blaOXA-23-like in the exDNA fraction. Additionally, qPCR's susceptibility to inhibition and contamination emphasizes the superior robustness of dPCR. This research highlights the need for improved monitoring and the implementation of advanced treatment technologies to mitigate ARG dissemination in wastewater.}, } @article {pmid39113256, year = {2024}, author = {Hossain, AKMZ and Chowdhury, AMMA}, title = {Understanding the Evolution and Transmission Dynamics of Antibiotic Resistance Genes: A Comprehensive Review.}, journal = {Journal of basic microbiology}, volume = {}, number = {}, pages = {e2400259}, doi = {10.1002/jobm.202400259}, pmid = {39113256}, issn = {1521-4028}, abstract = {Antibiotic resistance poses a formidable challenge to global public health, necessitating comprehensive understanding and strategic interventions. This review explores the evolution and transmission dynamics of antibiotic resistance genes, with a focus on Bangladesh. The indiscriminate use of antibiotics, compounded by substandard formulations and clinical misdiagnosis, fuels the emergence and spread of resistance in the country. Studies reveal high resistance rates among common pathogens, emphasizing the urgent need for targeted interventions and rational antibiotic use. Molecular assessments uncover a diverse array of antibiotic resistance genes in environmental reservoirs, highlighting the complex interplay between human activities and resistance dissemination. Horizontal gene transfer mechanisms, particularly plasmid-mediated conjugation, facilitate the exchange of resistance determinants among bacterial populations, driving the evolution of multidrug-resistant strains. The review discusses clinical implications, emphasizing the interconnectedness of environmental and clinical settings in resistance dynamics. Furthermore, bioinformatic and experimental evidence elucidates novel mechanisms of resistance gene transfer, underscoring the dynamic nature of resistance evolution. In conclusion, combating antibiotic resistance requires a multifaceted approach, integrating surveillance, stewardship, and innovative research to preserve the efficacy of antimicrobial agents and safeguard public health.}, } @article {pmid39103341, year = {2024}, author = {Hu, K and Chou, CW and Wilke, CO and Finkelstein, IJ}, title = {Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6653}, pmid = {39103341}, issn = {2041-1723}, support = {R01 GM124141/GM/NIGMS NIH HHS/United States ; R01GM088344//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 GM088344/GM/NIGMS NIH HHS/United States ; F-1808//Welch Foundation/ ; R01GM124141//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*DNA Transposable Elements/genetics ; *Escherichia coli/genetics/metabolism ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *Gene Transfer, Horizontal ; *CRISPR-Associated Proteins/metabolism/genetics ; Escherichia coli Proteins/genetics/metabolism ; }, abstract = {CASTs use both CRISPR-associated proteins and Tn7-family transposons for RNA-guided vertical and horizontal transmission. CASTs encode minimal CRISPR arrays but can't acquire new spacers. Here, we report that CASTs can co-opt defense-associated CRISPR arrays for horizontal transmission. A bioinformatic analysis shows that CASTs co-occur with defense-associated CRISPR systems, with the highest prevalence for type I-B and type V CAST sub-types. Using an E. coli quantitative transposition assay and in vitro reconstitution, we show that CASTs can use CRISPR RNAs from these defense systems. A high-resolution structure of the type I-F CAST-Cascade in complex with a type III-B CRISPR RNA reveals that Cas6 recognizes direct repeats via sequence-independent π - π interactions. In addition to using heterologous CRISPR arrays, type V CASTs can also transpose via an unguided mechanism, even when the S15 co-factor is over-expressed. Over-expressing S15 and the trans-activating CRISPR RNA or a single guide RNA reduces, but does not abrogate, off-target integration for type V CASTs. Our findings suggest that some CASTs may exploit defense-associated CRISPR arrays and that this fact must be considered when porting CASTs to heterologous bacterial hosts. More broadly, this work will guide further efforts to engineer the activity and specificity of CASTs for gene editing applications.}, } @article {pmid39102038, year = {2024}, author = {Olanrewaju, OS and Molale-Tom, LG and Bezuidenhout, CC}, title = {Genomic diversity, antibiotic resistance, and virulence in South African Enterococcus faecalis and Enterococcus lactis isolates.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {10}, pages = {289}, pmid = {39102038}, issn = {1573-0972}, mesh = {South Africa ; *Genome, Bacterial ; *Enterococcus faecalis/genetics/drug effects/pathogenicity/isolation & purification ; Virulence/genetics ; *Genetic Variation ; *Anti-Bacterial Agents/pharmacology ; *Virulence Factors/genetics ; Humans ; Drug Resistance, Bacterial/genetics ; Genomic Islands/genetics ; Gram-Positive Bacterial Infections/microbiology ; Enterococcus/genetics/drug effects/pathogenicity/isolation & purification/classification ; Phylogeny ; Gene Transfer, Horizontal ; Genomics ; Microbial Sensitivity Tests ; }, abstract = {This study presents the empirical findings of an in-depth genomic analysis of Enterococcus faecalis and Enterococcus lactis isolates from South Africa. It offers valuable insights into their genetic characteristics and their significant implications for public health. The study uncovers nuanced variations in the gene content of these isolates, despite their similar GC contents, providing a comprehensive view of the evolutionary diversity within the species. Genomic islands are identified, particularly in E. faecalis, emphasizing its propensity for horizontal gene transfer and genetic diversity, especially in terms of antibiotic resistance genes. Pangenome analysis reveals the existence of a core genome, accounting for a modest proportion of the total genes, with 2157 core genes, 1164 shell genes, and 4638 cloud genes out of 7959 genes in 52 South African E. faecalis genomes (2 from this study, 49 south Africa genomes downloaded from NCBI, and E. faecalis reference genome). Detecting large-scale genomic rearrangements, including chromosomal inversions, underscores the dynamic nature of bacterial genomes and their role in generating genetic diversity. The study uncovers an array of antibiotic resistance genes, with trimethoprim, tetracycline, glycopeptide, and multidrug resistance genes prevalent, raising concerns about the effectiveness of antibiotic treatment. Virulence gene profiling unveils a diverse repertoire of factors contributing to pathogenicity, encompassing adhesion, biofilm formation, stress resistance, and tissue damage. These empirical findings provide indispensable insights into these bacteria's genomic dynamics, antibiotic resistance mechanisms, and virulence potential, underlining the pressing need to address antibiotic resistance and implement robust control measures.}, } @article {pmid39101807, year = {2024}, author = {Dhurve, G and Behera, SR and Kodetham, G and Siddavattam, D}, title = {Outer membrane vesicles of Acinetobacter baumannii DS002 carry circular DNA similar to bovine meat and milk factors (BMMFs) and SPHINX 2.36 and probably play a role in interdomain lateral gene transfer.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0081724}, doi = {10.1128/spectrum.00817-24}, pmid = {39101807}, issn = {2165-0497}, abstract = {UNLABELLED: The discovery of Replication Competent Circular DNA molecules in mammalian cells and tissues is being linked to debilitating diseases, such as multiple sclerosis (MS), bovine spongiform encephalopathy (BSE), and colorectal cancer (CRC). These circular DNA molecules, otherwise known as bovine meat and milk factors (BMMFs) and Slow Progressive Hidden INfections of variable (X) latency (SPHINX), bear significant (80%) sequence similarity with the plasmids of Acinetobacter baumannii strains. Nanostructures, such as bacterial outer membrane vesicles (OMVs) serve as vehicles for transporting biomolecular cargo and have the potential to facilitate interkingdom lateral mobility of DNA. Strengthening the proposed hypothesis, this study demonstrates that OMVs derived from A. baumannii DS002 carrying four plasmids and genome (pTS236) of phage, AbDs1, successfully reached different parts of the body, including the central nervous system, following the injection of fluorescein isothiocyanate (FITC)-labeled OMVs into experimental mice. Out of the four OMV-associated plasmids, three (pTS4586, pTS9900, and pTS134338) were identified within the lumen, and the fourth one (pTS11291) was found on the surface of OMVs. In addition to the indigenous plasmids, the phage-encoded protein, Orf96, anchored on the surface of the OMVs by establishing a strong interaction with the OMV-associated porin, OmpA. Intriguingly, a subset of labeled OMVs, when incubated with Neuro2A cells, translocated across the membrane and reached to the cytoplasmic space of the cells. Collectively, the experimental evidence presented herein underscores the promising potential of OMVs as vehicles for delivering molecular cargo containing plasmids and phage genomes to diverse mammalian tissues and cells.

IMPORTANCE: Several independent studies have demonstrated the existence of replication competent circular DNA molecules of bacterial and viral origin in mammalian cells and tissues. However, studies about their origin and lateral mobility to mammalian cells are scarce. Our work describes the existence of circular DNA, similar to that of DNA molecules identified in mammalian cells, OMVs derived from soil isolate of A. baumannii DS002. Furthermore, the work also provides visual evidence that demonstrates the passage of labeled OMVs to different organs of experimental mice within hours after intravenously administering OMVs into experimental mice. Some of the labeled OMVs have even crossed the membrane of Neuro2A, suggesting the existence of interkingdom horizontal mobility between bacteria and mammals.}, } @article {pmid39101574, year = {2024}, author = {Rappaport, HB and Oliverio, AM}, title = {Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life.}, journal = {Genome biology and evolution}, volume = {16}, number = {8}, pages = {}, pmid = {39101574}, issn = {1759-6653}, mesh = {*Eukaryota/genetics ; *Extremophiles/genetics ; Adaptation, Physiological/genetics ; Genomics ; Genome ; Evolution, Molecular ; Phylogeny ; }, abstract = {From hydrothermal vents, to glaciers, to deserts, research in extreme environments has reshaped our understanding of how and where life can persist. Contained within the genomes of extremophilic organisms are the blueprints for a toolkit to tackle the multitude of challenges of survival in inhospitable environments. As new sequencing technologies have rapidly developed, so too has our understanding of the molecular and genomic mechanisms that have facilitated the success of extremophiles. Although eukaryotic extremophiles remain relatively understudied compared to bacteria and archaea, an increasing number of studies have begun to leverage 'omics tools to shed light on eukaryotic life in harsh conditions. In this perspective paper, we highlight a diverse breadth of research on extremophilic lineages across the eukaryotic tree of life, from microbes to macrobes, that are collectively reshaping our understanding of molecular innovations at life's extremes. These studies are not only advancing our understanding of evolution and biological processes but are also offering a valuable roadmap on how emerging technologies can be applied to identify cellular mechanisms of adaptation to cope with life in stressful conditions, including high and low temperatures, limited water availability, and heavy metal habitats. We shed light on patterns of molecular and organismal adaptation across the eukaryotic tree of life and discuss a few promising research directions, including investigations into the role of horizontal gene transfer in eukaryotic extremophiles and the importance of increasing phylogenetic diversity of model systems.}, } @article {pmid39100236, year = {2024}, author = {Bhattacharya, A and Aluquin, A and Kennedy, DA}, title = {Exceptions to the rule: When does resistance evolution not undermine antibiotic therapy in human bacterial infections?.}, journal = {Evolution letters}, volume = {8}, number = {4}, pages = {478-493}, pmid = {39100236}, issn = {2056-3744}, abstract = {The use of antibiotics to treat bacterial infections often imposes strong selection for antibiotic resistance. However, the prevalence of antibiotic resistance varies greatly across different combinations of pathogens and drugs. What underlies this variation? Systematic reviews, meta-analyses, and literature surveys capable of integrating data across many studies have tried to answer this question, but the vast majority of these studies have focused only on cases where resistance is common or problematic. Yet much could presumably be learned from the cases where resistance is infrequent or absent. Here we conducted a literature survey and a systematic review to study the evolution of antibiotic resistance across a wide range of pathogen-by-drug combinations (57 pathogens and 53 antibiotics from 15 drug classes). Using Akaike information criterion-based model selection and model-averaged parameter estimation we explored 14 different factors posited to be associated with resistance evolution. We find that the most robust predictors of high resistance are nosocomial transmission (i.e., hospital-acquired pathogens) and indirect transmission (e.g., vector-, water-, air-, or vehicle-borne pathogens). While the former was to be expected based on prior studies, the positive correlation between high resistance frequencies and indirect transmission is, to our knowledge, a novel insight. The most robust predictor of low resistance is zoonosis from wild animal reservoirs. We also found partial support that resistance was associated with pathogen type, horizontal gene transfer, commensalism, and human-to-human transmission. We did not find support for correlations between resistance and environmental reservoirs, mechanisms of drug action, and global drug use. This work explores the relative explanatory power of various pathogen and drug factors on resistance evolution, which is necessary to identify priority targets of stewardship efforts to slow the spread of drug-resistant pathogens.}, } @article {pmid39100235, year = {2024}, author = {Ciach, MA and Pawłowska, J and Górecki, P and Muszewska, A}, title = {The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities.}, journal = {Evolution letters}, volume = {8}, number = {4}, pages = {526-538}, pmid = {39100235}, issn = {2056-3744}, abstract = {Numerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand the hosts' metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided an extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), a similar characterization is still missing. In order to fill this gap, we have designed a computational pipeline to obtain a statistical sample of reliable HGT events with a low false discovery rate. We have analyzed 44 EDF proteomes and identified 829 xenologs in fungi ranging from Chytridiomycota to Mucoromycota. We have identified several patterns and statistical properties of EDF HGT. We show that HGT is driven by bursts of gene exchange and duplication, resulting in highly divergent numbers and molecular properties of xenologs between fungal lineages. Ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. Endosymbiotic bacteria can be a source of useful xenologs, as exemplified by NOD-like receptors transferred to Mortierellomycota. Closely related fungi have similar rates of intronization of xenologs. Posttransfer gene fusions and losses of protein domains are common and may influence the encoded proteins' functions. We argue that there is no universal approach for HGT identification and inter- and intra-kingdom transfers require tailored identification methods. Our results help to better understand how and to what extent HGT has shaped the metabolic, adaptive, and immune capabilities of fungi.}, } @article {pmid39098155, year = {2024}, author = {Wang, H and Gao, J and Ren, H and Zhao, Y and Wang, Y and An, J and Chen, H and Wang, Q}, title = {Whatever does not kill them makes them stronger: Using quaternary ammonia antimicrobials to alleviate the inhibition of ammonia oxidation under perfluorooctanoic acid stress.}, journal = {Water research}, volume = {263}, number = {}, pages = {122171}, doi = {10.1016/j.watres.2024.122171}, pmid = {39098155}, issn = {1879-2448}, abstract = {Perfluorooctanoic acid (PFOA), benzalkyl dimethylammonium compounds (BAC) and antibiotic resistance genes (ARGs) have negative effects on biological sewage treatment. The performance of nitrification systems under stress of PFOA (0.1-5 mg/L) or/and BAC (0.2-10 mg/L) was explored during 84-day experiments using four sequencing batch reactors, in this study. Low (0.1 mg/L) concentration PFOA had a positive influence on ammonia removal, while medium and high (2 and 5 mg/L) concentrations PFOA caused severe inhibition. Meanwhile, PFOA stress resulted in the enrichment of ARGs in water (w-ARGs). BAC (0-10 mg/L) had no obvious influence on ammonia removal. However, BAC promoted the reduction of ARGs and the bacterial community was the main participator (48.07%) for the spread of ARGs. Interestingly, the joint stress of PFOA and BAC increased the ammonia-oxidizing bacteria (AOB) activity from 5.81 ± 0.19 and 6.05 ± 0.79 mg N/(g MLSS·h) to 7.09 ± 0.87 and 7.23 ± 0.29 mg N/(g MLSS·h) in medium and high concentrations, compared to single stress of PFOA, which was observed for the first time. BAC could reduce bioavailability of PFOA through competitive adsorption and decreasing sludge hydrophobicity by the lower β-Sheet and α-Helix in tightly bound protein. Furthermore, the joint stress of PFOA and BAC was able to intensify the proliferation of w-ARGs and extracellular ARGs in sludge, and developed the most active horizontal gene transfer mediated by intl1 compared to single stress of PFOA or BAC. The batch tests verified the detoxification capacity of BAC on nitrification under 2.5 mg/L PFOA (48 h exposing), and the maximum alleviation of AOB activity was achieved at BAC and PFOA mass ratio of 2:1. In summary, BAC could be used to alleviate the inhibition of PFOA on ammonia oxidation, providing an efficient and sustainable approach in wastewater treatment.}, } @article {pmid39096995, year = {2024}, author = {Tian, J and Xu, L and Sun, JQ}, title = {Taxonomic characterization and comparative genomic analysis of a novel Devosia species revealed that phenolic acid-degrading traits are ubiquitous in the Devosia genus.}, journal = {Environmental research}, volume = {}, number = {}, pages = {119724}, doi = {10.1016/j.envres.2024.119724}, pmid = {39096995}, issn = {1096-0953}, abstract = {Phenolic acids (PAs) are widely distributed allelochemicals in various environments. To better understand the fate of PAs in environments, a halotolerant PAs-degrading bacterium (named strain RR2S18[T]) isolated from rhizosphere soil was identified as a novel species of Devosia, named Devosia rhizosphaerae sp. nov. The strain initially degraded PAs into central ring-fission intermediates (protocatechuic acid) using the CoA-dependent non-β-oxidation pathway. The produced ring-fission intermediates were then consecutively degraded by an ortho-cleavage reaction and the β-ketoadipic acid pathway. A comparative genomics analysis of 62 Devosia strains revealed that PAs-degrading genes were ubiquitous in their genomes, indicating that PAs degradation is universal among members of this genus. The analysis also suggested that the genes involved in CoA-dependent non-β-oxidation are inherent to Devosia strains, while those involved in ring-fission and β-ketoadipic acid pathways were obtained by horizontal gene transfer.}, } @article {pmid39095425, year = {2024}, author = {Landa, CR and Ariza-Mateos, A and Briones, C and Perales, C and Wagner, A and Domingo, E and Gómez, J}, title = {Adapting the rhizome concept to an extended definition of viral quasispecies and the implications for molecular evolution.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {17914}, pmid = {39095425}, issn = {2045-2322}, mesh = {*Rhizome/virology ; *Evolution, Molecular ; *Quasispecies/genetics ; *Phylogeny ; RNA Viruses/genetics/classification ; Gene Transfer, Horizontal ; Mutation ; Genome, Viral ; }, abstract = {The rhizome concept proposed by Gilles Deleuze and Félix Guattari offers a novel perspective on the organization and interdependence of complex constellations of heterogeneous entities, their mapping and their ruptures. The emphasis of the present study is placed on the dynamics of contacts and communication among such entities that arise from experimentation, without any favored hierarchy or origin. When applied to biological evolution, the rhizome concept integrates all types of heterogeneity resulting from "symbiotic" relationships among living beings (or their genomic material), horizontal genetic transfer, recombination and mutation, and breaks away from the approach that gives rise to the phylogenetic tree of life. It has already been applied to describe the dynamics and evolution of RNA viruses. Thus, here we introduce a novel framework for the interpretation the viral quasispecies concept, which explains the evolution of RNA virus populations as the result of dynamic interconnections and multifaceted interdependence between highly heterogeneous viral sequences and its inherently heterogeneous host cells. The rhizome network perspective underlines even further the medical implications of the broad mutant spectra of viruses that are in constant flow, given the multiple pathways they have available for fitness loss and gain.}, } @article {pmid39095161, year = {2025}, author = {Guo, Z and Tang, X and Wang, W and Luo, Z and Zeng, Y and Zhou, N and Yu, Z and Wang, D and Song, B and Zhou, C and Xiong, W}, title = {The photo-based treatment technology simultaneously removes resistant bacteria and resistant genes from wastewater.}, journal = {Journal of environmental sciences (China)}, volume = {148}, number = {}, pages = {243-262}, doi = {10.1016/j.jes.2024.01.005}, pmid = {39095161}, issn = {1001-0742}, mesh = {*Wastewater/chemistry ; *Waste Disposal, Fluid/methods ; Bacteria ; Disinfection/methods ; Drug Resistance, Bacterial/genetics ; Ultraviolet Rays ; Water Purification/methods ; }, abstract = {Because of the recent widespread usage of antibiotics, the acquisition and dissemination of antibiotic-resistance genes (ARGs) were prevalent in the majority of habitats. Generally, the biological wastewater treatment processes used in wastewater treatment plants have a limited efficiencies of antibiotics resistant bacteria (ARB) disinfection and ARGs degradation and even promote the proliferation of ARGs. Problematically, ARB and ARGs in effluent pose potential risks if they are not further treated. Photocatalytic oxidation is considered a promising disinfection technology, where the photocatalytic process generates many free radicals that enhance the interaction between light and deoxyribonucleic acid (DNA) for ARB elimination and subsequent degradation of ARGs. This review aims to illustrate the progress of photocatalytic oxidation technology for removing antibiotics resistant (AR) from wastewater in recent years. We discuss the sources and transfer of ARGs in wastewater. The overall removal efficiencies of ultraviolet radiation (UV)/chlorination, UV/ozone, UV/H2O2, and UV/sulfate-radical based system for ARB and ARGs, as well as the experimental parameters and removal mechanisms, are systematically discussed. The contribution of photocatalytic materials based on TiO2 and g-C3N4 to the inactivation of ARB and degradation of ARGs is highlighted, producing many free radicals to attack ARB and ARGs while effectively limiting the horizontal gene transfer (HGT) in wastewater. Finally, based on the reviewed studies, future research directions are proposed to realize specific photocatalytic oxidation technology applications and overcome current challenges.}, } @article {pmid39093595, year = {2024}, author = {Wu, J and Meng, L and Gaïa, M and Hikida, H and Okazaki, Y and Endo, H and Ogata, H}, title = {Gene transfer among viruses substantially contributes to gene gain of giant viruses.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msae161}, pmid = {39093595}, issn = {1537-1719}, abstract = {The phylum Nucleocytoviricota comprises a diverse group of double-stranded DNA viruses that display a wide range of gene repertoires. Although these gene repertoires determine the characteristics of individual viruses, the evolutionary processes that have shaped the gene repertoires of extant viruses since their common ancestor are poorly characterized. In this study, we aimed to address this gap in knowledge by using amalgamated likelihood estimation (ALE), a probabilistic tree reconciliation method that infers evolutionary scenarios by distinguishing origination, gene duplications, virus-to-virus horizontal gene transfer (vHGT), and gene losses. We analyzed over 4,700 gene families from 195 genomes spanning all known viral orders. The evolutionary reconstruction suggests a history of extensive gene gains and losses during the evolution of these viruses, notably with vHGT contributing to gene gains at a comparable level to duplications and originations. The vHGT frequently occurred between phylogenetically closely related viruses, as well as between distantly related viruses with an overlapping host range. We observed a pattern of massive gene duplications that followed vHGTs for gene families that was potentially related to host range control and virus-host arms race. These results suggest that vHGT represents a previously overlooked, yet important, evolutionary force that integrates the evolutionary paths of multiple viruses and affects shaping of Nucleocytoviricota virus gene repertoires.}, } @article {pmid39082809, year = {2024}, author = {Kanno, K and Kuriki, R and Yasuno, Y and Shinada, T and Ito, T and Hemmi, H}, title = {Archaeal mevalonate pathway in the uncultured bacterium Candidatus Promineifilum breve belonging to the phylum Chloroflexota.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0110624}, doi = {10.1128/aem.01106-24}, pmid = {39082809}, issn = {1098-5336}, abstract = {The archaeal mevalonate pathway is a recently discovered modified version of the eukaryotic mevalonate pathway. This pathway is widely conserved in archaea, except for some archaeal lineages possessing the eukaryotic or other modified mevalonate pathways. Although the pathway seems almost exclusive to the domain Archaea, the whole set of homologous genes of the pathway is found in the metagenome-assembled genome sequence of an uncultivated bacterium, Candidatus Promineifilum breve, of the phylum Chloroflexota. To prove the existence of the archaea-specific pathway in the domain Bacteria, we confirmed the activities of the enzymes specific to the pathway, phosphomevalonate dehydratase and anhydromevalonate phosphate decarboxylase, because only these two enzymes are absent in closely related Chloroflexota bacteria that possess a different type of modified mevalonate pathway. The activity of anhydromevalonate phosphate decarboxylase was evaluated by carotenoid production via the archaeal mevalonate pathway reconstituted in Escherichia coli cells, whereas that of phosphomevalonate dehydratase was confirmed by an in vitro assay using the recombinant enzyme after purification and iron-sulfur cluster reconstruction. Phylogenetic analyses of some mevalonate pathway-related enzymes suggest an evolutionary route for the archaeal mevalonate pathway in Candidatus P. breve, which probably involves horizontal gene transfer events.IMPORTANCEThe recent discovery of various modified mevalonate pathways in microorganisms, such as archaea and Chloroflexota bacteria, has shed light on the complexity of the evolution of metabolic pathways, including those involved in primary metabolism. The fact that the archaeal mevalonate pathway, which is almost exclusive to the domain Archaea, exists in a Chloroflexota bacterium provides valuable insights into the molecular evolution of the mevalonate pathways and associated enzymes. Putative genes probably involved in the archaeal mevalonate pathway have also been found in the metagenome-assembled genomes of Chloroflexota bacteria. Such genes can contribute to metabolic engineering for the bioproduction of valuable isoprenoids because the archaeal mevalonate pathway is known to be an energy-saving metabolic pathway that consumes less ATP than other mevalonate pathways do.}, } @article {pmid38823494, year = {2024}, author = {Tang, C and Shen, S and Yang, W and Shi, Q and Ding, L and Han, R and Hu, F}, title = {Dynamic evolution of ceftazidime-avibactam resistance from a single patient through the IncX3_NDM-5 plasmid transfer and blaKPC mutation.}, journal = {International journal of antimicrobial agents}, volume = {64}, number = {2}, pages = {107228}, doi = {10.1016/j.ijantimicag.2024.107228}, pmid = {38823494}, issn = {1872-7913}, mesh = {*Ceftazidime/pharmacology ; *Azabicyclo Compounds/pharmacology ; *Drug Combinations ; *Plasmids/genetics ; Humans ; *Klebsiella pneumoniae/genetics/drug effects ; *beta-Lactamases/genetics ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; *Enterobacter cloacae/genetics/drug effects ; *Mutation ; *Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/genetics/drug effects ; Klebsiella Infections/microbiology/drug therapy ; Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects ; }, abstract = {The rapid dissemination of carbapenem-resistant Enterobacterales (CRE) especially carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a great threat to global public health. Ceftazidime-avibactam, a novel β-lactam/β-lactamase inhibitor combination, has been widely used due to its excellent antibacterial activity against KPC-producing K. pneumoniae. However, several resistance mechanisms have been reported since its use. Here, we conducted a series of in vitro experiments to reveal and demonstrate the dynamic evolution of ceftazidime-avibactam resistance including interspecies IncX3_NDM-5 plasmid transfer between Enterobacter cloacae and K. pneumoniae and blaKPC mutation from blaKPC-2 to blaKPC-33. Through the analysis of conjugation frequency and fitness cost, the IncX3_NDM-5 plasmid in this study showed strong transmissibility and stability in E. coli EC600 and clinical strain K. pneumoniae 5298 as recipient strain. With increasing ceftazidime-avibactam concentration, the conjugation frequency remained at 10[-3]-10[-5], while the mutation frequency of K. pneumoniae 5298 was 10[-6]-10[-8] at the same concentration. Further plasmid analysis (the IncX3_NDM plasmid from this study and other 658 plasmids from the NCBI database) revealed the diverse origin and genetic structure of blaNDM-5 carrying plasmids. E. coli (42.9%), China (43.9%), IncX3 (66.6%) are the most common strains, regions, and Inc types respectively. By analysing of genetic environment detected in IncX3 plasmids, the dominant structures (168/258, 65.1%) were identified: ISKox3-IS26-blaNDM-5-IS5-ISAba125-Tn3000-Tn3. In additon, several structural variations were found in the core gene structure. In conclusion, the high fitness and transmissibility of the IncX3_NDM-5 plasmids were noteworthy. More importantly, the diverse ceftazidime-avibactam resistance mechanisms including blaNDM-5 tranfer and blaKPC-2 mutation highlighted the importance of the continuous monitoring of antimicrobial susceptibility and carbapenemases subtype during ceftazidime-avibactam treatment.}, } @article {pmid39080678, year = {2024}, author = {Rajput, M and Pandey, M and Dixit, R and Shukla, VK}, title = {Is cross-species horizontal gene transfer responsible for gallbladder carcinogenesis.}, journal = {World journal of surgical oncology}, volume = {22}, number = {1}, pages = {201}, pmid = {39080678}, issn = {1477-7819}, mesh = {Humans ; *Gene Transfer, Horizontal ; *Gallbladder Neoplasms/genetics/pathology/virology ; Carcinogenesis/genetics ; RNA, Antisense/genetics ; Gene Expression Regulation, Neoplastic ; Transcriptome ; }, abstract = {BACKGROUND: Cross-species horizontal gene transfer (HGT) involves the transfer of genetic material between different species of organisms. In recent years, mounting evidence has emerged that cross-species HGT does take place and may play a role in the development and progression of diseases.

METHODS: Transcriptomic data obtained from patients with gallbladder cancer (GBC) was assessed for the differential expression of antisense RNAs (asRNAs). The Basic Local Alignment Search Tool (BLAST) was used for cross-species analysis with viral, bacterial, fungal, and ancient human genomes to elucidate the evolutionary cross species origins of these differential asRNAs. Functional enrichment analysis and text mining were conducted and a network of asRNAs targeting mRNAs was constructed to understand the function of differential asRNAs better.

RESULTS: A total of 17 differentially expressed antisense RNAs (asRNAs) were identified in gallbladder cancer tissue compared to that of normal gallbladder. BLAST analysis of 15 of these asRNAs (AFAP1-AS1, HMGA2-AS1, MNX1-AS1, SLC2A1-AS1, BBOX1-AS1, ELFN1-AS1, TRPM2-AS, DNAH17-AS1, DCST1-AS1, VPS9D1-AS1, MIR1-1HG-AS1, HAND2-AS1, PGM5P4-AS1, PGM5P3-AS1, and MAGI2-AS) showed varying degree of similarities with bacterial and viral genomes, except for UNC5B-AS1 and SOX21-AS1, which were conserved during evolution. Two of these 15 asRNAs, (VPS9D1-AS1 and SLC2A1-AS1) exhibited a high degree of similarity with viral genomes (Chikungunya virus, Human immunodeficiency virus 1, Stealth virus 1, and Zika virus) and bacterial genomes including (Staphylococcus sp., Bradyrhizobium sp., Pasteurella multocida sp., and, Klebsiella pneumoniae sp.), indicating potential HGT during evolution.

CONCLUSION: The results provide novel evidence supporting the hypothesis that differentially expressed asRNAs in GBC exhibit varying sequence similarity with bacterial, viral, and ancient human genomes, indicating a potential shared evolutionary origin. These non-coding genes are enriched with methylation and were found to be associated with cancer-related pathways, including the P53 and PI3K-AKT signaling pathways, suggesting their possible involvement in tumor development.}, } @article {pmid39079455, year = {2024}, author = {Russell, SL and Penunuri, G and Condon, C}, title = {Diverse genetic conflicts mediated by molecular mimicry and computational approaches to detect them.}, journal = {Seminars in cell & developmental biology}, volume = {165}, number = {}, pages = {1-12}, doi = {10.1016/j.semcdb.2024.07.001}, pmid = {39079455}, issn = {1096-3634}, abstract = {In genetic conflicts between intergenomic and selfish elements, driver and killer elements achieve biased survival, replication, or transmission over sensitive and targeted elements through a wide range of molecular mechanisms, including mimicry. Driving mechanisms manifest at all organismal levels, from the biased propagation of individual genes, as demonstrated by transposable elements, to the biased transmission of genomes, as illustrated by viruses, to the biased transmission of cell lineages, as in cancer. Targeted genomes are vulnerable to molecular mimicry through the conserved motifs they use for their own signaling and regulation. Mimicking these motifs enables an intergenomic or selfish element to control core target processes, and can occur at the sequence, structure, or functional level. Molecular mimicry was first appreciated as an important phenomenon more than twenty years ago. Modern genomics technologies, databases, and machine learning approaches offer tremendous potential to study the distribution of molecular mimicry across genetic conflicts in nature. Here, we explore the theoretical expectations for molecular mimicry between conflicting genomes, the trends in molecular mimicry mechanisms across known genetic conflicts, and outline how new examples can be gleaned from population genomic datasets. We discuss how mimics involving short sequence-based motifs or gene duplications can evolve convergently from new mutations. Whereas, processes that involve divergent domains or fully-folded structures occur among genomes by horizontal gene transfer. These trends are largely based on a small number of organisms and should be reevaluated in a general, phylogenetically independent framework. Currently, publicly available databases can be mined for genotypes driving non-Mendelian inheritance patterns, epistatic interactions, and convergent protein structures. A subset of these conflicting elements may be molecular mimics. We propose approaches for detecting genetic conflict and molecular mimicry from these datasets.}, } @article {pmid39078126, year = {2024}, author = {Ai, C and Cui, P and Liu, C and Wu, J and Xu, Y and Liang, X and Yang, Q and Tang, X and Zhou, S and Liao, H and Friman, V-P}, title = {Viral and thermal lysis facilitates transmission of antibiotic resistance genes during composting.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0069524}, doi = {10.1128/aem.00695-24}, pmid = {39078126}, issn = {1098-5336}, abstract = {UNLABELLED: While the distribution of extracellular ARGs (eARGs) in the environment has been widely reported, the factors governing their release remain poorly understood. Here, we combined multi-omics and direct experimentation to test whether the release and transmission of eARGs are associated with viral lysis and heat during cow manure composting. Our results reveal that the proportion of eARGs increased 2.7-fold during composting, despite a significant and concomitant reduction in intracellular ARG abundances. This relative increase of eARGs was driven by composting temperature and viral lysis of ARG-carrying bacteria based on metagenome-assembled genome (MAG) analysis. Notably, thermal lysis of mesophilic bacteria carrying ARGs was a key factor in releasing eARGs at the thermophilic phase, while viral lysis played a relatively stronger role during the non-thermal phase of composting. Furthermore, MAG-based tracking of ARGs in combination with direct transformation experiments demonstrated that eARGs released during composting pose a potential transmission risk. Our study provides bioinformatic and experimental evidence of the undiscovered role of temperature and viral lysis in co-driving the spread of ARGs in compost microbiomes via the horizontal transfer of environmentally released DNA.

IMPORTANCE: The spread of antibiotic resistance genes (ARGs) is a critical global health concern. Understanding the factors influencing the release of extracellular ARGs (eARGs) is essential for developing effective strategies. In this study, we investigated the association between viral lysis, heat, and eARG release during composting. Our findings revealed a substantial increase in eARGs despite reduced intracellular ARG abundance. Composting temperature and viral lysis were identified as key drivers, with thermal lysis predominant during the thermophilic phase and viral lysis during non-thermal phases. Moreover, eARGs released during composting posed a transmission risk through horizontal gene transfer. This study highlights the significance of temperature and phage lysis in ARG spread, providing valuable insights for mitigating antibiotic resistance threats.}, } @article {pmid38598855, year = {2024}, author = {Hsieh, SC and Peters, JE}, title = {Natural and Engineered Guide RNA-Directed Transposition with CRISPR-Associated Tn7-Like Transposons.}, journal = {Annual review of biochemistry}, volume = {93}, number = {1}, pages = {139-161}, doi = {10.1146/annurev-biochem-030122-041908}, pmid = {38598855}, issn = {1545-4509}, mesh = {*DNA Transposable Elements/genetics ; *CRISPR-Cas Systems ; *RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; *Transposases/metabolism/genetics ; Gene Editing/methods ; Bacteria/genetics ; Plasmids/metabolism/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; }, abstract = {CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated nuclease) defense systems have been naturally coopted for guide RNA-directed transposition on multiple occasions. In all cases, cooption occurred with diverse elements related to the bacterial transposon Tn7. Tn7 tightly controls transposition; the transposase is activated only when special targets are recognized by dedicated target-site selection proteins. Tn7 and the Tn7-like elements that coopted CRISPR-Cas systems evolved complementary targeting pathways: one that recognizes a highly conserved site in the chromosome and a second pathway that targets mobile plasmids capable of cell-to-cell transfer. Tn7 and Tn7-like elements deliver a single integration into the site they recognize and also control the orientation of the integration event, providing future potential for use as programmable gene-integration tools. Early work has shown that guide RNA-directed transposition systems can be adapted to diverse hosts, even within microbial communities, suggesting great potential for engineering these systems as powerful gene-editing tools.}, } @article {pmid39073917, year = {2024}, author = {Gao, L and Liu, L and Lv, AP and Fu, L and Lian, ZH and Nunoura, T and Hedlund, BP and Xu, QY and Wu, D and Yang, J and Ali, M and Li, MM and Liu, YH and Antunes, A and Jiang, HC and Cheng, L and Jiao, JY and Li, WJ and Fang, BZ}, title = {Reversed oxidative TCA (roTCA) for carbon fixation by an Acidimicrobiia strain from a saline lake.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae147}, pmid = {39073917}, issn = {1751-7370}, abstract = {Acidimicrobiia are widely distributed in nature and suggested to be autotrophic via the Calvin-Benson-Bassham (CBB) cycle. However, direct evidence of chemolithoautotrophy in Acidimicrobiia is lacking. Here, we report a chemolithoautotrophic enrichment from a saline lake, and the subsequent isolation and characterization of a chemolithoautotroph, Salinilacustristhrix flava EGI L10123T, which belongs to a new Acidimicrobiia family. Although strain EGI L10123T is autotrophic, neither its genome nor Acidimicrobiia metagenome-assembled genomes (MAGs) from the enrichment culture encode genes necessary for the CBB cycle. Instead, genomic, transcriptomic, enzymatic, and stable-isotope probing data hinted at the activity of the reversed oxidative TCA (roTCA) coupled with the oxidation of sulfide as the electron donor. Phylogenetic analysis and ancestral character reconstructions of Acidimicrobiia suggested that the essential CBB gene rbcL was acquired through multiple horizontal gene transfer events from diverse microbial taxa. In contrast, genes responsible for sulfide- or hydrogen-dependent roTCA carbon fixation were already present in the last common ancestor of extant Acidimicrobiia. These findings imply the possibility of roTCA carbon fixation in Acidimicrobiia and the ecological importance of Acidimicrobiia. Further research in the future is necessary to confirm whether these characteristics are truly widespread across the clade.}, } @article {pmid39071422, year = {2024}, author = {Robinson, LR and Mcdevitt, CJ and Regan, MR and Quail, SL and Wadsworth, CB}, title = {In vitro evolution of ciprofloxacin resistance in Neisseria commensals and derived mutation population dynamics in natural Neisseria populations.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39071422}, issn = {2692-8205}, support = {R15 AI174182/AI/NIAID NIH HHS/United States ; }, abstract = {Commensal Neisseria are members of a healthy human oropharyngeal microbiome; however, they also serve as a reservoir of antimicrobial resistance for their pathogenic relatives. Despite their known importance as sources of novel genetic variation for pathogens, we still do not understand the full suite of resistance mutations commensal species can harbor. Here, we use in vitro selection to assess the mutations that emerge in response to ciprofloxacin selection in commensal Neisseria by passaging 4 replicates of 4 different species in the presence of a selective antibiotic gradient for 20 days; then categorized derived mutations with whole genome sequencing. 10/16 selected cells lines across the 4 species evolved ciprofloxacin resistance (≥ 1 ug/ml); with resistance-contributing mutations primarily emerging in DNA gyrase subunit A and B (gyrA and gyrB), topoisomerase IV subunits C and E (parC and parE), and the multiple transferable efflux pump repressor (mtrR). Of note, these derived mutations appeared in the same loci responsible for ciprofloxacin reduced susceptibility in the pathogenic Neisseria, suggesting conserved mechanisms of resistance across the genus. Additionally, we tested for zoliflodacin cross-resistance in evolved strain lines and found 6 lineages with elevated zoliflodacin minimum inhibitory concentrations. Finally, to interrogate the likelihood of experimentally derived mutations emerging and contributing to resistance in natural Neisseria, we used a population-based approach and identified GyrA 91I as a substitution circulating within commensal Neisseria populations and ParC 85C in a single gonococcal isolate. Small clusters of gonococcal isolates had commensal-like alleles at parC and parE, indicating recent cross-species recombination events.}, } @article {pmid39071318, year = {2024}, author = {Sloan, DB and Broz, AK and Kuster, SA and Muthye, V and Peñafiel-Ayala, A and Marron, JR and Lavrov, DV and Brieba, LG}, title = {Expansion of the MutS Gene Family in Plants.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.07.17.603841}, pmid = {39071318}, issn = {2692-8205}, abstract = {UNLABELLED: The MutS gene family is distributed across the tree of life and is involved in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded the set of MutS genes in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes. Land plants, green algae, red algae, and glaucophytes share cyanobacterial-like MutS1 and MutS2 genes that presumably were gained via plastid endosymbiotic gene transfer. MutS1 was subsequently lost in some taxa, including seed plants, whereas MutS2 was duplicated in Viridiplantae (i.e., land plants and green algae) with widespread retention of both resulting paralogs. Viridiplantae also have two anciently duplicated copies of the eukaryotic MSH6 gene (i.e., MSH6 and MSH7) and acquired MSH1 via horizontal gene transfer - potentially from a nucleocytovirus. Despite sharing the same name, "plant MSH1 " is not directly related to the gene known as MSH1 in some fungi and animals, which may be an ancestral eukaryotic gene acquired via mitochondrial endosymbiosis and subsequently lost in most eukaryotic lineages. There has been substantial progress in understanding the functions of MSH1 and MSH6 / MSH7 in plants, but the roles of the cyanobacterial-like MutS1 and MutS2 genes remain uncharacterized. Known functions of bacterial homologs and predicted protein structures, including fusions to diverse nuclease domains, provide hypotheses about potential molecular mechanisms. Because most plant-specific MutS proteins are targeted to the mitochondria and/or plastids, the expansion of this family appears to have played a large role in shaping plant organelle genetics.

ONE-SENTENCE SUMMARY: Plants are distinguished from other eukaryotes by a functionally diverse complement of MutS proteins gained via a combination of gene duplication, endosymbiotic gene transfer, and horizontal gene transfer.}, } @article {pmid38964386, year = {2024}, author = {Shi, J and Sun, C and An, T and Jiang, C and Mei, S and Lv, B}, title = {Unraveling the effect of micro/nanoplastics on the occurrence and horizontal transfer of environmental antibiotic resistance genes: Advances, mechanisms and future prospects.}, journal = {The Science of the total environment}, volume = {947}, number = {}, pages = {174466}, doi = {10.1016/j.scitotenv.2024.174466}, pmid = {38964386}, issn = {1879-1026}, mesh = {*Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Microplastics ; Anti-Bacterial Agents ; Bacteria/drug effects ; Genes, Bacterial ; }, abstract = {Microplastics can not only serve as vectors of antibiotic resistance genes (ARGs), but also they and even nanoplastics potentially affect the occurrence of ARGs in indigenous environmental microorganisms, which have aroused great concern for the development of antibiotic resistance. This article specifically reviews the effects of micro/nanoplastics (concentration, size, exposure time, chemical additives) and their interactions with other pollutants on environmental ARGs dissemination. The changes of horizontal genes transfer (HGT, i.e., conjugation, transformation and transduction) of ARGs caused by micro/nanoplastics were also summarized. Further, this review systematically sums up the mechanisms of micro/nanoplastics regulating HGT process of ARGs, including reactive oxygen species production, cell membrane permeability, transfer-related genes expression, extracellular polymeric substances production, and ARG donor-recipient adsorption/contaminants adsorption/biofilm formation. The underlying mechanisms in changes of bacterial communities induced by micro/nanoplastics were also discussed as it was an important factor for structuring the profile of ARGs in the actual environment, including causing environmental stress, providing carbon sources, forming biofilms, affecting pollutants distribution and environmental factors. This review contributes to a systematical understanding of the potential risks of antibiotic resistance dissemination caused by micro/nanoplastics and provokes thinking about perspectives for future research and the management of micro/nanoplastics and plastics.}, } @article {pmid39071313, year = {2024}, author = {Yang, XY and Shen, Z and Wang, C and Nakanishi, K and Fu, TM}, title = {DdmDE eliminates plasmid invasion by DNA-guided DNA targeting.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.07.20.604412}, pmid = {39071313}, issn = {2692-8205}, abstract = {Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, bacteria have developed various defense systems, including prokaryotic Argonautes (pAgo) and the D NA D efense M odule DdmDE system. Through biochemical analysis, structural determination, and in vivo plasmid clearance assays, we elucidate the assembly and activation mechanisms of DdmDE, which eliminates small, multicopy plasmids. We demonstrate that DdmE, a pAgo-like protein, acts as a catalytically inactive, DNA-guided, DNA-targeting defense module. In the presence of guide DNA, DdmE targets plasmids and recruits a dimeric DdmD, which contains nuclease and helicase domains. Upon binding to DNA substrates, DdmD transitions from an autoinhibited dimer to an active monomer, which then translocates along and cleaves the plasmids. Together, our findings reveal the intricate mechanisms underlying DdmDE-mediated plasmid clearance, offering fundamental insights into bacterial defense systems against plasmid invasions.}, } @article {pmid39067739, year = {2024}, author = {Chen, X and Song, X and Liang, Y and Wang, F and Pan, C and Wei, Z}, title = {Evaluation of the potential horizontal gene transfer ability during chicken manure and pig manure composting.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {124621}, doi = {10.1016/j.envpol.2024.124621}, pmid = {39067739}, issn = {1873-6424}, abstract = {Resistance genes have been identified as emerging pollutants due to their ability to rapidly spread in the environment through horizontal gene transfer (HGT). Microbial community serves as the pivotal factor influencing the frequency of HGT during manure composting. However, the characteristics of HGT in microbial community from different types of manure were unclear. Therefore, this study aimed to evaluate the potential risk of HGT in bacterial community through the co-composting of chicken manure and pig manure in different proportions. The experimental results showed that the abundance of sulfonamide antibiotic resistance genes and integrase genes was higher during pig manure composting than those during chicken manure composting. In addition, the addition of pig manure also increased resistance genes abundance during chicken manure composting. These results suggested that the potential HGT risk was greater during pig manure composting. Furthermore, microbial analysis of co-composting suggested bacterial community of pig manure was more competitive and adaptable than that of chicken manure. Ultimately, statistical analysis indicated that compared to chicken manure composting, the potential ability of HGT was greater during pig manure composting. This study provided the vital theoretical support and scientific guidance for mitigating the HGT risk during manure composting.}, } @article {pmid38920383, year = {2024}, author = {Rakibova, Y and Dunham, DT and Seed, KD and Freddolino, L}, title = {Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae.}, journal = {mSphere}, volume = {9}, number = {7}, pages = {e0001124}, doi = {10.1128/msphere.00011-24}, pmid = {38920383}, issn = {2379-5042}, support = {R35 GM128637/GM/NIGMS NIH HHS/United States ; R01AI127652//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2018257700//National Science Foundation (NSF)/ ; AI134678//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*Bacterial Proteins/genetics/metabolism ; *Vibrio cholerae/genetics/pathogenicity/metabolism ; *Gene Expression Regulation, Bacterial ; *Cholera/microbiology ; DNA-Binding Proteins/genetics/metabolism ; Humans ; Transcription, Genetic ; Virulence ; Virulence Factors/genetics ; Gene Transfer, Horizontal ; }, abstract = {UNLABELLED: Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control and expression of such genetic elements is critical for the bacteria to thrive in the different environmental niches they occupy. H-NS, the histone-like nucleoid structuring protein, is the best-studied xenogeneic silencer of HAEs in gamma-proteobacteria. Although H-NS and other highly abundant nucleoid-associated proteins (NAPs) have been shown to play important roles in regulating HAEs and virulence in model bacteria, we still lack a comprehensive understanding of how different NAPs modulate transcription in V. cholerae. By obtaining genome-wide measurements of protein occupancy and active transcription in a clinical isolate of V. cholerae, harboring recently discovered HAEs encoding for phage defense systems, we show that a lack of H-NS causes a robust increase in the expression of genes found in many HAEs. We further found that TsrA, a protein with partial homology to H-NS, regulates virulence genes primarily through modulation of H-NS activity. We also identified few sites that are affected by TsrA independently of H-NS, suggesting TsrA may act with diverse regulatory mechanisms. Our results demonstrate how the combinatorial activity of NAPs is employed by a clinical isolate of an important pathogen to regulate recently discovered HAEs.

IMPORTANCE: New strains of the bacterial pathogen Vibrio cholerae, bearing novel horizontally acquired elements (HAEs), frequently emerge. HAEs provide beneficial traits to the bacterium, such as antibiotic resistance and defense against invading bacteriophages. Xenogeneic silencers are proteins that help bacteria harness new HAEs and silence those HAEs until they are needed. H-NS is the best-studied xenogeneic silencer; it is one of the nucleoid-associated proteins (NAPs) in gamma-proteobacteria and is responsible for the proper regulation of HAEs within the bacterial transcriptional network. We studied the effects of H-NS and other NAPs on the HAEs of a clinical isolate of V. cholerae. Importantly, we found that H-NS partners with a small and poorly characterized protein, TsrA, to help domesticate new HAEs involved in bacterial survival and in causing disease. A proper understanding of the regulatory state in emerging isolates of V. cholerae will provide improved therapies against new isolates of the pathogen.}, } @article {pmid39067603, year = {2024}, author = {Miaomiao, L and Ikuro, K}, title = {Impact of chlorine disinfection on intracellular and extracellular antimicrobial resistance genes in wastewater treatment and water reclamation.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {175046}, doi = {10.1016/j.scitotenv.2024.175046}, pmid = {39067603}, issn = {1879-1026}, abstract = {Wastewater treatment plants and water reclamation facilities are reservoirs of antimicrobial resistance genes (ARGs). These ARGs are not limited solely to intracellular DNA (inARGs) but include extracellular DNA (exARGs) present in wastewater. The release of exARGs from cells can be exacerbated by treatment processes, including chlorine disinfection, which disrupts bacterial cells. Given the potential for exARGs to drive horizontal gene transfer and contribute to the proliferation of antimicrobial resistance, it is imperative to recognize these fractions as emerging environmental pollutants. In this study, we conducted a comprehensive year-long assessment of both inARGs and exARGs, further differentiating between dissolved exARGs (Dis_exARGs) and exARGs adsorbed onto particulate matter (Ads_exARGs), within a full-scale wastewater treatment and water reclamation facility. The results revealed that Ads_exARGs comprised up to 30 % of the total ARGs in raw sewage with high biomass content. Generally, treatments at low and high doses of chlorine increased the abundance of Dis_exARGs and Ads_exARGs. The fate of ARG levels that varied depending on the type of ARGs suggested variations in the susceptibility of the host bacteria to chlorination. Moreover, co-occurrence of several potential opportunistic pathogenic bacteria and ARGs were observed. Therefore, we propose higher doses of chlorination as a prerequisite for the effective removal of inARGs and exARGs.}, } @article {pmid39066295, year = {2024}, author = {Li, W and Tahiri, N}, title = {Host-Virus Cophylogenetic Trajectories: Investigating Molecular Relationships between Coronaviruses and Bat Hosts.}, journal = {Viruses}, volume = {16}, number = {7}, pages = {}, pmid = {39066295}, issn = {1999-4915}, support = {326911//Fonds de recherche du Québec/ ; RGPIN-2022-04322//Natural Sciences and Engineering Research Council/ ; }, mesh = {*Chiroptera/virology ; Animals ; *Phylogeny ; *Coronavirus/genetics/classification/physiology ; Evolution, Molecular ; Host-Pathogen Interactions/genetics ; Spike Glycoprotein, Coronavirus/genetics/metabolism ; Host Specificity ; Coronavirus Infections/virology ; }, abstract = {Bats, with their virus tolerance, social behaviors, and mobility, are reservoirs for emerging viruses, including coronaviruses (CoVs) known for genetic flexibility. Studying the cophylogenetic link between bats and CoVs provides vital insights into transmission dynamics and host adaptation. Prior research has yielded valuable insights into phenomena such as host switching, cospeciation, and other dynamics concerning the interaction between CoVs and bats. Nonetheless, a distinct gap exists in the current literature concerning a comparative cophylogenetic analysis focused on elucidating the contributions of sequence fragments to the co-evolution between hosts and viruses. In this study, we analyzed the cophylogenetic patterns of 69 host-virus connections. Among the 69 host-virus links examined, 47 showed significant cophylogeny based on ParaFit and PACo analyses, affirming strong associations. Focusing on two proteins, ORF1ab and spike, we conducted a comparative analysis of host and CoV phylogenies. For ORF1ab, the specific window ranged in multiple sequence alignment (positions 520-680, 770-870, 2930-3070, and 4910-5080) exhibited the lowest Robinson-Foulds (RF) distance (i.e., 84.62%), emphasizing its higher contribution in the cophylogenetic association. Similarly, within the spike region, distinct window ranges (positions 0-140, 60-180, 100-410, 360-550, and 630-730) displayed the lowest RF distance at 88.46%. Our analysis identified six recombination regions within ORF1ab (positions 360-1390, 550-1610, 680-1680, 700-1710, 2060-3090, and 2130-3250), and four within the spike protein (positions 10-510, 50-560, 170-710, and 230-730). The convergence of minimal RF distance regions with combination regions robustly affirms the pivotal role of recombination in viral adaptation to host selection pressures. Furthermore, horizontal gene transfer reveals prominent instances of partial gene transfer events, occurring not only among variants within the same host species but also crossing host species boundaries. This suggests a more intricate pattern of genetic exchange. By employing a multifaceted approach, our comprehensive strategy offers a nuanced understanding of the intricate interactions that govern the co-evolutionary dynamics between bat hosts and CoVs. This deeper insight enhances our comprehension of viral evolution and adaptation mechanisms, shedding light on the broader dynamics that propel viral diversity.}, } @article {pmid39061350, year = {2024}, author = {Drane, K and Sheehan, M and Whelan, A and Ariel, E and Kinobe, R}, title = {The Role of Wastewater Treatment Plants in Dissemination of Antibiotic Resistance: Source, Measurement, Removal and Risk Assessment.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {39061350}, issn = {2079-6382}, support = {2256.95982.2331//Townsville City Council, Townsville Australia/ ; }, abstract = {Antibiotic Resistance Genes (ARGs) are contaminants of emerging concern with marked potential to impact public and environmental health. This review focusses on factors that influence the presence, abundance, and dissemination of ARGs within Wastewater Treatment Plants (WWTPs) and associated effluents. Antibiotic-Resistant Bacteria (ARB) and ARGs have been detected in the influent and the effluent of WWTPs worldwide. Different levels of wastewater treatment (primary, secondary, and tertiary) show different degrees of removal efficiency of ARGs, with further differences being observed when ARGs are captured as intracellular or extracellular forms. Furthermore, routinely used molecular methodologies such as quantitative polymerase chain reaction or whole genome sequencing may also vary in resistome identification and in quantifying ARG removal efficiencies from WWTP effluents. Additionally, we provide an overview of the One Health risk assessment framework, as well as future strategies on how WWTPs can be assessed for environmental and public health impact.}, } @article {pmid39061343, year = {2024}, author = {Fahy, S and O'Connor, JA and Sleator, RD and Lucey, B}, title = {From Species to Genes: A New Diagnostic Paradigm.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {39061343}, issn = {2079-6382}, abstract = {Molecular diagnostics has the potential to revolutionise the field of clinical microbiology. Microbial identification and nomenclature have, for too long, been restricted to phenotypic characterisation. However, this species-level view fails to wholly account for genetic heterogeneity, a result of lateral gene transfer, mediated primarily by mobile genetic elements. This genetic promiscuity has helped to drive virulence development, stress adaptation, and antimicrobial resistance in several important bacterial pathogens, complicating their detection and frustrating our ability to control them. We argue that, as clinical microbiologists at the front line, we must embrace the molecular technologies that allow us to focus specifically on the genetic elements that cause disease rather than the bacterial species that express them. This review focuses on the evolution of microbial taxonomy since the introduction of molecular sequencing, the role of mobile genetic elements in antimicrobial resistance, the current and emerging assays in clinical laboratories, and the comparison of phenotypic versus genotypic analyses. In essence, it is time now to refocus from species to genes as part of a new diagnostic paradigm.}, } @article {pmid38032214, year = {2023}, author = {Kubori, T}, title = {A two-component system serves as a central hub for connecting energy metabolism and plasmid dissemination in bacteria.}, journal = {mBio}, volume = {14}, number = {6}, pages = {e0247423}, pmid = {38032214}, issn = {2150-7511}, support = {//Takeda Science Foundation (TSF)/ ; }, mesh = {*Plasmids/genetics ; *Acinetobacter baumannii/genetics/metabolism ; *Energy Metabolism/genetics ; *Conjugation, Genetic ; Bacterial Proteins/genetics/metabolism ; Type IV Secretion Systems/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Gene Expression Regulation, Bacterial ; }, abstract = {Mobile genetic elements such as conjugative plasmids play a key role in the acquisition of antibiotic resistance by pathogenic bacteria. Resistance genes on plasmids can be transferred between bacteria using specialized conjugation machinery. Acinetobacter baumannii, the most common bacterium associated with nosocomial infections, harbors a large conjugative plasmid that encodes a type IV secretion system (T4SS). Feng et al. recently found that the A. baumannii T4SS is specialized for plasmid transfer, suggesting that it may be involved in multidrug resistance (Z. Feng, L. Wang, Q. Guan, X. Chu, and Z.-Q. Luo, mBio e02276-23, 2023, https://doi.org/10.1128/mbio.02276-23), T4SS-encoding genes are shown to be controlled by a versatile GacA/S two-component regulatory system. GacA/S is also found to regulate genes involved in central metabolism. The coordinated regulation of metabolism and plasmid conjugation may be a bacterial strategy for adapting to selective pressure from antibiotics.}, } @article {pmid39061274, year = {2024}, author = {Ghazawi, A and Anes, F and Mouftah, S and Elbediwi, M and Baig, A and Alketbi, M and Almazrouei, F and Alhashmi, M and Alzarooni, N and Manzoor, A and Habib, I and Strepis, N and Nabi, A and Khan, M}, title = {Genomic Study of High-Risk Clones of Enterobacter hormaechei Collected from Tertiary Hospitals in the United Arab Emirates.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, doi = {10.3390/antibiotics13070592}, pmid = {39061274}, issn = {2079-6382}, support = {G00004620 and G00004164//United Arab Emirates University/ ; }, abstract = {Enterobacter hormaechei has emerged as a significant pathogen within healthcare settings due to its ability to develop multidrug resistance (MDR) and survive in hospital environments. This study presents a genome-based analysis of carbapenem-resistant Enterobacter hormaechei isolates from two major hospitals in the United Arab Emirates. Eight isolates were subjected to whole-genome sequencing (WGS), revealing extensive resistance profiles including the blaNDM-1, blaOXA-48, and blaVIM-4 genes. Notably, one isolate belonging to ST171 harbored dual carbapenemase genes, while five isolates exhibited colistin resistance without mcr genes. The presence of the type VI secretion system (T6SS), various adhesins, and virulence genes contributes to the virulence and competitive advantage of the pathogen. Additionally, our isolates (87.5%) possessed ampC β-lactamase genes, predominantly blaACT genes. The genomic context of blaNDM-1, surrounded by other resistance genes and mobile genetic elements, highlights the role of horizontal gene transfer (HGT) in the spread of resistance. Our findings highlight the need for rigorous surveillance, strategic antibiotic stewardship, and hospital-based WGS to manage and mitigate the spread of these highly resistant and virulent pathogens. Accurate identification and monitoring of Enterobacter cloacae complex (ECC) species and their resistance mechanisms are crucial for effective infection control and treatment strategies.}, } @article {pmid39060998, year = {2024}, author = {Seth-Smith, H and Bommana, S and Dean, D and Read, TD and Marti, H}, title = {Chlamydia suis undergoes interclade recombination promoting Tet-island exchange.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {724}, pmid = {39060998}, issn = {1471-2164}, support = {323530_177579//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, abstract = {BACKGROUND: The obligate intracellular bacterial family Chlamydiaceae comprises a number of different species that cause disease in various vertebrate hosts including humans. Chlamydia suis, primarily found in the gastrointestinal tract of pigs, is the only species of the Chlamydiaceae family to have naturally gained tetracycline resistance (TetR), through a genomic island (Tet-island), integrated into the middle of chromosomal invasin-like gene inv. Previous studies have hypothesised that the uptake of the Tet-island from a host outside the Chlamydiaceae family was a unique event, followed by spread among C. suis through homologous recombination. In vitro recombination studies have shown that Tet-island exchange between C. suis strains is possible. Our aim in this study was to gain a deeper understanding of the interclade recombination of the Tet-island, among currently circulating C. suis field strains compared to in vitro-generated recombinants, using published whole genome sequences of C. suis field strains (n = 35) and in vitro-generated recombinants (n = 63).

RESULTS: We found that the phylogeny of inv better reflected the phylogeny of the Tet-island than that of the whole genome, supporting recombination rather than site-specific insertion as the means of transfer. There were considerable differences between the distribution of recombinations within in vitro-generated strains compared to that within the field strains. These differences are likely because in vitro-generated recombinants were selected for a tetracycline and rifamycin/rifampicin resistant background, leading to the largest peak of recombination across the Tet-island. Finally, we found that interclade recombinations across the Tet-island were more variable in length downstream of the Tet-island than upstream.

CONCLUSIONS: Our study supports the hypothesis that the occurrence of TetR strains in both clades of C. suis came about through interclade recombination after a single ancestral horizontal gene transfer event.}, } @article {pmid39058093, year = {2024}, author = {Peñil-Celis, A and Tagg, KA and Webb, HE and Redondo-Salvo, S and Francois Watkins, L and Vielva, L and Griffin, C and Kim, JY and Folster, JP and Garcillan-Barcia, MP and de la Cruz, F}, title = {Mobile genetic elements define the non-random structure of the Salmonella enterica serovar Typhi pangenome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0036524}, doi = {10.1128/msystems.00365-24}, pmid = {39058093}, issn = {2379-5077}, abstract = {Bacterial relatedness measured using select chromosomal loci forms the basis of public health genomic surveillance. While approximating vertical evolution through this approach has proven exceptionally valuable for understanding pathogen dynamics, it excludes a fundamental dimension of bacterial evolution-horizontal gene transfer. Incorporating the accessory genome is the logical remediation and has recently shown promise in expanding epidemiological resolution for enteric pathogens. Employing k-mer-based Jaccard index analysis, and a novel genome length distance metric, we computed pangenome (i.e., core and accessory) relatedness for the globally important pathogen Salmonella enterica serotype Typhi (Typhi), and graphically express both vertical (homology-by-descent) and horizontal (homology-by-admixture) evolutionary relationships in a reticulate network of over 2,200 U.S. Typhi genomes. This analysis revealed non-random structure in the Typhi pangenome that is driven predominantly by the gain and loss of mobile genetic elements, confirming and expanding upon known epidemiological patterns, revealing novel plasmid dynamics, and identifying avenues for further genomic epidemiological exploration. With an eye to public health application, this work adds important biological context to the rapidly improving ways of analyzing bacterial genetic data and demonstrates the value of the accessory genome to infer pathogen epidemiology and evolution.IMPORTANCEGiven bacterial evolution occurs in both vertical and horizontal dimensions, inclusion of both core and accessory genetic material (i.e., the pangenome) is a logical step toward a more thorough understanding of pathogen dynamics. With an eye to public, and indeed, global health relevance, we couple contemporary tools for genomic analysis with decades of research on mobile genetic elements to demonstrate the value of the pangenome, known and unknown, annotated, and hypothetical, for stratification of Salmonella enterica serovar Typhi (Typhi) populations. We confirm and expand upon what is known about Typhi epidemiology, plasmids, and antimicrobial resistance dynamics, and offer new avenues of exploration to further deduce Typhi ecology and evolution, and ultimately to reduce the incidence of human disease.}, } @article {pmid39056664, year = {2024}, author = {Aguirre-Carvajal, K and Munteanu, CR and Armijos-Jaramillo, V}, title = {Database Bias in the Detection of Interdomain Horizontal Gene Transfer Events in Pezizomycotina.}, journal = {Biology}, volume = {13}, number = {7}, pages = {}, doi = {10.3390/biology13070469}, pmid = {39056664}, issn = {2079-7737}, support = {PRG.BIO.23.14.01//Universidad de Las Américas/ ; }, abstract = {Horizontal gene transfer (HGT) is a widely acknowledged phenomenon in prokaryotes for generating genetic diversity. However, the impact of this process in eukaryotes, particularly interdomain HGT, is a topic of debate. Although there have been observed biases in interdomain HGT detection, little exploration has been conducted on the effects of imbalanced databases. In our study, we conducted experiments to assess how different databases affect the detection of interdomain HGT using proteomes from the Pezizomycotina fungal subphylum as our focus group. Our objective was to simulate the database imbalance commonly found in public biological databases, where bacterial and eukaryotic sequences are unevenly represented, and demonstrate that an increase in uploaded eukaryotic sequences leads to a decrease in predicted HGTs. For our experiments, four databases with varying proportions of eukaryotic sequences but consistent proportions of bacterial sequences were utilized. We observed a significant reduction in detected interdomain HGT candidates as the proportion of eukaryotes increased within the database. Our data suggest that the imbalance in databases bias the interdomain HGT detection and highlights challenges associated with confirming the presence of interdomain HGT among Pezizomycotina fungi and potentially other groups within Eukarya.}, } @article {pmid39053184, year = {2024}, author = {Checcucci, A and Buscaroli, E and Modesto, M and Luise, D and Blasioli, S and Scarafile, D and Di Vito, M and Bugli, F and Trevisi, P and Braschi, I and Mattarelli, P}, title = {The swine waste resistome: Spreading and transfer of antibiotic resistance genes in Escherichia coli strains and the associated microbial communities.}, journal = {Ecotoxicology and environmental safety}, volume = {283}, number = {}, pages = {116774}, doi = {10.1016/j.ecoenv.2024.116774}, pmid = {39053184}, issn = {1090-2414}, abstract = {The overuse of antimicrobials in livestock farming has led to the development of resistant bacteria and the spread of antibiotic-resistant genes (ARGs) among animals. When manure containing these antibiotics is applied to agricultural fields, it creates a selective pressure that promotes the acquisition of ARGs by bacteria, primarily through horizontal gene transfer. Most research on ARGs focuses on their role in clinical antibiotic resistance and their transfer from environmental sources to bacteria associated with humans, such as Escherichia coli. The study investigates the spread of antibiotic-resistant genes (ARGs) through class 1 integrons in 27 Escherichia coli strains from pig manure. It focuses on six common ARGs (ermB, cmlA, floR, qnrS, tetA, and TEM) and the class 1 integron gene, assessing their prevalence in manure samples from three pig farms. The study found correlations and anticorrelations among these genes, indicating a predisposition of the integron in spreading certain ARGs. Specifically, cmlA and tetA genes were positively correlated with each other and negatively with int1, suggesting they are not transferred via Int1. Farm B had the highest int1 counts and a higher abundance of the TEM gene, but lower levels of cmlA and tetA genes. The results underscore the complexity of predicting ARG spread in agricultural environments and the associated health risks to humans through the food chain. The study's results offer valuable insights into the antibiotic-resistant genes (ARGs) profile in swine livestock, potentially aiding in the development of methods to trace ARGs in the environment.}, } @article {pmid39052705, year = {2024}, author = {Wan, Y and Myall, AC and Boonyasiri, A and Bolt, F and Ledda, A and Mookerjee, S and Weiße, AY and Getino, M and Turton, JF and Abbas, H and Prakapaite, R and Sabnis, A and Abdolrasouli, A and Malpartida-Cardenas, K and Miglietta, L and Donaldson, H and Gilchrist, M and Hopkins, KL and Ellington, MJ and Otter, JA and Larrouy-Maumus, G and Edwards, AM and Rodriguez-Manzano, J and Didelot, X and Barahona, M and Holmes, AH and Jauneikaite, E and Davies, F}, title = {Integrated Analysis of Patient Networks and Plasmid Genomes to Investigate a Regional, Multispecies Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both blaIMP and mcr-9 Genes.}, journal = {The Journal of infectious diseases}, volume = {230}, number = {1}, pages = {e159-e170}, doi = {10.1093/infdis/jiae019}, pmid = {39052705}, issn = {1537-6613}, support = {//Faculty of Medicine, Siriraj Hospital, Mahidol University/ ; MR/T005254/1/MRC_/Medical Research Council/United Kingdom ; MRF-145-0004-TPG-AVISO/MRF/MRF/United Kingdom ; EP/N014529///EPSRC Centre for Mathematics of Precision Healthcare/ ; //National Institute for Health Research/ ; //Imperial Biomedical Research Centre/ ; //Rosetrees Trust/ ; M683//Stoneygate Trust/ ; /WT_/Wellcome Trust/United Kingdom ; PSN109//Imperial College London/ ; //Imperial Health Charity/ ; //NIHR Health Protection Research Unit in Genomics and Enabling Data/ ; //NIHR Health Protection Research Unit/ ; NIHR200915//University of Oxford/ ; //UK Health Security Agency/ ; }, mesh = {Humans ; *Plasmids/genetics ; *beta-Lactamases/genetics ; *Enterobacteriaceae Infections/epidemiology/microbiology/transmission ; *Disease Outbreaks ; *Bacterial Proteins/genetics ; London/epidemiology ; Anti-Bacterial Agents/pharmacology ; Phylogeny ; Genome, Bacterial ; Male ; Female ; Middle Aged ; Microbial Sensitivity Tests ; Adult ; Enterobacteriaceae/genetics/drug effects ; Aged ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation & purification ; Colistin/pharmacology ; }, abstract = {BACKGROUND: Carbapenemase-producing Enterobacterales (CPE) are challenging in healthcare, with resistance to multiple classes of antibiotics. This study describes the emergence of imipenemase (IMP)-encoding CPE among diverse Enterobacterales species between 2016 and 2019 across a London regional network.

METHODS: We performed a network analysis of patient pathways, using electronic health records, to identify contacts between IMP-encoding CPE-positive patients. Genomes of IMP-encoding CPE isolates were overlaid with patient contacts to imply potential transmission events.

RESULTS: Genomic analysis of 84 Enterobacterales isolates revealed diverse species (predominantly Klebsiella spp, Enterobacter spp, and Escherichia coli); 86% (72 of 84) harbored an IncHI2 plasmid carrying blaIMP and colistin resistance gene mcr-9 (68 of 72). Phylogenetic analysis of IncHI2 plasmids identified 3 lineages showing significant association with patient contacts and movements between 4 hospital sites and across medical specialties, which was missed in initial investigations.

CONCLUSIONS: Combined, our patient network and plasmid analyses demonstrate an interspecies, plasmid-mediated outbreak of blaIMPCPE, which remained unidentified during standard investigations. With DNA sequencing and multimodal data incorporation, the outbreak investigation approach proposed here provides a framework for real-time identification of key factors causing pathogen spread. Plasmid-level outbreak analysis reveals that resistance spread may be wider than suspected, allowing more interventions to stop transmission within hospital networks.SummaryThis was an investigation, using integrated pathway networks and genomics methods, of the emergence of imipenemase-encoding carbapenemase-producing Enterobacterales among diverse Enterobacterales species between 2016 and 2019 in patients across a London regional hospital network, which was missed on routine investigations.}, } @article {pmid39052112, year = {2024}, author = {Li, H and Liu, B and Li, M and Shen, M}, title = {Livestock and poultry breeding farms as a fixed and underestimated source of antibiotic resistance genes.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {39052112}, issn = {1614-7499}, abstract = {The excessive use of antibiotics, disinfectants, and drugs in livestock and poultry breeding has resulted in a rise in the presence of antibiotic resistance genes (ARGs). Antibiotic-resistant bacteria (ARB) and ARGs have been widely found in animal feces, farm wastewater, and farm air. ARGs can not only spread across media through adsorption and migration, but also transfer resistance across bacterial genera through horizontal gene transfer. Livestock breeding has become a fixed and unavoidable source of ARGs in the environment. Existing technologies for controlling ARGs, such as composting, disinfection, and sewage treatment, are not efficient in removing ARB and ARGs from waste. Furthermore, the remaining ARGs still possess a strong capacity for dissemination. At present, antibiotics used in animal husbandry are difficult to replace in a short period of time. The growth and potential risks of resistance genes in livestock and poultry breeding sources in the receiving environment are not yet clear. In this paper, we summarize the current situation of ARGs in the livestock and poultry breeding environment. We also explain the key environmental processes, main influencing factors, and corresponding ecological risks associated with ARGs in this environment. The advantages and disadvantages of current technologies for the removal of ARGs are primarily discussed. There is a particular emphasis on clarifying the spatiotemporal evolution patterns and environmental process mechanisms of ARGs, as well as highlighting the importance and urgency of developing efficient pollution control technologies.}, } @article {pmid39052074, year = {2024}, author = {Allman, ES and Baños, H and Garrote-Lopez, M and Rhodes, JA}, title = {Identifiability of Level-1 Species Networks from Gene Tree Quartets.}, journal = {Bulletin of mathematical biology}, volume = {86}, number = {9}, pages = {110}, pmid = {39052074}, issn = {1522-9602}, support = {DMS-2051760//National Science Foundation/ ; DMS-2331660//National Science Foundation/ ; P20GM103395//Foundation for the National Institutes of Health/ ; }, mesh = {*Phylogeny ; *Mathematical Concepts ; *Models, Genetic ; *Gene Transfer, Horizontal ; Evolution, Molecular ; Genetic Speciation ; Gene Regulatory Networks ; Computer Simulation ; Hybridization, Genetic ; }, abstract = {When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several recently proposed methods are based on quartet concordance factors-the probabilities that a tree relating a gene sampled from the species displays the possible 4-taxon relationships. Building on earlier results, we investigate what level-1 network features are identifiable from concordance factors under the network multispecies coalescent model. We obtain results on both topological features of the network, and numerical parameters, uncovering a number of failures of identifiability related to 3-cycles in the network. Addressing these identifiability issues is essential for designing statistically consistent inference methods.}, } @article {pmid39044460, year = {2024}, author = {Roulet, ME and Ceriotti, LF and Gatica-Soria, L and Sanchez-Puerta, MV}, title = {Horizontally transferred mitochondrial DNA tracts become circular by microhomology-mediated repair pathways.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.19984}, pmid = {39044460}, issn = {1469-8137}, support = {PICT2020-01018//Fondo para la Investigación Científica y Tecnológica/ ; 06/A092-T1//Secretaría de Investigación, Internacionales y Posgrado, Universidad Nacional de Cuyo/ ; }, abstract = {The holoparasitic plant Lophophytum mirabile exhibits remarkable levels of mitochondrial horizontal gene transfer (HGT). Gathering comparative data from other individuals and host plants can provide insights into the HGT process. We sequenced the mitochondrial genome (mtDNA) from individuals of two species of Lophophytum and from mimosoid hosts. We applied a stringent phylogenomic approach to elucidate the origin of the whole mtDNAs, estimate the timing of the transfers, and understand the molecular mechanisms involved. Ancestral and recent HGT events replaced and enlarged the multichromosomal mtDNA of Lophophytum spp., with the foreign DNA ascending to 74%. A total of 14 foreign mitochondrial chromosomes originated from continuous regions in the host mtDNA flanked by short direct repeats. These foreign tracts are circularized by microhomology-mediated repair pathways and replicate independently until they are lost or they eventually recombine with other chromosomes. The foreign noncoding chromosomes are variably present in the population and likely evolve by genetic drift. We present the 'circle-mediated HGT' model in which foreign mitochondrial DNA tracts become circular and are maintained as plasmid-like molecules. This model challenges the conventional belief that foreign DNA must be integrated into the recipient genome for successful HGT.}, } @article {pmid39042422, year = {2024}, author = {Alves, J and Dry, I and White, JH and Dryden, DTF and Lynskey, NN}, title = {Generation of tools for expression and purification of the phage-encoded Type I restriction enzyme inhibitor, Ocr.}, journal = {Microbiology (Reading, England)}, volume = {170}, number = {7}, pages = {}, doi = {10.1099/mic.0.001465}, pmid = {39042422}, issn = {1465-2080}, mesh = {*Recombinant Proteins/genetics/metabolism/isolation & purification ; Viral Proteins/genetics/metabolism ; Bacteriophages/genetics/enzymology ; Streptococcus pyogenes/genetics/enzymology/metabolism ; Transformation, Bacterial ; Deoxyribonucleases, Type I Site-Specific/metabolism/genetics ; Gene Expression ; Escherichia coli/genetics/metabolism ; }, abstract = {DNA manipulation is an essential tool in molecular microbiology research that is dependent on the ability of bacteria to take up and preserve foreign DNA by horizontal gene transfer. This process can be significantly impaired by the activity of bacterial restriction modification systems; bacterial operons comprising paired enzymatic activities that protectively methylate host DNA, while cleaving incoming unmodified foreign DNA. Ocr is a phage-encoded protein that inhibits Type I restriction modification systems, the addition of which significantly improves bacterial transformation efficiency. We recently established an improved and highly efficient transformation protocol for the important human pathogen group A Streptococcus using commercially available recombinant Ocr protein, manufacture of which has since been discontinued. In order to ensure the continued availability of Ocr protein within the research community, we have generated tools and methods for in-house Ocr production and validated the activity of the purified recombinant protein.}, } @article {pmid39039821, year = {2024}, author = {Bohl, V and Mogk, A}, title = {When the going gets tough, the tough get going-Novel bacterial AAA+ disaggregases provide extreme heat resistance.}, journal = {Environmental microbiology}, volume = {26}, number = {7}, pages = {e16677}, doi = {10.1111/1462-2920.16677}, pmid = {39039821}, issn = {1462-2920}, support = {MO970/7-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Bacterial Proteins/metabolism/genetics ; HSP70 Heat-Shock Proteins/metabolism/genetics ; Thermotolerance ; Hot Temperature ; Bacteria/genetics/metabolism ; Endopeptidase Clp/metabolism/genetics ; Heat-Shock Proteins/metabolism/genetics ; Heat-Shock Response ; }, abstract = {Heat stress can lead to protein misfolding and aggregation, potentially causing cell death due to the loss of essential proteins. Bacteria, being particularly exposed to environmental stress, are equipped with disaggregases that rescue these aggregated proteins. The bacterial Hsp70 chaperone DnaK and the ATPase associated with diverse cellular activities protein ClpB form the canonical disaggregase in bacteria. While this combination operates effectively during physiological heat stress, it is ineffective against massive aggregation caused by temperature-based sterilization protocols used in the food industry and clinics. This leaves bacteria unprotected against these thermal processes. However, bacteria that can withstand extreme, man-made stress conditions have emerged. These bacteria possess novel ATPase associated with diverse cellular activities disaggregases, ClpG and ClpL, which are key players in extreme heat resistance. These disaggregases, present in selected Gram-negative or Gram-positive bacteria, respectively, function superiorly by exhibiting increased thermal stability and enhanced threading power compared to DnaK/ClpB. This enables ClpG and ClpL to operate at extreme temperatures and process large and tight protein aggregates, thereby contributing to heat resistance. The genes for ClpG and ClpL are often encoded on mobile genomic islands or conjugative plasmids, allowing for their rapid spread among bacteria via horizontal gene transfer. This threatens the efficiency of sterilization protocols. In this review, we describe the various bacterial disaggregases identified to date, characterizing their commonalities and the specific features that enable these novel disaggregases to provide stress protection against extreme stress conditions.}, } @article {pmid39039101, year = {2024}, author = {Brown, CL and Maile-Moskowitz, A and Lopatkin, AJ and Xia, K and Logan, LK and Davis, BC and Zhang, L and Vikesland, PJ and Pruden, A}, title = {Author Correction: Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6166}, doi = {10.1038/s41467-024-50577-6}, pmid = {39039101}, issn = {2041-1723}, } @article {pmid39038713, year = {2024}, author = {Sun, B and Bai, Z and Li, R and Song, M and Zhang, J and Wang, J and Zhuang, X}, title = {Efficient elimination of antibiotic resistome in livestock manure by semi-permeable membrane covered hyperthermophilic composting.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {131134}, doi = {10.1016/j.biortech.2024.131134}, pmid = {39038713}, issn = {1873-2976}, abstract = {Livestock manure is a hotspot for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and an important contributor to antibiotic resistance in non-clinical settings. This study investigated the effectiveness and potential mechanisms of a novel composting technology, semi-permeable membrane covered hyperthermophilic composting (smHTC), in removal of ARGs and MGEs in chicken manure. Results showed that smHTC was more efficient in removal of ARGs and MGEs (92% and 93%) compared to conventional thermophilic composting (cTC) (76% and 92%). The efficient removal in smHTC is attributed to direct or indirect negative effects caused by the high temperature, including reducing the involvement of bio-available heavy metals (HMs) in co-selection processes of antibiotic resistance, decreasing the bacterial abundance and diversity, suppressing the horizontal gene transfer and killing potential ARGs hosts. Overall, smHTC can efficiently remove the resistome in livestock manure, reducing the risk to crops and humans from ARGs residues in compost products.}, } @article {pmid39038196, year = {2024}, author = {Mori, BA and Coutu, C and Erlandson, MA and Hegedus, DD}, title = {Exploring the contribution of the salivary gland and midgut to digestion in the swede midge (Contarinia nasturtii) through a genomics-guided approach.}, journal = {Archives of insect biochemistry and physiology}, volume = {116}, number = {3}, pages = {e22135}, doi = {10.1002/arch.22135}, pmid = {39038196}, issn = {1520-6327}, support = {//Alberta Canola Producers Commission/ ; //Alberta Barley Commission/ ; //Alberta Wheat Commission/ ; 545088//NSERC Industrial Research Chair/ ; RGPIN-2021-02479//NSERC/ ; //Agriculture & Agri-Food Canada Genomics Research and Development Initiative/ ; //Alberta Pulse Growers Commission/ ; }, mesh = {Animals ; *Salivary Glands/metabolism/enzymology ; *Larva/genetics/metabolism/growth & development ; *Diptera/genetics/enzymology/metabolism ; Transcriptome ; Digestion ; Genomics ; Gastrointestinal Tract/metabolism ; Insect Proteins/metabolism/genetics ; }, abstract = {The larvae of Contarinia nasturtii (Kieffer) (Diptera: Cecidomyiidae), the swede midge, targets the meristem of brassica crops where they induce the formation of galls and disrupt seed and vegetable production. Previously, we examined the salivary gland transcriptome of newly-hatched first instar larvae as they penetrated the host and initiated gall formation. Here we examine the salivary gland and midgut transcriptome of third instar larvae and provide evidence for cooperative nutrient acquisition beginning with secretion of enzymes and feeding facilitators followed by gastrointestinal digestion. Sucrose, presumably obtained from the phloem, appeared to be a major nutrient source as several α-glucosidases (sucrases, maltases) and β-fructofuranosidases (invertases) were identified. Genes encoding β-fructofuranosidases/invertases were among the most highly expressed in both tissues and represented two distinct gene families that may have originated via horizontal gene transfer from bacteria. The importance of the phloem as a nutrient source is underscored by the expression of genes encoding regucalcin and ARMET (arginine-rich mutated in early stages of tumor) which interfere with calcium signalling and prevent sieve tube occlusion. Lipids, proteins, and starch appear to serve as a secondary nutrient sources. Genes encoding enzymes involved in the detoxification of glucosinolates (myrosinases, arylsulfatases, and glutathione-S-transferases) were expressed indicative of Brassicaceae host specialization. The midgut expressed simple peritrophins and mucins typical of those found in Type II peritrophic matrices, the first such description for a gall midge.}, } @article {pmid39038013, year = {2024}, author = {Berg, A and Berntsson, RP and Barandun, J}, title = {Nematocida displodere mechanosensitive ion channel of small conductance 2 assembles into a unique 6-channel super-structure in vitro.}, journal = {PloS one}, volume = {19}, number = {7}, pages = {e0301951}, doi = {10.1371/journal.pone.0301951}, pmid = {39038013}, issn = {1932-6203}, mesh = {*Ion Channels/metabolism/chemistry/genetics ; *Cryoelectron Microscopy ; Animals ; Caenorhabditis elegans/metabolism/genetics ; Microsporidia/metabolism/genetics ; Mechanotransduction, Cellular ; }, abstract = {Mechanosensitive ion channels play an essential role in reacting to environmental signals and sustaining cell integrity by facilitating ion flux across membranes. For obligate intracellular pathogens like microsporidia, adapting to changes in the host environment is crucial for survival and propagation. Despite representing a eukaryote of extreme genome reduction, microsporidia have expanded the gene family of mechanosensitive ion channels of small conductance (mscS) through repeated gene duplication and horizontal gene transfer. All microsporidian genomes characterized to date contain mscS genes of both eukaryotic and bacterial origin. Here, we investigated the cryo-electron microscopy structure of the bacterially derived mechanosensitive ion channel of small conductance 2 (MscS2) from Nematocida displodere, an intracellular pathogen of Caenorhabditis elegans. MscS2 is the most compact MscS-like channel known and assembles into a unique superstructure in vitro with six heptameric MscS2 channels. Individual MscS2 channels are oriented in a heterogeneous manner to one another, resembling an asymmetric, flexible six-way cross joint. Finally, we show that microsporidian MscS2 still forms a heptameric membrane channel, however the extreme compaction suggests a potential new function of this MscS-like protein.}, } @article {pmid39037483, year = {2024}, author = {de Carvalho, A and Giambiagi-deMarval, M and Rossi, CC}, title = {Mammaliicoccus sciuri's Pan-Immune System and the Dynamics of Horizontal Gene Transfer Among Staphylococcaceae: a One-Health CRISPR Tale.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {}, number = {}, pages = {}, pmid = {39037483}, issn = {1976-3794}, support = {408564/2023-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 304839/2022-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; E-26/010.000172/2016; 010.00128/2016; E-26.210.875/2016//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 101056/2018; 001463/2019; 211.554/2019; 201.071/2020//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 200.895/2021//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; E-26/204.925/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; APQ-03498-22//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 23038.002486/2018-26//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {Recently emancipated from the Staphylococcus genus due to genomic differences, Mammaliicoccus sciuri, previously classified as an occasional pathogen, emerges as a significant player in the landscape of resistance gene dissemination among Staphylococcaceae. Despite its classification, its role remained enigmatic. In this study, we delved into the genomic repertoire of M. sciuri to unravel its contribution to resistance and virulence gene transfer in the context of One Health. Through comprehensive analysis of publicly available genomes, we unveiled a diverse pan-immune system adept at defending against exogenous genetic elements, yet concurrently fostering horizontal gene transfer (HGT). Specifically, exploration of CRISPR-Cas systems, with spacer sequences as molecular signatures, elucidated a global dissemination pattern spanning environmental, animal, and human hosts. Notably, we identified the integration of CRISPR-Cas systems within SCCmecs (Staphylococcal Cassette Chromosome mec), harboring key genes associated with pathogenicity and resistance, especially the methicillin resistance gene mecA, suggesting a strategic adaptation to outcompete other mobile genetic elements. Our findings underscored M. sciuri's active engagement in HGT dynamics and evolutionary trajectories within Staphylococcaceae, emphasizing its central role in shaping microbial communities and highlighting the significance of understanding its implications in the One Health framework, an interdisciplinary approach that recognizes the interconnectedness of human, animal, and environmental health to address global health challenges.}, } @article {pmid39035534, year = {2024}, author = {Gheorghe-Barbu, I and Surleac, M and Barbu, IC and Paraschiv, S and Bănică, LM and Rotaru, LI and Vrâncianu, CO and Niță Lazăr, M and Oțelea, D and Chifiriuc, MC}, title = {Decoding the resistome, virulome and mobilome of clinical versus aquatic Acinetobacter baumannii in southern Romania.}, journal = {Heliyon}, volume = {10}, number = {13}, pages = {e33372}, pmid = {39035534}, issn = {2405-8440}, abstract = {Acinetobacter baumannii, a notorious opportunistic pathogen, presents a formidable challenge in both clinical and environmental fields due to its resilience and ability to acquire resistance. This study undertook a comprehensive analysis of 183 A. baumannii isolates collected between 2019 and 2022 from intra-hospital infections (IHI), hospital sewages (Hs), wastewater treatment plants (WWTP), and adjacent river waters from two Southern cities, focusing on their resistome, virulome, and mobilome through isolation on chromogenic media, identification by MALDI-TOF-MS and antibiotic susceptibility testing by disk diffusion) followed by genotypic characterization [Whole Genome Sequencing (WGS), 3rd generation sequencing through the MinION (ONT) platform, pangenome description, and respectively horizontal gene transfer through conjugation assays]. Our findings reveal significant genomic plasticity and the prevalence of high-risk international clones, underlining the potential of these isolates to act as reservoirs for antibiotic resistance genes (ARGs) that could be dynamically exchanged between clinical and environmental settings through mobile genetic elements (MGEs) such as the pMAL1 plasmids and the critical role of WWTPs in the persistence and spread of A. baumannii. Moreover, our study presents the first report of the co-occurrence of bla OXA-23 and bla OXA-72 in A. baumannii ST2 clone. Thus, our research underscores the necessity for integrated surveillance and targeted interventions across healthcare and environmental sectors to mitigate the risk posed by this adaptable pathogen.}, } @article {pmid39030691, year = {2024}, author = {Gan, D and Lin, Z and Zeng, L and Deng, H and Walsh, TR and Zhou, S and Yang, QE}, title = {Housefly gut microbiomes as a reservoir and facilitator for the spread of antibiotic resistance.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae128}, pmid = {39030691}, issn = {1751-7370}, abstract = {Arthropods, such as houseflies, play a significant role on the dissemination of antimicrobial resistance (AMR); however, their impact has often been overlooked in comparison to other AMR vectors. Understanding the contribution of arthropods to the spread of AMR is critical for implementing robust policies to mitigate the spread of AMR across "One Health" sectors. Herein, we investigated the in-situ transfer of a gfp-labelled AMR plasmid (IncA/C carrying a mcr-8 gene, pA/C_MCR-8) in the gut microbiota of housefly (Musca domestica) by applying single-cell sorting, 16S rRNA gene amplicon sequencing, and whole genome sequencing. Our findings demonstrate that the pA/C_MCR-8 positive E. coli donor strain is capable of colonizing the gut microbiome of houseflies and persists in the housefly intestine for five days, however, no transfer was detectable above the detection threshold of 10-5 per cell. The conjugative plasmid, pA/C_MCR-8 demonstrated a high transfer frequency ranging from 4.1 × 10-3 to 5.0 × 10-3 per cell in vitro, and exhibited transfer across various bacterial phyla, primarily encompassing Pseudomonadota and Bacillota. Phylogenic analysis has revealed that Providencia stuartii, a human opportunistic pathogen, was a notable recipient of pA/C_MCR-8. The conjugation assays further revealed that newly formed P. stuartii transconjugants readily transfer pA/C_MCR-8 to other clinically relevant pathogens (e.g. Klebsiella pneumoniae). Our findings indicate the potential transfer of AMR plasmids from houseflies to human opportunistic pathogens and further advocates the adoption of a One Health approach in developing infection control policies that address AMR across clinical settings.}, } @article {pmid39030685, year = {2024}, author = {Echeveste Medrano, MJ and Leu, AO and Pabst, M and Lin, Y and Mcllroy, SJ and Tyson, GW and van Ede, J and Sánchez-Andrea, I and Jetten, MSM and Jansen, R and Welte, CU}, title = {Osmoregulation in freshwater anaerobic methane oxidizing archaea under salt stress.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae137}, pmid = {39030685}, issn = {1751-7370}, abstract = {Climate change-driven sea level rise threatens freshwater ecosystems and elicits salinity stress in microbiomes. Methane emissions in these systems are largely mitigated by methane-oxidizing microorganisms. Here, we characterized the physiological and metabolic response of freshwater methanotrophic archaea to salt stress. In our microcosm experiments, inhibition of methanotrophic archaea started at 1%. However, during gradual increase of salt up to 3% in a reactor over 12 weeks, the culture continued to oxidize methane. Using gene expression profiles and metabolomics, we identified a pathway for salt-stress response that produces the osmolyte of anaerobic methanotrophic archaea: N(ε)-acetyl-β-L-lysine. An extensive phylogenomic analysis on N(ε)-acetyl-β-L-lysine-producing enzymes revealed that they are widespread across both bacteria and archaea, indicating a potential horizontal gene transfer and a link to BORG extrachromosomal elements. Physicochemical analysis of bioreactor biomass further indicated the presence of sialic acids and the consumption of intracellular polyhydroxyalkanoates in anaerobic methanotrophs during salt stress.}, } @article {pmid39029947, year = {2024}, author = {Azizpour, A and Balaji, A and Treangen, TJ and Segarra, S}, title = {Graph-based self-supervised learning for repeat detection in metagenomic assembly.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.279136.124}, pmid = {39029947}, issn = {1549-5469}, abstract = {Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene duplication, and gene loss/gain complicate accurate genome assembly from metagenomic communities. Detecting repeats is a crucial first step in overcoming these challenges. To address this issue, we propose GraSSRep, a novel approach that leverages the assembly graph's structure through graph neural networks (GNNs) within a self-supervised learning framework to classify DNA sequences into repetitive and non-repetitive categories. Specifically, we frame this problem as a node classification task within a metagenomic assembly graph. In a self-supervised fashion, we rely on a high-precision (but low-recall) heuristic to generate pseudo-labels for a small proportion of the nodes. We then use those pseudo-labels to train a GNN embedding and a random forest classifier to propagate the labels to the remaining nodes. In this way, GraSSRep combines sequencing features with predefined and learned graph features to achieve state-of-the-art performance in repeat detection. We evaluate our method using simulated and synthetic metagenomic datasets. The results on the simulated data highlight our GraSSRep's robustness to repeat attributes, demonstrating its effectiveness in handling the complexity of repeated sequences. Additionally, our experiments with synthetic metagenomic datasets reveal that incorporating the graph structure and the GNN enhances our detection performance. Finally, in comparative analyses, GraSSRep outperforms existing repeat detection tools with respect to precision and recall.}, } @article {pmid37345922, year = {2023}, author = {Bosch, DE and Abbasian, R and Parajuli, B and Peterson, SB and Mougous, JD}, title = {Structural disruption of Ntox15 nuclease effector domains by immunity proteins protects against type VI secretion system intoxication in Bacteroidales.}, journal = {mBio}, volume = {14}, number = {4}, pages = {e0103923}, pmid = {37345922}, issn = {2150-7511}, support = {K08 AI159619/AI/NIAID NIH HHS/United States ; P30 GM124169/GM/NIGMS NIH HHS/United States ; R01 AI080609/AI/NIAID NIH HHS/United States ; S10 OD021832/OD/NIH HHS/United States ; }, mesh = {*Type VI Secretion Systems/metabolism/genetics ; *Bacterial Proteins/genetics/metabolism/chemistry/immunology ; Humans ; Gene Transfer, Horizontal ; }, abstract = {Bacteroidales use type VI secretion systems (T6SS) to competitively colonize and persist in the colon. We identify a horizontally transferred T6SS with Ntox15 family nuclease effector (Tde1) that mediates interbacterial antagonism among Bacteroidales, including several derived from a single human donor. Expression of cognate (Tdi1) or orphan immunity proteins in acquired interbacterial defense systems protects against Tde1-dependent attack. We find that immunity protein interaction induces a large effector conformational change in Tde nucleases, disrupting the active site and altering the DNA-binding site. Crystallographic snapshots of isolated Tde1, the Tde1/Tdi1 complex, and homologs from Phocaeicola vulgatus (Tde2/Tdi2) illustrate a conserved mechanism of immunity inserting into the central core of Tde, splitting the nuclease fold into two subdomains. The Tde/Tdi interface and immunity mechanism are distinct from all other polymorphic toxin-immunity interactions of known structure. Bacteroidales abundance has been linked to inflammatory bowel disease activity in prior studies, and we demonstrate that Tde and T6SS structural genes are each enriched in fecal metagenomes from ulcerative colitis subjects. Genetically mobile Tde1-encoding T6SS in Bacteroidales mediate competitive growth and may be involved in inflammatory bowel disease. Broad immunity is conferred by Tdi1 homologs through a fold-disrupting mechanism unique among polymorphic effector-immunity pairs of known structure. IMPORTANCE Bacteroidales are related to inflammatory bowel disease severity and progression. We identify type VI secretion system (T6SS) nuclease effectors (Tde) which are enriched in ulcerative colitis and horizontally transferred on mobile genetic elements. Tde-encoding T6SSs mediate interbacterial competition. Orphan and cognate immunity proteins (Tdi) prevent intoxication by multiple Tde through a new mechanism among polymorphic toxin systems. Tdi inserts into the effector central core, splitting Ntox15 into two subdomains and disrupting the active site. This mechanism may allow for evolutionary diversification of the Tde/Tdi interface as observed in colicin nuclease-immunity interactions, promoting broad neutralization of Tde by orphan Tdi. Tde-dependent T6SS interbacterial antagonism may contribute to Bacteroidales diversity in the context of ulcerative colitis.}, } @article {pmid39028534, year = {2024}, author = {da Rosa, EEB and Kremer, FS}, title = {The mobilome landscape of biocide-resistance in Brazilian ESKAPE isolates.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {39028534}, issn = {1678-4405}, support = {Coordenação de Aperfeiçoamento de Pessoal de Nível Superior//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {The increasing frequency of antibiotic-resistant bacteria is a constant threat to global human health. Therefore, the pathogens of the ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Enterobacter spp.) are among the most relevant causes of hospital infections responsible for millions of deaths every year. However, little has been explored about the danger of microorganisms resistant to biocides such as antiseptics and disinfectants. Widely used in domestic, industrial, and hospital environments, these substances reach the environment and can cause selective pressure for resistance genes and induce cross-resistance to antibiotics, further aggravating the problem. Therefore, it is necessary to use innovative and efficient strategies to monitor the spread of genes related to resistance to biocides. Whole genome sequencing and bioinformatics analysis aiming to search for sequences encoding resistance mechanisms are essential to help monitor and combat these pathogens. Thus, this work describes the construction of a bioinformatics tool that integrates different databases to identify gene sequences that may confer some resistance advantage about biocides. Furthermore, the tool analyzed all the genomes of Brazilian ESKAPE isolates deposited at NCBI and found a series of different genes related to resistance to benzalkonium chloride, chlorhexidine, and triclosan, which were the focus of this work. As a result, the presence of resistance genes was identified in different types of biological samples, environments, and hosts. Regarding mobile genetic elements (MGEs), around 52% of isolates containing genes related to resistance to these compounds had their genes identified in plasmids, and 48.7% in prophages. These data show that resistance to biocides can be a silent, underestimated danger spreading across different environments and, therefore, requires greater attention.}, } @article {pmid39025839, year = {2024}, author = {Nowell, RW and Rodriguez, F and Hecox-Lea, BJ and Mark Welch, DB and Arkhipova, IR and Barraclough, TG and Wilson, CG}, title = {Bdelloid rotifers deploy horizontally acquired biosynthetic genes against a fungal pathogen.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5787}, pmid = {39025839}, issn = {2041-1723}, support = {NE/J01933X/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/S010866/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/M01651X/1//RCUK | Natural Environment Research Council (NERC)/ ; LTF-733-2010//European Molecular Biology Organization (EMBO)/ ; R01GM111917//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R21AG046899//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; }, mesh = {*Gene Transfer, Horizontal ; Animals ; *Rotifera/genetics/metabolism ; Biosynthetic Pathways/genetics ; Peptide Synthases/genetics/metabolism ; Polyketides/metabolism ; Phylogeny ; Multigene Family ; }, abstract = {Coevolutionary antagonism generates relentless selection that can favour genetic exchange, including transfer of antibiotic synthesis and resistance genes among bacteria, and sexual recombination of disease resistance alleles in eukaryotes. We report an unusual link between biological conflict and DNA transfer in bdelloid rotifers, microscopic animals whose genomes show elevated levels of horizontal gene transfer from non-metazoan taxa. When rotifers were challenged with a fungal pathogen, horizontally acquired genes were over twice as likely to be upregulated as other genes - a stronger enrichment than observed for abiotic stressors. Among hundreds of upregulated genes, the most markedly overrepresented were clusters resembling bacterial polyketide and nonribosomal peptide synthetases that produce antibiotics. Upregulation of these clusters in a pathogen-resistant rotifer species was nearly ten times stronger than in a susceptible species. By acquiring, domesticating, and expressing non-metazoan biosynthetic pathways, bdelloids may have evolved to resist natural enemies using antimicrobial mechanisms absent from other animals.}, } @article {pmid39021167, year = {2024}, author = {Barcan, AS and Barcan, RA and Vamanu, E}, title = {Genomic Insights into Bacterial Antimicrobial Resistance Transmission and Mitigation Strategies.}, journal = {Current pharmaceutical biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113892010304596240629102419}, pmid = {39021167}, issn = {1873-4316}, abstract = {The rapid emergence and global spread of antimicrobial resistance in recent years have raised significant concerns about the future of modern medicine. Superbugs and multidrugresistant bacteria have become endemic in many parts of the world, raising the specter of untreatable infections. The overuse and misuse of antimicrobials over the past 80 years have undoubtedly contributed to the development of antimicrobial resistance, placing immense pressure on healthcare systems worldwide. Nonetheless, the molecular mechanisms underlying antimicrobial resistance in bacteria have existed since ancient times. Some of these mechanisms and processes have served as the precursors of current resistance determinants, highlighting the ongoing arms race between bacteria and their antimicrobial adversaries. Moreover, the environment harbors many putative resistance genes, yet we cannot still predict which of these genes will emerge and manifest as pathogenic resistance phenotypes. The presence of antibiotics in natural habitats, even at sub-inhibitory concentrations, may provide selective pressures that favor the emergence of novel antimicrobial resistance apparatus and, thus, underscores the need for a comprehensive understanding of the factors driving the persistence and spread of antimicrobial resistance. As the development of antimicrobial strategies that evade resistance is urgently needed, a clear perception of these critical factors could ultimately pave the way for the design of innovative therapeutic targets.}, } @article {pmid39012117, year = {2024}, author = {Zalewska, M and Błażejewska, A and Gawor, J and Adamska, D and Goryca, K and Szeląg, M and Kalinowski, P and Popowska, M}, title = {A newly identified IncY plasmid from multi-drug-resistant Escherichia coli isolated from dairy cattle feces in Poland.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0087724}, doi = {10.1128/spectrum.00877-24}, pmid = {39012117}, issn = {2165-0497}, abstract = {UNLABELLED: Comprehensive whole-genome sequencing was performed on two multi-drug-resistant Escherichia coli strains isolated from cattle manure from a typical dairy farm in Poland in 2020. The identified strains are resistant to beta-lactams, aminoglycosides, tetracyclines, trimethoprim/sulfamethoxazole, and fluoroquinolones. The complete sequences of the harbored plasmids revealed antibiotic-resistance genes located within many mobile genetic elements (e.g., insertional sequences or transposons) and genes facilitating conjugal transfer or promoting horizontal gene transfer. These plasmids are hitherto undescribed. Similar plasmids have been identified, but not in Poland. The identified plasmids carried resistance genes, including the tetracycline resistance gene tet(A), aph family aminoglycoside resistance genes aph(3″)-lb and aph (6)-ld, beta-lactam resistance genes blaTEM-1 and blaCTX-M-15, sulfonamide resistance gene sul2, fluoroquinolone resistance gene qnrS1, and the trimethoprim resistance gene dfrA14. The characterized resistance plasmids were categorized into the IncY incompatibility group, indicating a high possibility for dissemination among the Enterobacteriaceae. While similar plasmids (99% identity) have been found in environmental and clinical samples, none have been identified in farm animals. These findings are significant within the One Health framework, as they underline the potential for antimicrobial-resistant E. coli from livestock and food sources to be transmitted to humans and vice versa. It highlights the need for careful monitoring and strategies to limit the spread of antibiotic resistance in the One Health approach.

IMPORTANCE: This study reveals the identification of new strains of antibiotic-resistant Escherichia coli in cattle manure from a dairy farm in Poland, offering critical insights into the spread of drug resistance. Through whole-genome sequencing, researchers discovered novel plasmids within these bacteria, which carry genes resistant to multiple antibiotics. These findings are particularly alarming, as these plasmids can transfer between different bacterial species, potentially escalating the spread of antibiotic resistance. This research underscores the vital connection between the health of humans, animals, and the environment, emphasizing the concept of One Health. It points to the critical need for global vigilance and strategies to curb the proliferation of antibiotic resistance. By showcasing the presence of these strains and their advanced resistance mechanisms, the study calls for enhanced surveillance and preventive actions in both agricultural practices and healthcare settings to address the imminent challenge of antibiotic-resistant bacteria.}, } @article {pmid39012101, year = {2024}, author = {Duran-Bedolla, J and Téllez-Sosa, J and Bocanegra-Ibarias, P and Schilmann, A and Bravo-Romero, S and Reyna-Flores, F and Villa-Reyes, T and Barrios-Camacho, H}, title = {Citrobacter spp. and Enterobacter spp. as reservoirs of carbapenemase blaNDM and blaKPC resistance genes in hospital wastewater.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0116524}, doi = {10.1128/aem.01165-24}, pmid = {39012101}, issn = {1098-5336}, abstract = {UNLABELLED: Antibiotic resistance has emerged as a global threat to public health, generating a growing interest in investigating the presence of antibiotic-resistant bacteria in environments influenced by anthropogenic activities. Wastewater treatment plants in hospital serve as significant reservoirs of antimicrobial-resistant bacteria, where a favorable environment is established, promoting the proliferation and transfer of resistance genes among different bacterial species. In our study, we isolated a total of 243 strains from 5 hospital wastewater sites in Mexico, belonging to 21 distinct Gram-negative bacterial species. The presence of β-lactamase was detected in 46.9% (114/243) of the isolates, which belonging to the Enterobacteriaceae family. We identified a total of 169 β-lactamase genes; blaTEM in 33.1%, blaCTX-M in 25.4%, blaKPC in 25.4%, blaNDM 8.8%, blaSHV in 5.3%, and blaOXA-48 in 1.1% distributed in 12 different bacteria species. Among the 114 of the isolates, 50.8% were found to harbor at least one carbapenemase and were discharged into the environment. The carbapenemase blaKPC was found in six Citrobacter spp. and E. coli, while blaNDM was detected in two distinct Enterobacter spp. and E. coli. Notably, blaNDM-1 was identified in a 110 Kb IncFII conjugative plasmid in E. cloacae, E. xiangfangensis, and E. coli within the same hospital wastewater. In conclusion, hospital wastewater showed the presence of Enterobacteriaceae carrying a high frequency of carbapenemase blaKPC and blaNDM. We propose that hospital wastewater serves as reservoirs for resistance mechanism within bacterial communities and creates an optimal environment for the exchange of this resistance mechanism among different bacterial strains.

IMPORTANCE: The significance of this study lies in its findings regarding the prevalence and diversity of antibiotic-resistant bacteria and genes identified in hospital wastewater in Mexico. The research underscores the urgent need for enhanced surveillance and prevention strategies to tackle the escalating challenge of antibiotic resistance, particularly evident through the elevated frequencies of carbapenemase genes such as blaKPC and blaNDM within the Enterobacteriaceae family. Moreover, the identification of these resistance genes on conjugative plasmids highlights the potential for widespread transmission via horizontal gene transfer. Understanding the mechanisms of antibiotic resistance in hospital wastewater is crucial for developing targeted interventions aimed at reducing transmission, thereby safeguarding public health and preserving the efficacy of antimicrobial therapies.}, } @article {pmid39011898, year = {2024}, author = {Yuan, W and Yu, J and Li, Z}, title = {Rapid functional activation of horizontally transferred eukaryotic intron-containing genes in the bacterial recipient.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkae628}, pmid = {39011898}, issn = {1362-4962}, support = {2020YFA0908000//National Key Research and Development Program of China/ ; TSBICIP-CXRC-001//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project/ ; 2060302//The ability establishment of sustainable use for valuable Chinese medicine resources/ ; }, abstract = {Horizontal gene transfer has occurred across all domains of life and contributed substantially to the evolution of both prokaryotes and eukaryotes. Previous studies suggest that many horizontally transferred eukaryotic genes conferred selective advantages to bacterial recipients, but how these eukaryotic genes evolved into functional bacterial genes remained unclear, particularly how bacteria overcome the expressional barrier posed by eukaryotic introns. Here, we first confirmed that the presence of intron would inactivate the horizontally transferred gene in Escherichia coli even if this gene could be efficiently transcribed. Subsequent large-scale genetic screens for activation of gene function revealed that activation events could rapidly occur within several days of selective cultivation. Molecular analysis of activation events uncovered two distinct mechanisms how bacteria overcome the intron barrier: (i) intron was partially deleted and the resulting stop codon-removed mutation led to one intact foreign protein or (ii) intron was intactly retained but it mediated the translation initiation and the interaction of two split small proteins (derived from coding sequences up- and downstream of intron, respectively) to restore gene function. Our findings underscore the likelihood that horizontally transferred eukaryotic intron-containing genes could rapidly acquire functionality if they confer a selective advantage to the prokaryotic recipient.}, } @article {pmid39010965, year = {2024}, author = {Jinnai, M and Yamaguchi, T and Minh, DTN and Hoang, ON and Le Thi, H and Thanh, PN and Hoai, PH and Do, PN and Van, CD and Kumeda, Y and Hase, A and Nakayama, T}, title = {Edible river fish-derived extended-spectrum β-lactamase (ESBL)-producing Enterobacterales harboring transferable plasmids encoding bla CTX-M-15, bla CTX-M-27, and bla CTX-M-55.}, journal = {One health (Amsterdam, Netherlands)}, volume = {18}, number = {}, pages = {100685}, pmid = {39010965}, issn = {2352-7714}, abstract = {Transmission of extended-spectrum β-lactamase (ESBL) genes has increased the global prevalence of ESBL-producing bacteria, especially in developing countries. Human infection with these bacteria may be food-mediated but has not been fully elucidated. Therefore, we aimed to examine ESBL-producing bacteria in edible river fish and elucidate their potential for horizontal gene transfer. A total of 173 ESBL-producing Enterobacterales were isolated (Escherichia coli [n = 87], Klebsiella pneumoniae [n = 52], Enterobacter cloacae complex [n = 18], Citrobacter freundii complex [n = 14], Atlantibacter hermannii [n = 1] and Serratia fonticola [n = 1]) from 56 of 80 fish intestinal contents sampled. Among the bacterial bla CTX-M genotypes, bla CTX-M-55 was the most predominant, followed by bla CTX-M-15, bla CTX-M-27, and bla CTX-M-65. Furthermore, we found that ESBL-producing Enterobacterales were able to transfer their bla CTX-M genes to E. coli. In summary, our results suggest that ESBL-producing Enterobacterales transfer bla CTX-M to indigenous gut E. coli in humans, following the consumption of contaminated fish.}, } @article {pmid39007976, year = {2024}, author = {Zalewska, M and Błażejewska, A and Gawor, J and Adamska, D and Goryca, K and Szeląg, M and Kalinowski, P and Popowska, M}, title = {The IncC and IncX1 resistance plasmids present in multi-drug resistant Escherichia coli strains isolated from poultry manure in Poland.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {39007976}, issn = {1614-7499}, support = {2017/25/Z/NZ7/03026//Narodowym Centrum Nauki/ ; }, abstract = {The study describes the whole-genome sequencing of two antibiotic-resistant representative Escherichia coli strains, isolated from poultry manure in 2020. The samples were obtained from a commercial chicken meat production facility in Poland. The antibiotic resistance profile was characterized by co-resistance to β-lactam antibiotics, aminoglycosides, and fluoroquinolones. The three identified resistance plasmids (R-plasmids), pECmdr13.2, pECmdr13.3, and pECmdr14.1, harbored various genes conferring resistance to tetracyclines (tetR[A]) for, aminoglycoside (aph, aac, and aad families), β-lactam (blaCMY-2, blaTEM-176), sulfonamide (sul1, sul2), fluoroquinolone (qnrS1), and phenicol (floR). These plasmids, which have not been previously reported in Poland, were found to carry IS26 insertion elements, the intI1-integrase gene, and conjugal transfer genes, facilitating horizontal gene transfer. Plasmids pECmdr13.2 and pECmdr14.1 also possessed a mercury resistance gene operon related to transposon Tn6196; this promotes plasmid persistence even without antibiotic selection pressure due to co-selection mechanisms such as co-resistance. The chicken manure-derived plasmids belonged to the IncX1 (narrow host range) and IncC (broad host range) incompatibility groups. Similar plasmids have been identified in various environments, clinical isolates, and farm animals, including cattle, swine, and poultry. This study holds significant importance for the One Health approach, as it highlights the potential for antibiotic-resistant bacteria from livestock and food sources, particularly E. coli, to transfer through the food chain to humans and vice versa.}, } @article {pmid39001714, year = {2024}, author = {Williams, TA and Davin, AA and Szánthó, LL and Stamatakis, A and Wahl, NA and Woodcroft, BJ and Soo, RM and Eme, L and Sheridan, PO and Gubry-Rangin, C and Spang, A and Hugenholtz, P and Szöllősi, GJ}, title = {Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae129}, pmid = {39001714}, issn = {1751-7370}, abstract = {In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree, and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution, and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature and oxygen use, offer enormous potential for understanding the rich tapestry of microbial life.}, } @article {pmid38992783, year = {2024}, author = {Klimov, PB and Hubert, J and Erban, T and Alejandra Perotti, M and Braig, HR and Flynt, A and He, Q and Cui, Y}, title = {Genomic and metagenomic analyses of the domestic mite Tyrophagus putrescentiae identify it as a widespread environmental contaminant and a host of a basal, mite-specific Wolbachia lineage (supergroup Q).}, journal = {International journal for parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijpara.2024.07.001}, pmid = {38992783}, issn = {1879-0135}, abstract = {Tyrophagus putrescentiae (mould mite) is a global, microscopic trophic generalist that commonly occurs in various human-created habitats, causing allergies and damaging stored food. Its ubiquity and extraordinary ability to penetrate research samples or cultures through air currents or by active walking through tights spaces (such as treads of screw caps) may lead to sample contamination and introduction of its DNA to research materials in the laboratory. This prompts a thorough investigation into potential sequence contamination in public genomic databases. The trophic success of T. putrescentiae is primarily attributed to the symbiotic bacteria housed in specialized internal mite structures, facilitating adaptation to varied nutritional niches. However, recent work suggests that horizontal transfer of bacterial/fungal genes related to nutritional functionality may also contribute to the mite's trophic versatility. This aspect requires independent confirmation. Additionally, T. putrescentiae harbors an uncharacterized and genetically divergent bacterium, Wolbachia, displaying blocking and microbiome-modifying effects. The phylogenomic position and supergroup assignment of this bacterium are unknown. Here, we sequenced and assembled the T. putrescentiae genome, analyzed its microbiome, and performed detailed phylogenomic analyses of the mite-specific Wolbachia. We show that T. putrescentiae DNA is a substantial source of contamination of research samples. Its DNA may inadvertently be co-extracted with the DNA of the target organism, eventually leading to sequence contamination in public databases. We identified a diversity of bacterial species associated with T. putrescentiae, including those capable of rapidly developing antibiotic resistance, such as Escherichia coli. Despite the presence of diverse bacterial communities in T. putrescentiae, we did not detect any recent horizontal gene transfers in this mite species and/or in astigmatid (domestic) mites in general. Our phylogenomic analysis of Wolbachia recovered a basal, mite-specific lineage (supergroup Q) represented by two Wolbachia spp. from the mould mite and a gall-inducing plant mite. Fluorescence in situ hybridization confirmed the presence of Wolbachia inside the mould mite. The discovery of an early derivative Wolbachia lineage (supergroup Q) in two phylogenetically unrelated and ecologically dissimilar mites suggests that this endosymbiotic bacterial lineage formed a long-term association with mites. This finding provides a unique insight into the early evolution and host associations of Wolbachia. Further discoveries of Wolbachia diversity in acariform mites are anticipated.}, } @article {pmid38992444, year = {2024}, author = {Soni, K and Jyoti, K and Kumar, A and Chandra, R}, title = {Coexistence of multidrug resistance and ESBL encoding genes - blaTEM, blaSHV, and blaCTX-M; its amplification and dispersion in the environment via municipal wastewater treatment plant.}, journal = {Chemosphere}, volume = {362}, number = {}, pages = {142829}, doi = {10.1016/j.chemosphere.2024.142829}, pmid = {38992444}, issn = {1879-1298}, abstract = {Municipal wastewater treatment plants (MWWTPs) are a global source of antibiotic resistance genes (ARGs), collecting wastewater from a variety of sources, including hospital wastewater, domestic wastewater, runoff from agricultural and livestock farms, etc. These sources are contaminated with organic and inorganic pollutants, ARGs and antibiotic-resistant bacteria (ARB). Such pollutants aided eutrophication and encouraged bacterial growth. During bacterial growth horizontal gene transfer (HGT) and vertical gene transfer (VGT) of ARGs and extended-spectrum β-lactamase (ESBL) encoding genes may facilitate, resulting in the spread of antibiotic resistance exponentially. The current study investigated the prevalence of multidrug resistance (MDR) and ESBL encoding genes in various treatment units of MWWTP and their spread in the environment. A total of three sampling sites (BUT, BRO, and BFB) were chosen, and 33 morphologically distinct bacterial colonies were isolated. 14 of the 33 isolates tested positive for antibiotic resistance and were further tested for the coexistence of MDR and ESBL production. The selected 14 isolates showed the highest resistance to trimethoprim (85.71%), followed by ciprofloxacin, azithromycin, and ampicillin (71.42%), tetracycline (57.14%), and vancomycin, gentamicin, and colistin sulphate (50%). A total of 9 isolates (64.28%) were phenotypically positive for ESBL production (BUT2, BUT3, BUT5, BRO1, BRO2, BRO3, BRO4, BRO5 and BFB1). The molecular detection of ESBL encoding genes, i.e. blaTEM, blaSHV, and blaCTX-M was carried out. The most prevalent gene was blaTEM (69.23%), followed by blaSHV (46.15%), and blaCTX-M (23.07%). In this study, 9 isolates (64.28%) out of 14 showed the coexistence of MDR and ESBL encoding genes, namely BUT3, BUT4, BUT5, BUT6, BUT7, BRO1, BRO2, BRO4, and BFB1. The coexistence of ESBL encoding genes and resistance to other antibiotic classes exacerbates human health and the environment.}, } @article {pmid38992349, year = {2024}, author = {Nazir, R and Shua, D and Shen, JP and Hu, HW and Wang, J and He, JZ}, title = {Effect of meddling ARBs on ARGs dynamics in fungal infested soil and their selective dispersal along spatially distant mycelial networks.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {174594}, doi = {10.1016/j.scitotenv.2024.174594}, pmid = {38992349}, issn = {1879-1026}, abstract = {During the recent times, environmental antibiotic resistance genes (ARGs) and their potential transfer to other bacterial hosts of pathogenic importance are of serious concern. However, the dissemination strategies of such ARGs are largely unknown. We tested that saprotrophic soil fungi differentially enriched antibiotic resistant bacteria (ARBs) and subsequently contributed in spatial distribution of selective ARGs. Wafergen qPCR analysis of 295 different ARGs was conducted for manure treated pre-sterilized soil incubated or not with selected bacterial-fungal consortia. The qPCR assay detected unique ARGs specifically found in the mycosphere of ascomycetous and basidiomycetous fungi. Both fungi exerted potentially different selection pressures on ARBs, resulting in different patterns of ARGs dissemination (to distant places) along their respective growing fungal highways. The relative abundance of mobile genetic elements (MGEs) was significantly decreased along fungal highways compared to the respective inoculation points. Moreover, the decrease in MGEs and ARGs (along fungal highways) was more prominent over time which depicts the continuous selection pressure of growing fungi on ARBs for enrichment of particular ARGs in mycosphere. Such data also indicate the potential role of saprotrophic soil fungi to facilitate horizontal gene transfer within mycospheric environmental settings. Our study, therefore, advocates to emphasize the future investigations for such (bacteria-fungal) interactive microbial consortia for potential (spatial) dissemination of resistance determinants which may ultimately increase the exposure risks of ARGs.}, } @article {pmid38990885, year = {2024}, author = {Windels, A and Franceus, J and Pleiss, J and Desmet, T}, title = {CANDy: Automated analysis of domain architectures in carbohydrate-active enzymes.}, journal = {PloS one}, volume = {19}, number = {7}, pages = {e0306410}, doi = {10.1371/journal.pone.0306410}, pmid = {38990885}, issn = {1932-6203}, mesh = {*Protein Domains ; Glycoside Hydrolases/chemistry/metabolism/genetics ; Catalytic Domain ; Software ; Carbohydrate Metabolism ; Carbohydrates/chemistry ; Animals ; }, abstract = {Carbohydrate-active enzymes (CAZymes) can be found in all domains of life and play a crucial role in metabolic and physiological processes. CAZymes often possess a modular structure, comprising not only catalytic domains but also associated domains such as carbohydrate-binding modules (CBMs) and linker domains. By exploring the modular diversity of CAZy families, catalysts with novel properties can be discovered and further insight in their biological functions and evolutionary relationships can be obtained. Here we present the carbohydrate-active enzyme domain analysis tool (CANDy), an assembly of several novel scripts, tools and databases that allows users to analyze the domain architecture of all protein sequences in a given CAZy family. CANDy's usability is shown on glycoside hydrolase family 48, a small yet underexplored family containing multi-domain enzymes. Our analysis reveals the existence of 35 distinct domain assemblies, including eight known architectures, with the remaining assemblies awaiting characterization. Moreover, we substantiate the occurrence of horizontal gene transfer from prokaryotes to insect orthologs and provide evidence for the subsequent removal of auxiliary domains, likely through a gene fission event. CANDy is available at https://github.com/PyEED/CANDy.}, } @article {pmid38987681, year = {2024}, author = {Elgayar, FA and Gouda, MK and Badran, AA and El Halfawy, NM}, title = {Pathogenomics analysis of high-risk clone ST147 multidrug-resistant Klebsiella pneumoniae isolated from a patient in Egypt.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {256}, pmid = {38987681}, issn = {1471-2180}, mesh = {*Klebsiella pneumoniae/genetics/drug effects/isolation & purification/classification ; Humans ; Egypt ; *Drug Resistance, Multiple, Bacterial/genetics ; *Klebsiella Infections/microbiology/epidemiology ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; *Virulence Factors/genetics ; *Whole Genome Sequencing ; *Genome, Bacterial/genetics ; beta-Lactamases/genetics ; Bacterial Proteins/genetics ; Plasmids/genetics ; }, abstract = {BACKGROUND: The emergence of multi-drug-resistant Klebsiella pneumoniae (MDR-KP) represents a serious clinical health concern. Antibiotic resistance and virulence interactions play a significant role in the pathogenesis of K. pneumoniae infections. Therefore, tracking the clinical resistome and virulome through monitoring antibiotic resistance genes (ARG) and virulence factors in the bacterial genome using computational analysis tools is critical for predicting the next epidemic.

METHODS: In the current study, one hundred extended spectrum β-lactamase (ESBL)-producing clinical isolates were collected from Mansoura University Hospital, Egypt, in a six-month period from January to June 2022. One isolate was selected due to the high resistance phenotype, and the genetic features of MDR-KP recovered from hospitalized patient were investigated. Otherwise, the susceptibility to 25 antimicrobials was determined using the DL Antimicrobial Susceptibility Testing (AST) system. Whole genome sequencing (WGS) using Illumina NovaSeq 6000 was employed to provide genomic insights into K. pneumoniae WSF99 clinical isolate.

RESULTS: The isolate K. pneumoniae WSF99 was phenotypically resistant to the antibiotics under investigation via antibiotic susceptibility testing. WGS analysis revealed that WSF99 total genome length was 5.7 Mb with an estimated 5,718 protein-coding genes and a G + C content of 56.98 mol%. Additionally, the allelic profile of the WSF99 isolate was allocated to the high-risk clone ST147. Furthermore, diverse antibiotic resistance genes were determined in the genome that explain the high-level resistance phenotypes. Several β-lactamase genes, including blaCTX-M-15, blaTEM-1, blaTEM-12, blaSHV-11, blaSHV-67, and blaOXA-9, were detected in the WSF99 isolate. Moreover, a single carbapenemase gene, blaNDM-5, was predicted in the genome, positioned within a mobile cassette. In addition, other resistance genes were predicted in the genome including, aac(6')-Ib, aph(3')-VI, sul1, sul2, fosA, aadA, arr-2, qnrS1, tetA and tetC. Four plasmid replicons CoIRNAI, IncFIB(K), IncFIB(pQil), and IncR were predicted in the genome. The draft genome analysis revealed the occurrence of genetic mobile elements positioned around the ARGs, suggesting the ease of dissemination via horizontal gene transfer.

CONCLUSIONS: This study reports a comprehensive pathogenomic analysis of MDR-KP isolated from a hospitalized patient. These findings could be relevant for future studies investigating the diversity of antimicrobial resistance and virulence in Egypt.}, } @article {pmid38986507, year = {2024}, author = {Irusan, D and Akshay, SD and Shetty, VP and Karunasagar, I and Deekshit, VK and Rohit, A}, title = {Analysis of mcr family of colistin resistance genes in Gram-negative isolates from a tertiary care hospital in India.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxae172}, pmid = {38986507}, issn = {1365-2672}, abstract = {AIM: Colistin serves as the drug of last resort for combating numerous multidrug-resistant (MDR) Gram-negative infections. Its efficacy is hampered by the prevalent issue of colistin resistance, which severely limits treatment options for critically ill patients. Identifying resistance genes is crucial for controlling resistance spread, with horizontal gene transfer being the primary mechanism among bacteria. This study aimed to assess the prevalence of plasmid-mediated mcr genes associated with colistin resistance in Gram-negative bacteria, utilizing both genotypic and phenotypic tests.

METHODS AND RESULTS: The clinical isolates (n=913) were obtained from a tertiary care center in Chennai, India. Colistin resistance was seen among Gram-negative isolates. These strains underwent screening for mcr-1, mcr-3, mcr-4, and mcr-5 genes via conventional PCR. Additionally, mcr-positive isolates were confirmed through Sanger sequencing and phenotypic testing. The bacterial isolates predominantly comprised Klebsiella pneumoniae (62.43%), Escherichia coli (19.71%), Pseudomonas aeruginosa (10.73%), Acinetobacter baumannii (4.81%), along with other species. All isolates exhibited multidrug resistance to three or more antibiotic classes. Colistin resistance, determined via broth microdilution (BMD) using CLSI guidelines, was observed in 13.08% of the isolates studied. Notably, mcr-5 was detected in K. pneumoniae in PCR, despite their absence in Sanger sequencing and phenotypic tests (including the combined-disk test, colistin MIC in the presence of EDTA, and Zeta potential assays). This finding underscores the importance of employing multiple diagnostic approaches to accurately identify colistin resistance mechanisms.

CONCLUSION AND IMPACT: The study highlights a concerning prevalence of colistin resistance among Enterobacterales, especially those producing carbapenemase, thereby impacting mortality rates. Nonetheless, further investigations are warranted to elucidate common mechanisms of colistin resistance and to evaluate the efficacy of screening techniques in detecting isolates carrying mcr genes responsible for enzyme-mediated lipopolysaccharide (LPS) modification.}, } @article {pmid38986416, year = {2024}, author = {Chi, W and Zou, Y and Qiu, T and Shi, W and Tang, L and Xu, M and Wu, H and Luan, X}, title = {Horizontal gene transfer plays a crucial role in the development of antibiotic resistance in an antibiotic-free shrimp farming system.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {135150}, doi = {10.1016/j.jhazmat.2024.135150}, pmid = {38986416}, issn = {1873-3336}, abstract = {Antibiotic selective pressure in aquaculture systems often results in the antibiotic resistance genes (ARGs) proliferation. Nonetheless, a paucity of data exists concerning the mechanisms of ARGs development in aquaculture systems without the influences of antibiotics. This study utilized metagenomic approaches to elucidate the dynamics and transfer mechanisms of ARGs throughout the aquaculture of Pacific white shrimp. A marked change in the resistome was observed throughout the aquaculture without antibiotics. The total ARGs relative abundance increased from 0.05 to 0.33 by day 90 of cultivation, with even higher in mixed wastewater (0.44). Both bacterial communities and mobile genetic elements play pivotal roles in the development of ARGs. Metagenome-assembled genomes showed enrichment of environmentally intrinsic ARGs on chromosomes including macB and mdtK. The plasmid-mediated horizontal transfer was recognized as a principal factor contributing to the rise of ARGs, particularly for tetG and floR, and this led to an escalation of resistance risk, peaking at a risks core of 35.43 on day 90. This study demonstrates that horizontal gene transfer plays a crucial role in ARGs development without antibiotic pressure, which can provide a theoretical foundation for controlling ARGs proliferation in aquaculture systems.}, } @article {pmid38942024, year = {2024}, author = {Harder, CB and Miyauchi, S and Virágh, M and Kuo, A and Thoen, E and Andreopoulos, B and Lu, D and Skrede, I and Drula, E and Henrissat, B and Morin, E and Kohler, A and Barry, K and LaButti, K and Salamov, A and Lipzen, A and Merényi, Z and Hegedüs, B and Baldrian, P and Stursova, M and Weitz, H and Taylor, A and Koriabine, M and Savage, E and Grigoriev, IV and Nagy, LG and Martin, F and Kauserud, H}, title = {Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations.}, journal = {Cell genomics}, volume = {4}, number = {7}, pages = {100586}, doi = {10.1016/j.xgen.2024.100586}, pmid = {38942024}, issn = {2666-979X}, mesh = {*Genome, Fungal/genetics ; *Agaricales/genetics ; Phylogeny ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Plants/microbiology/genetics ; }, abstract = {Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.}, } @article {pmid38983623, year = {2024}, author = {Chin, HS and Ravi Varadharajulu, N and Lin, ZH and Chen, WY and Zhang, ZH and Arumugam, S and Lai, CY and Yu, SS}, title = {Isolation, molecular identification, and genomic analysis of Mangrovibacter phragmitis strain ASIOC01 from activated sludge harboring the bioremediation prowess of glycerol and organic pollutants in high-salinity.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1415723}, pmid = {38983623}, issn = {1664-302X}, abstract = {The physiological and genotypic characteristics of Mangrovibacter (MGB) remain largely unexplored, including their distribution and abundance within ecosystems. M. phragmitis (MPH) ASIOC01 was successfully isolated from activated sludge (AS), which was pre-enriched by adding 1,3-dichloro-2-propanol and 3-chloro-1,2-propanediol as carbon sources. The new isolate, MPH ASIOC01, exhibited resilience in a medium containing sodium chloride concentration up to 11% (with optimal growth observed at 3%) and effectively utilizing glycerol as their sole carbon source. However, species delimitation of MGBs remains challenging due to high 16S rRNA sequence similarity (greater than 99% ANI) among different MGBs. In contrast, among the housekeeping gene discrepancies, the tryptophan synthase beta chain gene can serve as a robust marker for fast species delimitation among MGBs. Furthermore, the complete genome of MPH ASIOC01 was fully sequenced and circlized as a single contig using the PacBio HiFi sequencing method. Comparative genomics revealed genes potentially associated with various phenotypic features of MGBs, such as nitrogen-fixing, phosphate-solubilizing, cellulose-digesting, Cr-reducing, and salt tolerance. Computational analysis suggested that MPH ASIOC01 may have undergone horizontal gene transfer events, possibly contributing unique traits such as antibiotic resistance. Finally, our findings also disclosed that the introduction of MPH ASIOC01 into AS can assist in the remediation of wastewater chemical oxygen demand, which was evaluated using gas chromatograph-mass spectrometry. To the best of our knowledge, this study offers the most comprehensive understanding of the phenotypic and genotypic features of MGBs to date.}, } @article {pmid38980659, year = {2024}, author = {Poddar, BJ and Khardenavis, AA}, title = {Genomic Insights into the Landfill Microbial Community: Denitrifying Activity Supporting One-Carbon Utilization.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {38980659}, issn = {1559-0291}, support = {EMR/2016/006589//SERB, New Delhi/ ; }, abstract = {In spite of the developments in understanding of denitrifying methylotrophy in the recent years, challenges still exist in unravelling the overall biochemistry of nitrate-dependent methane oxidation in novel or poorly characterized/not-yet-cultured bacteria. In the present study, landfill site was mined for novel C1-carbon-metabolizing bacteria which can use nitrate/nitrite as an electron acceptor. A high-throughput rapid plate assay identified three bacterial isolates with eminent ability for nitrate-dependent methane metabolism under anaerobic conditions. Taxonomic identification by whole-genome sequence-based overall genome relatedness indices accurately assigned the isolates AAK_M13, AAK_M29, and AAK_M39 at the species level to Enterobacter cloacae, Bacillus subtilis, and Bacillus halotolerans, respectively. Several genes encoding sub-components involved in alcohol utilization and denitrification pathways, such as adh, fdh, fdo, nar, nir, and nor, were identified in all the genomes. Though no gene clusters encoding MMO/AMO were annotated, sequencing of PCR amplicons revealed similarity with pMMO/AMO gene using translated nucleotide sequence of strains AAK_M29 and AAK_M39, while strain AAK_M13 showed similarity with XRE family transcriptional regulator. This suggests the horizontal gene transfer and/or presence of a truncated version of a housekeeping enzyme encoded by genes exhibiting partial sequence similarity with pMMO genes that mimicked its function at greenhouse gas emission sites. Owing to lack of conclusive evidence for presence of methane metabolism genes in the selected isolates, further experiment was performed to validate their nitrate-dependent methane oxidation capacities. Bacillus subtilis AAK_M29, Bacillus halotolerans AAK_M39, and Enterobacter cloacae AAK_M13 could oxidize 60%, 75%, and 85% of the added methane respectively accompanied by high nitrate reduction (56-62%) thus supporting the correlation between these two activities. The remarkable ability of these isolates for nitrate-dependent methane metabolism has highlighted their role in ecological contribution and biotechnological potential to serve as methane and nitrate sinks in the landfill sites.}, } @article {pmid38977308, year = {2024}, author = {Vakirlis, N and Kupczok, A}, title = {Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.278977.124}, pmid = {38977308}, issn = {1549-5469}, abstract = {Species-specific genes, also known as orphans, are ubiquitous across life's domains. In prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in external elements such as viruses followed by horizontal gene transfer, whereas the scenario of native origination, through rapid divergence or de novo, is mostly dismissed. However, quantitative evidence supporting either scenario is lacking. Here, we systematically analyzed genomes from 4644 human gut microbiome species and identified more than 600,000 unique SSOGs, representing an average of 2.6% of a given species' pangenome. These sequences are mostly rare within each species yet show signs of purifying selection. Overall, SSOGs use optimal codons less frequently, and their proteins are more disordered than those of conserved genes (i.e., non-SSOGs). Importantly, across species, the GC content of SSOGs closely matches that of conserved ones. In contrast, the ∼5% of SSOGs that share similarity to known viral sequences have distinct characteristics, including lower GC content. Thus, SSOGs with similarity to viruses differ from the remaining SSOGs, contrasting an external origination scenario for most of them. By examining the orthologous genomic region in closely related species, we show that a small subset of SSOGs likely evolved natively de novo and find that these genes also differ in their properties from the remaining SSOGs. Our results challenge the notion that external elements are the dominant source of prokaryotic genetic novelty and will enable future studies into the biological role and relevance of species-specific genes in the human gut.}, } @article {pmid38975782, year = {2024}, author = {Price, CTD and Hanford, HE and Al-Quadan, T and Santic, M and Shin, CJ and Da'as, MSJ and Abu Kwaik, Y}, title = {Amoebae as training grounds for microbial pathogens.}, journal = {mBio}, volume = {}, number = {}, pages = {e0082724}, doi = {10.1128/mbio.00827-24}, pmid = {38975782}, issn = {2150-7511}, abstract = {Grazing of amoebae on microorganisms represents one of the oldest predator-prey dynamic relationships in nature. It represents a genetic "melting pot" for an ancient and continuous multi-directional inter- and intra-kingdom horizontal gene transfer between amoebae and its preys, intracellular microbial residents, endosymbionts, and giant viruses, which has shaped the evolution, selection, and adaptation of microbes that evade degradation by predatory amoeba. Unicellular phagocytic amoebae are thought to be the ancient ancestors of macrophages with highly conserved eukaryotic processes. Selection and evolution of microbes within amoeba through their evolution to target highly conserved eukaryotic processes have facilitated the expansion of their host range to mammals, causing various infectious diseases. Legionella and environmental Chlamydia harbor an immense number of eukaryotic-like proteins that are involved in ubiquitin-related processes or are tandem repeats-containing proteins involved in protein-protein and protein-chromatin interactions. Some of these eukaryotic-like proteins exhibit novel domain architecture and novel enzymatic functions absent in mammalian cells, such as ubiquitin ligases, likely acquired from amoebae. Mammalian cells and amoebae may respond similarly to microbial factors that target highly conserved eukaryotic processes, but mammalian cells may undergo an accidental response to amoeba-adapted microbial factors. We discuss specific examples of microbes that have evolved to evade amoeba predation, including the bacterial pathogens- Legionella, Chlamydia, Coxiella, Rickettssia, Francisella, Mycobacteria, Salmonella, Bartonella, Rhodococcus, Pseudomonas, Vibrio, Helicobacter, Campylobacter, and Aliarcobacter. We also discuss the fungi Cryptococcus, and Asperigillus, as well as amoebae mimiviruses/giant viruses. We propose that amoeba-microbe interactions will continue to be a major "training ground" for the evolution, selection, adaptation, and emergence of microbial pathogens equipped with unique pathogenic tools to infect mammalian hosts. However, our progress will continue to be highly dependent on additional genomic, biochemical, and cellular data of unicellular eukaryotes.}, } @article {pmid38971740, year = {2024}, author = {Bhat, A and Sharma, R and Desigan, K and Lucas, MM and Mishra, A and Bowers, RM and Woyke, T and Epstein, B and Tiffin, P and Pueyo, JJ and Paape, T}, title = {Horizontal gene transfer of the Mer operon is associated with large effects on the transcriptome and increased tolerance to mercury in nitrogen-fixing bacteria.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {247}, pmid = {38971740}, issn = {1471-2180}, support = {Quantitative Plant Science Initiative (QPSI)//U.S. Department of Energy/ ; Quantitative Plant Science Initiative (QPSI)//U.S. Department of Energy/ ; Quantitative Plant Science Initiative (QPSI)//U.S. Department of Energy/ ; Quantitative Plant Science Initiative (QPSI)//U.S. Department of Energy/ ; 3092-53000-001-00D//U.S. Department of Agriculture/ ; 3092-53000-001-00D//U.S. Department of Agriculture/ ; }, mesh = {*Gene Transfer, Horizontal ; *Mercury/metabolism/toxicity ; *Operon ; *Transcriptome ; *Symbiosis ; Nitrogen-Fixing Bacteria/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Nitrogen Fixation ; Rhizobium leguminosarum/genetics/metabolism ; Soil Microbiology ; }, abstract = {BACKGROUND: Mercury (Hg) is highly toxic and has the potential to cause severe health problems for humans and foraging animals when transported into edible plant parts. Soil rhizobia that form symbiosis with legumes may possess mechanisms to prevent heavy metal translocation from roots to shoots in plants by exporting metals from nodules or compartmentalizing metal ions inside nodules. Horizontal gene transfer has potential to confer immediate de novo adaptations to stress. We used comparative genomics of high quality de novo assemblies to identify structural differences in the genomes of nitrogen-fixing rhizobia that were isolated from a mercury (Hg) mine site that show high variation in their tolerance to Hg.

RESULTS: Our analyses identified multiple structurally conserved merA homologs in the genomes of Sinorhizobium medicae and Rhizobium leguminosarum but only the strains that possessed a Mer operon exhibited 10-fold increased tolerance to Hg. RNAseq analysis revealed nearly all genes in the Mer operon were significantly up-regulated in response to Hg stress in free-living conditions and in nodules. In both free-living and nodule environments, we found the Hg-tolerant strains with a Mer operon exhibited the fewest number of differentially expressed genes (DEGs) in the genome, indicating a rapid and efficient detoxification of Hg from the cells that reduced general stress responses to the Hg-treatment. Expression changes in S. medicae while in bacteroids showed that both rhizobia strain and host-plant tolerance affected the number of DEGs. Aside from Mer operon genes, nif genes which are involved in nitrogenase activity in S. medicae showed significant up-regulation in the most Hg-tolerant strain while inside the most Hg-accumulating host-plant. Transfer of a plasmid containing the Mer operon from the most tolerant strain to low-tolerant strains resulted in an immediate increase in Hg tolerance, indicating that the Mer operon is able to confer hyper tolerance to Hg.

CONCLUSIONS: Mer operons have not been previously reported in nitrogen-fixing rhizobia. This study demonstrates a pivotal role of the Mer operon in effective mercury detoxification and hypertolerance in nitrogen-fixing rhizobia. This finding has major implications not only for soil bioremediation, but also host plants growing in mercury contaminated soils.}, } @article {pmid38971360, year = {2024}, author = {Zhang, W and Geng, J and Sun, M and Jiang, C and Lin, H and Chen, H and Yang, Y}, title = {Distinct species turnover patterns shaped the richness of antibiotic resistance genes on eight different microplastic polymers.}, journal = {Environmental research}, volume = {}, number = {}, pages = {119562}, doi = {10.1016/j.envres.2024.119562}, pmid = {38971360}, issn = {1096-0953}, abstract = {Elucidating the formation mechanism of plastisphere antibiotic resistance genes (ARGs) on different polymers is necessary to understand the ecological risks of plastisphere ARGs. Here, we explored the turnover and assembly mechanism of plastisphere ARGs on 8 different microplastic polymers (4 biodegradable (bMPs) and 4 non-biodegradable microplastics (nMPs)) by metagenomic sequencing. Our study revealed the presence of 479 ARGs with abundance ranging from 41.37 to 58.17 copies/16S rRNA gene in all plastispheres. These ARGs were predominantly multidrug resistance genes. The richness of plastisphere ARGs on different polymers had a significant correlation with the contribution of species turnover to plastisphere ARGs β diversity. Furthermore, polymer type was the most critical factor affecting the composition of plastisphere ARGs. More opportunistic pathogens carrying diverse ARGs on BMPs (PBAT, PBS, and PHA) with higher horizontal gene transfer potential may further magnify the ecological risks and human health threats. For example, the opportunistic pathogens Riemerella anatipestifer, Vibrio campbellii, and Vibrio cholerae are closely related to human production and life, which were the important potential hosts of many plastisphere ARGs and mobile genetic elements on BMPs. Thus, we emphasize the urgency of developing the formation mechanism of plastisphere ARGs and the necessity of controlling BMPs and ARG pollution, especially BMPs, with ever-increasing usage in daily life.}, } @article {pmid38969684, year = {2024}, author = {Salem, S and Abdelsalam, NA and Shata, AH and Mouftah, SF and Cobo-Díaz, JF and Osama, D and Atteya, R and Elhadidy, M}, title = {Unveiling the microevolution of antimicrobial resistance in selected Pseudomonas aeruginosa isolates from Egyptian healthcare settings: A genomic approach.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {15500}, pmid = {38969684}, issn = {2045-2322}, support = {CRP/EGY22-03//CRP-ICGEB grant/ ; }, mesh = {*Pseudomonas aeruginosa/genetics/drug effects/isolation & purification ; Egypt/epidemiology ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; Pseudomonas Infections/microbiology/epidemiology ; Biofilms/drug effects/growth & development ; Whole Genome Sequencing/methods ; Genomics/methods ; Genome, Bacterial ; Evolution, Molecular ; Drug Resistance, Bacterial/genetics ; Multilocus Sequence Typing ; Polymorphism, Single Nucleotide ; Drug Resistance, Multiple, Bacterial/genetics ; Phylogeny ; }, abstract = {The incidence of Pseudomonas aeruginosa infections in healthcare environments, particularly in low-and middle-income countries, is on the rise. The purpose of this study was to provide comprehensive genomic insights into thirteen P. aeruginosa isolates obtained from Egyptian healthcare settings. Phenotypic analysis of the antimicrobial resistance profile and biofilm formation were performed using minimum inhibitory concentration and microtiter plate assay, respectively. Whole genome sequencing was employed to identify sequence typing, resistome, virulome, and mobile genetic elements. Our findings indicate that 92.3% of the isolates were classified as extensively drug-resistant, with 53.85% of these demonstrating strong biofilm production capabilities. The predominant clone observed in the study was ST773, followed by ST235, both of which were associated with the O11 serotype. Core genome multi-locus sequence typing comparison of these clones with global isolates suggested their potential global expansion and adaptation. A significant portion of the isolates harbored Col plasmids and various MGEs, all of which were linked to antimicrobial resistance genes. Single nucleotide polymorphisms in different genes were associated with the development of antimicrobial resistance in these isolates. In conclusion, this pilot study underscores the prevalence of extensively drug-resistant P. aeruginosa isolates and emphasizes the role of horizontal gene transfer facilitated by a diverse array of mobile genetic elements within various clones. Furthermore, specific insertion sequences and mutations were found to be associated with antibiotic resistance.}, } @article {pmid38968733, year = {2024}, author = {Li, Y and Zhang, S and Chen, Z and Huang, W and Liu, Q and Fang, H and Chi, B and Yang, N and Zhang, Q}, title = {Deciphering the impact of organic loading rate and digestate recirculation on the occurrence patterns of antibiotics and antibiotic resistance genes in dry anaerobic digestion of kitchen waste.}, journal = {Water research}, volume = {261}, number = {}, pages = {122005}, doi = {10.1016/j.watres.2024.122005}, pmid = {38968733}, issn = {1879-2448}, abstract = {Organic loading rate (OLR) is crucial for determining the stability of dry anaerobic digestion (AD). Digestate recirculation contributes to reactor stability and enhances methane production. Nevertheless, the understanding of how OLR and digestate recirculation affect the abundance and diversity of antibiotics and antibiotic resistance genes (ARGs), as well as the mechanisms involved in the dissemination of ARGs, remains limited. This study thoroughly investigated this critical issue through a long-term pilot-scale experiment. The metabolome analyses revealed the enrichment of various antibiotics, such as aminoglycoside, tetracycline, and macrolide, under low OLR conditions (OLR ≤ 4.0 g·VS/L·d) and the reactor instability. Antibiotics abundance decreased by approximately 19.66-31.69 % during high OLR operation (OLR ≥ 6.0 g·VS/L·d) with digestate recirculation. The metagenome analyses demonstrated that although low OLR promoted reactor stability, it facilitated the proliferation of antibiotic-resistant bacteria, such as Pseudomonas, and triggered functional profiles related to ATP generation, oxidative stress response, EPS secretion, and cell membrane permeability, thereby facilitating horizontal gene transfer (HGT) of ARGs. However, under stable operation at an OLR of 6.0 g·VS/L·d, there was a decrease in ARGs abundance but a notable increase in human pathogenic bacteria (HPB) and mobile genetic elements (MGEs). Subsequently, during reactor instability, the abundance of ARGs and HPB increased. Notably, during digestate recirculation at OLR levels of 6.0 and 7.0 g·VS/L·d, the process attenuated the risk of ARGs spread by reducing the diversity of ARGs hosts, minimizing interactions among ARGs hosts, ARGs, and MGEs, and weakening functional profiles associated with HGT of ARGs. Overall, digestate recirculation aids in reducing the abundance of antibiotics and ARGs under high OLR conditions. These findings provide advanced insights into how OLR and digestate recirculation affect the occurrence patterns of antibiotics and ARGs in dry AD.}, } @article {pmid38965531, year = {2024}, author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV}, title = {Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {148}, pmid = {38965531}, issn = {1741-7007}, support = {Intramural Research Program//U.S. National Library of Medicine/ ; }, mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Biodiversity ; Symbiosis/genetics ; Models, Theoretical ; Models, Biological ; }, abstract = {BACKGROUND: Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation.

RESULTS: To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment.

CONCLUSIONS: The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity.}, } @article {pmid38964677, year = {2024}, author = {Xu, G and Yang, S}, title = {Evolution of orphan and atypical histidine kinases and response regulators for microbial signaling diversity.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {133635}, doi = {10.1016/j.ijbiomac.2024.133635}, pmid = {38964677}, issn = {1879-0003}, abstract = {Two-component signaling systems (TCS) are the predominant means of microbes for sensing and responding to environmental stimuli. Typically, TCS is comprised of a sensor histidine kinase (HK) and a cognate response regulator (RR), which might have coevolved together. They usually involve the phosphoryl transfer signaling mechanism. However, there are also some orphan and atypical HK and RR homologs, and their evolutionary origins are still not very clear. They are not associated with cognate pairs or lack the conserved residues for phosphoryl transfer, but they could receive or respond to signals from other regulators. The objective of this study is to reveal the evolutionary history of these orphan and atypical HK and RR homologs. Structural, domain, sequence, and phylogenetic analyses indicated that their evolution process might undergo gene duplication, divergence, and domain shuffling. Meanwhile, lateral gene transfer might also be involved for their gene distribution. Evolution of orphan and atypical HK and RR homologs have increased their signaling diversity, which could be helpful for microbial adaption in complex environments.}, } @article {pmid38964571, year = {2024}, author = {Xu, C and Hu, C and Li, F and Liu, W and Xu, Y and Shi, D}, title = {Antibiotic resistance genes risks in relation to host pathogenicity and mobility in a typical hospital wastewater treatment process.}, journal = {Environmental research}, volume = {259}, number = {}, pages = {119554}, doi = {10.1016/j.envres.2024.119554}, pmid = {38964571}, issn = {1096-0953}, abstract = {Hospital wastewaters (HWWs) serve as critical reservoirs for disseminating antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB). However, the dynamics and noteworthy shifts of ARGs and their associated pathogenicity, mobility, and resistome risks during HWWs treatment processes remain poorly understood. Utilizing metagenomic sequencing and assembly, we identified 817 ARG subtypes conferring resistance to 20 classes of antibiotics across 18 HWW samples from influent to effluent. Genes encoding resistance to multidrug, aminoglycoside and beta_lactam were the most prevalent ARG types, reflecting patterns observed in clinical settings. On-site treatment efforts decreased the relative abundance of ARGs by 77.4% from influent to secondary sedimentation, whereas chlorine disinfection significantly increased their abundance in the final effluent. Deterministic processes primarily drove the taxonomic assembly, with Proteobacteria being the most abundant phylum and serving as the primary host for 15 ARG types. Contig-based analysis further revealed 114 pathogenic ARB, with Escherichia coli, Pseudomonas alcaligenes, and Pseudomonas aeruginosa exhibiting multidrug-resistant. The contributions of host bacteria and pathogenic ARB varied throughout wastewater treatment. In addition, 7.10%-31.0 % ARGs were flanked by mobile genetic elements (MGEs), predominantly mediated by transposase (74.1%). Notably, tnpA exhibited the highest potential for ARG dissemination, frequently co-occurring with beta-lactam resistance genes (35.2%). Considering ARG profiles, pathogenic hosts, and transferability, raw influent exhibited the highest antibiotic resistome risk index (ARRI), followed by the final effluent. Chlorine disinfection exacerbated resistome risks by inducing potential pathogenic ARB and mobile ARGs, posing threats to the receiving environment. This study delineates ARG occurrence patterns, highlights mechanisms of ARG carriage and horizontal gene transfer, and provides insights for assessing resistance risks and prioritizing interventions in clinical settings.}, } @article {pmid38964320, year = {2024}, author = {Kadibalban, AS and Landan, G and Dagan, T}, title = {The extent and characteristics of DNA transfer between plasmids and chromosomes.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2024.06.030}, pmid = {38964320}, issn = {1879-0445}, abstract = {Plasmids are extrachromosomal genetic elements that reside in prokaryotes. The acquisition of plasmids encoding beneficial traits can facilitate short-term survival in harsh environmental conditions or long-term adaptation of new ecological niches. Due to their ability to transfer between cells, plasmids are considered agents of gene transfer. Nonetheless, the frequency of DNA transfer between plasmids and chromosomes remains understudied. Using a novel approach for detection of homologous loci between genome pairs, we uncover gene sharing with the chromosome in 1,974 (66%) plasmids residing in 1,016 (78%) taxonomically diverse isolates. The majority of homologous loci correspond to mobile elements, which may be duplicated in the host chromosomes in tens of copies. Neighboring shared genes often encode similar functional categories, indicating the transfer of multigene functional units. Rare transfer events of antibiotics resistance genes are observed mainly with mobile elements. The frequent erosion of sequence similarity in homologous regions indicates that the transferred DNA is often devoid of function. DNA transfer between plasmids and chromosomes thus generates genetic variation that is akin to workings of endosymbiotic gene transfer in eukaryotic evolution. Our findings imply that plasmid contribution to gene transfer most often corresponds to transfer of the plasmid entity rather than transfer of protein-coding genes between plasmids and chromosomes.}, } @article {pmid38963857, year = {2024}, author = {Weimann, A and Dinan, AM and Ruis, C and Bernut, A and Pont, S and Brown, K and Ryan, J and Santos, L and Ellison, L and Ukor, E and Pandurangan, AP and Krokowski, S and Blundell, TL and Welch, M and Blane, B and Judge, K and Bousfield, R and Brown, N and Bryant, JM and Kukavica-Ibrulj, I and Rampioni, G and Leoni, L and Harrison, PT and Peacock, SJ and Thomson, NR and Gauthier, J and Fothergill, JL and Levesque, RC and Parkhill, J and Floto, RA}, title = {Evolution and host-specific adaptation of Pseudomonas aeruginosa.}, journal = {Science (New York, N.Y.)}, volume = {385}, number = {6704}, pages = {eadi0908}, doi = {10.1126/science.adi0908}, pmid = {38963857}, issn = {1095-9203}, mesh = {*Pseudomonas aeruginosa/genetics/physiology/pathogenicity ; *Pseudomonas Infections/microbiology ; Humans ; *Cystic Fibrosis/microbiology ; Evolution, Molecular ; Adaptation, Physiological ; Gene Transfer, Horizontal ; Host Specificity ; Host Adaptation ; Macrophages/microbiology/immunology ; }, abstract = {The major human bacterial pathogen Pseudomonas aeruginosa causes multidrug-resistant infections in people with underlying immunodeficiencies or structural lung diseases such as cystic fibrosis (CF). We show that a few environmental isolates, driven by horizontal gene acquisition, have become dominant epidemic clones that have sequentially emerged and spread through global transmission networks over the past 200 years. These clones demonstrate varying intrinsic propensities for infecting CF or non-CF individuals (linked to specific transcriptional changes enabling survival within macrophages); have undergone multiple rounds of convergent, host-specific adaptation; and have eventually lost their ability to transmit between different patient groups. Our findings thus explain the pathogenic evolution of P. aeruginosa and highlight the importance of global surveillance and cross-infection prevention in averting the emergence of future epidemic clones.}, } @article {pmid38962965, year = {2024}, author = {Diamant, I and Adani, B and Sylman, M and Rahav, G and Gal-Mor, O}, title = {The transcriptional regulation of the horizontally acquired iron uptake system, yersiniabactin and its contribution to oxidative stress tolerance and pathogenicity of globally emerging salmonella strains.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2369339}, doi = {10.1080/19490976.2024.2369339}, pmid = {38962965}, issn = {1949-0984}, mesh = {Animals ; *Oxidative Stress ; *Iron/metabolism ; Mice ; *Bacterial Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; *Salmonella enterica/genetics/metabolism/pathogenicity ; Virulence/genetics ; Phenols/metabolism ; Thiazoles/metabolism ; Humans ; Salmonella Infections/microbiology ; Gene Transfer, Horizontal ; Female ; Virulence Factors/genetics/metabolism ; Plasmids/genetics ; }, abstract = {The bacterial species Salmonella enterica (S. enterica) is a highly diverse pathogen containing more than 2600 distinct serovars, which can infect a wide range of animal and human hosts. Recent global emergence of multidrug resistant strains, from serovars Infantis and Muenchen is associated with acquisition of the epidemic megaplasmid, pESI that augments antimicrobial resistance and pathogenicity. One of the main pESI's virulence factors is the potent iron uptake system, yersiniabactin encoded by fyuA, irp2-irp1-ybtUTE, ybtA, and ybtPQXS gene cluster. Here we show that yersiniabactin, has an underappreciated distribution among different S. enterica serovars and subspecies, integrated in their chromosome or carried by different conjugative plasmids, including pESI. While the genetic organization and the coding sequence of the yersiniabactin genes are generally conserved, a 201-bp insertion sequence upstream to ybtA, was identified in pESI. Despite this insertion, pESI-encoded yersiniabactin is regulated by YbtA and the ancestral Ferric Uptake Regulator (Fur), which binds directly to the ybtA and irp2 promoters. Furthermore, we show that yersiniabactin genes are specifically induced during the mid-late logarithmic growth phase and in response to iron-starvation or hydrogen peroxide. Concurring, yersiniabactin was found to play a previously unknown role in oxidative stress tolerance and to enhance intestinal colonization of S. Infantis in mice. These results indicate that yersiniabactin contributes to Salmonella fitness and pathogenicity in vivo and is likely to play a role in the rapid dissemination of pESI among globally emerging Salmonella lineages.}, } @article {pmid38962322, year = {2024}, author = {Sobh, G and Araj, GF and Finianos, M and Sourenian, T and Hrabak, J and Pappagianitsis, CC and Chaar, ME and Bitar, I}, title = {Molecular characterization of carbapenem and ceftazidime-avibactam-resistant Enterobacterales and horizontal spread of bla NDM-5 gene at a Lebanese medical center.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1407246}, pmid = {38962322}, issn = {2235-2988}, mesh = {*Ceftazidime/pharmacology ; *Azabicyclo Compounds/pharmacology ; Humans ; Lebanon ; *beta-Lactamases/genetics/metabolism ; *Klebsiella pneumoniae/genetics/drug effects ; *Whole Genome Sequencing ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics/drug effects ; *Carbapenems/pharmacology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Drug Combinations ; Plasmids/genetics ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; Genome, Bacterial ; Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects/isolation & purification ; Bacterial Proteins/genetics/metabolism ; Tertiary Care Centers ; }, abstract = {INTRODUCTION: In the battle against multidrug-resistant bacterial infections, ceftazidime- avibactam (CZA) stands as a pivotal defense, particularly against carbapenemresistant (CR) Gram-negative pathogens. However, the rise in resistance against this drug poses a significant threat to its effectiveness, highlighting the critical need for in-depth studies about its resistance mechanisms.

METHODS: This research focuses on the genomic characterization of CR- and CZA-resistant Escherichia coli (n=26) and Klebsiella pneumoniae (n=34) strains, harboring the blaNDM and/or blaOXA-48-like genes, at a major Lebanese tertiary care medical center, using whole genome sequencing (WGS).

RESULTS: Our findings revealed a notable prevalence of blaNDM in all K. pneumoniae strains isolates, with 27 of these also harboring blaOXA-48. On the other hand, E. coli strains predominantly carried the blaNDM-5 gene. Whole genome sequencing (WGS) identified a predominance of ST383 among K. pneumoniae strains, which possessed a multi-replicon IncFIB-IncHI1B plasmid harboring the blaNDM-5. Additionally, various Inc group plasmids in K. pneumoniae across multiple sequence types were found to carry the blaNDM. Similarly, diverse STs of E. coli were observed to carry blaNDM-5 on different plasmids.

DISCUSSION: The study underscores NDM carbapenemases as a paramount resistance mechanism in Lebanon,jeopardizing critical last-resort treatments. It also illuminates the role of varied sequence types and mobile genetic elements in the spread of NDM resistance,stressing the urgent need for strategies to mitigate this threat, especially in nosocomial infections.}, } @article {pmid38961341, year = {2024}, author = {Yang, Y and Zhou, P and Tian, D and Wang, W and Zhou, Y and Jiang, X}, title = {CRISPR-Cas3 and type I restriction-modification team up against blaKPC-IncF plasmid transfer in Klebsiella pneumoniae.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {240}, pmid = {38961341}, issn = {1471-2180}, support = {82102439//National Natural Science Foundation of China/ ; 82202564//National Natural Science Foundation of China/ ; 82172315//National Natural Science Foundation of China/ ; 22YF1437500//Shanghai Sailing Program/ ; }, mesh = {*Klebsiella pneumoniae/genetics ; *Plasmids/genetics ; *CRISPR-Cas Systems ; *Conjugation, Genetic ; beta-Lactamases/genetics ; DNA Restriction-Modification Enzymes/genetics ; China ; Klebsiella Infections/microbiology ; Gene Transfer, Horizontal ; Humans ; Genome, Bacterial/genetics ; }, abstract = {OBJECTIVE: We explored whether the Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification (R-M) systems are compatible and act together to resist plasmid attacks.

METHODS: 932 global whole-genome sequences from GenBank, and 459 K. pneumoniae isolates from six provinces of China, were collected to investigate the co-distribution of CRISPR-Cas, R-M systems, and blaKPC plasmid. Conjugation and transformation assays were applied to explore the anti-plasmid function of CRISPR and R-M systems.

RESULTS: We found a significant inverse correlation between the presence of CRISPR and R-M systems and blaKPC plasmids in K. pneumoniae, especially when both systems cohabited in one host. The multiple matched recognition sequences of both systems in blaKPC-IncF plasmids (97%) revealed that they were good targets for both systems. Furthermore, the results of conjugation assay demonstrated that CRISPR-Cas and R-M systems in K. pneumoniae could effectively hinder blaKPC plasmid invasion. Notably, CRISPR-Cas and R-M worked together to confer a 4-log reduction in the acquisition of blaKPC plasmid in conjugative events, exhibiting robust synergistic anti-plasmid immunity.

CONCLUSIONS: Our results indicate the synergistic role of CRISPR and R-M in regulating horizontal gene transfer in K. pneumoniae and rationalize the development of antimicrobial strategies that capitalize on the immunocompromised status of KPC-KP.}, } @article {pmid38960277, year = {2024}, author = {Li, W and Wang, Y and Zhao, K and Xu, L and Shi, T and Ma, B and Lv, X}, title = {Host-virus coevolution drives soil microbial function succession along a millennium land reclamation chronosequence.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2024.06.022}, pmid = {38960277}, issn = {2090-1224}, abstract = {INTRODUCTION: Gene exchange between viruses and hosts plays an important role in driving virus-host coevolution, enabling adaptation of both viruses and hosts to environmental changes. However, the mechanisms and functional significance of virus-host gene exchanges over long-term scales remain largely unexplored.

OBJECTIVE: The present study aimed to gain insights into the role of viruses in virus-host interactions and coevolution by monitoring virome dynamics along a millennium-long land reclamation chronosequence.

METHODS: We collected 24 soil samples from 8 stages of a millennium-long land reclamation chronosequence, including non-reclamation, and reclamation periods of 10, 50, 100, 300, 500, 700, and 1000 years. We characterized their metagenomes, and identified DNA viruses within these metagenomes.

RESULTS: Our findings reveal a significant shift in viral community composition after 50 years of land reclamation, but soil viral diversity reached a stable phase approximately 300 years after the initial reclamation. Analysis of the virus-host network showed a scale-free degree distribution and a reduction in complexity over time, with generalist viruses emerging as key facilitators of horizontal gene transfer.

CONCLUSION: These findings highlight the integral role of viruses, especially generalist types, in mediating gene exchanges between viruses and hosts, thereby influencing the coevolutionary dynamics in soil ecosystems over significant timescales. This study offers novel insights into long-term virus-host interactions, showing how the virome responds to environmental changes, driving shifts in various microbial functions in reclaimed land.}, } @article {pmid38949703, year = {2024}, author = {Saula, AY and Knight, G and Bowness, R}, title = {Within-Host Mathematical Models of Antibiotic Resistance.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2833}, number = {}, pages = {79-91}, pmid = {38949703}, issn = {1940-6029}, mesh = {*Bacteria/genetics/drug effects ; Humans ; *Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Models, Theoretical ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Host-Pathogen Interactions/genetics ; }, abstract = {Mathematical models have been used to study the spread of infectious diseases from person to person. More recently studies are developing within-host modeling which provides an understanding of how pathogens-bacteria, fungi, parasites, or viruses-develop, spread, and evolve inside a single individual and their interaction with the host's immune system.Such models have the potential to provide a more detailed and complete description of the pathogenesis of diseases within-host and identify other influencing factors that may not be detected otherwise. Mathematical models can be used to aid understanding of the global antibiotic resistance (ABR) crisis and identify new ways of combating this threat.ABR occurs when bacteria respond to random or selective pressures and adapt to new environments through the acquisition of new genetic traits. This is usually through the acquisition of a piece of DNA from other bacteria, a process called horizontal gene transfer (HGT), the modification of a piece of DNA within a bacterium, or through. Bacteria have evolved mechanisms that enable them to respond to environmental threats by mutation, and horizontal gene transfer (HGT): conjugation; transduction; and transformation. A frequent mechanism of HGT responsible for spreading antibiotic resistance on the global scale is conjugation, as it allows the direct transfer of mobile genetic elements (MGEs). Although there are several MGEs, the most important MGEs which promote the development and rapid spread of antimicrobial resistance genes in bacterial populations are plasmids and transposons. Each of the resistance-spread-mechanisms mentioned above can be modeled allowing us to understand the process better and to define strategies to reduce resistance.}, } @article {pmid38948848, year = {2024}, author = {Lv, C and Abdullah, M and Chen, W and Zhou, N and Cheng, Z and Chen, Y and Li, M and Simpson, KW and Elsaadi, A and Zhu, Y and Lipkin, SM and Chang, YF}, title = {Genomic characterization of Escherichia coli harbor a polyketide synthase (pks) island associated with colorectal cancer (CRC) development.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.06.16.599199}, pmid = {38948848}, issn = {2692-8205}, abstract = {The E. coli strain harboring the polyketide synthase (Pks) island encodes the genotoxin colibactin, a secondary metabolite reported to have severe implications for human health and for the progression of colorectal cancer. The present study involved whole-genome-wide comparison and phylogenetic analysis of pks harboring E. coli isolates to gain insight into the distribution and evolution of these organism. Fifteen E. coli strains isolated from patients with ulcerative colitis were sequenced, 13 of which harbored pks islands. In addition, 2,654 genomes from the public database were also screened for pks harboring E. coli genomes, 158 of which were pks -positive isolates. Whole-genome-wide comparison and phylogenetic analysis revealed that 171 (158+13) pks -positive isolates belonged to phylogroup B2, and most of the isolates associated to sequence types ST73 and ST95. One isolate from an ulcerative colitis (UC) patient was of the sequence type ST8303. The maximum likelihood tree based on the core genome of pks -positive isolates revealed horizontal gene transfer across sequence types and serotypes. Virulome and resistome analyses revealed the preponderance of virulence genes and a reduced number of antimicrobial genes in Pks -positive isolates. This study strongly contributes to understanding the evolution of pks islands in E. coli .}, } @article {pmid38947372, year = {2024}, author = {Gómez-Gaviria, M and Contreras-López, LM and Aguilera-Domínguez, JI and Mora-Montes, HM}, title = {Strategies of Pharmacological Repositioning for the Treatment of Medically Relevant Mycoses.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {2641-2658}, pmid = {38947372}, issn = {1178-6973}, abstract = {Fungal infections represent a worldwide concern for public health, due to their prevalence and significant increase in cases each year. Among the most frequent mycoses are those caused by members of the genera Candida, Cryptococcus, Aspergillus, Histoplasma, Pneumocystis, Mucor, and Sporothrix, which have been treated for years with conventional antifungal drugs, such as flucytosine, azoles, polyenes, and echinocandins. However, these microorganisms have acquired the ability to evade the mechanisms of action of these drugs, thus hindering their treatment. Among the most common evasion mechanisms are alterations in sterol biosynthesis, modifications of drug transport through the cell wall and membrane, alterations of drug targets, phenotypic plasticity, horizontal gene transfer, and chromosomal aneuploidies. Taking into account these problems, some research groups have sought new therapeutic alternatives based on drug repositioning. Through repositioning, it is possible to use existing pharmacological compounds for which their mechanism of action is already established for other diseases, and thus exploit their potential antifungal activity. The advantage offered by these drugs is that they may be less prone to resistance. In this article, a comprehensive review was carried out to highlight the most relevant repositioning drugs to treat fungal infections. These include antibiotics, antivirals, anthelmintics, statins, and anti-inflammatory drugs.}, } @article {pmid38946899, year = {2024}, author = {Ji, J and Zhu, Y and Zhao, F and Zhang, J and Yao, B and Zhu, M and Yu, Y and Zhang, J and Fu, Y}, title = {Co-colonization of different species harboring KPC or NDM carbapenemase in the same host gut: insight of resistance evolution by horizontal gene transfer.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1416454}, pmid = {38946899}, issn = {1664-302X}, abstract = {INTRODUCTION: The dissemination of carbapenem-resistant Enterobacteriales (CRE) in nosocomial settings is primarily associated with the horizontal transfer of plasmids. However, limited research has focused on the in-host transferability of carbapenem resistance. In this study, ten isolates were collected from gut specimens of five individuals, each hosting two different species, including Escherichia coli, Klebsiella pneumoniae, Klebsiella aerogenes, Enterobacter cloacae, or Citrobacter koseri.

METHODS: Species identification and antimicrobial susceptibility were determined by MALDI-TOF MS and broth microdilution method. Carbapenemase genes were detected and localized using PCR, S1-PFGE and southern blot. The transferability of carbapenemase genes between species was investigated through filter mating experiments, and the genetic contexts of the plasmids were analyzed using whole genome sequencing.

RESULTS AND DISCUSSION: Our results revealed that each of the ten isolates harbored a carbapenemase gene, including bla NDM-5, bla NDM-1, or bla KPC-2, on a plasmid. Five different plasmids were successfully transferred to recipient cells of E. coli, K. pneumoniae or A. baumannii by transconjugation. The genetic contexts of the carbapenemase gene were remarkably similar between the two CRE isolates from each individual. This study highlights the potential for interspecies plasmid transmission in human gut, emphasizing the colonization of CRE as a significant risk factor for the dissemination of carbapenemase genes within the host. These findings underscore the need for appropriate intestinal CRE screening and colonization prevention.}, } @article {pmid38944065, year = {2024}, author = {Marchetti, A and Orlando, M and Bombardi, L and Fusco, S and Mangiagalli, M and Lotti, M}, title = {Evolutionary history and activity towards oligosaccharides and polysaccharides of GH3 glycosidases from an Antarctic marine bacterium.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {133449}, doi = {10.1016/j.ijbiomac.2024.133449}, pmid = {38944065}, issn = {1879-0003}, abstract = {Glycoside hydrolases (GHs) are pivotal in the hydrolysis of the glycosidic bonds of sugars, which are the main carbon and energy sources. The genome of Marinomonas sp. ef1, an Antarctic bacterium, contains three GHs belonging to family 3. These enzymes have distinct architectures and low sequence identity, suggesting that they originated from separate horizontal gene transfer events. M-GH3_A and M-GH3_B, were found to differ in cold adaptation and substrate specificity. M-GH3_A is a bona fide cold-active enzyme since it retains 20 % activity at 10 °C and exhibits poor long-term thermal stability. On the other hand, M-GH3_B shows mesophilic traits with very low activity at 10 °C (< 5 %) and higher long-term thermal stability. Substrate specificity assays highlight that M-GH3_A is a promiscuous β-glucosidase mainly active on cellobiose and cellotetraose, whereas M-GH3_B is a β-xylosidase active on xylan and arabinoxylan. Structural analysis suggests that such functional differences are due to their differently shaped active sites. The active site of M-GH3_A is wider but has a narrower entrance compared to that of M-GH3_B. Genome-based prediction of metabolic pathways suggests that Marinomonas sp. ef1 can use monosaccharides derived from the GH3-catalyzed hydrolysis of oligosaccharides either as a carbon source or for producing osmolytes.}, } @article {pmid38942826, year = {2024}, author = {Boukouvala, S and Kontomina, E and Olbasalis, I and Patriarcheas, D and Tzimotoudis, D and Arvaniti, K and Manolias, A and Tsatiri, MA and Basdani, D and Zekkas, S}, title = {Insights into the genomic and functional divergence of NAT gene family to serve microbial secondary metabolism.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {14905}, pmid = {38942826}, issn = {2045-2322}, support = {3712//Hellenic Foundation for Research and Innovation (H.F.R.I.)/ ; MIS-5000432//State Scholarships Foundation (ΙΚΥ)/ ; }, mesh = {*Multigene Family ; *Secondary Metabolism/genetics ; *Bacteria/genetics/metabolism ; Archaea/genetics/metabolism ; Phylogeny ; Arylamine N-Acetyltransferase/genetics/metabolism ; Fungi/genetics ; Genomics/methods ; Gene Transfer, Horizontal ; }, abstract = {Microbial NAT enzymes, which employ acyl-CoA to acylate aromatic amines and hydrazines, have been well-studied for their role in xenobiotic metabolism. Some homologues have also been linked to secondary metabolism, but this function of NAT enzymes is not as well-known. For this comparative study, we surveyed sequenced microbial genomes to update the list of formally annotated NAT genes, adding over 4000 new sequences (mainly bacterial, but also archaeal, fungal and protist) and portraying a broad but not universal distribution of NATs in the microbiocosmos. Localization of NAT sequences within microbial gene clusters was not a rare finding, and this association was evident across all main types of biosynthetic gene clusters (BGCs) implicated in secondary metabolism. Interrogation of the MIBiG database for experimentally characterized clusters with NAT genes further supports that secondary metabolism must be a major function for microbial NAT enzymes and should not be overlooked by researchers in the field. We also show that NAT sequences can be associated with bacterial plasmids potentially involved in horizontal gene transfer. Combined, our computational predictions and MIBiG literature findings reveal the extraordinary functional diversification of microbial NAT genes, prompting further research into their role in predicted BGCs with as yet uncharacterized function.}, } @article {pmid38942019, year = {2024}, author = {Mason, B and Hayward, DC and Moya, A and Cooke, I and Sorenson, A and Brunner, R and Andrade, N and Huerlimann, R and Bourne, DG and Schaeffer, P and Grinblat, M and Ravasi, T and Ueda, N and Tang, SL and Ball, EE and Miller, DJ}, title = {Microbiome manipulation by corals and other Cnidaria via quorum quenching.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2024.05.073}, pmid = {38942019}, issn = {1879-0445}, abstract = {A dynamic mucous layer containing numerous micro-organisms covers the surface of corals and has multiple functions including both removal of sediment and "food gathering."[1] It is likely to also act as the primary barrier to infection; various proteins and compounds with antimicrobial activity have been identified in coral mucus, though these are thought to be largely or exclusively of microbial origin. As in Hydra,[2] anti-microbial peptides (AMPs) are likely to play major roles in regulating the microbiomes of corals.[3][,][4] Some eukaryotes employ a complementary but less obvious approach to manipulate their associated microbiome by interfering with quorum signaling, effectively preventing bacteria from coordinating gene expression across a population. Our investigation of immunity in the reef-building coral Acropora millepora,[5] however, led to the discovery of a coral gene referred to here as AmNtNH1 that can inactivate a range of acyl homoserine lactones (AHLs), common bacterial quorum signaling molecules, and is induced on immune challenge of adult corals and expressed during the larval settlement process. Closely related proteins are widely distributed within the Scleractinia (hard corals) and some other cnidarians, with multiple paralogs in Acropora, but their closest relatives are bacterial, implying that these are products of one or more lateral gene transfer events post-dating the cnidarian-bilaterian divergence. The deployment by corals of genes used by bacteria to compete with other bacteria reflects a mechanism of microbiome manipulation previously unknown in Metazoa but that may apply more generally.}, } @article {pmid38941922, year = {2024}, author = {Li, B and Ni, S and Liu, Y and Lin, J and Wang, X}, title = {The histone-like nucleoid-structuring protein encoded by the plasmid pMBL6842 regulates both plasmid stability and host physiology of Pseudoalteromonas rubra SCSIO 6842.}, journal = {Microbiological research}, volume = {286}, number = {}, pages = {127817}, doi = {10.1016/j.micres.2024.127817}, pmid = {38941922}, issn = {1618-0623}, abstract = {Plasmids orchestrate bacterial adaptation across diverse environments and facilitate lateral gene transfer within bacterial communities. Their presence can perturb host metabolism, creating a competitive advantage for plasmid-free cells. Plasmid stability hinges on efficient replication and partition mechanisms. While plasmids commonly encode histone-like nucleoid-structuring (H-NS) family proteins, the precise influence of plasmid-encoded H-NS proteins on stability remains elusive. In this study, we examined the conjugative plasmid pMBL6842, harboring the hns gene, and observed its positive regulation of parAB transcription, critical for plasmid segregation. Deletion of hns led to rapid plasmid loss, which was remedied by hns complementation. Further investigations unveiled adverse effects of hns overexpression on the bacterial host. Transcriptome analysis revealed hns's role in regulating numerous bacterial genes, impacting both host growth and swimming motility in the presence of the hns gene. Therefore, our study unveils the multifaceted roles of H-NS in both plasmid stability and host physiology, underscoring its biological significance and paving the way for future inquiries into the involvement of H-NS in horizontal gene transfer events.}, } @article {pmid38940556, year = {2024}, author = {Sun, W-S and Torrens, G and Ter Beek, J and Cava, F and Berntsson, RP-A}, title = {Breaking barriers: pCF10 type 4 secretion system relies on a self-regulating muramidase to modulate the cell wall.}, journal = {mBio}, volume = {}, number = {}, pages = {e0048824}, doi = {10.1128/mbio.00488-24}, pmid = {38940556}, issn = {2150-7511}, abstract = {Conjugative type 4 secretion systems (T4SSs) are the main driver for the spread of antibiotic resistance genes and virulence factors in bacteria. To deliver the DNA substrate to recipient cells, it must cross the cell envelopes of both donor and recipient bacteria. In the T4SS from the enterococcal conjugative plasmid pCF10, PrgK is known to be the active cell wall degrading enzyme. It has three predicted extracellular hydrolase domains: metallo-peptidase (LytM), soluble lytic transglycosylase (SLT), and cysteine, histidine-dependent amidohydrolases/peptidases (CHAP). Here, we report the structure of the LytM domain and show that its active site is degenerate and lacks the active site metal. Furthermore, we show that only the predicted SLT domain is functional in vitro and that it unexpectedly has a muramidase instead of a lytic transglycosylase activity. While we did not observe any peptidoglycan hydrolytic activity for the LytM or CHAP domain, we found that these domains downregulated the SLT muramidase activity. The CHAP domain was also found to be involved in PrgK dimer formation. Furthermore, we show that PrgK interacts with PrgL, which likely targets PrgK to the rest of the T4SS. The presented data provides important information for understanding the function of Gram-positive T4SSs.IMPORTANCEAntibiotic resistance is a large threat to human health and is getting more prevalent. One of the major contributors to the spread of antibiotic resistance among different bacteria is type 4 secretion systems (T4SS). However, mainly T4SSs from Gram-negative bacteria have been studied in detail. T4SSs from Gram-positive bacteria, which stand for more than half of all hospital-acquired infections, are much less understood. The significance of our research is in identifying the function and regulation of a cell wall hydrolase, a key component of the pCF10 T4SS from Enterococcus faecalis. This system is one of the best-studied Gram-positive T4SSs, and this added knowledge aids in our understanding of horizontal gene transfer in E. faecalis as well as other medically relevant Gram-positive bacteria.}, } @article {pmid38940543, year = {2024}, author = {Jian, J and Wang, Z and Chen, C and Workman, CT and Fang, X and Larsen, TO and Guo, J and Sonnenschein, EC}, title = {Two high-quality Prototheca zopfii genomes provide new insights into their evolution as obligate algal heterotrophs and their pathogenicity.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0414823}, doi = {10.1128/spectrum.04148-23}, pmid = {38940543}, issn = {2165-0497}, abstract = {UNLABELLED: The majority of the nearly 10,000 described species of green algae are photoautotrophs; however, some species have lost their ability to photosynthesize and become obligate heterotrophs that rely on parasitism for survival. Two high-quality genomes of the heterotrophic algae Prototheca zopfii Pz20 and Pz23 were obtained using short- and long-read genomic as well as transcriptomic data. The genome sizes were 31.2 Mb and 31.3 Mb, respectively, and contig N50 values of 1.99 Mb and 1.26 Mb. Although P. zopfii maintained its plastid genome, the transition to heterotrophy led to a reduction in both plastid and nuclear genome size, including the loss of photosynthesis-related genes from both the nuclear and plastid genomes and the elimination of genes encoding for carotenoid oxygenase and pheophorbide an oxygenase. The loss of genes, including basic leucine-zipper (bZIP) transcription factors, flavin adenine dinucleotide-linked oxidase, and helicase, could have played a role in the transmission of autotrophy to heterotrophs and in the processes of abiotic stress resistance and pathogenicity. A total of 66 (1.37%) and 73 (1.49%) genes were identified as potential horizontal gene transfer events in the two P. zopfii genomes, respectively. Genes for malate synthase and isocitrate lyase, which are horizontally transferred from bacteria, may play a pivotal role in carbon and nitrogen metabolism as well as the pathogenicity of Prototheca and non-photosynthetic organisms. The two high-quality P. zopfii genomes provide new insights into their evolution as obligate heterotrophs and pathogenicity.

IMPORTANCE: The genus Prototheca, characterized by its heterotrophic nature and pathogenicity, serves as an exemplary model for investigating pathobiology. The limited understanding of the protothecosis infectious disease is attributed to the lack of genomic resources. Using HiFi long-read sequencing, both nuclear and plastid genomes were generated for two strains of P. zopfii. The findings revealed a concurrent reduction in both plastid and nuclear genome size, accompanied by the loss of genes associated with photosynthesis, carotenoid oxygenase, basic leucine-zipper (bZIP) transcription factors, and others. The analysis of horizontal gene transfer revealed the presence of 1.37% and 1.49% bacterial genes, including malate synthase and isocitrate lyase, which play crucial roles in carbon and nitrogen metabolism, as well as pathogenicity and obligate heterotrophy. The two high-quality P. zopfii genomes represent valuable resources for investigating their adaptation and evolution as obligate heterotrophs, as well as for developing future prevention and treatment strategies against protothecosis.}, } @article {pmid38940156, year = {2024}, author = {Curry, KD and Yu, FB and Vance, SE and Segarra, S and Bhaya, D and Chikhi, R and Rocha, EPC and Treangen, TJ}, title = {Reference-free structural variant detection in microbiomes via long-read co-assembly graphs.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {Supplement_1}, pages = {i58-i67}, doi = {10.1093/bioinformatics/btae224}, pmid = {38940156}, issn = {1367-4811}, support = {//Ken Kennedy Institute Recruiting/ ; //Rice University Wagoner Foreign Study Scholarship/ ; P01-AI152999/GF/NIH HHS/United States ; //National Institute of Allergy and Infectious Diseases/ ; IIS-2239114//NSF/ ; //NSF/ ; EF-2126387//MIM Universal Rules of Live/ ; //European Union's Horizon 2020/ ; 872539//Marie Skłodowska-Curie/ ; //Carnegie Institution for Science/ ; //Department of Energy Joint Genome Institute/ ; //Office of Science/ ; //Department of Energy/ ; 2023333162//NSF/ ; }, mesh = {*Microbiota/genetics ; *Metagenome ; *Genome, Bacterial ; Metagenomics/methods ; Gene Transfer, Horizontal ; Bacteria/genetics ; Algorithms ; }, abstract = {MOTIVATION: The study of bacterial genome dynamics is vital for understanding the mechanisms underlying microbial adaptation, growth, and their impact on host phenotype. Structural variants (SVs), genomic alterations of 50 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to the absence of clear reference genomes and the presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing all metagenomic samples in a series (time or other metric) into a single co-assembly graph. The log fold change in graph coverage between successive samples is then calculated to call SVs that are thriving or declining.

RESULTS: We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, particularly as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between successive time and temperature samples, suggesting host advantage. Our approach leverages previous work in assembly graph structural and coverage patterns to provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial gene flux.

rhea is open source and available at: https://github.com/treangenlab/rhea.}, } @article {pmid38936370, year = {2024}, author = {Yu, T and Xu, X and Liu, Y and Wang, X and Wu, S and Qiu, Z and Liu, X and Pan, X and Gu, C and Wang, S and Dong, L and Li, W and Yao, X}, title = {Multi-omics signatures reveal genomic and functional heterogeneity of Cutibacterium acnes in normal and diseased skin.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2024.06.002}, pmid = {38936370}, issn = {1934-6069}, abstract = {Cutibacterium acnes is the most abundant bacterium of the human skin microbiome since adolescence, participating in both skin homeostasis and diseases. Here, we demonstrate individual and niche heterogeneity of C. acnes from 1,234 isolate genomes. Skin disease (atopic dermatitis and acne) and body site shape genomic differences of C. acnes, stemming from horizontal gene transfer and selection pressure. C. acnes harbors characteristic metabolic functions, fewer antibiotic resistance genes and virulence factors, and a more stable genome compared with Staphylococcus epidermidis. Integrated genome, transcriptome, and metabolome analysis at the strain level unveils the functional characteristics of C. acnes. Consistent with the transcriptome signature, C. acnes in a sebum-rich environment induces toxic and pro-inflammatory effects on keratinocytes. L-carnosine, an anti-oxidative stress metabolite, is up-regulated in the C. acnes metabolome from atopic dermatitis and attenuates skin inflammation. Collectively, our study reveals the joint impact of genes and the microenvironment on C. acnes function.}, } @article {pmid38936366, year = {2024}, author = {Garric, S and Ratin, M and Marie, D and Foulon, V and Probert, I and Rodriguez, F and Six, C}, title = {Impaired photoacclimation in a kleptoplastidic dinoflagellate reveals physiological limits of early stages of endosymbiosis.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2024.05.066}, pmid = {38936366}, issn = {1879-0445}, abstract = {Dinophysis dinoflagellates are predators of Mesodinium ciliates, from which they retain only the plastids of cryptophyte origin. The absence of nuclear photosynthetic cryptophyte genes in Dinophysis raises intriguing physiological and evolutionary questions regarding the functional dynamics of these temporary kleptoplastids within a foreign cellular environment. In an experimental setup including two light conditions, the comparative analysis with Mesodinium rubrum and the cryptophyte Teleaulax amphioxeia revealed that Dinophysis acuminata possessed a smaller and less dynamic functional photosynthetic antenna for green light, a function performed by phycoerythrin. We showed that the lack of the cryptophyte nucleus prevented the synthesis of the phycoerythrin α subunit, thereby hindering the formation of a complete phycoerythrin in Dinophysis. In particular, biochemical analyses showed that Dinophysis acuminata synthesized a poorly stable, incomplete phycoerythrin composed of chromophorylated β subunits, with impaired performance. We show that, consequently, a continuous supply of new plastids is crucial for growth and effective photoacclimation in this organism. Transcriptome analyses revealed that all examined strains of Dinophysis spp. have acquired the cryptophyte pebA and pebB genes through horizontal gene transfer, suggesting a potential ability to synthesize the phycobilin pigments bound to the cryptophyte phycoerythrin. By emphasizing that a potential long-term acquisition of the cryptophyte plastid relies on establishing genetic independence for essential functions such as light harvesting, this study highlights the intricate molecular challenges inherent in the enslavement of organelles and the processes involved in the diversification of photosynthetic organisms through endosymbiosis.}, } @article {pmid38936185, year = {2024}, author = {Hu, CJ and Lv, YQ and Xian, WD and Jiao, JY and Lian, ZH and Tan, S and Li, MM and Luo, ZH and Liu, ZT and Lv, AP and Liu, L and Ali, M and Liu, WQ and Li, WJ}, title = {Multi-omics insights into the function and evolution of sodium benzoate biodegradation pathway in Benzoatithermus flavus gen. nov., sp. nov. from hot spring.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {135017}, doi = {10.1016/j.jhazmat.2024.135017}, pmid = {38936185}, issn = {1873-3336}, abstract = {Biodegradation stands as an eco-friendly and effective approach for organic contaminant remediation. However, research on microorganisms degrading sodium benzoate contaminants in extreme environments remains limited. In this study, we report to display the isolation of a novel hot spring enriched cultures with sodium benzoate (400 mg/L) as the sole carbon source. The results revealed that the phylum Pseudomonadota was the potential sodium benzoate degrader and a novel genus within the family Geminicoccaceae of this phylum. The isolated strain was named Benzoatithermus flavus SYSU G07066[T] and was isolated from HNT-2 hot spring samples. Genomic analysis revealed that SYSU G07066[T] carried benABC genes and physiological experiments indicated the ability to utilize sodium benzoate as a sole carbon source for growth, which was further confirmed by transcriptomic data with expression of benABC. Phylogenetic analysis suggested that Horizontal Gene Transfer (HGT) plays a significant role in acquiring sodium benzoate degradation capability among prokaryotes, and SYSU G07066[T] might have acquired benABC genes through HGT from the family Acetobacteraceae. The discovery of the first microorganism with sodium benzoate degradation function from a hot spring enhances our understanding of the diverse functions within the family Geminicoccaceae. This study unearths the first novel genus capable of efficiently degrading sodium benzoate and its evolution history at high temperatures, holding promising industrial applications, and provides a new perspective for further exploring the application potential of hot spring "microbial dark matter".}, } @article {pmid38936038, year = {2024}, author = {Wang, F and Huang, W and Zhang, M and Zhang, Q and Luo, Y and Chen, J and Su, Y and Huang, H and Fang, F and Luo, J}, title = {Disinfectant polyhexamethylene guanidine triggered simultaneous efflux pump antibiotic- and metal-resistance genes propagation during sludge anaerobic digestion.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {357}, number = {}, pages = {124453}, doi = {10.1016/j.envpol.2024.124453}, pmid = {38936038}, issn = {1873-6424}, abstract = {The environmental transmission of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) exerted devastating threats to global public health, and their interactions with other emerging contaminants (ECs) have raised increasing concern. This study investigated that the abundances of ARGs and MRGs with the predominant type of efflux pump were simultaneously increased (8.4-59.1%) by disinfectant polyhexamethylene guanidine (PHMG) during waste activated sludge (WAS) anaerobic digestion. The aggregation of the same microorganisms (i.e., Hymenobacter and Comamonas) and different host bacteria (i.e., Azoarcus and Thauera) were occurred upon exposure to PHMG, thereby increasing the co-selection and propagation of MRGs and ARGs by vertical gene transfer. Moreover, PHMG enhanced the process of horizontal gene transfer (HGT), facilitating their co-transmission by the same mobile genetic elements (20.2-223.7%). Additionally, PHMG up-regulated the expression of critical genes (i.e., glnB, trpG and gspM) associated with the HGT of ARGs and MRGs (i.e., two-component regulatory system and quorum sensing) and exocytosis system (i.e., bacterial secretion system). Structural equation model analysis further verified that the key driver for the simultaneous enrichment of ARGs and MRGs under PHMG stress was microbial community structure. The study gives new insights into the aggravated environmental risks and mechanisms of ECs in sludge digestion system, providing guidance for subsequent regulation and control of ECs.}, } @article {pmid38936019, year = {2024}, author = {Liu, Y and Song, X and Hou, X and Wang, Y and Cao, X}, title = {Effect of Mn-HA on ARGs and MRGs in nitrogen-culturing sludge.}, journal = {Journal of environmental management}, volume = {365}, number = {}, pages = {121615}, doi = {10.1016/j.jenvman.2024.121615}, pmid = {38936019}, issn = {1095-8630}, abstract = {The simultaneous escalation in ARGs (antibiotic resistance genes) and MRGs (metal resistance genes) further complicates the intricate network of factors contributing to the proliferation of microbial resistance. Manganese, which has been reported to affect the resistance of bacteria to antibiotics and metals, plays a vital role in microbial nitrogen metabolism. Moreover, nitrifying and denitrifying populations are potential hosts for ARGs. In this study, manganese was introduced in its prevalent organic chelated form in the environment (Manganese humus chelates, Mn-HA) to a N metabolism sludge to explore the effect of manganese on MRGs and ARGs dissemination. Metagenomics results revealed that manganese availability enhances nitrogen metabolism, while a decrease in ARGs was noted which may be attributed to the inhibition of horizontal gene transfer (HGT), reflected in the reduced integrase -encoded gene int. Population analysis revealed that nitrifier and denitrifier genus harbor MRGs and ARGs, indicating that nitrifier and denitrifier are hosts of MRGs and ARGs. This raises the question of whether the prevalence of ARGs is always increased in metal-contained environments.}, } @article {pmid38935608, year = {2024}, author = {Randriantseheno, LN and Andrianaivoarimanana, V and Pizarro-Cerdá, J and Wagner, DM and Rajerison, M}, title = {Review of genotyping methods for Yersinia pestis in Madagascar.}, journal = {PLoS neglected tropical diseases}, volume = {18}, number = {6}, pages = {e0012252}, doi = {10.1371/journal.pntd.0012252}, pmid = {38935608}, issn = {1935-2735}, mesh = {*Yersinia pestis/genetics/classification/isolation & purification ; Madagascar/epidemiology ; *Plague/microbiology/epidemiology ; Humans ; Animals ; Genotype ; Genotyping Techniques/methods ; }, abstract = {BACKGROUND: Plague, a zoonotic disease caused by Yersinia pestis, was responsible for 3 historical human pandemics that killed millions of people. It remains endemic in rodent populations in Africa, Asia, North America, and South America but human plague is rare in most of these locations. However, human plague is still highly prevalent in Madagascar, which typically records a significant part of all annual global cases. This has afforded an opportunity to study contemporary human plague in detail using various typing methods for Y. pestis.

AIM: This review aims to summarize the methods that have been used to type Y. pestis in Madagascar along with the major discoveries that have been made using these approaches.

METHODS: Pubmed and Google Scholar were used to search for the keywords: "typing Yersinia pestis Madagascar," "evolution Yersinia pestis Madagascar," and "diversity Yersinia pestis Madagascar." Eleven publications were relevant to our topic and further information was retrieved from references cited in those publications.

RESULTS: The history of Y. pestis typing in Madagascar can be divided in 2 periods: the pre-genomics and genomics eras. During the pre-genomics era, ribotyping, direct observation of plasmid content and plasmid restriction fragment length polymorphisms (RFLP) were employed but only revealed a limited amount of diversity among Malagasy Y. pestis strains. Extensive diversity only started to be revealed in the genomics era with the use of clustered regularly interspaced palindromic repeats (CRISPR), multiple-locus variable number tandem repeats (VNTR) analysis (MLVA), and single-nucleotide polymorphisms (SNPs) discovered from whole genome sequences. These higher-resolution genotyping methods have made it possible to highlight the distribution and persistence of genotypes in the different plague foci of Madagascar (Mahajanga and the Central and Northern Highlands) by genotyping strains from the same locations across years, to detect transfers between foci, to date the emergence of genotypes, and even to document the transmission of antimicrobial resistant (AMR) strains during a pneumonic plague outbreak. Despite these discoveries, there still remain topics that deserve to be explored, such as the contribution of horizontal gene transfer to the evolution of Malagasy Y. pestis strains and the evolutionary history of Y. pestis in Madagascar.

CONCLUSIONS: Genotyping of Y. pestis has yielded important insights on plague in Madagascar, particularly since the advent of whole-genome sequencing (WGS). These include a better understanding of plague persistence in the environment, antimicrobial AMR and multi-drug resistance in Y. pestis, and the person-to-person spread of pneumonic plague. Considering that human plague is still a significant public health threat in Madagascar, these insights can be useful for controlling and preventing human plague in Madagascar and elsewhere, and also are relevant for understanding the historical pandemics and the possible use of Y. pestis as a biological weapon.}, } @article {pmid38935220, year = {2024}, author = {Parra, B and Lutz, VT and Brøndsted, L and Carmona, JL and Palomo, A and Nesme, J and Van Hung Le, V and Smets, BF and Dechesne, A}, title = {Characterization and Abundance of Plasmid-Dependent Alphatectivirus Bacteriophages.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {85}, pmid = {38935220}, issn = {1432-184X}, support = {101026675//European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant/ ; 002200000279//VRID Postdoctorado from Vicerrectoría de Investigación y Desarrollo, Universidad de Concepción/ ; P-PhanFARE (23046)//Villum Fonden/ ; }, mesh = {*Plasmids/genetics ; *Wastewater/virology/microbiology ; *Bacteriophages/genetics/isolation & purification/physiology/classification ; Genome, Viral ; Escherichia coli/virology/genetics ; Host Specificity ; Pseudomonas putida/virology/genetics ; Salmonella enterica/virology/genetics ; Phylogeny ; }, abstract = {Antimicrobial resistance (AMR) is a major public health threat, exacerbated by the ability of bacteria to rapidly disseminate antimicrobial resistance genes (ARG). Since conjugative plasmids of the incompatibility group P (IncP) are ubiquitous mobile genetic elements that often carry ARG and are broad-host-range, they are important targets to prevent the dissemination of AMR. Plasmid-dependent phages infect plasmid-carrying bacteria by recognizing components of the conjugative secretion system as receptors. We sought to isolate plasmid-dependent phages from wastewater using an avirulent strain of Salmonella enterica carrying the conjugative IncP plasmid pKJK5. Irrespective of the site, we only obtained bacteriophages belonging to the genus Alphatectivirus. Eleven isolates were sequenced, their genomes analyzed, and their host range established using S. enterica, Escherichia coli, and Pseudomonas putida carrying diverse conjugative plasmids. We confirmed that Alphatectivirus are abundant in domestic and hospital wastewater using culture-dependent and culture-independent approaches. However, these results are not consistent with their low or undetectable occurrence in metagenomes. Therefore, overall, our results emphasize the importance of performing phage isolation to uncover diversity, especially considering the potential of plasmid-dependent phages to reduce the spread of ARG carried by conjugative plasmids, and to help combat the AMR crisis.}, } @article {pmid38934605, year = {2024}, author = {Burcham, ZM}, title = {Comparative genomic analysis of an emerging Pseudomonadaceae member, Thiopseudomonas alkaliphila.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0415723}, doi = {10.1128/spectrum.04157-23}, pmid = {38934605}, issn = {2165-0497}, abstract = {Thiopseudomonas alkaliphila, an organism recently classified within the Pseudomonadaceae family, has been detected in diverse sources such as human tissues, animal guts, industrial fermenters, and decomposition environments, suggesting a diverse ecological role. However, a large knowledge gap exists in how T. alkaliphila functions. In this comparative genomic analysis, adaptations indicative of habitat specificity among strains and genomic similarity to known opportunistic pathogens are revealed. Genomic investigation reveals a core metabolic utilization of multiple oxidative and non-oxidative catabolic pathways, suggesting adaptability to varied environments and carbon sources. The genomic repertoire of T. alkaliphila includes secondary metabolites, such as antimicrobials and siderophores, indicative of its involvement in microbial competition and resource acquisition. Additionally, the presence of transposases, prophages, plasmids, and Clustered Regularly Interspaced Short Palindromic Repeats-Cas systems in T. alkaliphila genomes suggests mechanisms for horizontal gene transfer and defense against viral predation. This comprehensive genomic analysis expands our understanding on the ecological functions, community interactions, and potential virulence of T. alkaliphila, while emphasizing its adaptability and diverse capabilities across environmental and host-associated ecosystems.IMPORTANCEAs the microbial world continues to be explored, new organisms will emerge with beneficial and/or pathogenetic impact. Thiopseudomonas alkaliphila is a species originally isolated from clinical human tissue and fluid samples but has not been attributed to disease. Since its classification, T. alkaliphila has been found in animal guts, animal waste, decomposing remains, and biogas fermentation reactors. This is the first study to provide an in-depth view of the metabolic potential of publicly available genomes belonging to this species through a comparative genomics and draft pangenome calculation approach. It was found that T. alkaliphila is metabolically versatile and likely adapts to diverse energy sources and environments, which may make it useful for bioremediation and in industrial settings. A range of virulence factors and antibiotic resistances were also detected, suggesting T. alkaliphila may operate as an undescribed opportunistic pathogen.}, } @article {pmid38930473, year = {2024}, author = {Otero-Olarra, JE and Díaz-Cárdenas, G and Aguilera-Arreola, MG and Curiel-Quesada, E and Pérez-Valdespino, A}, title = {Aeromonas trota Is Highly Refractory to Acquire Exogenous Genetic Material.}, journal = {Microorganisms}, volume = {12}, number = {6}, pages = {}, doi = {10.3390/microorganisms12061091}, pmid = {38930473}, issn = {2076-2607}, abstract = {Aeromonas trota is sensitive to most antibiotics and the sole species of this genus susceptible to ampicillin. This susceptibility profile could be related to its inability to acquire exogenous DNA. In this study, A. trota isolates were analyzed to establish their capacity to incorporate foreign DNA. Fourteen strains were identified as A. trota by multilocus phylogenetic analysis (MLPA). Minimal inhibitory concentrations of antibiotics (MIC) were assessed, confirming the susceptibility to most antibiotics tested. To explore their capacity to be transformed, A. trota strains were used as recipients in different horizontal transfer assays. Results showed that around fifty percent of A. trota strains were able to incorporate pBAMD1-2 and pBBR1MCS-3 plasmids after conjugal transfer. In all instances, conjugation frequencies were very low. Interestingly, several isoforms of plasmid pBBR1MCS-3 were observed in transconjugants. Strains could not receive pAr-32, a native plasmid from A. salmonicida. A. trota strains were unable to receive DNA by means of electroporation, natural transformation or vesiduction. These results confirm that A. trota species are extremely refractory to horizontal gene transfer, which could be associated to plasmid instability resulting from oligomerization or to the presence of defense systems against exogenous genetic material in their genomes. To explain the poor results of horizontal gene transfer (HGT), selected genomes were sequenced and analyzed, revealing the presence of defense systems, which could prevent the stable incorporation of exogenous DNA in A. trota.}, } @article {pmid38927231, year = {2024}, author = {Amábile-Cuevas, CF and Lund-Zaina, S}, title = {Non-Canonical Aspects of Antibiotics and Antibiotic Resistance.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/antibiotics13060565}, pmid = {38927231}, issn = {2079-6382}, abstract = {The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.}, } @article {pmid38927226, year = {2024}, author = {Gestels, Z and Abdellati, S and Kenyon, C and Manoharan-Basil, SS}, title = {Ciprofloxacin Concentrations 100-Fold Lower than the MIC Can Select for Ciprofloxacin Resistance in Neisseria subflava: An In Vitro Study.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/antibiotics13060560}, pmid = {38927226}, issn = {2079-6382}, support = {Unknown//PRESTIP/ ; }, abstract = {Neisseria gonorrhoeae can acquire antimicrobial resistance (AMR) through horizontal gene transfer (HGT) from other Neisseria spp. such as commensals like Neisseria subflava. Low doses of antimicrobials in food could select for AMR in N. subflava, which could then be transferred to N. gonorrhoeae. In this study, we aimed to determine the lowest concentration of ciprofloxacin that can induce ciprofloxacin resistance (minimum selection concentration-MSC) in a N. subflava isolate (ID-Co000790/2, a clinical isolate collected from a previous community study conducted at ITM). In this study, Neisseria subflava was serially passaged on gonococcal (GC) medium agar plates containing ciprofloxacin concentrations ranging from 1:100 to 1:10,000 below its ciprofloxacin MIC (0.006 µg/mL) for 6 days. After 6 days of serial passaging at ciprofloxacin concentrations of 1/100th of the MIC, 24 colonies emerged on the plate containing 0.06 µg/mL ciprofloxacin, which corresponds to the EUCAST breakpoint for N. gonorrhoeae. Their ciprofloxacin MICs were between 0.19 to 0.25 µg/mL, and whole genome sequencing revealed a missense mutation T91I in the gyrA gene, which has previously been found to cause reduced susceptibility to fluoroquinolones. The N. subflava MSCde novo was determined to be 0.06 ng/mL (0.00006 µg/mL), which is 100×-fold lower than the ciprofloxacin MIC. The implications of this finding are that the low concentrations of fluoroquinolones found in certain environmental samples, such as soil, river water, and even the food we eat, may be able to select for ciprofloxacin resistance in N. subflava.}, } @article {pmid38927197, year = {2024}, author = {Yaikhan, T and Suwannasin, S and Singkhamanan, K and Chusri, S and Pomwised, R and Wonglapsuwan, M and Surachat, K}, title = {Genomic Characterization of Multidrug-Resistant Enterobacteriaceae Clinical Isolates from Southern Thailand Hospitals: Unraveling Antimicrobial Resistance and Virulence Mechanisms.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/antibiotics13060531}, pmid = {38927197}, issn = {2079-6382}, support = {B13F670075//the NSRF via the Program Management Unit for Human Resources & Institutional Development, Research Innovation/ ; //the Postdoctoral Fellowship from Prince of Songkla University/ ; B13F660074//the NSRF via the Program Management Unit for Human Resources & Institutional Development, Research and Innovation/ ; }, abstract = {The emergence and spread of antimicrobial resistance (AMR) among Enterobacteriaceae pose significant threats to global public health. In this study, we conducted a short-term surveillance effort in Southern Thailand hospitals to characterize the genomic diversity, AMR profiles, and virulence factors of Enterobacteriaceae strains. We identified 241 carbapenem-resistant Enterobacteriaceae, of which 12 were selected for whole-genome sequencing (WGS) and genome analysis. The strains included Proteus mirabilis, Serratia nevei, Klebsiella variicola, Klebsiella aerogenes, Klebsiella indica, Klebsiella grimontii, Phytobacter ursingii, Phytobacter palmae, Kosakonia spp., and Citrobacter freundii. The strains exhibited high levels of multidrug resistance, including resistance to carbapenem antibiotics. Whole-genome sequencing revealed a diverse array of antimicrobial resistance genes (ARGs), with strains carrying genes for ß-lactamase, efflux pumps, and resistance to other antibiotic classes. Additionally, stress response, metal tolerance, and virulence-associated genes were identified, highlighting the adaptability and pathogenic potential of these strains. A plasmid analysis identified several plasmid replicons, including IncA/C2, IncFIB(K), and Col440I, as well as several plasmids identical to those found globally, indicating the potential for the horizontal gene transfer of ARGs. Importantly, this study also identified a novel species of Kosakonia spp. PSU27, adding to the understanding of the genetic diversity and resistance mechanisms of Enterobacteriaceae in Southern Thailand. The results reported in this study highlight the critical importance of implementing effective antimicrobial management programs and developing innovative treatment approaches to urgently tackle AMR.}, } @article {pmid38927185, year = {2024}, author = {Peng, J and Feng, J and Ji, H and Kong, X and Hong, J and Zhu, L and Qian, H}, title = {Emergence of Rarely Reported Extensively Drug-Resistant Salmonella Enterica Serovar Paratyphi B among Patients in East China.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/antibiotics13060519}, pmid = {38927185}, issn = {2079-6382}, support = {National Major S&T Projects(2018ZX10714-002)//Ministry of Science and Technology of the People's Republic of China/ ; Ym2023040//Jiangsu Preventive Medicine Association/ ; }, abstract = {BACKGROUND: In recent years, global concern over increasing multidrug resistance (MDR) among various Salmonella serotypes has grown significantly. However, reports on MDR Salmonella Paratyphi B remain scarce, let alone the extensively drug-resistant (XDR) strains.

METHODS: In this retrospective study, we investigated the isolates of Salmonella Paratyphi B in Jiangsu Province over the past decade and carried out antimicrobial susceptibility tests, then the strains were sequenced and bioinformatics analyses were performed.

RESULTS: 27 Salmonella Paratyphi B strains were identified, of which the predominant STs were ST42 (11), ST86 (10), and ST2814 (5). Among these strains, we uncovered four concerning XDR Salmonella Paratyphi B ST2814 strains (4/5) which were previously unreported. These alarmingly resistant isolates showed resistance to all three major antibiotic classes for Salmonella treatment and even the last resort treatment tigecycline. Bioinformatics analysis revealed high similarity between the plasmids harbored by these XDR strains and diverse Salmonella serotypes and Escherichia coli from China and neighboring regions. Notably, these four plasmids carried the ramAp gene responsible for multiple antibiotic resistance by regulating the AcrAB-TolC pump, predominantly originating from China. Additionally, a distinct MDR ST42(1/11) strain with an ICE on chromosome was also identified. Furthermore, phylogenetic analysis of global ST42/ST2814 isolates highlighted the regional specificity of these strains, with Jiangsu isolates clustering together with domestic isolates and XDR ST2814 forming a distinct branch, suggesting adaptation to local antibiotic pressures.

CONCLUSIONS: This research underscores the pressing need for closely monitoring the MDR/XDR Salmonella Paratyphi B, particularly the emerging ST2814 strains in Jiangsu Province, to effectively curb its spread and protect public health. Moreover, surveillance should be strengthened across different ecological niches and genera to track resistance genes and horizontal gene transfer elements under the concept of "ONE HEALTH".}, } @article {pmid38926391, year = {2024}, author = {Brown, CL and Maile-Moskowitz, A and Lopatkin, AJ and Xia, K and Logan, LK and Davis, BC and Zhang, L and Vikesland, PJ and Pruden, A}, title = {Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5412}, pmid = {38926391}, issn = {2041-1723}, support = {1545756//National Science Foundation (NSF)/ ; 2004751//National Science Foundation (NSF)/ ; 2125798//National Science Foundation (NSF)/ ; 4813//Water Research Foundation (WRF)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Sewage/microbiology ; *Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/metabolism ; Water Purification/methods ; Metagenomics/methods ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid/methods ; Drug Resistance, Bacterial/genetics ; Selection, Genetic ; }, abstract = {Activated sludge is the centerpiece of biological wastewater treatment, as it facilitates removal of sewage-associated pollutants, fecal bacteria, and pathogens from wastewater through semi-controlled microbial ecology. It has been hypothesized that horizontal gene transfer facilitates the spread of antibiotic resistance genes within the wastewater treatment plant, in part because of the presence of residual antibiotics in sewage. However, there has been surprisingly little evidence to suggest that sewage-associated antibiotics select for resistance at wastewater treatment plants via horizontal gene transfer or otherwise. We addressed the role of sewage-associated antibiotics in promoting antibiotic resistance using lab-scale sequencing batch reactors fed field-collected wastewater, metagenomic sequencing, and our recently developed bioinformatic tool Kairos. Here, we found confirmatory evidence that fluctuating levels of antibiotics in sewage are associated with horizontal gene transfer of antibiotic resistance genes, microbial ecology, and microdiversity-level differences in resistance gene fate in activated sludge.}, } @article {pmid38922012, year = {2024}, author = {Kerek, Á and Németh, V and Szabó, Á and Papp, M and Bányai, K and Kardos, G and Kaszab, E and Bali, K and Nagy, Z and Süth, M and Jerzsele, Á}, title = {Monitoring Changes in the Antimicrobial-Resistance Gene Set (ARG) of Raw Milk and Dairy Products in a Cattle Farm, from Production to Consumption.}, journal = {Veterinary sciences}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/vetsci11060265}, pmid = {38922012}, issn = {2306-7381}, support = {RRF-2.3.1-21-2022-00001//National Recovery Fund/ ; }, abstract = {Raw milk and dairy products can serve as potential vectors for transmissible bacterial, viral and protozoal diseases, alongside harboring antimicrobial-resistance genes. This study monitors the changes in the antimicrobial-resistance gene pool in raw milk and cheese, from farm to consumer, utilizing next-generation sequencing. Five parallel sampling runs were conducted to assess the resistance gene pool, as well as phage or plasmid carriage and potential mobility. In terms of taxonomic composition, in raw milk the Firmicutes phylum made up 41%, while the Proteobacteria phylum accounted for 58%. In fresh cheese, this ratio shifted to 93% Firmicutes and 7% Proteobacteria. In matured cheese, the composition was 79% Firmicutes and 21% Proteobacteria. In total, 112 antimicrobial-resistance genes were identified. While a notable reduction in the resistance gene pool was observed in the freshly made raw cheese compared to the raw milk samples, a significant growth in the resistance gene pool occurred after one month of maturation, surpassing the initial gene frequency. Notably, the presence of extended-spectrum beta-lactamase (ESBL) genes, such as OXA-662 (100% coverage, 99.3% identity) and OXA-309 (97.1% coverage, 96.2% identity), raised concerns; these genes have a major public health relevance. In total, nineteen such genes belonging to nine gene families (ACT, CMY, EC, ORN, OXA, OXY, PLA, RAHN, TER) have been identified. The largest number of resistance genes were identified against fluoroquinolone drugs, which determined efflux pumps predominantly. Our findings underscore the importance of monitoring gene pool variations throughout the product pathway and the potential for horizontal gene transfer in raw products. We advocate the adoption of a new approach to food safety investigations, incorporating next-generation sequencing techniques.}, } @article {pmid38918632, year = {2024}, author = {Mei, Z and Wang, F and Bhosle, A and Dong, D and Mehta, R and Ghazi, A and Zhang, Y and Liu, Y and Rinott, E and Ma, S and Rimm, EB and Daviglus, M and Willett, WC and Knight, R and Hu, FB and Qi, Q and Chan, AT and Burk, RD and Stampfer, MJ and Shai, I and Kaplan, RC and Huttenhower, C and Wang, DD}, title = {Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {38918632}, issn = {1546-170X}, support = {R00DK119412//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01NR01999//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AG077489//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P30DK046200//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 897161//American Heart Association (American Heart Association, Inc.)/ ; 209933838//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; R24DK110499//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; }, abstract = {The association of gut microbial features with type 2 diabetes (T2D) has been inconsistent due in part to the complexity of this disease and variation in study design. Even in cases in which individual microbial species have been associated with T2D, mechanisms have been unable to be attributed to these associations based on specific microbial strains. We conducted a comprehensive study of the T2D microbiome, analyzing 8,117 shotgun metagenomes from 10 cohorts of individuals with T2D, prediabetes, and normoglycemic status in the United States, Europe, Israel and China. Dysbiosis in 19 phylogenetically diverse species was associated with T2D (false discovery rate < 0.10), for example, enriched Clostridium bolteae and depleted Butyrivibrio crossotus. These microorganisms also contributed to community-level functional changes potentially underlying T2D pathogenesis, for example, perturbations in glucose metabolism. Our study identifies within-species phylogenetic diversity for strains of 27 species that explain inter-individual differences in T2D risk, such as Eubacterium rectale. In some cases, these were explained by strain-specific gene carriage, including loci involved in various mechanisms of horizontal gene transfer and novel biological processes underlying metabolic risk, for example, quorum sensing. In summary, our study provides robust cross-cohort microbial signatures in a strain-resolved manner and offers new mechanistic insights into T2D.}, } @article {pmid38436262, year = {2024}, author = {Harmer, CJ and Hall, RM}, title = {IS26 and the IS26 family: versatile resistance gene movers and genome reorganizers.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {88}, number = {2}, pages = {e0011922}, doi = {10.1128/mmbr.00119-22}, pmid = {38436262}, issn = {1098-5557}, support = {GNT1194879//DHAC | National Health and Medical Research Council (NHMRC)/ ; }, mesh = {*DNA Transposable Elements/genetics ; *Gram-Negative Bacteria/genetics ; Genome, Bacterial ; Drug Resistance, Bacterial/genetics ; Transposases/metabolism/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; }, abstract = {SUMMARYIn Gram-negative bacteria, the insertion sequence IS26 is highly active in disseminating antibiotic resistance genes. IS26 can recruit a gene or group of genes into the mobile gene pool and support their continued dissemination to new locations by creating pseudo-compound transposons (PCTs) that can be further mobilized by the insertion sequence (IS). IS26 can also enhance expression of adjacent potential resistance genes. IS26 encodes a DDE transposase but has unique properties. It forms cointegrates between two separate DNA molecules using two mechanisms. The well-known copy-in (replicative) route generates an additional IS copy and duplicates the target site. The recently discovered and more efficient and targeted conservative mechanism requires an IS in both participating molecules and does not generate any new sequence. The unit of movement for PCTs, known as a translocatable unit or TU, includes only one IS26. TU formed by homologous recombination between the bounding IS26s can be reincorporated via either cointegration route. However, the targeted conservative reaction is key to generation of arrays of overlapping PCTs seen in resistant pathogens. Using the copy-in route, IS26 can also act on a site in the same DNA molecule, either inverting adjacent DNA or generating an adjacent deletion plus a circular molecule carrying the DNA segment lost and an IS copy. If reincorporated, these circular molecules create a new PCT. IS26 is the best characterized IS in the IS26 family, which includes IS257/IS431, ISSau10, IS1216, IS1006, and IS1008 that are also implicated in spreading resistance genes in Gram-positive and Gram-negative pathogens.}, } @article {pmid38918467, year = {2024}, author = {Grodner, B and Shi, H and Farchione, O and Vill, AC and Ntekas, I and Diebold, PJ and Wu, DT and Chen, CY and Kim, DM and Zipfel, WR and Brito, IL and De Vlaminck, I}, title = {Spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {38918467}, issn = {2058-5276}, support = {1DP2AI138242//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1R33CA235302//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1R33CA235302//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; S10OD018516//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1R33CA235302//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; }, abstract = {The exchange of mobile genetic elements (MGEs) facilitates the spread of functional traits including antimicrobial resistance within bacterial communities. Tools to spatially map MGEs and identify their bacterial hosts in complex microbial communities are currently lacking, limiting our understanding of this process. Here we combined single-molecule DNA fluorescence in situ hybridization (FISH) with multiplexed ribosomal RNA-FISH to enable simultaneous visualization of both MGEs and bacterial taxa. We spatially mapped bacteriophage and antimicrobial resistance (AMR) plasmids and identified their host taxa in human oral biofilms. This revealed distinct clusters of AMR plasmids and prophage, coinciding with densely packed regions of host bacteria. Our data suggest spatial heterogeneity in bacterial taxa results in heterogeneous MGE distribution within the community, with MGE clusters resulting from horizontal gene transfer hotspots or expansion of MGE-carrying strains. Our approach can help advance the study of AMR and phage ecology in biofilms.}, } @article {pmid38917629, year = {2024}, author = {Liu, F and Shen, Y and Hou, Y and Wu, J and Ting, Y and Nie, C and Tong, M}, title = {Elimination of representative antibiotic-resistant bacteria, antibiotic resistance genes and ciprofloxacin from water via photoactivation of periodate using FeS2.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {134982}, doi = {10.1016/j.jhazmat.2024.134982}, pmid = {38917629}, issn = {1873-3336}, abstract = {The propagation of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) induced by the release of antibiotics poses great threats to ecological safety and human health. In this study, periodate (PI)/FeS2/simulated sunlight (SSL) system was employed to remove representative ARB, ARGs and antibiotics in water. 1 × 10[7] CFU mL[-1] of gentamycin-resistant Escherichia coli was effectively disinfected below limit of detection in PI/FeS2/SSL system under different water matrix and in real water samples. Sulfadiazine-resistant Pseudomonas and Gram-positive Bacillus subtilis could also be efficiently sterilized. Theoretical calculation showed that (110) facet was the most reactive facet on FeS2 to activate PI for the generation of reactive species (·OH, ·O2[-], h[+] and Fe(IV)=O) to damage cell membrane and intracellular enzyme defense system. Both intracellular and extracellular ARGs could be degraded and the expression levels of multidrug resistance-related genes were downregulated during the disinfection process. Thus, horizontal gene transfer (HGT) of ARB was inhibited. Moreover, PI/FeS2/SSL system could disinfect ARB in a continuous flow reactor and in an enlarged reactor under natural sunlight irradiation. PI/FeS2/SSL system could also effectively degrade the HGT-promoting antibiotic (ciprofloxacin) via hydroxylation and ring cleavage process. Overall, PI/FeS2/SSL exhibited great promise for the elimination of antibiotic resistance from water.}, } @article {pmid38915079, year = {2024}, author = {Wu, CS and Wang, RJ and Chaw, SM}, title = {Integration of large and diverse angiosperm DNA fragments into Asian Gnetum mitogenomes.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {140}, pmid = {38915079}, issn = {1741-7007}, support = {No. 2022B1111040003//Guangdong Provincial Key R&D Programme/ ; }, mesh = {*Phylogeny ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Gnetum/genetics ; DNA, Plant/genetics ; Evolution, Molecular ; Magnoliopsida/genetics ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in West African, South American, and Southeast Asian rainforests. Only a single acquisition of an angiosperm mitochondrial intron has been documented to date in Asian Gnetum mitogenomes. We wanted to develop a more comprehensive understanding of frequency and fragment length distribution of such events as well as their evolutionary history in this genus.

RESULTS: We sequenced and assembled mitogenomes from five Asian Gnetum species. These genomes vary remarkably in size and foreign DNA content. We identified 15 mitochondrion-derived and five plastid-derived (MTPT) foreign genes. Our phylogenetic analyses strongly indicate that these foreign genes were transferred from diverse eudicots-mostly from the Rubiaceae genus Coptosapelta and ten genera of Malpighiales. This indicates that Asian Gnetum has experienced multiple independent HGT events. Patterns of sequence evolution strongly suggest DNA-mediated transfer between mitochondria as the primary mechanism giving rise to these HGT events. Most Asian Gnetum species are lianas and often entwined with sympatric angiosperms. We therefore propose that close apposition of Gnetum and angiosperm stems presents opportunities for interspecific cell-to-cell contact through friction and wounding, leading to HGT.

CONCLUSIONS: Our study reveals that multiple HGT events have resulted in massive amounts of angiosperm mitochondrial DNA integrated into Asian Gnetum mitogenomes. Gnetum and its neighboring angiosperms are often entwined with each other, possibly accounting for frequent HGT between these two phylogenetically remote lineages.}, } @article {pmid38914331, year = {2024}, author = {Haffiez, N and Kalantar, E and Zakaria, BS and Azizi, SMM and Farner, JM and Dhar, BR}, title = {Impact of aging of primary and secondary polystyrene nanoplastics on the transmission of antibiotic resistance genes in anaerobic digestion.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {174213}, doi = {10.1016/j.scitotenv.2024.174213}, pmid = {38914331}, issn = {1879-1026}, abstract = {Sewage sludge is a significant reservoir of nano/microplastics (NPs/MPs) and antibiotic resistance genes (ARGs). Research has revealed that NPs/MPs may exert an inhibitory effect on anaerobic digestion (AD) of sludge. Moreover, NPs/MPs can influence microbial community diversity and composition, potentially increasing ARGs dissemination. The morphological changes to NPs/MPs surface due to aging contribute to modifying hydrophobic properties. To date, there is limited comprehension regarding how various surface properties of NPs influence ARGs dissemination during AD. This study investigated the impact of primary aged/non-aged and secondary aged/non-aged polystyrene nanoplastics (PSNPs) on ARGs and mobile genetic elements (MGEs) propagation during AD. The findings indicated that the UV-aging process resulted in surface oxidation and distinct morphological characteristics in both primary and secondary PSNPs, while the surface oxidation effect was more pronounced in the secondary aged PSNPs. High concentrations (150 μg/L) of primary and secondary PSNPs inhibited methane production, with secondary PSNPs causing greater inhibition by 16 to 20 % compared to control. In contrast, low concentration (25 μg/L) had negligible or slightly positive effects on methane production. PSNPs at 150 μg/L reduced total VFA concentration, indicating an inhibitory effect on the fermentation step in the AD process. Primary and secondary PSNPs exhibited changes in EPS characteristics. ARGs abundance was enriched in reactors amended with PSNPs, with the highest abundance of 8.54 × 10[5] copies/g sludge observed in the secondary aged PSNPs (150 μg/L) reactor. Reactors exposed to aged PSNPs exhibited a relatively higher abundance of ARGs compared to reactors exposed to non-aged PSNPs. Exposure to PSNPs increased the microbial community diversity within the digesters and triggered the enrichment of Comamonadaceae and Syntrophaceae, belonging to Proteobacteria phylum. On the other hand, archaeal communities tended to shift towards hydrogenotrophic methanogens in PSNPs reactors. The correlation analysis showed that Comamonadaceae were positively correlated with the majority of ARGs and intl1. A positive correlation was observed between MGEs and most ARGs, suggesting that the increased proliferation of ARGs under PSNPs exposure may be linked to the abundance of MGEs, which in turn promotes the growth of hosts carrying ARGs. These findings suggest that aged and non-aged NPs could substantially impact the spread of ARGs and MGEs, which also led to notable alterations in the composition of the microbial community. Overall, this study provides valuable insights into the multifaceted impacts of PSNPs with various characteristics on AD processes, microbial communities, and ARGs proliferation, highlighting the urgent need for comprehensive assessments of NPs pollutants in the environment.}, } @article {pmid38913753, year = {2024}, author = {Maier, JL and Gin, C and Callahan, B and Sheriff, EK and Duerkop, BA and Kleiner, M}, title = {Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella.}, journal = {PLoS pathogens}, volume = {20}, number = {6}, pages = {e1012301}, doi = {10.1371/journal.ppat.1012301}, pmid = {38913753}, issn = {1553-7374}, abstract = {Salmonella enterica Serovar Typhimurium (Salmonella) and its bacteriophage P22 are a model system for the study of horizontal gene transfer by generalized transduction. Typically, the P22 DNA packaging machinery initiates packaging when a short sequence of DNA, known as the pac site, is recognized on the P22 genome. However, sequences similar to the pac site in the host genome, called pseudo-pac sites, lead to erroneous packaging and subsequent generalized transduction of Salmonella DNA. While the general genomic locations of the Salmonella pseudo-pac sites are known, the sequences themselves have not been determined. We used visualization of P22 sequencing reads mapped to host Salmonella genomes to define regions of generalized transduction initiation and the likely locations of pseudo-pac sites. We searched each genome region for the sequence with the highest similarity to the P22 pac site and aligned the resulting sequences. We built a regular expression (sequence match pattern) from the alignment and used it to search the genomes of two P22-susceptible Salmonella strains-LT2 and 14028S-for sequence matches. The final regular expression successfully identified pseudo-pac sites in both LT2 and 14028S that correspond with generalized transduction initiation sites in mapped read coverages. The pseudo-pac site sequences identified in this study can be used to predict locations of generalized transduction in other P22-susceptible hosts or to initiate generalized transduction at specific locations in P22-susceptible hosts with genetic engineering. Furthermore, the bioinformatics approach used to identify the Salmonella pseudo-pac sites in this study could be applied to other phage-host systems.}, } @article {pmid38878435, year = {2024}, author = {Zhang, X and Ma, L and Zhang, XX}, title = {Neglected risks of enhanced antimicrobial resistance and pathogenicity in anaerobic digestion during transition from thermophilic to mesophilic.}, journal = {Journal of hazardous materials}, volume = {475}, number = {}, pages = {134886}, doi = {10.1016/j.jhazmat.2024.134886}, pmid = {38878435}, issn = {1873-3336}, mesh = {Anaerobiosis ; *Drug Resistance, Bacterial/genetics ; Temperature ; Methane/metabolism ; Bacteria/genetics/pathogenicity/metabolism/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Virulence Factors/genetics ; Gene Transfer, Horizontal ; Enterobacteriaceae/genetics/pathogenicity/drug effects/metabolism ; Genes, Bacterial ; }, abstract = {Minimization of antibiotic resistance genes (ARGs) and potential pathogenic antibiotic-resistant bacteria (PARB) during anaerobic digestion (AD) is significantly impacted by temperature. However, knowledge on how ARGs and PARB respond to temperature transition from thermophilic to mesophilic is limited. Here, we combined metagenomic-based with culture-based approaches and revealed the risks of antimicrobial resistance and pathogenicity during transition from 55 °C to 35 °C for AD, with strategies of sharp (ST, one-step by 20 °C/d) and mild (MT, step-wise by 1 °C/d). Results indicated a lower decrease in methane production with MT (by 38.9%) than ST (by 88.8%). Phenotypic assays characterized a significant propagation of multi-resistant lactose-fermenting Enterobacteriaceae and indicator pathogens after both transitions, especially via ST. Further genomic evidence indicated a significant increase of ARGs (29.4-fold), virulence factor genes (1.8-fold) and PARB (65.3-fold) after ST, while slight enrichment via MT. Bacterial succession and enhanced horizontal transfer mediated by mobile genetic elements promoted ARG propagation in AD during transition, which was synchronously exacerbated through horizontal transfer mechanisms mediated by cellular physiological responses (oxidative stress, membrane permeability, bacterial conjugation and transformation) and co-selection mechanisms of biomethanation metabolic functions (acidogenesis and acetogenesis). This study reveals temperature-dependent resistome and pathogenicity development in AD, facilitating microbial risk control.}, } @article {pmid38771049, year = {2024}, author = {Muñoz-Gutiérrez, I and Cantu, L and Shanahan, J and Girguis, M and de la Cruz, M and Mota-Bravo, L}, title = {Cryptic environmental conjugative plasmid recruits a novel hybrid transposon resulting in a new plasmid with higher dispersion potential.}, journal = {mSphere}, volume = {9}, number = {6}, pages = {e0025224}, doi = {10.1128/msphere.00252-24}, pmid = {38771049}, issn = {2379-5042}, support = {GM136498//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*Plasmids/genetics ; *DNA Transposable Elements/genetics ; *Escherichia coli/genetics/drug effects ; *Conjugation, Genetic ; *Anti-Bacterial Agents/pharmacology ; Lakes/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; }, abstract = {UNLABELLED: Cryptic conjugative plasmids lack antibiotic-resistance genes (ARGs). These plasmids can capture ARGs from the vast pool of the environmental metagenome, but the mechanism to recruit ARGs remains to be elucidated. To investigate the recruitment of ARGs by a cryptic plasmid, we sequenced and conducted mating experiments with Escherichia coli SW4848 (collected from a lake) that has a cryptic IncX (IncX4) plasmid and an IncF (IncFII/IncFIIB) plasmid with five genes that confer resistance to aminoglycosides (strA and strB), sulfonamides (sul2), tetracycline [tet(A)], and trimethoprim (dfrA5). In a conjugation experiment, a novel hybrid Tn21/Tn1721 transposon of 22,570 bp (designated Tn7714) carrying the five ARG mobilized spontaneously from the IncF plasmid to the cryptic IncX plasmid. The IncF plasmid was found to be conjugative when it was electroporated into E. coli DH10B (without the IncX plasmid). Two parallel conjugations with the IncF and the new IncX (carrying the novel Tn7714 transposon) plasmids in two separate E. coli DH10B as donors and E. coli J53 as the recipient revealed that the conjugation rate of the new IncX plasmid (with the novel Tn7714 transposon and five ARGs) is more than two orders of magnitude larger than the IncF plasmid. For the first time, this study shows experimental evidence that cryptic environmental plasmids can capture and transfer transposons with ARGs to other bacteria, creating novel multidrug-resistant conjugative plasmids with higher dispersion potential.

IMPORTANCE: Cryptic conjugative plasmids are extrachromosomal DNA molecules without antibiotic-resistance genes (ARGs). Environmental bacteria carrying cryptic plasmids with a high conjugation rate threaten public health because they can capture clinically relevant ARGs and rapidly spread them to pathogenic bacteria. However, the mechanism to recruit ARG by cryptic conjugative plasmids in environmental bacteria has not been observed experimentally. Here, we document the first translocation of a transposon with multiple clinically relevant ARGs to a cryptic environmental conjugative plasmid. The new multidrug-resistant conjugative plasmid has a conjugation rate that is two orders of magnitude higher than the original plasmid that carries the ARG (i.e., the new plasmid from the environment can spread ARG more than two orders of magnitude faster). Our work illustrates the importance of studying the mobilization of ARGs in environmental bacteria. It sheds light on how cryptic conjugative plasmids recruit ARGs, a phenomenon at the root of the antibiotic crisis.}, } @article {pmid38911822, year = {2024}, author = {Banerjee, P and Eulenstein, O and Friedberg, I}, title = {Discovering genomic islands in unannotated bacterial genomes using sequence embedding.}, journal = {Bioinformatics advances}, volume = {4}, number = {1}, pages = {vbae089}, pmid = {38911822}, issn = {2635-0041}, abstract = {MOTIVATION: Genomic islands (GEIs) are clusters of genes in bacterial genomes that are typically acquired by horizontal gene transfer. GEIs play a crucial role in the evolution of bacteria by rapidly introducing genetic diversity and thus helping them adapt to changing environments. Specifically of interest to human health, many GEIs contain pathogenicity and antimicrobial resistance genes. Detecting GEIs is, therefore, an important problem in biomedical and environmental research. There have been many previous studies for computationally identifying GEIs. Still, most of these studies rely on detecting anomalies in the unannotated nucleotide sequences or on a fixed set of known features on annotated nucleotide sequences.

RESULTS: Here, we present TreasureIsland, which uses a new unsupervised representation of DNA sequences to predict GEIs. We developed a high-precision boundary detection method featuring an incremental fine-tuning of GEI borders, and we evaluated the accuracy of this framework using a new comprehensive reference dataset, Benbow. We show that TreasureIsland's accuracy rivals other GEI predictors, enabling efficient and faster identification of GEIs in unannotated bacterial genomes.

TreasureIsland is available under an MIT license at: https://github.com/FriedbergLab/GenomicIslandPrediction.}, } @article {pmid38910035, year = {2024}, author = {Zarlenga, DS and Hoberg, EP and Thompson, P and Rosenthal, B}, title = {Trichinella: Becoming a parasite.}, journal = {Veterinary parasitology}, volume = {}, number = {}, pages = {110220}, doi = {10.1016/j.vetpar.2024.110220}, pmid = {38910035}, issn = {1873-2550}, abstract = {Phylogenetic evidence indicates that free-living nematodes gave rise to parasitic nematodes where parasitism evolved independently at least 15 times. The high level of genetic and biological diversity among parasites dictates an equally high level of diversity in the transition to parasitism. We previously hypothesized that horizontal gene transfer (HGT) played an important role in the evolution of parasitism among early ancestors of Trichinella, mediated by an interplay of ecological and evolutionary pathways that contributed to persistence and diversification. We propose that host selection may have been associated with the metabolism of ammonia and engender a new paradigm whereby the reprogrammed nurse cell is capable of generating cyanate thereby enabling the importance of the Trichinella cyanase in the longevity of the cell. Parasites and parasitism have revealed considerable resilience against a backdrop of climate change and environmental perturbation. Here we provide a putative link between key periods in the evolution of Trichinella and major geological and climatological events dating back 500 million years. A useful lens for exploring such ideas, the Stockholm Paradigm, integrates Ecological Fitting (a foundation for host colonization and diversification), the Oscillation Hypothesis (recurring shifts between trends in generalization and specialization relative to host range), the Geographic Mosaic Theory of Coevolution (microevolutionary co-adaptive processes), and the Taxon Pulse Hypothesis (alternating events of biotic expansion i.e., exploitation in evolutionary and ecological time). Here we examine how one or more of these interactive theories, in a phylogenetic-historical context and in conjunction with HGT, may help explain the scope and depth of diversity among Trichinella genotypes.}, } @article {pmid38908181, year = {2024}, author = {Wu, Y and Niu, Q and Liu, Y and Zheng, X and Long, M and Chen, Y}, title = {Chlorinated organophosphorus flame retardants induce the propagation of antibiotic resistance genes in sludge fermentation systems: Insight of chromosomal mutation and microbial traits.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {134971}, doi = {10.1016/j.jhazmat.2024.134971}, pmid = {38908181}, issn = {1873-3336}, abstract = {Waste activated sludge (WAS) is a critical reservoir for antibiotic resistance genes (ARGs) due to the prevalent misuse of antibiotics. Horizontal gene transfer (HGT) is the primary mechanism for ARGs spread through mobile genetic elements (MGEs). However, the role of non-antibiotic organophosphorus flame retardants (Cl-OFRs) in ARG transmission in the WAS fermentation system remains unclear. This study examines the effects of tris(2-chloroethyl) phosphate (TCEP), a representative Cl-OFR, on ARG dynamics in WAS fermentation using molecular docking and metagenomic analysis. The results showed a 33.4 % increase in ARG abundance in the presence of TCEP. Interestingly, HGT did not appear to be the primary mechanism of ARG dissemination under TCEP stress, as evidenced by a 2.51 % decrease in MGE abundance. TCEP binds to sludge through hydrogen bonds with a binding energy of - 3.6 kJ/mol, leading to microbial damage and an increase in the proportion of non-viable cells. This interaction prompts a microbial shift toward Firmicutes with thick cell walls, which are significant ARG carriers. Additionally, TCEP induces chromosomal mutations through oxidative stress and the SOS response, contributing to ARG formation. Microorganisms also develop multidrug resistance mechanisms to expel TCEP and mitigate its toxicity. This study provides a comprehensive understanding of Cl-OFRs effects on the ARGs fates in WAS fermentation system and offers guidance for the safe and efficient treatment of Cl-OFRs and WAS.}, } @article {pmid38906294, year = {2024}, author = {Yao, S and Yu, J and Zhang, T and Xie, J and Yan, C and Ni, X and Guo, B and Cui, C}, title = {Comprehensive analysis of distribution characteristics and horizontal gene transfer elements of blaNDM-1-carrying bacteria.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {173907}, doi = {10.1016/j.scitotenv.2024.173907}, pmid = {38906294}, issn = {1879-1026}, abstract = {The worldwide dissemination of New Delhi metallo-β-lactamase-1 (NDM-1), which mediates resistance to almost all clinical β-lactam antibiotics, is a major public health problem. The global distribution, species, sources, and potential transfer risk of blaNDM-1-carrying bacteria are unclear. Results of a comprehensive analysis of literature in 2010-2022 showed that a total of 6002 blaNDM-1 carrying bacteria were widely distributed around 62 countries with a high trend in the coastal areas. Opportunistic pathogens or pathogens like Klebsiella sp., Escherichia sp., Acinetobacter sp. and Pseudomonas sp. were the four main species indicating the potential microbial risk. Source analysis showed that 86.45 % of target bacteria were isolated from the source of hospital (e.g., Hospital patients and wastewater) and little from surface water (5.07 %) and farms (3.98 %). A plasmid-encoded blaNDM-1Acinetobacter sp. with the resistance mechanisms of antibiotic efflux pump, antibiotic target change and antibiotic degradation was isolated from the wastewater of a typical tertiary hospital. Insertion sequences (IS3 and IS30) located in the adjacent 5 kbp of blaNDM-1-bleMBL gene cluster indicating the transposon-mediated horizontal gene transfer risk. These results showed that the worldwide spread of blaNDM-1-carrying bacteria and its potential horizontal gene transfer risk deserve good control.}, } @article {pmid38905247, year = {2024}, author = {Mohamed, DS and Abd El-Baky, RM and El-Mokhtar, MA and Ghanem, SK and Yahia, R and Alqahtani, AM and Abourehab, MAS and Ahmed, EF}, title = {Influence of selected non-antibiotic pharmaceuticals on antibiotic resistance gene transfer in Escherichia coli.}, journal = {PloS one}, volume = {19}, number = {6}, pages = {e0304980}, pmid = {38905247}, issn = {1932-6203}, mesh = {*Escherichia coli/drug effects/genetics ; *Gene Transfer, Horizontal ; *Plasmids/genetics ; Metoclopramide/pharmacology ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics/drug effects ; Conjugation, Genetic ; Drug Resistance, Microbial/genetics/drug effects ; }, abstract = {BACKGROUND: Antibiotic resistance genes (ARGs) transfer rapidly among bacterial species all over the world contributing to the aggravation of antibiotic resistance crisis. Antibiotics at sub-inhibitory concentration induce horizontal gene transfer (HRT) between bacteria, especially through conjugation. The role of common non-antibiotic pharmaceuticals in the market in disseminating antibiotic resistance is not well studied.

OBJECTIVES: In this work, we indicated the effect of some commonly used non-antibiotic pharmaceuticals including antiemetic (metoclopramide HCl) and antispasmodics (hyoscine butyl bromide and tiemonium methyl sulfate) on the plasmid-mediated conjugal transfer of antibiotic resistance genes between pathogenic E. coli in the gastric intestinal tract (GIT).

METHODS: Broth microdilution assay was used to test the antibacterial activity of the tested non-antibiotic pharmaceuticals. A conjugation mating system was applied in presence of the studied non-antibiotic pharmaceuticals to test their effect on conjugal transfer frequency. Plasmid extraction and PCR were performed to confirm the conjugation process. Transmission electron microscopy (TEM) was used for imaging the effect of non-antibiotic pharmaceuticals on bacterial cells.

RESULTS: No antibacterial activity was reported for the used non-antibiotic pharmaceuticals. Plasmid-mediated conjugal transfer between isolates was induced by metoclopramide HCl but suppressed by hyoscine butyl bromide. Tiemonium methylsulfate slightly promoted conjugal transfer. Aggregation between cells and periplasmic bridges was clear in the case of metoclopramide HCl while in presence of hyoscine butyl bromide little affinity was observed.

CONCLUSION: This study indicates the contribution of non-antibiotic pharmaceuticals to the dissemination and evolution of antibiotic resistance at the community level. Metoclopramide HCl showed an important role in the spread of antibiotic resistance.}, } @article {pmid38904756, year = {2024}, author = {Kaur, J and Verma, H and Kaur, J and Lata, P and Dhingra, GG and Lal, R}, title = {In Silico Analysis of the Phylogenetic and Physiological Characteristics of Sphingobium indicum B90A: A Hexachlorocyclohexane-Degrading Bacterium.}, journal = {Current microbiology}, volume = {81}, number = {8}, pages = {233}, pmid = {38904756}, issn = {1432-0991}, mesh = {*Phylogeny ; *Sphingomonadaceae/genetics/metabolism/classification ; *Genome, Bacterial ; *Hexachlorocyclohexane/metabolism ; *Computer Simulation ; *Biodegradation, Environmental ; Genomic Islands ; Gene Transfer, Horizontal ; }, abstract = {The study focuses on the in silico genomic characterization of Sphingobium indicum B90A, revealing a wealth of genes involved in stress response, carbon monoxide oxidation, β-carotene biosynthesis, heavy metal resistance, and aromatic compound degradation, suggesting its potential as a bioremediation agent. Furthermore, genomic adaptations among nine Sphingomonad strains were explored, highlighting shared core genes via pangenome analysis, including those related to the shikimate pathway and heavy metal resistance. The majority of genes associated with aromatic compound degradation, heavy metal resistance, and stress response were found within genomic islands across all strains. Sphingobium indicum UT26S exhibited the highest number of genomic islands, while Sphingopyxis alaskensis RB2256 had the maximum fraction of its genome covered by genomic islands. The distribution of lin genes varied among the strains, indicating diverse genetic responses to environmental pressures. Additionally, in silico evidence of horizontal gene transfer (HGT) between plasmids pSRL3 and pISP3 of the Sphingobium and Sphingomonas genera, respectively, has been provided. The manuscript offers novel insights into strain B90A, highlighting its role in horizontal gene transfer and refining evolutionary relationships among Sphingomonad strains. The discovery of stress response genes and the czcABCD operon emphasizes the potential of Sphingomonads in consortia development, supported by genomic island analysis.}, } @article {pmid38904697, year = {2024}, author = {Bhattacharjee, A and Singh, AK}, title = {Delineating the Acquired Genetic Diversity and Multidrug Resistance in Alcaligenes from Poultry Farms and Nearby Soil.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {}, number = {}, pages = {}, pmid = {38904697}, issn = {1976-3794}, support = {OLP-2035//Council for Scientific and Industrial Research/ ; OLP-2081//Council for Scientific and Industrial Research/ ; GPP-0423//DST-SERB/ ; }, abstract = {Alcaligenes faecalis is one of the most important and clinically significant environmental pathogens, increasing in importance due to its isolation from soil and nosocomial environments. The Gram-negative soil bacterium is associated with skin endocarditis, bacteremia, dysentery, meningitis, endophthalmitis, urinary tract infections, and pneumonia in patients. With emerging antibiotic resistance in A. faecalis, it has become crucial to understand the origin of such resistance genes within this clinically significant environmental and gut bacterium. In this research, we studied the impact of antibiotic overuse in poultry and its effect on developing resistance in A. faecalis. We sampled soil and faecal materials from five poultry farms, performed whole genome sequencing & analysis and identified four strains of A. faecalis. Furthermore, we characterized the genes in the genomic islands of A. faecalis isolates. We found four multidrug-resistant A. faecalis strains that showed resistance against vancomycin (MIC >1000 μg/ml), ceftazidime (50 μg/ml), colistin (50 μg/ml) and ciprofloxacin (50 μg/ml). From whole genome comparative analysis, we found more than 180 resistance genes compared to the reference sequence. Parts of our assembled contigs were found to be similar to different bacteria which included pbp1A and pbp2 imparting resistance to amoxicillin originally a part of Helicobacter and Bordetella pertussis. We also found the Mycobacterial insertion element IS6110 in the genomic islands of all four genomes. This prominent insertion element can be transferred and induce resistance to other bacterial genomes. The results thus are crucial in understanding the transfer of resistance genes in the environment and can help in developing regimes for antibiotic use in the food and poultry industry.}, } @article {pmid38903782, year = {2024}, author = {Ott, LC and Mellata, M}, title = {Short-chain fatty acids inhibit bacterial plasmid transfer through conjugation in vitro and in ex vivo chicken tissue explants.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1414401}, doi = {10.3389/fmicb.2024.1414401}, pmid = {38903782}, issn = {1664-302X}, abstract = {The animal gut acts as a potent reservoir for spreading and maintaining conjugative plasmids that confer antimicrobial resistance (AMR), fitness, and virulence attributes. Interventions that inhibit the continued emergence and expansion of AMR and virulent strains in agricultural and clinical environments are greatly desired. This study aims to determine the presence and efficacy of short-chain fatty acids (SCFA) inhibitory effects on the conjugal transfer of AMR plasmids. In vitro broth conjugations were conducted between donor Escherichia coli strains carrying AMP plasmids and the plasmid-less Escherichia coli HS-4 recipient strain. Conjugations were supplemented with ddH2O or SCFAs at 1, 0.1, 0.01, or 0.001 molar final concentration. The addition of SCFAs completely inhibited plasmid transfer at 1 and 0.1 molar and significantly (p < 0.05) reduced transfer at 0.01 molar, regardless of SCFA tested. In explant models for the chicken ceca, either ddH2O or a final concentration of 0.025 M SCFAs were supplemented to the explants infected with donor and recipient E. coli. In every SCFA tested, significant decreases in transconjugant populations compared to ddH2O-treated control samples were observed with minimal effects on donor and recipient populations. Finally, significant reductions in transconjugants for plasmids of each incompatibility type (IncP1ε, IncFIβ, and IncI1) tested were detected. This study demonstrates for the first time the broad inhibition ability of SCFAs on bacterial plasmid transfer and eliminates AMR with minimal effect on bacteria. Implementing interventions that increase the concentrations of SCFAs in the gut may be a viable method to reduce the risk, incidence, and rate of AMR emergence in agricultural and human environments.}, } @article {pmid38903098, year = {2024}, author = {Sastre-Dominguez, J and DelaFuente, J and Toribio-Celestino, L and Herencias, C and Herrador-Gomez, P and Costas, C and Hernandez-Garcia, M and Canton, R and Rodriguez-Beltran, J and Santos-Lopez, A and San Millan, A}, title = {Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.03.01.582297}, pmid = {38903098}, abstract = {Plasmids are extrachromosomal genetic elements commonly found in bacteria. Plasmids are known to fuel bacterial evolution through horizontal gene transfer (HGT), but recent analyses indicate that they can also promote intragenomic adaptations. However, the role of plasmids as catalysts of bacterial evolution beyond HGT remains poorly explored. In this study, we investigate the impact of a widespread conjugative plasmid, pOXA-48, on the evolution of various multidrug-resistant clinical enterobacteria. Combining experimental and within-patient evolution analyses, we unveil that plasmid pOXA-48 promotes bacterial evolution through the transposition of plasmid-encoded insertion sequence 1 (IS1) elements. Specifically, IS1-mediated gene inactivations expedite the adaptation rate of clinical strains in vitro and foster within-patient adaptation in the gut microbiota. We decipher the mechanism underlying the plasmid-mediated surge in IS1 transposition, revealing a negative feedback loop regulated by the genomic copy number of IS1. Given the overrepresentation of IS elements in bacterial plasmids, our findings propose that plasmid-mediated IS transposition represents a crucial mechanism for swift bacterial adaptation.}, } @article {pmid38902796, year = {2024}, author = {Chaudhari, NM and Pérez-Carrascal, OM and Overholt, WA and Totsche, KU and Küsel, K}, title = {Genome streamlining in Parcubacteria transitioning from soil to groundwater.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {41}, pmid = {38902796}, issn = {2524-6372}, abstract = {BACKGROUND: To better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seepage waters to groundwater on genomic composition of ultra-small Parcubacteria, the dominating CPR class in seepage waters, using genome resolved metagenomics.

RESULTS: Bacterial metagenome-assembled genomes (MAGs), (318 total, 32 of Parcubacteria) were generated from seepage waters and compared directly to groundwater counterparts. The estimated average genome sizes of members of major phyla Proteobacteria, Bacteroidota and Cand. Patescibacteria (Candidate Phyla Radiation - CPR bacteria) were significantly higher in soil-seepage water as compared to their groundwater counterparts. Seepage water Parcubacteria (Paceibacteria) exhibited 1.18-fold greater mean genome size and 2-fold lower mean proportion of pseudogenes than those in groundwater. Bacteroidota and Proteobacteria also showed a similar trend of reduced genomes in groundwater compared to seepage. While exploring gene loss and adaptive gains in closely related CPR lineages in groundwater, we identified a membrane protein, and a lipoglycopeptide resistance gene unique to a seepage Parcubacterium genome. A nitrite reductase gene was also identified and was unique to the groundwater Parcubacteria genomes, likely acquired from other planktonic microbes via horizontal gene transfer.

CONCLUSIONS: Overall, our data suggest that bacteria in seepage waters, including ultra-small Parcubacteria, have significantly larger genomes and higher metabolic enrichment than their groundwater counterparts, highlighting possible genome streamlining of the latter in response to habitat selection in an oligotrophic environment.}, } @article {pmid38901473, year = {2024}, author = {Walt, HK and Ahn, SJ and Hoffmann, FG}, title = {Horizontally transferred glycoside hydrolase 26 may aid hemipteran insects in plant tissue digestion.}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {108134}, doi = {10.1016/j.ympev.2024.108134}, pmid = {38901473}, issn = {1095-9513}, abstract = {Glycoside hydrolases are enzymes that break down complex carbohydrates into simple sugars by catalyzing the hydrolysis of glycosidic bonds. There have been multiple instances of adaptive horizontal gene transfer of genes belonging to various glycoside hydrolase families from microbes to insects, as glycoside hydrolases can metabolize constituents of the carbohydrate-rich plant cell wall. In this study, we characterize the horizontal transfer of a gene from the glycoside hydrolase family 26 (GH26) from bacteria to insects of the order Hemiptera. Our phylogenies trace the horizontal gene transfer to the common ancestor of the superfamilies Pentatomoidea and Lygaeoidea, which include stink bugs and seed bugs. After horizontal transfer, the gene was assimilated into the insect genome as indicated by the gain of an intron, and a eukaryotic signal peptide. Subsequently, the gene has undergone independent losses and expansions in copy number in multiple lineages, suggesting an adaptive role of GH26s in some insects. Finally, we measured tissue-level gene expression of multiple stink bugs and the large milkweed bug using publicly available RNA-seq datasets. We found that the GH26 genes are highly expressed in tissues associated with plant digestion, especially in the principal salivary glands of the stink bugs. Our results are consistent with the hypothesis that this horizontally transferred GH26 was co-opted by the insect to aid in plant tissue digestion and that this HGT event was likely adaptive.}, } @article {pmid38896653, year = {2024}, author = {Elliott, JFK and McLeod, DV and Taylor, TB and Westra, ER and Gandon, S and Watson, BNJ}, title = {Conditions for the spread of CRISPR-Cas immune systems into bacterial populations.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae108}, pmid = {38896653}, issn = {1751-7370}, abstract = {Bacteria contain a wide variety of innate and adaptive immune systems which provide protection to the host against invading genetic material, including bacteriophages (phages). It is becoming increasingly clear that bacterial immune systems are frequently lost and gained through horizontal gene transfer (HGT). However, how and when new immune systems can become established in a bacterial population has remained largely unstudied. We developed a joint epidemiological and evolutionary model that predicts the conditions necessary for the spread of a CRISPR-Cas immune system into a bacterial population lacking this system. We find that whether bacteria carrying CRISPR-Cas will spread (increase in frequency) into a bacterial population depends on the abundance of phages and the difference in the frequency of phage resistance mechanisms between bacteria carrying a CRISPR-Cas immune system, and those not (denoted as ${f} _{\Delta } $). Specifically, the abundance of cells carrying CRISPR-Cas will increase if there is a higher proportion of phage resistance (either via CRISPR-Cas immunity or surface modification) in the CRISPR-Cas possessing population than in the cells lacking CRISPR-Cas. We experimentally validated these predictions using Pseudomonas aeruginosa PA14 and phage DMS3vir as a model. Specifically, by varying the initial ratios of different strains of bacteria that carry alternative forms of phage resistance we confirmed that the spread of cells carrying CRISPR-Cas through a population can be predicted based on phage density and the relative frequency of resistance phenotypes. Understanding which conditions promote the spread of CRISPR-Cas systems helps to predict when and where these defences can establish in bacterial populations after a horizontal gene transfer event, both in ecological and clinical contexts.}, } @article {pmid38896471, year = {2024}, author = {Lerminiaux, N and Mitchell, R and Katz, K and Fakharuddin, K and McGill, E and Mataseje, L}, title = {Plasmid genomic epidemiology of carbapenem-hydrolysing class D β-lactamase (CDHL)-producing Enterobacterales in Canada, 2010-2021.}, journal = {Microbial genomics}, volume = {10}, number = {6}, pages = {}, doi = {10.1099/mgen.0.001257}, pmid = {38896471}, issn = {2057-5858}, mesh = {*beta-Lactamases/genetics ; *Plasmids/genetics ; Canada/epidemiology ; Humans ; *Carbapenems/pharmacology ; *Whole Genome Sequencing ; *Bacterial Proteins/genetics ; *Enterobacteriaceae Infections/microbiology/epidemiology ; Enterobacteriaceae/genetics/drug effects/classification ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Cross Infection/microbiology/epidemiology ; }, abstract = {Carbapenems are last-resort antibiotics for treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance is a rising global threat due to the acquisition of carbapenemase genes. Oxacillinase-48 (bla OXA-48)-type carbapenemases are increasing in abundance in Canada and elsewhere; these genes are frequently found on mobile genetic elements and are associated with specific transposons. This means that alongside clonal dissemination, bla OXA-48-type genes can spread through plasmid-mediated horizontal gene transfer. We applied whole genome sequencing to characterize 249 bla OXA-48-type-producing Enterobacterales isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short- and long-read sequencing, we obtained 70 complete and circular bla OXA-48-type-encoding plasmids. Using MOB-suite, four major plasmids clustered were identified, and we further estimated a plasmid cluster for 91.9 % (147/160) of incomplete bla OXA-48-type-encoding contigs. We identified different patterns of carbapenemase mobilization across Canada, including horizontal transmission of bla OXA-181/IncX3 plasmids (75/249, 30.1 %) and bla OXA-48/IncL/M plasmids (47/249, 18.9 %), and both horizontal transmission and clonal transmission of bla OXA-232 for Klebsiella pneumoniae ST231 on ColE2-type/ColKP3 plasmids (25/249, 10.0 %). Our findings highlight the diversity of OXA-48-type plasmids and indicate that multiple plasmid clusters and clonal transmission have contributed to bla OXA-48-type spread and persistence in Canada.}, } @article {pmid38896033, year = {2024}, author = {Huang, B and Xiao, Y and Zhang, Y}, title = {Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae111}, pmid = {38896033}, issn = {1751-7370}, abstract = {Selenocysteine (Sec) is encoded by the UGA codon that normally functions as a stop signal and is specifically incorporated into selenoproteins via a unique recoding mechanism. The translational recoding of UGA as Sec is directed by an unusual RNA structure, the Sec insertion sequence (SECIS) element. Although archaea and eukaryotes adopt a similar Sec encoding machinery, the SECIS elements have no similarities to each other with regard to sequence and structure. We analyzed more than 400 Asgard archaeal genomes to examine the occurrence of both Sec encoding system and selenoproteins in this archaeal superphylum, the closest prokaryotic relatives of eukaryotes. A comprehensive map of Sec utilization trait has been generated, providing the most detailed understanding of the use of this nonstandard amino acid in Asgard archaea so far. By characterizing the selenoproteomes of all organisms, several selenoprotein-rich phyla and species were identified. Most Asgard archaeal selenoprotein genes possess eukaryotic SECIS-like structures with varying degrees of diversity. Moreover, euryarchaeal SECIS elements might originate from Asgard archaeal SECIS elements via lateral gene transfer, indicating a complex and dynamic scenario of the evolution of SECIS element within archaea. Finally, a roadmap for the transition of eukaryotic SECIS elements from archaea was proposed, and selenophosphate synthetase may serve as a potential intermediate for the generation of ancestral eukaryotic SECIS element. Our results offer new insights into a deeper understanding of the evolution of Sec insertion machinery.}, } @article {pmid38895488, year = {2024}, author = {Ellison, TJ and Ellison, CK}, title = {DNA binding is rate-limiting for natural transformation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.06.06.597730}, pmid = {38895488}, abstract = {UNLABELLED: Bacteria take up environmental DNA using dynamic appendages called type IV pili (T4P) to elicit horizontal gene transfer in a process called natural transformation. Natural transformation is widespread amongst bacteria yet determining how different factors universally contribute to or limit this process across species has remained challenging. Here we show that Acinetobacter baylyi , the most naturally transformable species, is highly transformable due to its ability to robustly bind nonspecific DNA via a dedicated orphan minor pilin, FimT. We show that, compared to its homologues, A. baylyi FimT contains multiple positively charged residues that additively promote DNA binding efficiency. Expression of A. baylyi FimT in a closely related Acinetobacter pathogen is sufficient to substantially improve its capacity for natural transformation, demonstrating that T4P-DNA binding is a rate-limiting step in this process. These results demonstrate the importance of T4P-DNA binding efficiency in driving natural transformation, establishing a key factor limiting horizontal gene transfer.

IMPORTANCE: Natural transformation is a multi-step, broadly conserved mechanism for horizontal gene transfer in which bacteria take up exogenous DNA from the environment and integrate it into their genome by homologous recombination. A complete picture of the factors that limit this behavior remain unclear due to variability between bacterial systems. In this manuscript, we provide clear and direct evidence that DNA binding by type IV pili prior to DNA uptake is a rate-limiting step of natural transformation. We show that increasing DNA binding in antibiotic resistant Acinetobacter pathogens can boost their transformation rates by 100-fold. In addition to expanding our understanding of the factors that limit transformation in the environment, these results will also contribute to a deeper understanding of the spread of antibiotic resistance genes in relevant human pathogens.}, } @article {pmid38895369, year = {2024}, author = {Klein, JA and Predeus, AV and Greissl, AR and Clark-Herrera, MM and Cruz, E and Cundiff, JA and Haeberle, AL and Howell, M and Lele, A and Robinson, DJ and Westerman, TL and Wrande, M and Wright, SJ and Green, NM and Vallance, BA and McClelland, M and Mejia, A and Goodman, AG and Elfenbein, JR and Knodler, LA}, title = {Pathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.06.07.595826}, pmid = {38895369}, abstract = {Providencia alcalifaciens is a Gram-negative bacterium found in a wide variety of water and land environments and organisms. It has been isolated as part of the gut microbiome of animals and insects, as well as from stool samples of patients with diarrhea. Specific P. alcalifaciens strains encode gene homologs of virulence factors found in other pathogenic members of the same Enterobacterales order, such as Salmonella enterica serovar Typhimurium and Shigella flexneri. Whether these genes are also pathogenic determinants in P. alcalifaciens is not known. Here we have used P. alcalifaciens 205/92, a clinical isolate, with in vitro and in vivo infection models to investigate P. alcalifaciens -host interactions at the cellular level. Our particular focus was the role of two type III secretion systems (T3SS) belonging to the Inv-Mxi/Spa family. T3SS 1b is widespread in Providencia spp. and encoded on the chromosome. T3SS 1a is encoded on a large plasmid that is present in a subset of P. alcalifaciens strains, which are primarily isolates from diarrheal patients. Using a combination of electron and fluorescence microscopy and gentamicin protection assays we show that P. alcalifaciens 205/92 is internalized into eukaryotic cells, rapidly lyses its internalization vacuole and proliferates in the cytosol. This triggers caspase-4 dependent inflammasome responses in gut epithelial cells. The requirement for the T3SS 1a in entry, vacuole lysis and cytosolic proliferation is host-cell type specific, playing a more prominent role in human intestinal epithelial cells as compared to macrophages. In a bovine ligated intestinal loop model, P. alcalifaciens colonizes the intestinal mucosa, inducing mild epithelial damage with negligible fluid accumulation. No overt role for T3SS 1a or T3SS 1b was seen in the calf infection model. However, T3SS 1b was required for the rapid killing of Drosophila melanogaster . We propose that the acquisition of two T3SS by horizontal gene transfer has allowed P. alcalifaciens to diversify its host range, from a highly virulent pathogen of insects to an opportunistic gastrointestinal pathogen of animals.}, } @article {pmid38891015, year = {2024}, author = {Zhou, H and Lu, Z and Liu, X and Bie, X and Xue, F and Tang, S and Feng, Q and Cheng, Y and Yang, J}, title = {Environmentally Relevant Concentrations of Tetracycline Promote Horizontal Transfer of Antimicrobial Resistance Genes via Plasmid-Mediated Conjugation.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, pmid = {38891015}, issn = {2304-8158}, support = {32272295//National Natural Science Foundation of China/ ; BE2022684//Jiangsu Provincial Key Research and Development Program/ ; KJ2024017//the Science and Technology Project of Jiangsu Provincial Administration for Market Regulation/ ; }, abstract = {The ubiquitous presence of antimicrobial-resistant organisms and antimicrobial resistance genes (ARGs) constitutes a major threat to global public safety. Tetracycline (TET) is a common antimicrobial agent that inhibits bacterial growth and is frequently detected in aquatic environments. Although TET may display coselection for resistance, limited knowledge is available on whether and how it might influence plasmid-mediated conjugation. Subinhibitory concentrations (3.9-250 ng/mL) of TET promoted horizontal gene transfer (HGT) via the mobilizable plasmid pVP52-1 from the donor Vibrio parahaemolyticus NJIFDCVp52 to the recipient Escherichia coli EC600 by 1.47- to 3.19-fold. The transcription levels of tetracycline resistance genes [tetA, tetR(A)], conjugation-related genes (traA, traD), outer membrane protein genes (ompA, ompK, ompV), reactive oxygen species (ROS)-related genes (oxyR, rpoS), autoinducer-2 (AI-2) synthesis gene (luxS), and SOS-related genes (lexA, recA) in the donor and recipient were significantly increased. Furthermore, the overproduced intracellular ROS generation and increased cell membrane permeability under TET exposure stimulated the conjugative transfer of ARGs. Overall, this study provides important insights into the contributions of TET to the spread of antimicrobial resistance.}, } @article {pmid38888367, year = {2024}, author = {Li, X and Gallardo, O and August, E and Dassa, B and Court, DL and Stavans, J and Arbel-Goren, R}, title = {Stability and gene strand bias of lambda prophages and chromosome organization in Escherichia coli.}, journal = {mBio}, volume = {}, number = {}, pages = {e0207823}, doi = {10.1128/mbio.02078-23}, pmid = {38888367}, issn = {2150-7511}, abstract = {Temperate phage-mediated horizontal gene transfer is a potent driver of genetic diversity in the evolution of bacteria. Most lambdoid prophages in Escherichia coli are integrated into the chromosome with the same orientation with respect to the direction of chromosomal replication, and their location on the chromosome is far from homogeneous. To better understand these features, we studied the interplay between lysogenic and lytic states of phage lambda in both native and inverted integration orientations at the wild-type integration site as well as at other sites on the bacterial chromosome. Measurements of free phage released by spontaneous induction showed that the stability of lysogenic states is affected by location and orientation along the chromosome, with stronger effects near the origin of replication. Competition experiments and range expansions between lysogenic strains with opposite orientations and insertion loci indicated that there are no major differences in growth. Moreover, measurements of the level of transcriptional bursts of the cI gene coding for the lambda phage repressor using single-molecule fluorescence in situ hybridization resulted in similar levels of transcription for both orientations and prophage location. We postulate that the preference for a given orientation and location is a result of a balance between the maintenance of lysogeny and the ability to lyse.IMPORTANCEThe integration of genetic material of temperate bacterial viruses (phages) into the chromosomes of bacteria is a potent evolutionary force, allowing bacteria to acquire in one stroke new traits and restructure the information in their chromosomes. Puzzlingly, this genetic material is preferentially integrated in a particular orientation and at non-random sites on the bacterial chromosome. The work described here reveals that the interplay between the maintenance of the stability of the integrated phage, its ability to excise, and its localization along the chromosome plays a key role in setting chromosomal organization in Escherichia coli.}, } @article {pmid38884912, year = {2024}, author = {Libante, V and Dechêne-Tempier, M and Leblond-Bourget, N and Payot, S}, title = {Detection and Quantification of Conjugative Transfer of Mobile Genetic Elements Carrying Antibiotic Resistance Genes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2815}, number = {}, pages = {79-91}, pmid = {38884912}, issn = {1940-6029}, mesh = {*Conjugation, Genetic ; *Interspersed Repetitive Sequences/genetics ; Gene Transfer, Horizontal ; Streptococcus suis/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Polymerase Chain Reaction/methods ; Genes, Bacterial ; }, abstract = {Multidrug resistance, due to acquired antimicrobial resistance genes, is increasingly reported in the zoonotic pathogen Streptococcus suis. Most of these resistance genes are carried by chromosomal Mobile Genetic Elements (MGEs), in particular, Integrative and Conjugative Elements (ICEs) and Integrative and Mobilizable Elements (IMEs). ICEs and IMEs frequently form tandems or nested composite elements, which make their identification difficult. To evaluate their mobility, it is necessary to (i) select the suitable donor-recipient pairs for mating assays, (ii) do PCR excision tests to confirm that the genetic element is able to excise from the chromosome as a circular intermediate, and (iii) evaluate the transfer of the genetic element by conjugation by doing mating assays. In addition to a dissemination of resistance genes between S. suis strains, MGEs can lead to a spreading of resistance genes in the environment and toward pathogenic bacteria. This propagation had to be considered in a One Health perspective.}, } @article {pmid38884260, year = {2024}, author = {Wang, S and Jiang, Y and Che, L and Wang, RH and Li, SC}, title = {Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkae515}, pmid = {38884260}, issn = {1362-4962}, support = {20220814183301001//Shenzhen Science and Technology Program/ ; 9667242//Applied Research/ ; 9440262//Hong Kong Innovation and Technology Fund/ ; }, abstract = {Horizontal gene transfer (HGT) phenomena pervade the gut microbiome and significantly impact human health. Yet, no current method can accurately identify complete HGT events, including the transferred sequence and the associated deletion and insertion breakpoints from shotgun metagenomic data. Here, we develop LocalHGT, which facilitates the reliable and swift detection of complete HGT events from shotgun metagenomic data, delivering an accuracy of 99.4%-verified by Nanopore data-across 200 gut microbiome samples, and achieving an average F1 score of 0.99 on 100 simulated data. LocalHGT enables a systematic characterization of HGT events within the human gut microbiome across 2098 samples, revealing that multiple recipient genome sites can become targets of a transferred sequence, microhomology is enriched in HGT breakpoint junctions (P-value = 3.3e-58), and HGTs can function as host-specific fingerprints indicated by the significantly higher HGT similarity of intra-personal temporal samples than inter-personal samples (P-value = 4.3e-303). Crucially, HGTs showed potential contributions to colorectal cancer (CRC) and acute diarrhoea, as evidenced by the enrichment of the butyrate metabolism pathway (P-value = 3.8e-17) and the shigellosis pathway (P-value = 5.9e-13) in the respective associated HGTs. Furthermore, differential HGTs demonstrated promise as biomarkers for predicting various diseases. Integrating HGTs into a CRC prediction model achieved an AUC of 0.87.}, } @article {pmid38882494, year = {2024}, author = {Xu, X and Feng, Q and Zhang, T and Gao, Y and Cheng, Q and Zhang, W and Wu, Q and Xu, K and Li, Y and Nguyen, N and Taft, DH and Mills, DA and Lemay, DG and Zhu, W and Mao, S and Zhang, A and Xu, K and Liu, J}, title = {Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life.}, journal = {iMeta}, volume = {3}, number = {2}, pages = {e169}, pmid = {38882494}, issn = {2770-596X}, abstract = {The infant gut microbiome is increasingly recognized as a reservoir of antibiotic resistance genes, yet the assembly of gut resistome in infants and its influencing factors remain largely unknown. We characterized resistome in 4132 metagenomes from 963 infants in six countries and 4285 resistance genes were observed. The inherent resistome pattern of healthy infants (N = 272) could be distinguished by two stages: a multicompound resistance phase (Months 0-7) and a tetracycline-mupirocin-β-lactam-dominant phase (Months 8-14). Microbial taxonomy explained 40.7% of the gut resistome of healthy infants, with Escherichia (25.5%) harboring the most resistance genes. In a further analysis with all available infants (N = 963), we found age was the strongest influencer on the resistome and was negatively correlated with the overall resistance during the first 3 years (p < 0.001). Using a random-forest approach, a set of 34 resistance genes could be used to predict age (R [2] = 68.0%). Leveraging microbial host inference analyses, we inferred the age-dependent assembly of infant resistome was a result of shifts in the gut microbiome, primarily driven by changes in taxa that disproportionately harbor resistance genes across taxa (e.g., Escherichia coli more frequently harbored resistance genes than other taxa). We performed metagenomic functional profiling and metagenomic assembled genome analyses whose results indicate that the development of gut resistome was driven by changes in microbial carbohydrate metabolism, with an increasing need for carbohydrate-active enzymes from Bacteroidota and a decreasing need for Pseudomonadota during infancy. Importantly, we observed increased acquired resistance genes over time, which was related to increased horizontal gene transfer in the developing infant gut microbiome. In summary, infant age was negatively correlated with antimicrobial resistance gene levels, reflecting a composition shift in the gut microbiome, likely driven by the changing need for microbial carbohydrate metabolism during early life.}, } @article {pmid38880617, year = {2024}, author = {Miyoshi, SI and Amako, K and Muraoka, M and Morinaga, H and Ueba, S}, title = {Mobile genetic elements associated with utilization of dichloromethane and methanol as energy sources in Cupriavidus metallidurans.}, journal = {Journal of microorganism control}, volume = {29}, number = {2}, pages = {55-65}, doi = {10.4265/jmc.29.2_55}, pmid = {38880617}, issn = {2758-6391}, mesh = {*Methanol/metabolism ; *Cupriavidus/genetics/metabolism/drug effects ; *Methylene Chloride/metabolism ; *Interspersed Repetitive Sequences/genetics ; Energy Metabolism/drug effects/genetics ; Genome, Bacterial/genetics ; Gene Transfer, Horizontal ; }, abstract = {Cupriavidus metallidurans strain PD11 isolated from laboratory waste drainage can use C1 compounds, such as dichloromethane (DCM) and methanol, as a sole carbon and energy source. However, strain CH34 (a type-strain) cannot grow in the medium supplemented with DCM. In the present study, we aimed to unravel the genetic elements underlying the utilization of C1 compounds by strain PD11. The genome subtraction approach indicated that only strain PD11 had several genes highly homologous to those of Herminiimonas arsenicoxydans strain ULPAs1. Moreover, a series of polymerase chain reaction (PCR) to detect the orthologs of H. arsenicoxydans genes and the comparative study of the genomes of three strains revealed that the 87.9 kb DNA fragment corresponding to HEAR1959 to HEAR2054 might be horizontally transferred to strain PD11. The 87.9 kb DNA fragment identified was found to contain three genes whose products were putatively involved in the metabolism of formaldehyde, a common intermediate of DCM and methanol. In addition, reverse transcription PCR analysis showed that all three genes were significantly expressed when strain PD11 was cultivated in the presence of DCM or methanol. These findings suggest that strain PD11 can effectively utilize the C1 compounds because of transfer of the mobile genetic elements from other bacterial species, for instance, from H. arsenicoxydans.}, } @article {pmid38880337, year = {2024}, author = {Sugimoto, TN and Jouraku, A and Mitsuhashi, W}, title = {Search for genes gained by horizontal gene transfer in an entomopoxvirus, with special reference to the analysis of the transfer of an ABC transporter gene.}, journal = {Virus research}, volume = {}, number = {}, pages = {199418}, doi = {10.1016/j.virusres.2024.199418}, pmid = {38880337}, issn = {1872-7492}, abstract = {Although it is generally believed that large DNA viruses capture genes by horizontal gene transfer (HGT), the detailed manner of such transfer has not been fully elucidated. Here, we searched for genes in the coleopteran entomopoxvirus (EV) Anomala cuprea entomopoxvirus (ACEV) that might have been gained by HGT. We classified the potential source organisms for HGT into three categories: the host A. cuprea; other organisms, including viruses unrelated to EVs; and organisms with uncertain host attribution. Of the open reading frames (ORFs) of the ACEV genome, 2.1% were suggested to have been gained from the host by ACEV or its recent ancestor via HGT; 8.7% were possibly from organisms other than the host, and 3.7% were possibly from the third category of organisms via HGT. The analysis showed that ACEV contains some interesting ORFs obtained by HGT, including a large ATP-binding cassette protein (ABC transporter) ORF and a tenascin ORF (IDs ACV025 and ACV123, respectively). We then performed a detailed analysis of the HGT of the ACEV large ABC transporter ORF-the largest of the ACEV ORFs. mRNA sequences obtained by RNA-seq from fat bodies-sites of ACEV replication-and midgut tissues-sites of initial infection-of the virus's host A. cuprea larvae were subjected to BLAST analysis. One type of ABC transporter ORF from the fat bodies and two types from the midgut tissues, one of which was identical to that in the fat bodies, had the greatest identity to the ABC transporter ORF of ACEV. The two types from the host had high levels of identity to each other (approximately 95% nucleotide sequence identity), strongly suggesting that the host ABC transporter group consisting of the two types was the origin of ACV025. We then determined the sequence (12,381 bp) containing a full-length gene of the A. cuprea ABC transporter. It turned out to be a transcription template for the abovementioned mRNA found in both tissues. In addition, we determined a large part (ca. 6.9 kb) of the template sequence for the mRNA found only in the midgut tissues. The results showed that the ACEV ABC transporter ORF is missing parts corresponding to introns of the host ABC transporter genes, indicating that the ORF was likely acquired by HGT in the form of mRNA. The presence of definite duplicated sequences adjacent to the ACEV ABC transporter genes-a sign of LINE-1 retrotransposon-mediated HGT-was not observed. An approximately 2-month ACV025 transcription experiment suggested that the transporter sequence is presumed to be continuously functional. The amino acid sequence of ACV025 suggests that its product might function in the regulation of phosphatide in the host-cell membranes.}, } @article {pmid38878503, year = {2024}, author = {Hu, Q and Zhang, L and Yang, R and Tang, J and Dong, G}, title = {Quaternary ammonium biocides promote conjugative transfer of antibiotic resistance gene in structure- and species-dependent manner.}, journal = {Environment international}, volume = {189}, number = {}, pages = {108812}, doi = {10.1016/j.envint.2024.108812}, pmid = {38878503}, issn = {1873-6750}, mesh = {*Disinfectants/pharmacology ; *Quaternary Ammonium Compounds/pharmacology ; *Escherichia coli/drug effects/genetics ; *Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; }, abstract = {The linkage between biocides and antibiotic resistance has been widely suggested in laboratories and various environments. However, the action mechanism of biocides on antibiotic resistance genes (ARGs) spread is still unclear. Thus, 6 quaternary ammonium biocides (QACs) with different bonded substituents or alkyl chain lengths were selected to assess their effects on the conjugation transfer of ARGs in this study. Two conjugation models with the same donor (E. coli DH5α (RP4)) into two receptors, E. coli MG1655 and pathogenic S. sonnei SE6-1, were constructed. All QACs were found to significantly promote intra- and inter-genus conjugative transfer of ARGs, and the frequency was highly impacted by their structure and receptors. At the same environmental exposure level (4 × 10[-1] mg/L), didecyl dimethyl ammonium chloride (DDAC (C10)) promoted the most frequency of conjugative transfer, while benzathine chloride (BEC) promoted the least. With the same donor, the enhanced frequency of QACs of intra-transfer is higher than inter-transfer. Then, the acquisition mechanisms of two receptors were further determined using biochemical combined with transcriptome analysis. For the recipient E. coli, the promotion of the intragenus conjugative transfer may be associated with increased cell membrane permeability, reactive oxygen species (ROS) production and proton motive force (PMF)-induced enhancement of flagellar motility. Whereas, the increase of cell membrane permeability and decreased flagellar motility due to PMF disruption but encouraged biofilm formation, maybe the main reasons for promoting intergenus conjugative transfer in the recipient S. sonnei. As one pathogenic bacterium, S. sonnei was first found to acquire ARGs by biocide exposure.}, } @article {pmid38878444, year = {2024}, author = {Li, W and Zeng, J and Zheng, N and Ge, C and Li, Y and Yao, H}, title = {Polyvinyl chloride microplastics in the aquatic environment enrich potential pathogenic bacteria and spread antibiotic resistance genes in the fish gut.}, journal = {Journal of hazardous materials}, volume = {475}, number = {}, pages = {134817}, doi = {10.1016/j.jhazmat.2024.134817}, pmid = {38878444}, issn = {1873-3336}, abstract = {Microplastics and antibiotics coexist in aquatic environments, especially in freshwater aquaculture areas. However, as the second largest production of polyvinyl chloride (PVC) in the world, the effects of co-exposure to microplastics particles and antibiotics on changes in antibiotic resistance gene (ARG) profiles and the microbial community structure of aquatic organism gut microorganisms are poorly understood. Therefore, in this study, carp (Cyprinus carpio) were exposed to single or combined PVC microplastic contamination and oxytetracycline (OTC) or sulfamethazine (SMZ) for 8 weeks. PVC microplastics can enrich potential pathogenic bacteria, such as Enterobacter and Acinetobacter, among intestinal microorganisms. The presence of PVC microplastics enhanced the selective enrichment and dissemination risk of ARGs. PVC microplastics combined with OTC (OPVC) treatment significantly increased the abundance of tetracycline resistance genes (1.40-fold) compared with that in the OTC exposure treatment, revealing an obvious co-selection effect. However, compared with those in the control group, the total abundance of ARGs and MGEs in the OPVC treatment groups were significantly lower, which was correlated with the reduced abundances of the potential host Enterobacter. Overall, our results emphasized the diffusion and spread of ARGs are more influenced by PVC microplastics than by antibiotics, which may lead to antibiotic resistance in aquaculture.}, } @article {pmid38878442, year = {2024}, author = {Ma, Y and Xu, S and Huang, Y and Du, J and Wang, J and Gao, B and Song, J and Ma, S and Jia, H and Zhan, S}, title = {The mechanism differences between sulfadiazine degradation and antibiotic resistant bacteria inactivation by iron-based graphitic biochar and peroxydisulfate system.}, journal = {Journal of hazardous materials}, volume = {475}, number = {}, pages = {134907}, doi = {10.1016/j.jhazmat.2024.134907}, pmid = {38878442}, issn = {1873-3336}, abstract = {In this study, the activation of peroxydisulfate (PS) by K2FeO4-activation biochar (KFeB) and acid-picking K2FeO4-activation biochar (AKFeB) was investigated to reveal the mechanism differences between iron site and graphitic structure in sulfadiazine (SDZ) degradation and ARB inactivation, respectively. KFeB/PS and AKFeB/PS systems had similar degradation property towards SDZ, but only KFeB/PS system showed excellent bactericidal property. The mechanism study demonstrated that dissolved SDZ was degraded through electron transfer pathway mediated by graphitic structure, while suspended ARB was inactivated through free radicals generated by iron-activated PS, accompanied by excellent removal on antibiotic resistance genes (ARGs). The significant decrease in conjugative transfer frequency indicated the reduced horizontal gene transfer risk of ARGs after treatment with KFeB/PS system. Transcriptome data suggested that membrane protein channel disruption and adenosine triphosphate synthesis inhibition were key reasons for conjugative transfer frequency reduction. Continuous flow reactor of KFeB/PS system can efficiently remove antibiotics and ARB, implying the potential application in practical wastewater purification. In conclusion, this study provides novel insights for classified and collaborative control of antibiotics and ARB by carbon-based catalysts driven persulfate advanced oxidation technology.}, } @article {pmid38878434, year = {2024}, author = {Chen, MM and Zhang, YQ and Cheng, LC and Zhao, FJ and Wang, P}, title = {Photoaged nanoplastics with multienzyme-like activities significantly shape the horizontal transfer of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {475}, number = {}, pages = {134884}, doi = {10.1016/j.jhazmat.2024.134884}, pmid = {38878434}, issn = {1873-3336}, abstract = {Nanoplastics (NPs), identified as emerging pollutants, pose a great risk to environment and global public health, exerting profound influences on the prevalence and dissemination of antibiotic resistance genes (ARGs). Despite evidence suggesting that nano-sized plastic particles can facilitate the horizontal gene transfer (HGT) of ARGs, it is imperative to explore strategies for inhibiting the transfer of ARGs. Currently, limited information exists regarding the characteristics of environmentally aged NPs and their impact on ARGs propagation. Herein, we investigated the impact of photo-aged NPs on the transfer of ARG-carrying plasmids into Escherichia coli (E. coli) cells. Following simulated sunlight irradiation, photo-aged nano-sized polystyrene plastics (PS NPs) exhibited multiple enzyme-like activities, including peroxidase (POD) and oxidase (OXD), leading to a burst of reactive oxygen species (ROS). At relatively low concentrations (0.1, 1 μg/mL), both pristine and aged PS NPs facilitated the transfer of pUC19 and pHSG396 plasmids within E. coli due to moderate ROS production and enhanced cell membrane permeability. Intriguingly, at relatively high concentrations (5, 10 μg/mL), aged PS NPs significantly suppressed plasmids transformation. The non-unidirectional impact of aged PS NPs involved the overproduction of ROS (•OH and •O2[-]) via nanozyme activity, directly degrading ARGs and damaging plasmid structure. Additionally, oxidative damage to bacteria resulted from the presence of much toxic free radicals, causing physical damage to cell membranes, reduction of the SOS response and restriction of adenosine-triphosphate (ATP) supply, ultimately leading to inactivation of recipient cells. This study unveils the intrinsic multienzyme-like activity of environmentally aged NPs, highlighting their potential to impede the transfer and dissemination of ARGs.}, } @article {pmid38878274, year = {2024}, author = {Vidal-Quist, JC and Ortego, F and Rombauts, S and Hernández-Crespo, P}, title = {The genome-wide response of Dermatophagoides pteronyssinus to cystatin A, a peptidase inhibitor from human skin, sheds light on its digestive physiology and allergenicity.}, journal = {Insect molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/imb.12931}, pmid = {38878274}, issn = {1365-2583}, abstract = {The digestive physiology of house dust mites (HDMs) is particularly relevant for their allergenicity since many of their allergens participate in digestion and are excreted into faecal pellets, a main source of exposure for allergic subjects. To gain insight into the mite dietary digestion, the genome of the HDM Dermatophagoides pteronyssinus was screened for genes encoding peptidases (n = 320), glycosylases (n = 77), lipases and esterases (n = 320), peptidase inhibitors (n = 65) and allergen-related proteins (n = 52). Basal gene expression and transcriptional responses of mites to dietary cystatin A, a cysteine endopeptidase inhibitor with previously shown antinutritional effect on mites, were analysed by RNAseq. The ingestion of cystatin A resulted in significant regulation of different cysteine endopeptidase and glycosylase genes. One Der p 1-like and two cathepsin B-like cysteine endopeptidase genes of high basal expression were induced, which suggests their prominent role in proteolytic digestion together with major allergen Der p 1. A number of genes putatively participating in the interaction of mites with their microbiota and acquired by horizontal gene transfer were repressed, including genes encoding the peptidase Der p 38, two 1,3-beta-glucanases, a lysozyme and a GH19 chitinase. Finally, the disruption of mite digestion resulted in the regulation of up to 17 allergen and isoallergen genes. Altogether, our results shed light on the putative role of specific genes in digestion and illustrate the connection between the digestive physiology of HDM and allergy.}, } @article {pmid38876022, year = {2024}, author = {Sivalingam, P and Sabatino, R and Sbaffi, T and Corno, G and Fontaneto, D and Borgomaneiro, G and Rogora, M and Crotti, E and Mapelli, F and Borin, S and Pilar, AL and Eckert, EM and Di Cesare, A}, title = {Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {475}, number = {}, pages = {134885}, doi = {10.1016/j.jhazmat.2024.134885}, pmid = {38876022}, issn = {1873-3336}, abstract = {Aquatic ecosystems are crucial in the antimicrobial resistance cycle. While intracellular DNA has been extensively studied to understand human activity's impact on antimicrobial resistance gene (ARG) dissemination, extracellular DNA is frequently overlooked. This study examines the effect of anthropogenic water pollution on microbial community diversity, the resistome, and ARG dissemination. We analyzed intracellular and extracellular DNA from wastewater treatment plant effluents and lake surface water by shotgun sequencing. We also conducted experiments to evaluate anthropogenic pollution's effect on transforming extracellular DNA (using Gfp-plasmids carrying ARGs) within a natural microbial community. Chemical analysis showed treated wastewater had higher anthropogenic pollution-related parameters than lake water. The richness of microbial community, antimicrobial resistome, and high-risk ARGs was greater in treated wastewaters than in lake waters both for intracellular and extracellular DNA. Except for the high-risk ARGs, richness was significantly higher in intracellular than in extracellular DNA. Several ARGs were associated with mobile genetic elements and located on plasmids. Furthermore, Gfp-plasmid transformation within a natural microbial community was enhanced by anthropogenic pollution levels. Our findings underscore anthropogenic pollution's pivotal role in shaping microbial communities and their antimicrobial resistome. Additionally, it may facilitate ARG dissemination through extracellular DNA plasmid uptake.}, } @article {pmid38871331, year = {2024}, author = {Wang, X and Li, J and Pan, X}, title = {How micro-/nano-plastics influence the horizontal transfer of antibiotic resistance genes - A review.}, journal = {The Science of the total environment}, volume = {944}, number = {}, pages = {173881}, doi = {10.1016/j.scitotenv.2024.173881}, pmid = {38871331}, issn = {1879-1026}, abstract = {Plastic debris such as microplastics (MPs) and nanoplastics (NPTs), along with antibiotic resistance genes (ARGs), are pervasive in the environment and are recognized as significant global health and ecological concerns. Micro-/nano-plastics (MNPs) have been demonstrated to favor the spread of ARGs by enhancing the frequency of horizontal gene transfer (HGT) through various pathways. This paper comprehensively and systematically reviews the current study with focus on the influence of plastics on the HGT of ARGs. The critical role of MNPs in the HGT of ARGs has been well illustrated in sewage sludge, livestock farms, constructed wetlands and landfill leachate. A summary of the performed HGT assay and the underlying mechanism of plastic-mediated transfer of ARGs is presented in the paper. MNPs could facilitate or inhibit HGT of ARGs, and their effects depend on the type, size, and concentration. This review provides a comprehensive insight into the effects of MNPs on the HGT of ARGs, and offers suggestions for further study. Further research should attempt to develop a standard HGT assay and focus on investigating the impact of different plastics, including the oligomers they released, under real environmental conditions on the HGT of ARGs.}, } @article {pmid38871190, year = {2024}, author = {Skalny, M and Rokowska, A and Szuwarzynski, M and Gajewska, M and Dziewit, L and Bajda, T}, title = {Nanoscale surface defects of goethite governing DNA adsorption process and formation of the Goethite-DNA conjugates.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {142602}, doi = {10.1016/j.chemosphere.2024.142602}, pmid = {38871190}, issn = {1879-1298}, abstract = {In urbanized areas, extracellular DNA (exDNA) is suspected of carrying genes with undesirable traits like virulence genes (VGs) or antibiotic resistance genes (ARGs), which can spread through horizontal gene transfer (HGT). Hence, it is crucial to develop novel approaches for the mitigation of exDNA in the environment. Our research explores the role of goethite, a common iron mineral with high adsorption capabilities, in exDNA adsorption processes. We compare well-crystalline, semi-crystalline, and nano goethites with varying particle sizes to achieve various specific surface areas (SSAs) (18.7 - 161.6 m[2]/g) and porosities. We conducted batch adsorption experiments using DNA molecules of varying chain lengths (DNA sizes: < 11 Kb, < 6 Kb, and < 3 Kb) and assessed the impact of Ca[2+] and biomacromolecules on the adsorption efficacy and mechanisms. Results show that porosity and pore structure significantly influence DNA adsorption capacity. Goethite with well-developed meso- and macroporosity demonstrated enhanced DNA adsorption. The accumulation of DNA on the goethite interface led to substantial aggregation in the system, thus the formation of DNA-goethite conjugates, indicating the bridging between mineral particles. DNA chain length, the presence of Ca[2+], and the biomacromolecule matrix also affected the adsorption capacity and mechanism. Interactions between DNA and positively charged biomacromolecules or Ca[2+] led to DNA compaction, allowing greater DNA accumulation in pores. However, a high concentration of biomacromolecules led to the saturation of the goethite surface, inhibiting DNA adsorption. AFM imaging of goethite particles after adsorption suggested the formation of the DNA multilayer. The study advances understanding of the environmental behavior of exDNA and its interaction with iron oxyhydroxides, offering insights into developing more effective methods for ARGs removal in wastewater treatment plants. By manipulating the textural properties of goethite, it's possible to enhance exDNA removal, potentially reducing the spread of biocontamination in urban and industrial environments.}, } @article {pmid38870897, year = {2024}, author = {Kennedy, NW and Comstock, LE}, title = {Mechanisms of bacterial immunity, protection, and survival during interbacterial warfare.}, journal = {Cell host & microbe}, volume = {32}, number = {6}, pages = {794-803}, doi = {10.1016/j.chom.2024.05.006}, pmid = {38870897}, issn = {1934-6069}, mesh = {*Bacteria/immunology/genetics ; *Bacterial Toxins/metabolism/immunology ; Gene Transfer, Horizontal ; Humans ; Microbial Viability ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/metabolism/genetics ; }, abstract = {Most bacteria live in communities, often with closely related strains and species with whom they must compete for space and resources. Consequently, bacteria have acquired or evolved mechanisms to antagonize competitors through the production of antibacterial toxins. Similar to bacterial systems that combat phage infection and mechanisms to thwart antibiotics, bacteria have also acquired and evolved features to protect themselves from antibacterial toxins. Just as there is a large body of research identifying and characterizing antibacterial proteins and toxin delivery systems, studies of bacterial mechanisms to resist and survive assault from competitors' weapons have also expanded tremendously. Emerging data are beginning to reveal protective processes and mechanisms that are as diverse as the toxins themselves. Protection against antibacterial toxins can be acquired by horizontal gene transfer, receptor or target alteration, induction of protective functions, physical barriers, and other diverse processes. Here, we review recent studies in this rapidly expanding field.}, } @article {pmid38870889, year = {2024}, author = {Zhang, P and Wang, Y and Lin, H and Liang, J and Wang, J and Bai, Y and Qu, J and Wang, A}, title = {Bacterial evolution in Biofiltration of drinking water treatment plant: Different response of phage and plasmid to varied water sources.}, journal = {Water research}, volume = {259}, number = {}, pages = {121887}, doi = {10.1016/j.watres.2024.121887}, pmid = {38870889}, issn = {1879-2448}, abstract = {Biofiltration in drinking water treatment (BDWT) are popular as it holds promise as an alternative to chemical treatments, yet our understanding of the key drivers and trends underlying bacterial evolution within this process remains limited. While plasmids and phages are recognized as the main vectors of horizontal gene transfer (HGT), their roles in shaping bacterial evolution in BDWT remain largely unknown. Here we leverage global metagenomic data to unravel the primary forces driving bacterial evolution in BDWT. Our results revealed that the primary vector of HGT varies depending on the type of source water (groundwater and surface water). Both plasmids and phages accelerated bacterial evolution in BDWT by enhancing genetic diversity within species, but they drove contrasting evolutionary trends in functional redundancy in different source water types. Specifically, trends towards and away from functional redundancy (indicated as gene-protein ratio) were observed in surface-water and groundwater biofilters, respectively. Virulent phages drove bacterial evolution through synergistic interactions with bacterial species capable of natural transformation and with certain natural compounds that disrupt bacterial cytoplasmic membranes. Genes relating to water purification (such as Mn(II)-oxidizing genes), microbial risks (antibiotic resistance genes), and chemical risk (polycyclic aromatic hydrocarbons) were enriched via HGT in BDWT, highlighting the necessity for heighted focus on these useful and risky objects. Overall, these discoveries enhance our understanding of bacterial evolution in BDWT and have implications for the optimization of water treatment strategies.}, } @article {pmid38861577, year = {2024}, author = {Elsen, S and Simon, V and Attrée, I}, title = {Cross-regulation and cross-talk of conserved and accessory two-component regulatory systems orchestrate Pseudomonas copper resistance.}, journal = {PLoS genetics}, volume = {20}, number = {6}, pages = {e1011325}, doi = {10.1371/journal.pgen.1011325}, pmid = {38861577}, issn = {1553-7404}, abstract = {Bacteria use diverse strategies and molecular machinery to maintain copper homeostasis and to cope with its toxic effects. Some genetic elements providing copper resistance are acquired by horizontal gene transfer; however, little is known about how they are controlled and integrated into the central regulatory network. Here, we studied two copper-responsive systems in a clinical isolate of Pseudomonas paraeruginosa and deciphered the regulatory and cross-regulation mechanisms. To do so, we combined mutagenesis, transcriptional fusion analyses and copper sensitivity phenotypes. Our results showed that the accessory CusRS two-component system (TCS) responds to copper and activates both its own expression and that of the adjacent nine-gene operon (the pcoA2 operon) to provide resistance to elevated levels of extracellular copper. The same locus was also found to be regulated by two core-genome-encoded TCSs-the copper-responsive CopRS and the zinc-responsive CzcRS. Although the target palindromic sequence-ATTCATnnATGTAAT-is the same for the three response regulators, transcriptional outcomes differ. Thus, depending on the operon/regulator pair, binding can result in different activation levels (from none to high), with the systems demonstrating considerable plasticity. Unexpectedly, although the classical CusRS and the noncanonical CopRS TCSs rely on distinct signaling mechanisms (kinase-based vs. phosphatase-based), we discovered cross-talk in the absence of the cognate sensory kinases. This cross-talk occurred between the proteins of these two otherwise independent systems. The cusRS-pcoA2 locus is part of an Integrative and Conjugative Element, and was found in other Pseudomonas strains where its expression could provide copper resistance under appropriate conditions. The results presented here illustrate how acquired genetic elements can become part of endogenous regulatory networks, providing a physiological advantage. They also highlight the potential for broader effects of accessory regulatory proteins through interference with core regulatory proteins.}, } @article {pmid38853947, year = {2024}, author = {Wendt, GR and Collins, JJ}, title = {Horizontal gene transfer of a functional cki homolog in the human pathogen Schistosoma mansoni.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38853947}, abstract = {Schistosomes are parasitic flatworms responsible for the neglected tropical disease schistosomiasis, causing devastating morbidity and mortality in the developing world. The parasites are protected by a skin-like tegument, and maintenance of this tegument is controlled by a schistosome ortholog of the tumor suppressor TP53. To understand mechanistically how p53-1 controls tegument production, we identified a cyclin dependent kinase inhibitor homolog (cki) that was co-expressed with p53-1. RNA interference of cki resulted in a hyperproliferation phenotype, that, in combination with p53-1 RNA interference yielded abundant tumor-like growths, indicating that cki and p53-1 are bona fide tumor suppressors in Schistosoma mansoni. Interestingly, cki homologs are widely present throughout parasitic flatworms but evidently absent from their free-living ancestors, suggesting this cki homolog came from an ancient horizontal gene transfer event. This in turn implies that the evolution of parasitism in flatworms may have been aided by a highly unusual means of metazoan genetic inheritance.}, } @article {pmid38843310, year = {2024}, author = {Coelho, MA and David-Palma, M and Shea, T and Bowers, K and McGinley-Smith, S and Mohammad, AW and Gnirke, A and Yurkov, AM and Nowrousian, M and Sun, S and Cuomo, CA and Heitman, J}, title = {Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis.}, journal = {PLoS biology}, volume = {22}, number = {6}, pages = {e3002682}, doi = {10.1371/journal.pbio.3002682}, pmid = {38843310}, issn = {1545-7885}, abstract = {In exploring the evolutionary trajectories of both pathogenesis and karyotype dynamics in fungi, we conducted a large-scale comparative genomic analysis spanning the Cryptococcus genus, encompassing both global human fungal pathogens and nonpathogenic species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species, covering virtually all known diversity within these genera. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at preadaptive pathogenic potential, our analysis found evidence of gene gain (via horizontal gene transfer) and gene loss in pathogenic Cryptococcus species, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the 2 genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5, or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes showed reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Overall, our findings advance our understanding of genetic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.}, } @article {pmid38754416, year = {2024}, author = {Benz, F and Camara-Wilpert, S and Russel, J and Wandera, KG and Čepaitė, R and Ares-Arroyo, M and Gomes-Filho, JV and Englert, F and Kuehn, JA and Gloor, S and Mestre, MR and Cuénod, A and Aguilà-Sans, M and Maccario, L and Egli, A and Randau, L and Pausch, P and Rocha, EPC and Beisel, CL and Madsen, JS and Bikard, D and Hall, AR and Sørensen, SJ and Pinilla-Redondo, R}, title = {Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans.}, journal = {Cell host & microbe}, volume = {32}, number = {6}, pages = {875-886.e9}, doi = {10.1016/j.chom.2024.04.016}, pmid = {38754416}, issn = {1934-6069}, mesh = {*CRISPR-Cas Systems ; *Plasmids/genetics ; *Klebsiella pneumoniae/genetics ; *Conjugation, Genetic ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; Bacteriophages/genetics ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Plasmid-encoded type IV-A CRISPR-Cas systems lack an acquisition module, feature a DinG helicase instead of a nuclease, and form ribonucleoprotein complexes of unknown biological functions. Type IV-A3 systems are carried by conjugative plasmids that often harbor antibiotic-resistance genes and their CRISPR array contents suggest a role in mediating inter-plasmid conflicts, but this function remains unexplored. Here, we demonstrate that a plasmid-encoded type IV-A3 system co-opts the type I-E adaptation machinery from its host, Klebsiella pneumoniae (K. pneumoniae), to update its CRISPR array. Furthermore, we reveal that robust interference of conjugative plasmids and phages is elicited through CRISPR RNA-dependent transcriptional repression. By silencing plasmid core functions, type IV-A3 impacts the horizontal transfer and stability of targeted plasmids, supporting its role in plasmid competition. Our findings shed light on the mechanisms and ecological function of type IV-A3 systems and demonstrate their practical efficacy for countering antibiotic resistance in clinically relevant strains.}, } @article {pmid38842312, year = {2024}, author = {Klepa, MS and diCenzo, GC and Hungria, M}, title = {Comparative genomic analysis of Bradyrhizobium strains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0026024}, doi = {10.1128/spectrum.00260-24}, pmid = {38842312}, issn = {2165-0497}, abstract = {Bradyrhizobium is known for fixing atmospheric nitrogen in symbiosis with agronomically important crops. This study focused on two groups of strains, each containing eight natural variants of the parental strains, Bradyrhizobium japonicum SEMIA 586 (=CNPSo 17) or Bradyrhizobium diazoefficiens SEMIA 566 (=CNPSo 10). CNPSo 17 and CNPSo 10 were used as commercial inoculants for soybean crops in Brazil at the beginning of the crop expansion in the southern region in the 1960s-1970s. Variants derived from these parental strains were obtained in the late 1980s through a strain selection program aimed at identifying elite strains adapted to a new cropping frontier in the central-western Cerrado region, with a higher capacity of biological nitrogen fixation (BNF) and competitiveness. Here, we aimed to detect genetic variations possibly related to BNF, competitiveness for nodule occupancy, and adaptation to the stressful conditions of the Brazilian Cerrado soils. High-quality genome assemblies were produced for all strains. The core genome phylogeny revealed that strains of each group are closely related, as confirmed by high average nucleotide identity values. However, variants accumulated divergences resulting from horizontal gene transfer, genomic rearrangements, and nucleotide polymorphisms. The B. japonicum group presented a larger pangenome and a higher number of nucleotide polymorphisms than the B. diazoefficiens group, possibly due to its longer adaptation time to the Cerrado soil. Interestingly, five strains of the B. japonicum group carry two plasmids. The genetic variability found in both groups is discussed considering the observed differences in their BNF capacity, competitiveness for nodule occupancy, and environmental adaptation.IMPORTANCEToday, Brazil is a global leader in the study and use of biological nitrogen fixation with soybean crops. As Brazilian soils are naturally void of soybean-compatible bradyrhizobia, strain selection programs were established, starting with foreign isolates. Selection searched for adaptation to the local edaphoclimatic conditions, higher efficiency of nitrogen fixation, and strong competitiveness for nodule occupancy. We analyzed the genomes of two parental strains of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens and eight variant strains derived from each parental strain. We detected two plasmids in five strains and several genetic differences that might be related to adaptation to the stressful conditions of the soils of the Brazilian Cerrado biome. We also detected genetic variations in specific regions that may impact symbiotic nitrogen fixation. Our analysis contributes to new insights into the evolution of Bradyrhizobium, and some of the identified differences may be applied as genetic markers to assist strain selection programs.}, } @article {pmid38839049, year = {2024}, author = {Middlebrook, EA and Katani, R and Fair, JM}, title = {OrthoPhyl - Streamlining large scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkae119}, pmid = {38839049}, issn = {2160-1836}, abstract = {There are a staggering number of publicly available bacterial genome sequences (at writing, 2.0 million assemblies in NCBI's GenBank alone), and the deposition rate continues to increase. This wealth of data begs for phylogenetic analyses to place these sequences within an evolutionary context. A phylogenetic placement not only aids in taxonomic classification, but informs the evolution of novel phenotypes, targets of selection, and horizontal gene transfer. Building trees from multi-gene codon alignments is a laborious task that requires bioinformatic expertise, rigorous curation of orthologs, and heavy computation. Compounding the problem is the lack of tools that can streamline these processes for building trees from large scale genomic data. Here we present OrthoPhyl, which takes bacterial genome assemblies and reconstructs trees from whole genome codon alignments. The analysis pipeline can analyze an arbitrarily large number of input genomes (>1200 tested here) by identifying a diversity spanning subset of assemblies and using these genomes to build gene models to infer orthologs in the full dataset. To illustrate the versatility of OrthoPhyl, we show three use-cases: E. coli/Shigella, Brucella/Ochrobactrum, and the order Rickettsiales. We compare trees generated with OrthoPhyl to trees generated with kSNP3 and GToTree along with published trees using alternative methods. We show that OrthoPhyl trees are consistent with other methods while incorporating more data, allowing for greater numbers of input genomes, and more flexibility of analysis.}, } @article {pmid38830804, year = {2024}, author = {Amirfard, KD and Moriyama, M and Suzuki, S and Sano, D}, title = {Effect of environmental factors on conjugative transfer of antibiotic resistance genes in aquatic settings.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxae129}, pmid = {38830804}, issn = {1365-2672}, abstract = {Antimicrobial-resistance genes (ARGs) are spread among bacteria by horizontal gene transfer (HGT), however, the effect of environmental factors on the dynamics of the ARG in water environments has not been very well understood. In this systematic review, we employed the regression tree algorithm to identify the environmental factors that facilitate/inhibit the transfer of ARGs via conjugation in planktonic/biofilm-formed bacterial cells based on the results of past relevant research. Escherichia coli strains were the most studied genus for conjugation experiments as donor/recipient in the intra-genera category. Conversely, Pseudomonas spp., Acinetobacter spp., and Salmonella spp. were studied primarily as recipients across inter-genera bacteria. The conjugation efficiency (ce) was found to be highly dependent on the incubation period. Some antibiotics, such as nitrofurantoin (at ≥ 0.2 µg ml -1) and kanamycin (at ≥ 9.5 mg l -1) as well as metallic compounds like mercury (II) chloride (HgCl2, ≥ 3 µmol l -1), and vanadium (III) chloride (VCl3, ≥ 50 µmol l -1) had enhancing effect on conjugation. The highest ce value (-0.90 log10) was achieved at 15-19 °C, with linoleic acid concentrations < 8 mg l -1, a recognized conjugation inhibitor. Identifying critical environmental factors affecting ARG dissemination in aquatic environments will accelerate strategies to control their proliferation and combat antibiotic resistance.}, } @article {pmid38830497, year = {2024}, author = {Zhang, X and Li, P and Wang, J and Fu, D and Zhao, B and Dong, W and Liu, Y}, title = {Comparative genomic and phylogenetic analyses of mitochondrial genomes of hawthorn (Crataegus spp.) in Northeast China.}, journal = {International journal of biological macromolecules}, volume = {272}, number = {Pt 1}, pages = {132795}, doi = {10.1016/j.ijbiomac.2024.132795}, pmid = {38830497}, issn = {1879-0003}, abstract = {Hawthorn (Crataegus spp.) plants are major sources of health food and medicines. Twenty species and seven variations of Crataegus are present in China. A variety of unique Crataegus species was found in their natural distribution in northeast China. In the present study, we assembled and annotated the mitochondrial genomes of five Crataegus species from northeastern China. The sizes of the newly sequenced mitochondrial genomes ranged from 245,907 bp to 410,837 bp. A total of 45-55 genes, including 12-19 transfer RNA genes, three ribosomal RNA genes, and 29-33 protein-coding genes (PCGs) were encoded by these mitochondrial genomes. Seven divergent hotspot regions were identified by comparative analyses: atp6, nad3, ccmFN, matR, nad1, nad5, and rps1. The most conserved genes among the Crataegus species, according to the whole-genome correlation analysis, were nad1, matR, nad5, ccmFN, cox1, nad4, trnQ-TTG, trnK-TTT, trnE-TTC, and trnM-CAT. Horizontal gene transfer between organellar genomes was common in Crataegus plants. Based on the phylogenetic trees of mitochondrial PCGs, C. maximowiczii, C. maximowiczii var. ninganensis, and C. bretschneideri shared similar maternal relationships. This study improves Crataegus mitochondrial genome resources and offers important insights into the taxonomy and species identification of this genus.}, } @article {pmid38830094, year = {2024}, author = {Attah, V and Milner, DS and Fang, Y and Yan, X and Leonard, G and Heitman, J and Talbot, NJ and Richards, TA}, title = {Duplication and neofunctionalization of a horizontally transferred xyloglucanase as a facet of the Red Queen coevolutionary dynamic.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {24}, pages = {e2218927121}, doi = {10.1073/pnas.2218927121}, pmid = {38830094}, issn = {1091-6490}, support = {PLP-2014-147//Leverhulme Trust/ ; URF/R/191005//Royal Society (The Royal Society)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Glycoside Hydrolases/metabolism/genetics ; *Phylogeny ; Phytophthora/pathogenicity/genetics ; Plant Diseases/microbiology/parasitology ; Evolution, Molecular ; Gene Duplication ; }, abstract = {Oomycete protists share phenotypic similarities with fungi, including the ability to cause plant diseases, but branch in a distant region of the tree of life. It has been suggested that multiple horizontal gene transfers (HGTs) from fungi-to-oomycetes contributed to the evolution of plant-pathogenic traits. These HGTs are predicted to include secreted proteins that degrade plant cell walls, a barrier to pathogen invasion and a rich source of carbohydrates. Using a combination of phylogenomics and functional assays, we investigate the diversification of a horizontally transferred xyloglucanase gene family in the model oomycete species Phytophthora sojae. Our analyses detect 11 xyloglucanase paralogs retained in P. sojae. Using heterologous expression in yeast, we show consistent evidence that eight of these paralogs have xyloglucanase function, including variants with distinct protein characteristics, such as a long-disordered C-terminal extension that can increase xyloglucanase activity. The functional variants analyzed subtend a phylogenetic node close to the fungi-to-oomycete transfer, suggesting the horizontally transferred gene was a bona fide xyloglucanase. Expression of three xyloglucanase paralogs in Nicotiana benthamiana triggers high-reactive oxygen species (ROS) generation, while others inhibit ROS responses to bacterial immunogens, demonstrating that the paralogs differentially stimulate pattern-triggered immunity. Mass spectrometry of detectable enzymatic products demonstrates that some paralogs catalyze the production of variant breakdown profiles, suggesting that secretion of variant xyloglucanases increases efficiency of xyloglucan breakdown as well as diversifying the damage-associated molecular patterns released. We suggest that this pattern of neofunctionalization and the variant host responses represent an aspect of the Red Queen host-pathogen coevolutionary dynamic.}, } @article {pmid38827508, year = {2024}, author = {Tang, N and Wei, D and Zeng, Y and Zhang, G and Wang, C and Feng, J and Song, Y}, title = {Understanding the rapid spread of antimicrobial resistance genes mediated by IS26.}, journal = {mLife}, volume = {3}, number = {1}, pages = {101-109}, pmid = {38827508}, issn = {2770-100X}, abstract = {Insertion sequences (ISs) promote the transmission of antimicrobial resistance genes (ARGs) across bacterial populations. However, their contributions and dynamics during the transmission of resistance remain unclear. In this study, we selected IS26 as a representative transposable element to decipher the relationship between ISs and ARGs and to investigate their transfer features and transmission trends. We retrieved 2656 translocatable IS 26 -bounded units with ARGs (tIS26-bUs-ARGs) in complete bacterial genomes from the NCBI RefSeq database. In total, 124 ARGs spanning 12 classes of antibiotics were detected, and the average contribution rate of IS26 to these genes was 41.2%. We found that IS 26 -bounded units (IS26-bUs) mediated extensive ARG dissemination within the bacteria of the Gammaproteobacteria class, showing strong transfer potential between strains, species, and even phyla. The IS26-bUs expanded in bacterial populations over time, and their temporal expansion trend was significantly correlated with antibiotic usage. This wide dissemination could be due to the nonspecific target site preference of IS26. Finally, we experimentally confirmed that the introduction of a single copy of IS26 could lead to the formation of a composite transposon mediating the transmission of "passenger" genes. These observations extend our knowledge of the IS26 and provide new insights into the mediating role of ISs in the dissemination of antibiotic resistance.}, } @article {pmid38823616, year = {2024}, author = {Peng, J and Wang, D and He, P and Wei, P and Zhang, L and Lan, W and Zhang, X and Guan, J and Chen, Y and Li, W and Zheng, Y and Li, Y and Chen, W and Zhao, Z and Jiang, L and Zhou, L}, title = {Seasonal Dynamics of Antibiotic Resistance Genes and Mobile Genetic Elements in a Subtropical Coastal Ecosystem: Implications for Environmental Health Risks.}, journal = {Environmental research}, volume = {}, number = {}, pages = {119298}, doi = {10.1016/j.envres.2024.119298}, pmid = {38823616}, issn = {1096-0953}, abstract = {Antibiotic resistance poses a considerable global public health concern, leading to heightened rates of illness and mortality. However, the impact of seasonal variations and environmental factors on the health risks associated with antibiotic resistance genes (ARGs) and their assembly mechanisms is not fully understood. Based on metagenomic sequencing, this study investigated the antibiotic resistome, mobile genetic elements (MGEs), and microbiomes in a subtropical coastal ecosystem of the Beibu Gulf, China, over autumn and winter, and explored the factors influencing seasonal changes in ARG and MGE abundance and diversity. Results indicated that ARG abundance and diversity were higher in winter than in autumn, with beta-lactam and multidrug resistance genes being the most diverse and abundant, respectively. Similarly, MGE abundance and diversity increased in winter and were strongly correlated with ARGs. In contrast, more pronounced associations between microbial communities, especially archaea, and the antibiotic resistome were observed in autumn than in winter. The co-occurrence network identified multiple interactions between MGEs and various multidrug efflux pumps in winter, suggesting a potential for ARG dissemination. Multivariate correlation analyses and path modeling indicated that environmental factors driving microbial community changes predominantly influenced antibiotic resistome assembly in autumn, while the relative importance of MGEs increased significantly in winter. These findings suggest an elevated health risk associated with antimicrobial resistance in the Beibu Gulf during winter, attributed to the dissemination of ARGs by horizontal gene transfer. The observed seasonal variations highlight the dynamic nature of antibiotic resistance dissemination in coastal ecosystems, emphasizing the need for comprehensive surveillance and management measures to address the growing threat of antimicrobial resistance in vulnerable environments.}, } @article {pmid38820540, year = {2024}, author = {Morel-Letelier, I and Yuen, B and Kück, AC and Camacho-García, YE and Petersen, JM and Lara, M and Leray, M and Eisen, JA and Osvatic, JT and Gros, O and Wilkins, LGE}, title = {Adaptations to nitrogen availability drive ecological divergence of chemosynthetic symbionts.}, journal = {PLoS genetics}, volume = {20}, number = {5}, pages = {e1011295}, doi = {10.1371/journal.pgen.1011295}, pmid = {38820540}, issn = {1553-7404}, abstract = {Bacterial symbionts, with their shorter generation times and capacity for horizontal gene transfer (HGT), play a critical role in allowing marine organisms to cope with environmental change. The closure of the Isthmus of Panama created distinct environmental conditions in the Tropical Eastern Pacific (TEP) and Caribbean, offering a "natural experiment" for studying how closely related animals evolve and adapt under environmental change. However, the role of bacterial symbionts in this process is often overlooked. We sequenced the genomes of endosymbiotic bacteria in two sets of sister species of chemosymbiotic bivalves from the genera Codakia and Ctena (family Lucinidae) collected on either side of the Isthmus, to investigate how differing environmental conditions have influenced the selection of symbionts and their metabolic capabilities. The lucinid sister species hosted different Candidatus Thiodiazotropha symbionts and only those from the Caribbean had the genetic potential for nitrogen fixation, while those from the TEP did not. Interestingly, this nitrogen-fixing ability did not correspond to symbiont phylogeny, suggesting convergent evolution of nitrogen fixation potential under nutrient-poor conditions. Reconstructing the evolutionary history of the nifHDKT operon by including other lucinid symbiont genomes from around the world further revealed that the last common ancestor (LCA) of Ca. Thiodiazotropha lacked nif genes, and populations in oligotrophic habitats later re-acquired the nif operon through HGT from the Sedimenticola symbiont lineage. Our study suggests that HGT of the nif operon has facilitated niche diversification of the globally distributed Ca. Thiodiazotropha endolucinida species clade. It highlights the importance of nitrogen availability in driving the ecological diversification of chemosynthetic symbiont species and the role that bacterial symbionts may play in the adaptation of marine organisms to changing environmental conditions.}, } @article {pmid38819554, year = {2024}, author = {Hellmuth, M and Stadler, PF}, title = {The Theory of Gene Family Histories.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2802}, number = {}, pages = {1-32}, pmid = {38819554}, issn = {1940-6029}, mesh = {*Phylogeny ; *Multigene Family ; *Gene Transfer, Horizontal ; *Evolution, Molecular ; Models, Genetic ; Computational Biology/methods ; }, abstract = {Most genes are part of larger families of evolutionary-related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene family histories, i.e., the precise dating of evolutionary events relative to phylogenetic tree of the underlying species has remained a challenging topic despite their importance as a basis for detailed investigations into adaptation and functional evolution of individual members of the gene family. The identification of orthologs, moreover, is a particularly important subproblem of the more general setting considered here. In the last few years, an extensive body of mathematical results has appeared that tightly links orthology, a formal notion of best matches among genes, and horizontal gene transfer. The purpose of this chapter is to broadly outline some of the key mathematical insights and to discuss their implication for practical applications. In particular, we focus on tree-free methods, i.e., methods to infer orthology or horizontal gene transfer as well as gene trees, species trees, and reconciliations between them without using a priori knowledge of the underlying trees or statistical models for the inference of phylogenetic trees. Instead, the initial step aims to extract binary relations among genes.}, } @article {pmid38818484, year = {2022}, author = {Zhou, Z and Liu, Y and Anantharaman, K and Li, M}, title = {The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis.}, journal = {mLife}, volume = {1}, number = {4}, pages = {374-381}, pmid = {38818484}, issn = {2770-100X}, abstract = {The division of organisms on the Tree of Life into either a three-domain (3D) tree or a two-domain (2D) tree has been disputed for a long time. Ever since the discovery of Archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as the evolutionary marker, there has been a great advance in our knowledge of not only the growing diversity of Archaea but also the evolutionary relationships between different lineages of living organisms. Here, we present this perspective to summarize the progress of archaeal diversity and changing notion of the Tree of Life. Meanwhile, we provide the latest progress in genomics/physiology-based discovery of Asgard archaeal lineages as the closest relative of Eukaryotes. Furthermore, we propose three major directions for future research on exploring the "next one" closest Eukaryote relative, deciphering the function of archaeal eukaryotic signature proteins and eukaryogenesis from both genomic and physiological aspects, and understanding the roles of horizontal gene transfer, viruses, and mobile elements in eukaryogenesis.}, } @article {pmid38818268, year = {2023}, author = {Konstantinidis, KT}, title = {Sequence-discrete species for prokaryotes and other microbes: A historical perspective and pending issues.}, journal = {mLife}, volume = {2}, number = {4}, pages = {341-349}, pmid = {38818268}, issn = {2770-100X}, abstract = {Whether prokaryotes, and other microorganisms, form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying, regulating, and communicating about these organisms. In the past decade, comparisons of thousands of genomes of isolates and hundreds of metagenomes have shown that prokaryotic diversity may be predominantly organized in such sequence-discrete clusters, albeit organisms of intermediate relatedness between the identified clusters are also frequently found. Accumulating evidence suggests, however, that the latter "intermediate" organisms show enough ecological and/or functional distinctiveness to be considered different species. Notably, the area of discontinuity between clusters often-but not always-appears to be around 85%-95% genome-average nucleotide identity, consistently among different taxa. More recent studies have revealed remarkably similar diversity patterns for viruses and microbial eukaryotes as well. This high consistency across taxa implies a specific mechanistic process that underlies the maintenance of the clusters. The underlying mechanism may be a substantial reduction in the efficiency of homologous recombination, which mediates (successful) horizontal gene transfer, around 95% nucleotide identity. Deviations from the 95% threshold (e.g., species showing lower intraspecies diversity) may be caused by ecological differentiation that imposes barriers to otherwise frequent gene transfer. While this hypothesis that clusters are driven by ecological differentiation coupled to recombination frequency (i.e., higher recombination within vs. between groups) is appealing, the supporting evidence remains anecdotal. The data needed to rigorously test the hypothesis toward advancing the species concept are also outlined.}, } @article {pmid38817968, year = {2024}, author = {Zhao, Y and Ding, WJ and Xu, L and Sun, JQ}, title = {A comprehensive comparative genomic analysis revealed that plant growth promoting traits are ubiquitous in strains of Stenotrophomonas.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1395477}, doi = {10.3389/fmicb.2024.1395477}, pmid = {38817968}, issn = {1664-302X}, abstract = {Stenotrophomonas strains, which are often described as plant growth promoting (PGP) bacteria, are ubiquitous in many environments. A total of 213 genomes of strains of Stenotrophomonas were analyzed using comparative genomics to better understand the ecological roles of these bacteria in the environment. The pan-genome of the 213 strains of Stenotrophomonas consists of 27,186 gene families, including 710 core gene families, 11,039 unique genes and 15,437 accessory genes. Nearly all strains of Stenotrophomonas harbor the genes for GH3-family cellulose degradation and GH2- and GH31-family hemicellulose hydrolase, as well as intact glycolysis and tricarboxylic acid cycle pathways. These abilities suggest that the strains of this genus can easily obtain carbon and energy from the environment. The Stenotrophomonas strains can respond to oxidative stress by synthesizing catalase, superoxide dismutase, methionine sulfoxide reductase, and disulfide isomerase, as well as managing their osmotic balance by accumulating potassium and synthesizing compatible solutes, such as betaine, trehalose, glutamate, and proline. Each Stenotrophomonas strain also contains many genes for resistance to antibiotics and heavy metals. These genes that mediate stress tolerance increase the ability of Stenotrophomonas strains to survive in extreme environments. In addition, many functional genes related to attachment and plant colonization, growth promotion and biocontrol were identified. In detail, the genes associated with flagellar assembly, motility, chemotaxis and biofilm formation enable the strains of Stenotrophomonas to effectively colonize host plants. The presence of genes for phosphate-solubilization and siderophore production and the polyamine, indole-3-acetic acid, and cytokinin biosynthetic pathways confer the ability to promote plant growth. These strains can produce antimicrobial compounds, chitinases, lipases and proteases. Each Stenotrophomonas genome contained 1-9 prophages and 17-60 genomic islands, and the genes related to antibiotic and heavy metal resistance and the biosynthesis of polyamines, indole-3-acetic acid, and cytokinin may be acquired by horizontal gene transfer. This study demonstrates that strains of Stenotrophomonas are highly adaptable for different environments and have strong potential for use as plant growth-promoting bacteria.}, } @article {pmid38817813, year = {2023}, author = {Li, L and Zhang, T}, title = {Roadmap to tackle antibiotic resistance in the environment under the One Health framework.}, journal = {mLife}, volume = {2}, number = {3}, pages = {224-228}, pmid = {38817813}, issn = {2770-100X}, abstract = {Antibiotic resistance has been recognized as a major challenge worldwide for humans. "One Health" has been recognized as a key concept for containment of antibiotic resistance. Under the framework, the role of the environment in the development of antibiotic resistance genes (ARGs) has become increasingly obvious. Despite numerous efforts, response to antibiotic resistance is considered to be inadequate, which is probably due to the lack of a clear roadmap. Here, we propose a "One Health" roadmap to combat antibiotic resistance in the environment through (1) understanding environmental resistome. The environmental gene pool has long been recognized as the single largest reservoir of both known and novel ARGs. (2) Standardizing ARG quantification. Systematic joint efforts based on standardized quantification are urgently needed to understand the true tempospatial profiles of the environmental resistome. (3) Identifying mechanisms of resistome development. Horizontal gene transfer and co-selection have been recognized as the two main mechanisms contributing to the environmental resistome. (4) Establishing a risk-assessment framework. The first critical step for large-scale cost-effective targeted ARG management in the environment is the risk assessment to identify the priority ARGs for control. (5) Formulating regulatory standards. By correlating the environmental ARG profile with public health, we may identify the indicator ARGs that can be integrated into current environmental quality standards. (6) Developing control strategies. Systematic analysis of available control technologies is required to identify the most feasible ones to curtail the spread of ARGs in the environment. The proposed roadmap under the "One Health" framework provides a guide to tackle antibiotic resistance in the environment.}, } @article {pmid38816863, year = {2024}, author = {Pontes, A and Paraíso, F and Silva, M and Lagoas, C and Aires, A and Brito, PH and Rosa, CA and Lachance, MA and Sampaio, JP and Gonçalves, C and Gonçalves, P}, title = {Extensive remodeling of sugar metabolism through gene loss and horizontal gene transfer in a eukaryotic lineage.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {128}, pmid = {38816863}, issn = {1741-7007}, support = {UIDB/04378/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0140/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/BIA-EVL/1100/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/BIA-EVL/0604/2021//Fundação para a Ciência e a Tecnologia/ ; 2023.09581.CPCA.A1//Fundação para a Ciência e a Tecnologia/ ; 2022.15871.CPCA.A2//Fundação para a Ciência e a Tecnologia/ ; UIDB/04378/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0140/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/BIA-EVL/1100/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/BIA-EVL/0604/2021//Fundação para a Ciência e a Tecnologia/ ; 2023.09581.CPCA.A1//Fundação para a Ciência e a Tecnologia/ ; 2022.15871.CPCA.A2//Fundação para a Ciência e a Tecnologia/ ; #406564/2022-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 0457499/2014-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 313088/2020-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 408733/2021//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; #406564/2022-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CNPq process numbers 0457499/2014-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 313088/2020-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 408733/2021//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; APQ-01525-14//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; APQ-02552-15//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; APQ-01525-14//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; APQ-02552-15//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; }, mesh = {*Gene Transfer, Horizontal ; Phylogeny ; Carbohydrate Metabolism/genetics ; Sugars/metabolism ; Evolution, Molecular ; Genome, Fungal ; }, abstract = {BACKGROUND: In yeasts belonging to the subphylum Saccharomycotina, genes encoding components of the main metabolic pathways, like alcoholic fermentation, are usually conserved. However, in fructophilic species belonging to the floral Wickerhamiella and Starmerella genera (W/S clade), alcoholic fermentation was uniquely shaped by events of gene loss and horizontal gene transfer (HGT).

RESULTS: Because HGT and gene losses were first identified when only eight W/S-clade genomes were available, we collected publicly available genome data and sequenced the genomes of 36 additional species. A total of 63 genomes, representing most of the species described in the clade, were included in the analyses. Firstly, we inferred the phylogenomic tree of the clade and inspected the genomes for the presence of HGT-derived genes involved in fructophily and alcoholic fermentation. We predicted nine independent HGT events and several instances of secondary loss pertaining to both pathways. To investigate the possible links between gene loss and acquisition events and evolution of sugar metabolism, we conducted phenotypic characterization of 42 W/S-clade species including estimates of sugar consumption rates and fermentation byproduct formation. In some instances, the reconciliation of genotypes and phenotypes yielded unexpected results, such as the discovery of fructophily in the absence of the cornerstone gene (FFZ1) and robust alcoholic fermentation in the absence of the respective canonical pathway.

CONCLUSIONS: These observations suggest that reinstatement of alcoholic fermentation in the W/S clade triggered a surge of innovation that goes beyond the utilization of xenologous enzymes, with fructose metabolism playing a key role.}, } @article {pmid38813783, year = {2024}, author = {Wolyniak, MJ and Frazier, RH and Gemborys, PK and Loehr, HE}, title = {Malate dehydrogenase: a story of diverse evolutionary radiation.}, journal = {Essays in biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1042/EBC20230076}, pmid = {38813783}, issn = {1744-1358}, support = {//Hampden-Sydney College Office of Undergraduate Research/ ; }, abstract = {Malate dehydrogenase (MDH) is a ubiquitous enzyme involved in cellular respiration across all domains of life. MDH's ubiquity allows it to act as an excellent model for considering the history of life and how the rise of aerobic respiration and eukaryogenesis influenced this evolutionary process. Here, we present the diversity of the MDH family of enzymes across bacteria, archaea, and eukarya, the relationship between MDH and lactate dehydrogenase (LDH) in the formation of a protein superfamily, and the connections between MDH and endosymbiosis in the formation of mitochondria and chloroplasts. The development of novel and powerful DNA sequencing techniques has challenged some of the conventional wisdom underlying MDH evolution and suggests a history dominated by gene duplication, horizontal gene transfer, and cryptic endosymbiosis events and adaptation to a diverse range of environments across all domains of life over evolutionary time. The data also suggest a superfamily of proteins that do not share high levels of sequential similarity but yet retain strong conservation of core function via key amino acid residues and secondary structural components. As DNA sequencing and 'big data' analysis techniques continue to improve in the life sciences, it is likely that the story of MDH will continue to refine as more examples of superfamily diversity are recovered from nature and analyzed.}, } @article {pmid38811160, year = {2024}, author = {Breidenstein, A and Lamy, A and Bader, CP and Sun, WS and Wanrooij, PH and Berntsson, RP}, title = {PrgE: an OB-fold protein from plasmid pCF10 with striking differences to prototypical bacterial SSBs.}, journal = {Life science alliance}, volume = {7}, number = {8}, pages = {}, pmid = {38811160}, issn = {2575-1077}, mesh = {*Plasmids/genetics ; *DNA-Binding Proteins/metabolism/genetics/chemistry ; *Bacterial Proteins/genetics/metabolism/chemistry ; *Enterococcus faecalis/genetics/metabolism ; *DNA, Single-Stranded/metabolism/genetics ; Protein Binding ; Conjugation, Genetic/genetics ; Type IV Secretion Systems/genetics/metabolism ; Models, Molecular ; Gene Transfer, Horizontal ; DNA, Bacterial/genetics/metabolism ; }, abstract = {A major pathway for horizontal gene transfer is the transmission of DNA from donor to recipient cells via plasmid-encoded type IV secretion systems (T4SSs). Many conjugative plasmids encode for a single-stranded DNA-binding protein (SSB) together with their T4SS. Some of these SSBs have been suggested to aid in establishing the plasmid in the recipient cell, but for many, their function remains unclear. Here, we characterize PrgE, a proposed SSB from the Enterococcus faecalis plasmid pCF10. We show that PrgE is not essential for conjugation. Structurally, it has the characteristic OB-fold of SSBs, but it has very unusual DNA-binding properties. Our DNA-bound structure shows that PrgE binds ssDNA like beads on a string supported by its N-terminal tail. In vitro studies highlight the plasticity of PrgE oligomerization and confirm the importance of the N-terminus. Unlike other SSBs, PrgE binds both double- and single-stranded DNA equally well. This shows that PrgE has a quaternary assembly and DNA-binding properties that are very different from the prototypical bacterial SSB, but also different from eukaryotic SSBs.}, } @article {pmid38818326, year = {2022}, author = {Da Cunha, V and Gaïa, M and Forterre, P}, title = {The expanding Asgard archaea and their elusive relationships with Eukarya.}, journal = {mLife}, volume = {1}, number = {1}, pages = {3-12}, pmid = {38818326}, issn = {2770-100X}, abstract = {The discovery of Asgard archaea and the exploration of their diversity over the last 6 years have deeply impacted the scientific community working on eukaryogenesis, rejuvenating an intense debate on the topology of the universal tree of life (uTol). Here, we discuss how this debate is impacted by two recent publications that expand the number of Asgard lineages and eukaryotic signature proteins (ESPs). We discuss some of the main difficulties that can impair the phylogenetic reconstructions of the uTol and suggest that the debate about its topology is not settled. We notably hypothesize the existence of horizontal gene transfers between ancestral Asgards and proto-eukaryotes that could result in the observed abnormal behaviors of some Asgard ESPs and universal marker proteins. This hypothesis is relevant regardless of the scenario considered regarding eukaryogenesis. It implies that the Asgards were already diversified before the last eukaryotic common ancestor and shared the same biotopes with proto-eukaryotes. We suggest that some Asgards might be still living in symbiosis today with modern Eukarya.}, } @article {pmid38810941, year = {2024}, author = {Zhang, Y and Liu, M and Zhang, J and Wu, J and Hong, L and Zhu, L and Long, J}, title = {Large-scale comparative analysis reveals phylogenomic preference of blaNDM-1 and blaKPC-2 transmission among Klebsiella pneumoniae.}, journal = {International journal of antimicrobial agents}, volume = {}, number = {}, pages = {107225}, doi = {10.1016/j.ijantimicag.2024.107225}, pmid = {38810941}, issn = {1872-7913}, abstract = {blaNDM-1 and blaKPC-2 are responsible for the global rise of carbapenem-resistant K. pneumoniae, posing a great challenge to public health. However, the impact of phylogenetic factors on blaNDM-1 and blaKPC-2 dissemination is not yet fully understood. Here, we established a global dataset of 4051 blaNDM-1+ or 10223 blaKPC-2+ K. pneumoniae genomes and compared their transmission mode on a global scale. The results showed that blaNDM-1+ K. pneumoniae genomes exhibited a broader geographical distribution and higher ST richness than blaKPC-2+, indicating higher transmissibility of the blaNDM-1 gene. Furthermore, blaNDM-1+ genomes displayed significant difference in ST lineage, antibiotic resistance genes composition, virulence genes composition, genetic environments with blaKPC-2+, suggesting their distinct dissemination mechanism. blaNDM-1+ genomes were predominantly associated with ST147 and ST16, whereas blaKPC-2+ genomes were mainly found in ST11 and ST258. Significantly different accessory genes were identified between blaNDM-1+ and blaKPC-2+ genomes. The preference for blaKPC-2 distribution across certain countries, ST lineages, and genetic environments underscores vertical spread as the primary mechanism driving the expansion of blaKPC-2. In contrast to blaKPC-2+, blaNDM-1+ genomes did not display such a strong preference, confirming that the blaNDM-1 dissemination mainly depended on horizontal gene transfer. Overall, our study demonstrates different phylogenetic drivers of blaNDM-1 and blaKPC-2 dissemination, providing new insights into their global transmission dynamic.}, } @article {pmid38808732, year = {2024}, author = {He, J and Yang, Z and Wang, M and Jia, R and Chen, S and Liu, M and Zhao, X and Yang, Q and Wu, Y and Zhang, S and Huang, J and Ou, X and Sun, D and Tian, B and He, Y and Wu, Z and Cheng, A and Zhu, D}, title = {Integrative and conjugative elements of Pasteurella multocida: Prevalence and signatures in population evolution.}, journal = {Virulence}, volume = {15}, number = {1}, pages = {2359467}, doi = {10.1080/21505594.2024.2359467}, pmid = {38808732}, issn = {2150-5608}, mesh = {*Pasteurella multocida/genetics/classification ; *Gene Transfer, Horizontal ; Animals ; *Phylogeny ; *Pasteurella Infections/microbiology/epidemiology/transmission ; *Genome, Bacterial ; DNA Transposable Elements ; Conjugation, Genetic ; Evolution, Molecular ; Poultry/microbiology ; Prevalence ; High-Throughput Nucleotide Sequencing ; }, abstract = {Pasteurella multocida (P. multocida) is a bacterial pathogen responsible for a range of infections in humans and various animal hosts, causing significant economic losses in farming. Integrative and conjugative elements (ICEs) are important horizontal gene transfer elements, potentially enabling host bacteria to enhance adaptability by acquiring multiple functional genes. However, the understanding of ICEs in P. multocida and their impact on the transmission of this pathogen remains limited. In this study, 42 poultry-sourced P. multocida genomes obtained by high-throughput sequencing together with 393 publicly available P. multocida genomes were used to analyse the horizontal transfer of ICEs. Eighty-two ICEs were identified in P. multocida, including SXT/R391 and Tn916 subtypes, as well as three subtypes of ICEHin1056 family, with the latter being widely prevalent in P. multocida and carrying multiple resistance genes. The correlations between insertion sequences and resistant genes in ICEs were also identified, and some ICEs introduced the carbapenem gene blaOXA-2 and the bleomycin gene bleO to P. multocida. Phylogenetic and collinearity analyses of these bioinformatics found that ICEs in P. multocida were transmitted vertically and horizontally and have evolved with host specialization. These findings provide insight into the transmission and evolution mode of ICEs in P. multocida and highlight the importance of understanding these elements for controlling the spread of antibiotic resistance.}, } @article {pmid38808121, year = {2024}, author = {Haimlich, S and Fridman, Y and Khandal, H and Savaldi-Goldstein, S and Levy, A}, title = {Widespread horizontal gene transfer between plants and bacteria.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae073}, pmid = {38808121}, issn = {2730-6151}, abstract = {Plants host a large array of commensal bacteria that interact with the host. The growth of both bacteria and plants is often dependent on nutrients derived from the cognate partners, and the bacteria fine-tune host immunity against pathogens. This ancient interaction is common in all studied land plants and is critical for proper plant health and development. We hypothesized that the spatial vicinity and the long-term relationships between plants and their microbiota may promote cross-kingdom horizontal gene transfer (HGT), a phenomenon that is relatively rare in nature. To test this hypothesis, we analyzed the Arabidopsis thaliana genome and its extensively sequenced microbiome to detect events of horizontal transfer of full-length genes that transferred between plants and bacteria. Interestingly, we detected 75 unique genes that were horizontally transferred between plants and bacteria. Plants and bacteria exchange in both directions genes that are enriched in carbohydrate metabolism functions, and bacteria transferred to plants genes that are enriched in auxin biosynthesis genes. Next, we provided a proof of concept for the functional similarity between a horizontally transferred bacterial gene and its Arabidopsis homologue in planta. The Arabidopsis DET2 gene is essential for biosynthesis of the brassinosteroid phytohormones, and loss of function of the gene leads to dwarfism. We found that expression of the DET2 homologue from Leifsonia bacteria of the Actinobacteria phylum in the Arabidopsis det2 background complements the mutant and leads to normal plant growth. Together, these data suggest that cross-kingdom HGT events shape the metabolic capabilities and interactions between plants and bacteria.}, } @article {pmid38802023, year = {2024}, author = {Ji, W and Ma, J and Zheng, Z and Al-Herrawy, AZ and Xie, B and Wu, D}, title = {Algae blooms with resistance in fresh water: Potential interplay between Microcystis and antibiotic resistance genes.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {173528}, doi = {10.1016/j.scitotenv.2024.173528}, pmid = {38802023}, issn = {1879-1026}, abstract = {Microcystis, a type of cyanobacteria known for producing microcystins (MCs), is experiencing a global increase in blooms. They have been recently recognized as potential contributors to the widespread of antibiotic resistance genes (ARGs). By reviewing approximately 150 pieces of recent studies, a hypothesis has been formulated suggesting that significant fluctuations in MCs concentrations and microbial community structure during Microcystis blooms could influence the dynamics of waterborne ARGs. Among all MCs, microcystin-LR (MC-LR) is the most widely distributed worldwide, notably abundant in reservoirs during summer. MCs inhibit protein phosphatases or increase reactive oxygen species (ROS), inducing oxidative stresses, enhancing membrane permeability, and causing DNA damage. This further enhances selective pressures and horizontal gene transfer (HGT) chances of ARGs. The mechanisms by which Microcystis regulates ARG dissemination have been systematically organized for the first time, focusing on the secretion of MCs and the alterations of bacterial community structure. However, several knowledge gaps remain, particularly concerning how MCs interfere with the electron transport chain and how Microcystis facilitates HGT of ARGs. Concurrently, the predominance of Microcystis forming the algal microbial aggregates is considered a hotspot for preserving and transferring ARGs. Yet, Microcystis can deplete the nutrients from other taxa within these aggregates, thereby reducing the density of ARG-carrying bacteria. Therefore, further studies are needed to explore the 'symbiotic - competitive' relationships between Microcystis and ARG-hosting bacteria under varied nutrient conditions. Addressing these knowledge gaps is crucial to understand the impacts of the algal aggregates on dynamics of waterborne antibiotic resistome, and underscores the need for effective control of Microcystis to curb the spread of antibiotic resistance. Constructed wetlands and photocatalysis represent advantageous strategies for halting the spread of ARGs from the perspective of Microcystis blooms, as they can effectively control Microcystis and MCs while maintaining the stability of aquatic ecosystem.}, } @article {pmid38789482, year = {2024}, author = {Puginier, C and Libourel, C and Otte, J and Skaloud, P and Haon, M and Grisel, S and Petersen, M and Berrin, JG and Delaux, PM and Dal Grande, F and Keller, J}, title = {Phylogenomics reveals the evolutionary origins of lichenization in chlorophyte algae.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4452}, pmid = {38789482}, issn = {2041-1723}, mesh = {*Lichens/genetics/microbiology ; *Phylogeny ; *Symbiosis/genetics ; *Chlorophyta/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Biological Evolution ; Transcriptome ; Glycoside Hydrolases/genetics/metabolism ; Genomics ; }, abstract = {Mutualistic symbioses have contributed to major transitions in the evolution of life. Here, we investigate the evolutionary history and the molecular innovations at the origin of lichens, which are a symbiosis established between fungi and green algae or cyanobacteria. We de novo sequence the genomes or transcriptomes of 12 lichen algal symbiont (LAS) and closely related non-symbiotic algae (NSA) to improve the genomic coverage of Chlorophyte algae. We then perform ancestral state reconstruction and comparative phylogenomics. We identify at least three independent gains of the ability to engage in the lichen symbiosis, one in Trebouxiophyceae and two in Ulvophyceae, confirming the convergent evolution of the lichen symbioses. A carbohydrate-active enzyme from the glycoside hydrolase 8 (GH8) family was identified as a top candidate for the molecular-mechanism underlying lichen symbiosis in Trebouxiophyceae. This GH8 was acquired in lichenizing Trebouxiophyceae by horizontal gene transfer, concomitantly with the ability to associate with lichens fungal symbionts (LFS) and is able to degrade polysaccharides found in the cell wall of LFS. These findings indicate that a combination of gene family expansion and horizontal gene transfer provided the basis for lichenization to evolve in chlorophyte algae.}, } @article {pmid38789462, year = {2024}, author = {Wranne, MS and Karami, N and Sriram, KK and Jaén-Luchoro, D and Yazdanshenas, S and Lin, YL and Kabbinale, A and Flach, CF and Westerlund, F and Åhrén, C}, title = {Comparison of CTX-M encoding plasmids present during the early phase of the ESBL pandemic in western Sweden.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {11880}, pmid = {38789462}, issn = {2045-2322}, support = {C4A 2020-02518//Västra Götalandsregionen/ ; ALF-965000//Västra Götalandsregionen/ ; 2021-00922//Svenska Forskningsrådet Formas/ ; 634890//EU Horizon 2020 program BeyondSeq/ ; }, mesh = {Sweden/epidemiology ; *Plasmids/genetics ; *beta-Lactamases/genetics ; *Escherichia coli/genetics ; Humans ; Pandemics ; Escherichia coli Infections/epidemiology/microbiology ; Gene Transfer, Horizontal ; Escherichia coli Proteins/genetics ; Whole Genome Sequencing ; }, abstract = {Plasmids encoding blaCTX-M genes have greatly shaped the evolution of E. coli producing extended-spectrum beta-lactamases (ESBL-E. coli) and adds to the global threat of multiresistant bacteria by promoting horizontal gene transfer (HGT). Here we screened the similarity of 47 blaCTX-M -encoding plasmids, from 45 epidemiologically unrelated and disperse ESBL-E. coli strains, isolated during the early phase (2009-2014) of the ESBL pandemic in western Sweden. Using optical DNA mapping (ODM), both similar and rare plasmids were identified. As many as 57% of the plasmids formed five ODM-plasmid groups of at least three similar plasmids per group. The most prevalent type (28%, IncIl, pMLST37) encoded blaCTX-M-15 (n = 10), blaCTX-M-3 (n = 2) or blaCTX-M-55 (n = 1). It was found in isolates of various sequence types (STs), including ST131. This could indicate ongoing local HGT as whole-genome sequencing only revealed similarities with a rarely reported, IncIl plasmid. The second most prevalent type (IncFII/FIA/FIB, F1:A2:B20) harboring blaCTX-M-27, was detected in ST131-C1-M27 isolates, and was similar to plasmids previously reported for this subclade. The results also highlight the need for local surveillance of plasmids and the importance of temporospatial epidemiological links so that detection of a prevalent plasmid is not overestimated as a potential plasmid transmission event in outbreak investigations.}, } @article {pmid38788585, year = {2024}, author = {Liu, T and Lee, S and Kim, M and Fan, P and Boughton, RK and Boucher, C and Jeong, KC}, title = {A study at the wildlife-livestock interface unveils the potential of feral swine as a reservoir for extended-spectrum β-lactamase-producing Escherichia coli.}, journal = {Journal of hazardous materials}, volume = {473}, number = {}, pages = {134694}, doi = {10.1016/j.jhazmat.2024.134694}, pmid = {38788585}, issn = {1873-3336}, abstract = {Wildlife is known to serve as carriers and sources of antimicrobial resistance (AMR). Due to their unrestricted movements and behaviors, they can spread antimicrobial resistant bacteria among livestock, humans, and the environment, thereby accelerating the dissemination of AMR. Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is one of major concerns threatening human and animal health, yet transmission mechanisms at the wildlife-livestock interface are not well understood. Here, we investigated the mechanisms of ESBL-producing bacteria spreading across various hosts, including cattle, feral swine, and coyotes in the same habitat range, as well as from environmental samples over a two-year period. We report a notable prevalence and clonal dissemination of ESBL-producing E. coli in feral swine and coyotes, suggesting their persistence and adaptation within wildlife hosts. In addition, in silico studies showed that horizontal gene transfer, mediated by conjugative plasmids and insertion sequences elements, may play a key role in spreading the ESBL genes among these bacteria. Furthermore, the shared gut resistome of cattle and feral swine suggests the dissemination of antibiotic resistance genes at the wildlife-livestock interface. Taken together, our results suggest that feral swine may serve as a reservoir of ESBL-producing E. coli.}, } @article {pmid38788579, year = {2024}, author = {Zhou, CS and Cao, GL and Liu, BF and Liu, W and Ma, WL and Ren, NQ}, title = {Deciphering the reduction of antibiotic resistance genes (ARGs) during medium-chain fatty acids production from waste activated sludge: Driven by inhibition of ARGs transmission and shift of microbial community.}, journal = {Journal of hazardous materials}, volume = {473}, number = {}, pages = {134676}, doi = {10.1016/j.jhazmat.2024.134676}, pmid = {38788579}, issn = {1873-3336}, abstract = {Medium-chain fatty acids (MCFAs) production from waste activated sludge (WAS) by chain extension (CE) is a promising technology. However, the effects and mechanisms of CE process on the fate of antibiotic resistance genes (ARGs) remain unclear. In this study, the results showed that the removal efficiency of ARGs was 81.15 % in CE process, suggesting its efficacy in reducing environmental risks. Further, the observed decrease in mobile genetic elements (MGEs) indicated that CE process restricted the horizontal gene transfer (HGT). Complementing this, the increase in soluble organic matters and extracellular 16 S rDNA confirmed that MCFAs production caused bacterial damage. Decreased intracellular ARGs and increased extracellular ARGs further revealed that MCFAs production impaired ARGs hosts, thereby limiting the vertical gene transfer (VGT) of ARGs. Shift of microbial community combined with co-occurrence network analysis demonstrated that functional bacteria without host potential for ARGs were enriched, but potential ARGs and MGEs hosts decreased, showing the role of functional bacterial phylogeny and selection pressure of MCFAs in reducing ARGs. Finally, partial least squares path model was used to systematic verify the mechanism of ARGs removal in CE process, which was attributed to the inhibition of ARGs transmission (HGT and VGT) and shift of microbial community.}, } @article {pmid38786183, year = {2024}, author = {Sabtcheva, S and Stoikov, I and Ivanov, IN and Donchev, D and Lesseva, M and Georgieva, S and Teneva, D and Dobreva, E and Christova, I}, title = {Genomic Characterization of Carbapenemase-Producing Enterobacter hormaechei, Serratia marcescens, Citrobacter freundii, Providencia stuartii, and Morganella morganii Clinical Isolates from Bulgaria.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {5}, pages = {}, pmid = {38786183}, issn = {2079-6382}, abstract = {Carbapenemase-producing Enterobacter spp. Serratia marcescens, Citrobacter freundii, Providencia spp., and Morganella morganii (CP-ESCPM) are increasingly identified as causative agents of nosocomial infections but are still not under systematic genomic surveillance. In this study, using a combination of whole-genome sequencing and conjugation experiments, we sought to elucidate the genomic characteristics and transferability of resistance genes in clinical CP-ESCPM isolates from Bulgaria. Among the 36 sequenced isolates, NDM-1 (12/36), VIM-4 (11/36), VIM-86 (8/36), and OXA-48 (7/36) carbapenemases were identified; two isolates carried both NDM-1 and VIM-86. The majority of carbapenemase genes were found on self-conjugative plasmids. IncL plasmids were responsible for the spread of OXA-48 among E. hormaechei, C. freundii, and S. marcescens. IncM2 plasmids were generally associated with the spread of NDM-1 in C. freundii and S. marcescens, and also of VIM-4 in C. freundii. IncC plasmids were involved in the spread of the recently described VIM-86 in P. stuartii isolates. IncC plasmids carrying blaNDM-1 and blaVIM-86 were observed too. blaNDM-1 was also detected on IncX3 in S. marcescens and on IncT plasmid in M. morganii. The significant resistance transfer rates we observed highlight the role of the ESCPM group as a reservoir of resistance determinants and stress the need for strengthening infection control measures.}, } @article {pmid38786161, year = {2024}, author = {Lamichhane, J and Choi, BI and Stegman, N and Fontes Noronha, M and Wolfe, AJ}, title = {Macrolide Resistance in the Aerococcus urinae Complex: Implications for Integrative and Conjugative Elements.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {5}, pages = {}, pmid = {38786161}, issn = {2079-6382}, support = {Pathnostics//Pathnostics/ ; }, abstract = {The recognition of the Aerococcus urinae complex (AUC) as an emerging uropathogen has led to growing concerns due to a limited understanding of its disease spectrum and antibiotic resistance profiles. Here, we investigated the prevalence of macrolide resistance within urinary AUC isolates, shedding light on potential genetic mechanisms. Phenotypic testing revealed a high rate of macrolide resistance: 45%, among a total of 189 urinary AUC isolates. Genomic analysis identified integrative and conjugative elements (ICEs) as carriers of the macrolide resistance gene ermA, suggesting horizontal gene transfer as a mechanism of resistance. Furthermore, comparison with publicly available genomes of related pathogens revealed high ICE sequence homogeneity, highlighting the potential for cross-species dissemination of resistance determinants. Understanding mechanisms of resistance is crucial for developing effective surveillance strategies and improving antibiotic use. Furthermore, the findings underscore the importance of considering the broader ecological context of resistance dissemination, emphasizing the need for community-level surveillance to combat the spread of antibiotic resistance within the urinary microbiome.}, } @article {pmid38786130, year = {2024}, author = {Monecke, S and Burgold-Voigt, S and Braun, SD and Diezel, C and Liebler-Tenorio, EM and Müller, E and Nassar, R and Reinicke, M and Reissig, A and Senok, A and Ehricht, R}, title = {Characterisation of PVL-Positive Staphylococcus argenteus from the United Arab Emirates.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {5}, pages = {}, pmid = {38786130}, issn = {2079-6382}, support = {13GW0456//Federal Ministry of Education and Research/ ; 13N15717//Federal Ministry of Education and Research/ ; }, abstract = {Staphylococcus argenteus is a recently described staphylococcal species that is related to Staphylococcus aureus but lacks the staphyloxanthin operon. It is able to acquire both resistance markers such as the SCCmec elements and mobile genetic elements carrying virulence-associated genes from S. aureus. This includes those encoding the Panton-Valentine leukocidin (PVL), which is associated mainly with severe and/or recurrent staphylococcal skin and soft tissue infections. Here, we describe the genome sequences of two PVL-positive, mecA-negative S. argenteus sequence type (ST) 2250 isolates from the United Arab Emirates in detail. The isolates were found in a dental clinic in the United Arab Emirates (UAE). Both were sequenced using Oxford Nanopore Technology (ONT). This demonstrated the presence of temperate bacteriophages in the staphylococcal genomes, including a PVL prophage. It was essentially identical to the published sequence of phiSa2wa_st78 (GenBank NC_055048), a PVL phage from an Australian S. aureus clonal complex (CC) 88 isolate. Besides the PVL prophage, one isolate carried another prophage and the second isolate carried two additional prophages, whereby the region between these two prophages was inverted. This "flipped" region comprised about 1,083,000 bp, or more than a third of the strain's genome, and it included the PVL prophage. Prophages were induced by Mitomycin C treatment and subjected to transmission electron microscopy (TEM). This yielded, in accordance to the sequencing results, one or, respectively, two distinct populations of icosahedral phages. It also showed prolate phages which presumptively might be identified as the PVL phage. This observation highlights the significance bacteriophages have as agents of horizontal gene transfer as well as the need for monitoring emerging staphylococcal strains, especially in cosmopolitan settings such as the UAE.}, } @article {pmid38783378, year = {2024}, author = {Brattig, N and Bergquist, R and Vienneau, D and Zhou, XN}, title = {Geography and health: role of human translocation and access to care.}, journal = {Infectious diseases of poverty}, volume = {13}, number = {1}, pages = {37}, pmid = {38783378}, issn = {2049-9957}, mesh = {Humans ; *Health Services Accessibility ; Animals ; *Zoonoses/epidemiology ; COVID-19/transmission/epidemiology ; Communicable Diseases/epidemiology/transmission ; SARS-CoV-2 ; Geography ; }, abstract = {Natural, geographical barriers have historically limited the spread of communicable diseases. This is no longer the case in today's interconnected world, paired with its unprecedented environmental and climate change, emphasising the intersection of evolutionary biology, epidemiology and geography (i.e. biogeography). A total of 14 articles of the special issue entitled "Geography and health: role of human translocation and access to care" document enhanced disease transmission of diseases, such as malaria, leishmaniasis, schistosomiasis, COVID-19 (Severe acute respiratory syndrome corona 2) and Oropouche fever in spite of spatiotemporal surveillance. High-resolution satellite images can be used to understand spatial distributions of transmission risks and disease spread and to highlight the major avenue increasing the incidence and geographic range of zoonoses represented by spill-over transmission of coronaviruses from bats to pigs or civets. Climate change and globalization have increased the spread and establishment of invasive mosquitoes in non-tropical areas leading to emerging outbreaks of infections warranting improved physical, chemical and biological vector control strategies. The translocation of pathogens and their vectors is closely connected with human mobility, migration and the global transport of goods. Other contributing factors are deforestation with urbanization encroaching into wildlife zones. The destruction of natural ecosystems, coupled with low income and socioeconomic status, increase transmission probability of neglected tropical and zoonotic diseases. The articles in this special issue document emerging or re-emerging diseases and surveillance of fever symptoms. Health equity is intricately connected to accessibility to health care and the targeting of healthcare resources, necessitating a spatial approach. Public health comprises successful disease management integrating spatial surveillance systems, including access to sanitation facilities. Antimicrobial resistance caused, e.g. by increased use of antibiotics in health, agriculture and aquaculture, or acquisition of resistance genes, can be spread by horizontal gene transfer. This editorial reviews the key findings of this 14-article special issue, identifies important gaps relevant to our interconnected world and makes a number of specific recommendations to mitigate the transmission risks of infectious diseases in the post-COVID-19 pandemic era.}, } @article {pmid38783210, year = {2024}, author = {Han, D and Ma, S and He, C and Yang, Y and Li, P and Lu, L}, title = {Unveiling the genetic architecture and transmission dynamics of a novel multidrug-resistant plasmid harboring blaNDM-5 in E. Coli ST167: implications for antibiotic resistance management.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {178}, pmid = {38783210}, issn = {1471-2180}, support = {2022B1154//Health Projects of Zhongshan City/ ; 2018B1081//Health Projects of Zhongshan City/ ; }, mesh = {*Plasmids/genetics ; *Escherichia coli/genetics/drug effects ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *beta-Lactamases/genetics ; Humans ; *Escherichia coli Infections/microbiology/transmission ; *Microbial Sensitivity Tests ; China ; Gene Transfer, Horizontal ; Carbapenems/pharmacology ; }, abstract = {BACKGROUND: The emergence of multidrug-resistant (MDR) Escherichia coli strains poses significant challenges in clinical settings, particularly when these strains harbor New Delhi metallo-ß-lactamase (NDM) gene, which confer resistance to carbapenems, a critical class of last-resort antibiotics. This study investigates the genetic characteristics and implications of a novel blaNDM-5-carrying plasmid pNDM-5-0083 isolated from an E. coli strain GZ04-0083 from clinical specimen in Zhongshan, China.

RESULTS: Phenotypic and genotypic evaluations confirmed that the E. coli ST167 strain GZ04-0083 is a multidrug-resistant organism, showing resistance to diverse classes of antibiotics including ß-lactams, carbapenems, fluoroquinolones, aminoglycosides, and sulfonamides, while maintaining susceptibility to monobactams. Investigations involving S1 pulsed-field gel electrophoresis, Southern blot analysis, and conjugation experiments, alongside genomic sequencing, confirmed the presence of the blaNDM-5 gene within a 146-kb IncFIB plasmid pNDM-5-0083. This evidence underscores a significant risk for the horizontal transfer of resistance genes among bacterial populations. Detailed annotations of genetic elements-such as resistance genes, transposons, and insertion sequences-and comparative BLAST analyses with other blaNDM-5-carrying plasmids, revealed a unique architectural configuration in the pNDM-5-0083. The MDR region of this plasmid shares a conserved gene arrangement (repA-IS15DIV-blaNDM-5-bleMBL-IS91-suI2-aadA2-dfrA12) with three previously reported plasmids, indicating a potential for dynamic genetic recombination and evolution within the MDR region. Additionally, the integration of virulence factors, including the iro and sit gene clusters and enolase, into its genetic architecture poses further therapeutic challenges by enhancing the strain's pathogenicity through improved host tissue colonization, immune evasion, and increased infection severity.

CONCLUSIONS: The detailed identification and characterization of pNDM-5-0083 enhance our understanding of the mechanisms facilitating the spread of carbapenem resistance. This study illuminates the intricate interplay among various genetic elements within the novel blaNDM-5-carrying plasmid, which are crucial for the stability and mobility of resistance genes across bacterial populations. These insights highlight the urgent need for ongoing surveillance and the development of effective strategies to curb the proliferation of antibiotic resistance.}, } @article {pmid38783209, year = {2024}, author = {Gevin, M and Latifi, A and Talla, E}, title = {The modular architecture of sigma factors in cyanobacteria: a framework to assess their diversity and understand their evolution.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {512}, pmid = {38783209}, issn = {1471-2164}, support = {ANR-21-CE20-0025-01//Agence Nationale de la Recherche/ ; ANR-21-CE20-0025-01//Agence Nationale de la Recherche/ ; ANR-21-CE20-0025-01//Agence Nationale de la Recherche/ ; }, mesh = {*Sigma Factor/genetics/metabolism ; *Evolution, Molecular ; *Cyanobacteria/genetics/metabolism ; *Phylogeny ; Bacterial Proteins/genetics/metabolism ; Genetic Variation ; }, abstract = {BACKGROUND: Bacterial RNA polymerase holoenzyme requires sigma70 factors to start transcription by identifying promoter elements. Cyanobacteria possess multiple sigma70 factors to adapt to a wide variety of ecological niches. These factors are grouped into two categories: primary sigma factor initiates transcription of housekeeping genes during normal growth conditions, while alternative sigma factors initiate transcription of specific genes under particular conditions. However, the present classification does not consider the modular organization of their structural domains, introducing therefore multiple functional and structural biases. A comprehensive analysis of this protein family in cyanobacteria is needed to address these limitations.

RESULTS: We investigated the structure and evolution of sigma70 factors in cyanobacteria, analyzing their modular architecture and variation among unicellular, filamentous, and heterocyst-forming morphotypes. 4,193 sigma70 homologs were found with 59 distinct modular patterns, including six essential and 29 accessory domains, such as DUF6596. 90% of cyanobacteria typically have 5 to 17 sigma70 homologs and this number likely depends on the strain morphotype, the taxonomic order and the genome size. We classified sigma70 factors into 12 clans and 36 families. According to taxonomic orders and phenotypic traits, the number of homologs within the 14 main families was variable, with the A.1 family including the primary sigma factor since this family was found in all cyanobacterial species. The A.1, A.5, C.1, E.1, J.1, and K.1 families were found to be key sigma families that distinguish heterocyst-forming strains. To explain the diversification and evolution of sigma70, we propose an evolutionary scenario rooted in the diversification of a common ancestor of the A1 family. This scenario is characterized by evolutionary events including domain losses, gains, insertions, and modifications. The high occurrence of the DUF6596 domain in bacterial sigma70 proteins, and its association with the highest prevalence observed in Actinobacteria, suggests that this domain might be important for sigma70 function. It also implies that the domain could have emerged in Actinobacteria and been transferred through horizontal gene transfer.

CONCLUSION: Our analysis provides detailed insights into the modular domain architecture of sigma70, introducing a novel robust classification. It also proposes an evolutionary scenario explaining their diversity across different taxonomical orders.}, } @article {pmid38781445, year = {2024}, author = {Vuruputoor, VS and Starovoitov, A and Cai, Y and Liu, Y and Rahmatpour, N and Hedderson, TA and Wilding, N and Wegrzyn, JL and Goffinet, B}, title = {Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkae104}, pmid = {38781445}, issn = {2160-1836}, abstract = {The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana is presented here. Assembled from 73x nanopore long reads and 163x BGI-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes (BUSCO: C:94.8%[D:13.9%]). This genome holds two genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants and are thus interpreted as resulting from two unique horizontal gene transfers from microbes. Further, Physcomitrellopsis africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens, but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses, during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily "short" timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant Physcomitrellopsis africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events.}, } @article {pmid38777914, year = {2024}, author = {Zhang, F and Shi, X and Xu, J and Yuan, W and Li, Z}, title = {Tandem gene duplication selected by activation of horizontally transferred gene in bacteria.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {340}, pmid = {38777914}, issn = {1432-0614}, support = {2020YFA0908000//The National Key R&D Program of China/ ; TSBICIP-CXRC-001//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project/ ; 2060302//Key project at central government level: The ability establishment of sustainable use for valuable Chinese medicine resource/ ; }, mesh = {*Gene Duplication ; *Gene Transfer, Horizontal ; *Escherichia coli/genetics/metabolism ; *Plasmids/genetics ; Bacteria/genetics/metabolism ; Gene Dosage ; Recombination, Genetic ; }, abstract = {Horizontal gene transfer occurs frequently in bacteria, but the mechanism driving activation and optimization of the expression of horizontally transferred genes (HTGs) in new recipient strains is not clear. Our previous study found that spontaneous tandem DNA duplication resulted in rapid activation of HTGs. Here, we took advantage of this finding to develop a novel technique for tandem gene duplication, named tandem gene duplication selected by activation of horizontally transferred gene in bacteria (TDAH), in which tandem duplication was selected by the activation of horizontally transferred selectable marker gene. TDAH construction does not contain any reported functional elements based on homologous or site-specific recombination and DNA amplification. TDAH only contains an essential selectable marker for copy number selection and 9-bp-microhomology border sequences for precise illegitimate recombination. One transformation and 3 days were enough to produce a high-copy strain, so its procedure is simple and fast. Without subsequent knockout of the endogenous recombination system, TDAH could also generate the relatively stable high-copy tandem duplication for plasmid-carried and genome-integrated DNA. TDAH also showed an excellent capacity for increase gene expression and worked well in different industrial bacteria. We also applied TDAH to select the optimal high copy number of ribA for vitamin B2 production in E. coli; the yield was improved by 3.5 times and remained stable even after 12 subcultures. TDAH is a useful tool for recombinant protein production and expression optimization of biosynthetic pathways. KEY POINTS: • We develop a novel and efficient technique (TDAH) for tandem gene duplication in bacterium. TDAH is based on the mechanism of HTG rapid activation. TDAH does not contain any reported functional elements based on homologous recombination and DNA amplification. TDAH only contains an essential selectable marker for copy number selection, so its construction and procedure are very simple and fast. • TDAH is the first reported selected and stable tandem-gene-duplication technique in which the selected high-copy plasmid-carried and genome-integrated DNA could remain stable without the subsequent knockout of recombination system. • TDAH showed an excellent capacity for regulating gene expression and worked well in different industrial bacteria, indicating it is a useful tool for recombinant protein production and expression optimization of biosynthetic pathways. • TDAH was applied to select the optimal high copy number of ribA for vitamin B2 production in E. coli; the yield was improved by 3.5-fold and remained stable even after 12 subcultures.}, } @article {pmid38772228, year = {2024}, author = {Xu, M and Gao, P and Gao, Y and Xiong, SJ and Chen, HQ and Shen, XX}, title = {Impacts of microplastic type on the fate of antibiotic resistance genes and horizontal gene transfer mechanism during anaerobic digestion.}, journal = {Journal of environmental management}, volume = {360}, number = {}, pages = {121090}, doi = {10.1016/j.jenvman.2024.121090}, pmid = {38772228}, issn = {1095-8630}, abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) are important pollutants in waste activated sludge (WAS), but their interactions during anaerobic digestion (AD) still need to be further explored. This study investigated variations in ARGs, mobile genetic elements (MGEs), and host bacteria during AD under the pressure of polyamide (PA), polyethylene (PE), and polypropylene (PP). The results showed that the MPs increased methane production by 11.7-35.5%, and decreased ARG abundance by 5.6-24.6%. Correlation analysis showed that the decrease of MGEs (plasmid, prophage, etc.) promoted the decrease of the abundance of multidrug, aminoglycoside and tetracycline resistance genes. Metagenomic annotation revealed that the reduction of key host bacteria (Arenimonas, Lautropia, etc.) reduced the abundance of major ARGs (rsmA, rpoB2, etc.). Moreover, PP MPs contributed to a reduction in the abundance of functional genes related to the production of reactive oxygen species, ATP synthesis, and cell membrane permeability, which was conducive to reducing the potential for horizontal gene transfer of ARGs. These findings provide insights into the treatment of organic waste containing MPs.}, } @article {pmid38772218, year = {2024}, author = {Kang, J and Zhang, C and Wan, S and Li, W and Zhao, W and Li, L and Shang, Y and Du, XD and Liu, D and Yao, H}, title = {Prevalence and characterization of aminoglycoside resistance gene aph(2")-If-carrying Campylobacter jejuni.}, journal = {International journal of food microbiology}, volume = {419}, number = {}, pages = {110747}, doi = {10.1016/j.ijfoodmicro.2024.110747}, pmid = {38772218}, issn = {1879-3460}, abstract = {Campylobacter jejuni is recognized as a significant foodborne pathogen, and recent studies have indicated a rising trend of aminoglycosides resistance gene aph(2″)-If among C. jejuni isolates from food-producing animals in China. However, systematic information about aph(2″)-If-positive C. jejuni from food-producing animals and other sources worldwide based on whole-genome analysis remains a knowledge gap. In this study, we aimed to analyze the worldwide distribution, genetic environment and phylogenetic tree of aph(2″)-If by utilizing Whole Genome Sequencing (WGS) data obtained, coupled with information in the GenBank database. A total of 160C. jejuni isolates in the GenBank database and 14C. jejuni isolates in our laboratory carrying aph(2″)-If gene were performed for further analysis. WGS analysis revealed the global distribution of aph(2″)-If among C. jejuni from 6 countries. Multilocus Sequence Typing(MLST) results indicated that 70 STs were involved in the dissemination of aph(2″)-If, with ST10086 being the predominant ST. Whole-genome Multilocus Sequence Typing(wg-MLST) analysis according to times, countries, and origins of C. jejuni isolation further demonstrated a close relationship between aph(2″)-If carrying C. jejuni isolates from farm and food. The findings also revealed the existence of 32 distinct types of genetic environments surrounding aph(2″)-If among these isolates. Notably, Type 30, characterized by the arrangement ISsag10-deoD-ant(9)-hp-hp-aph(2″)-If, emerged as the predominant genetic environment. In conclusion, our analysis provides the inaugural perspective on the worldwide distribution of aph(2″)-If. This resistance gene demonstrates horizontal transferability and regional diffusion in a clonal pattern. The close association observed among aph(2″)-If-positive C. jejuni strains isolated from poultry, food, and clinical environments underscores the potential for zoonotic transmission from these isolates.}, } @article {pmid38771034, year = {2024}, author = {Chong, TN and Shapiro, L}, title = {Bacterial cell differentiation enables population level survival strategies.}, journal = {mBio}, volume = {}, number = {}, pages = {e0075824}, doi = {10.1128/mbio.00758-24}, pmid = {38771034}, issn = {2150-7511}, abstract = {Clonal reproduction of unicellular organisms ensures the stable inheritance of genetic information. However, this means of reproduction lacks an intrinsic basis for genetic variation, other than spontaneous mutation and horizontal gene transfer. To make up for this lack of genetic variation, many unicellular organisms undergo the process of cell differentiation to achieve phenotypic heterogeneity within isogenic populations. Cell differentiation is either an inducible or obligate program. Induced cell differentiation can occur as a response to a stimulus, such as starvation or host cell invasion, or it can be a stochastic process. In contrast, obligate cell differentiation is hardwired into the organism's life cycle. Whether induced or obligate, bacterial cell differentiation requires the activation of a signal transduction pathway that initiates a global change in gene expression and ultimately results in a morphological change. While cell differentiation is considered a hallmark in the development of multicellular organisms, many unicellular bacteria utilize this process to implement survival strategies. In this review, we describe well-characterized cell differentiation programs to highlight three main survival strategies used by bacteria capable of differentiation: (i) environmental adaptation, (ii) division of labor, and (iii) bet-hedging.}, } @article {pmid38618896, year = {2024}, author = {Peng, X and Zhou, J and Lan, Z and Tan, R and Chen, T and Shi, D and Li, H and Yang, Z and Zhou, S and Jin, M and Li, JW and Yang, D}, title = {Carbonaceous particulate matter promotes the horizontal transfer of antibiotic resistance genes.}, journal = {Environmental science. Processes & impacts}, volume = {26}, number = {5}, pages = {915-927}, doi = {10.1039/d3em00547j}, pmid = {38618896}, issn = {2050-7895}, mesh = {*Particulate Matter/analysis ; *Gene Transfer, Horizontal ; *Air Pollutants/analysis ; Drug Resistance, Microbial/genetics ; Particle Size ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; }, abstract = {There is growing concern about the transfer of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in airborne particulate matter. In this study, we investigated the effects of various types of carbonaceous particulate matter (CPM) on the transfer of ARGs in vitro. The results showed that CPM promoted the transfer of ARGs, which was related to the concentration and particle size. Compared with the control group, the transfer frequency was 95.5, 74.7, 65.4, 14.7, and 3.8 times higher in G (graphene), CB (carbon black), NGP (nanographite powder), GP1.6 (graphite powder 1.6 micron), and GP45 (graphite powder 45 micron) groups, respectively. Moreover, the transfer frequency gradually increased with the increase in CPM concentration, while there was a negative relationship between the CPM particle size and conjugative transfer frequency. In addition, the results showed that CPM could promote the transfer of ARGs by increasing ROS, as well as activating the SOS response and expression of conjugative transfer-related genes (trbBp, trfAp, korA, kroB, and trbA). These findings are indicative of the potential risk of CPM for the transfer of ARGs in the environment, enriching our understanding of environmental pollution and further raising awareness of environmental protection.}, } @article {pmid38770060, year = {2024}, author = {Tamayo-Leiva, J and Alcorta, J and Sepúlveda, F and Fuentes-Alburquenque, S and Arroyo, JI and González-Pastor, JE and Díez, B}, title = {Structure and dispersion of the conjugative mobilome in surface ocean bacterioplankton.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae059}, pmid = {38770060}, issn = {2730-6151}, abstract = {Mobile genetic elements (MGEs), collectively referred to as the "mobilome", can have a significant impact on the fitness of microbial communities and therefore on ecological processes. Marine MGEs have mainly been associated with wide geographical and phylogenetic dispersal of adaptative traits. However, whether the structure of this mobilome exhibits deterministic patterns in the natural community is still an open question. The aim of this study was to characterize the structure of the conjugative mobilome in the ocean surface bacterioplankton by searching the publicly available marine metagenomes from the TARA Oceans survey, together with molecular markers, such as relaxases and type IV coupling proteins of the type IV secretion system (T4SS). The T4SS machinery was retrieved in more abundance than relaxases in the surface marine bacterioplankton. Moreover, among the identified MGEs, mobilizable elements were the most abundant, outnumbering self-conjugative sequences. Detection of a high number of incomplete T4SSs provides insight into possible strategies related to trans-acting activity between MGEs, and accessory functions of the T4SS (e.g. protein secretion), allowing the host to maintain a lower metabolic burden in the highly dynamic marine system. Additionally, the results demonstrate a wide geographical dispersion of MGEs throughout oceanic regions, while the Southern Ocean appears segregated from other regions. The marine mobilome also showed a high similarity of functions present in known plasmid databases. Moreover, cargo genes were mostly related to DNA processing, but scarcely associated with antibiotic resistance. Finally, within the MGEs, integrative and conjugative elements showed wider marine geographic dispersion than plasmids.}, } @article {pmid38769479, year = {2024}, author = {Talat, A and Khan, F and Khan, AU}, title = {Genome analyses of colistin-resistant high-risk blaNDM-5 producing Klebsiella pneumoniae ST147 and Pseudomonas aeruginosa ST235 and ST357 in clinical settings.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {174}, pmid = {38769479}, issn = {1471-2180}, mesh = {*Klebsiella pneumoniae/genetics/drug effects/isolation & purification ; *Pseudomonas aeruginosa/genetics/drug effects/isolation & purification ; *Colistin/pharmacology ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Whole Genome Sequencing ; *Microbial Sensitivity Tests ; *Pseudomonas Infections/microbiology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Genome, Bacterial/genetics ; *Klebsiella Infections/microbiology ; Gene Transfer, Horizontal ; India ; beta-Lactamases/genetics ; Plasmids/genetics ; }, abstract = {BACKGROUND: Colistin is a last-resort antibiotic used in extreme cases of multi-drug resistant (MDR) Gram-negative bacterial infections. Colistin resistance has increased in recent years and often goes undetected due to the inefficiency of predominantly used standard antibiotic susceptibility tests (AST). To address this challenge, we aimed to detect the prevalence of colistin resistance strains through both Vitek®2 and broth micro-dilution. We investigated 1748 blood, tracheal aspirate, and pleural fluid samples from the Intensive Care Unit (ICU), Neonatal Intensive Care Unit (NICU), and Tuberculosis and Respiratory Disease centre (TBRD) in an India hospital. Whole-genome sequencing (WGS) of extremely drug-resitant (XDR) and pan-drug resistant (PDR) strains revealed the resistance mechanisms through the Resistance Gene Identifier (RGI.v6.0.0) and Snippy.v4.6.0. Abricate.v1.0.1, PlasmidFinder.v2.1, MobileElementFinder.v1.0.3 etc. detected virulence factors, and mobile genetic elements associated to uncover the pathogenecity and the role of horizontal gene transfer (HGT).

RESULTS: This study reveals compelling insights into colistin resistance among global high-risk clinical isolates: Klebsiella pneumoniae ST147 (16/20), Pseudomonas aeruginosa ST235 (3/20), and ST357 (1/20). Vitek®2 found 6 colistin-resistant strains (minimum inhibitory concentrations, MIC = 4 μg/mL), while broth microdilution identified 48 (MIC = 32-128 μg/mL), adhering to CLSI guidelines. Despite the absence of mobile colistin resistance (mcr) genes, mechanisms underlying colistin resistance included mgrB deletion, phosphoethanolamine transferases arnT, eptB, ompA, and mutations in pmrB (T246A, R256G) and eptA (V50L, A135P, I138V, C27F) in K. pneumoniae. P. aeruginosa harbored phosphoethanolamine transferases basS/pmrb, basR, arnA, cprR, cprS, alongside pmrB (G362S), and parS (H398R) mutations. Both strains carried diverse clinically relevant antimicrobial resistance genes (ARGs), including plasmid-mediated blaNDM-5 (K. pneumoniae ST147) and chromosomally mediated blaNDM-1 (P. aeruginosa ST357).

CONCLUSION: The global surge in MDR, XDR and PDR bacteria necessitates last-resort antibiotics such as colistin. However, escalating resistance, particularly to colistin, presents a critical challenge. Inefficient colistin resistance detection methods, including Vitek2, alongside limited surveillance resources, accentuate the need for improved strategies. Whole-genome sequencing revealed alarming colistin resistance among K. pneumoniae and P. aeruginosa in an Indian hospital. The identification of XDR and PDR strains underscores urgency for enhanced surveillance and infection control. SNP analysis elucidated resistance mechanisms, highlighting the complexity of combatting resistance.}, } @article {pmid38767750, year = {2024}, author = {S, V and T, J and E, AP and A, MHA}, title = {Antibiotic resistance of heterotrophic bacteria from the sediments of adjoining high Arctic fjords, Svalbard.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {38767750}, issn = {1678-4405}, abstract = {Antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) are now considered major global threats. The Kongsfjorden and Krossfjorden are the interlinked fjords in the Arctic that are currently experiencing the effects of climate change and receiving input of pollutants from distant and regional sources. The present study focused on understanding the prevalence of antibiotic resistance of retrievable heterotrophic bacteria from the sediments of adjacent Arctic fjords Kongsfjorden and Krossfjorden. A total of 237 bacterial isolates were tested against 16 different antibiotics. The higher resistance observed towards Extended Spectrum β-lactam antibiotic (ESBL) includes ceftazidime (45.56%) followed by trimethoprim (27%) and sulphamethizole (24.05%). The extent of resistance was meagre against tetracycline (2.53%) and gentamycin (2.95%). The 16S rRNA sequencing analysis identified that Proteobacteria (56%) were the dominant antibiotic resistant phyla, followed by Firmicutes (35%), Actinobacteria (8%) and Bacteroidetes. The dominant resistant bacterial isolates are Bacillus cereus (10%), followed by Alcaligenes faecalis (6.47%), Cytobacillus firmus (5.75%) Salinibacterium sp. (5%) and Marinobacter antarcticus (5%). Our study reveals the prevalence of antibiotic resistance showed significant differences in both the inner and outer fjords of Kongsfjorden and Krossfjorden (p < 0.05). This may be the input of antibiotic resistance bacteria released into the fjords from the preserved permafrost due to the melting of glaciers, horizontal gene transfer, and human influence in the Arctic region act as a selection pressure for the development and dissemination of more antibiotic resistant bacteria in Arctic fjords.}, } @article {pmid38765968, year = {2024}, author = {Mancuso, CP and Baker, JS and Qu, E and Tripp, AD and Balogun, IO and Lieberman, TD}, title = {Intraspecies warfare restricts strain coexistence in human skin microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.05.07.592803}, pmid = {38765968}, abstract = {Determining why only a fraction of encountered or applied bacterial strains engraft in a given person's microbiome is crucial for understanding and engineering these communities [1] . Previous work has established that metabolism can determine colonization success in vivo [2-4] , but relevance of bacterial warfare in preventing engraftment has been less explored. Here, we demonstrate that intraspecies warfare presents a significant barrier to strain transmission in the skin microbiome by profiling 14,884 pairwise interactions between Staphylococcus epidermidis cultured from eighteen human subjects from six families. We find that intraspecies antagonisms are abundant; these interactions are mechanistically diverse, independent of the relatedness between strains, and consistent with rapid evolution via horizontal gene transfer. Ability to antagonize more strains is associated with reaching a higher fraction of the on-person S. epidermidis community. Moreover, antagonisms are significantly depleted among strains residing on the same person relative to random assemblages. Two notable exceptions, in which bacteria evolved to become sensitive to antimicrobials found on the same host, are explained by mutations that provide phage resistance, contextualizing the importance of warfare among other lethal selective pressures. Taken together, our results emphasize that accounting for intraspecies bacterial warfare is essential to the design of long-lasting probiotic therapeutics.}, } @article {pmid38695519, year = {2024}, author = {Garrido, V and Arrieta-Gisasola, A and Migura-García, L and Laorden, L and Grilló, MJ}, title = {Multidrug resistance in Salmonella isolates of swine origin: mobile genetic elements and plasmids associated with cephalosporin resistance with potential transmission to humans.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {5}, pages = {e0026424}, doi = {10.1128/aem.00264-24}, pmid = {38695519}, issn = {1098-5336}, support = {IIQ14061.RI1//Dirección General de Industria, Energia y Proyectos Estrategicos S3, Gobierno de Navarra (Department of Industry of the Government of Navarra)/ ; PA20/03//Centres de Recerca de Catalunya (CERCA)/ ; Grant PIF-19/290//Basque Country University (UPV/EHU)/ ; }, mesh = {Animals ; Swine/microbiology ; *Plasmids/genetics ; *Salmonella/genetics/drug effects/isolation & purification ; *Interspersed Repetitive Sequences ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Humans ; Cephalosporin Resistance/genetics ; Salmonella Infections, Animal/microbiology ; Spain ; Swine Diseases/microbiology ; Cephalosporins/pharmacology ; Gene Transfer, Horizontal ; }, abstract = {The emergence of foodborne Salmonella strains carrying antimicrobial resistance (AMR) in mobile genetic elements (MGE) is a significant public health threat in a One Health context requiring continuous surveillance. Resistance to ciprofloxacin and cephalosporins is of particular concern. Since pigs are a relevant source of foodborne Salmonella for human beings, we studied transmissible AMR genes and MGE in a collection of 83 strains showing 9 different serovars and 15 patterns of multidrug resistant (MDR) previously isolated from pigs raised in the conventional breeding system of Northern Spain. All isolates were susceptible to ciprofloxacin and three isolates carried blaCMY-2 or blaCTX-M-9 genes responsible for cefotaxime resistance. Filter mating experiments showed that the two plasmids carrying blaCTX-M-9 were conjugative while that carrying blaCMY-2 was self-transmissible by transformation. Whole-genome sequencing and comparative analyses were performed on the isolates and plasmids. The IncC plasmid pSB109, carrying blaCMY-2, was similar to one found in S. Reading from cattle, indicating potential horizontal transfer between serovars and animal sources. The IncHI2 plasmids pSH102 in S. Heidelberg and pSTM45 in S. Typhimurium ST34, carrying blaCTX-M-9, shared similar backbones and two novel "complex class 1 integrons" containing different AMR and heavy metal genes. Our findings emphasize the importance of sequencing techniques to identify emerging AMR regions in conjugative and stable plasmids from livestock production. The presence of MGE carrying clinically relevant AMR genes raises public health concerns, requiring monitoring to mitigate the emergence of bacteria carrying AMR genes and subsequent spread through animals and food.IMPORTANCEThe emergence of foodborne Salmonella strains carrying antimicrobial resistance (AMR) in mobile genetic elements (MGE) is a significant public health threat in a One Health context. Since pigs are a relevant source of foodborne Salmonella for humans, in this study, we investigate different aspects of AMR in a collection of 83 Salmonella showing nine different serovars and 15 patterns of multidrug resistant (MDR) isolated from pigs raised in the conventional breeding system. Our findings emphasize the importance of sequencing techniques to identify emerging AMR regions in conjugative and stable plasmids from livestock production. The presence of MGE carrying clinically relevant AMR genes raises public health concerns, requiring monitoring to mitigate the emergence of bacteria carrying AMR genes and subsequent spread through animals and food.}, } @article {pmid38626826, year = {2024}, author = {Zhang, J and Zhao, L and Wang, W and Zhang, Q and Wang, XT and Xing, DF and Ren, NQ and Lee, DJ and Chen, C}, title = {Large language model for horizontal transfer of resistance gene: From resistance gene prevalence detection to plasmid conjugation rate evaluation.}, journal = {The Science of the total environment}, volume = {931}, number = {}, pages = {172466}, doi = {10.1016/j.scitotenv.2024.172466}, pmid = {38626826}, issn = {1879-1026}, mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Pseudomonas/genetics ; }, abstract = {The burgeoning issue of plasmid-mediated resistance genes (ARGs) dissemination poses a significant threat to environmental integrity. However, the prediction of ARGs prevalence is overlooked, especially for emerging ARGs that are potentially evolving gene exchange hotspot. Here, we explored to classify plasmid or chromosome sequences and detect resistance gene prevalence by using DNABERT. Initially, the DNABERT fine-tuned in plasmid and chromosome sequences followed by multilayer perceptron (MLP) classifier could achieve 0.764 AUC (Area under curve) on external datasets across 23 genera, outperforming 0.02 AUC than traditional statistic-based model. Furthermore, Escherichia, Pseudomonas single genera based model were also be trained to explore its predict performance to ARGs prevalence detection. By integrating K-mer frequency attributes, our model could boost the performance to predict the prevalence of ARGs in an external dataset in Escherichia with 0.0281-0.0615 AUC and Pseudomonas with 0.0196-0.0928 AUC. Finally, we established a random forest model aimed at forecasting the relative conjugation transfer rate of plasmids with 0.7956 AUC, drawing on data from existing literature. It identifies the plasmid's repression status, cellular density, and temperature as the most important factors influencing transfer frequency. With these two models combined, they provide useful reference for quick and low-cost integrated evaluation of resistance gene transfer, accelerating the process of computer-assisted quantitative risk assessment of ARGs transfer in environmental field.}, } @article {pmid38765680, year = {2024}, author = {Tan, BSY and Mohan, L and Watthanaworawit, W and Ngamprasertchai, T and Nosten, FH and Ling, C and Bifani, P}, title = {Detection of florfenicol resistance in opportunistic Acinetobacter spp. infections in rural Thailand.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1368813}, pmid = {38765680}, issn = {1664-302X}, abstract = {Florfenicol (Ff) is an antimicrobial agent belonging to the class amphenicol used for the treatment of bacterial infections in livestock, poultry, and aquaculture (animal farming). It inhibits protein synthesis. Ff is an analog of chloramphenicol, an amphenicol compound on the WHO essential medicine list that is used for the treatment of human infections. Due to the extensive usage of Ff in animal farming, zoonotic pathogens have developed resistance to this antimicrobial agent. There are numerous reports of resistance genes from organisms infecting or colonizing animals found in human pathogens, suggesting a possible exchange of genetic materials. One of these genes is floR, a gene that encodes for an efflux pump that removes Ff from bacterial cells, conferring resistance against amphenicol, and is often associated with mobile genetic elements and other resistant determinants. In this study, we analyzed bacterial isolates recovered in rural Thailand from patients and environmental samples collected for disease monitoring. Whole genome sequencing was carried out for all the samples collected. Speciation and genome annotation was performed revealing the presence of the floR gene in the bacterial genome. The minimum inhibitory concentration (MIC) was determined for Ff and chloramphenicol. Chromosomal and phylogenetic analyses were performed to investigate the acquisition pattern of the floR gene. The presence of a conserved floR gene in unrelated Acinetobacter spp. isolated from human bacterial infections and environmental samples was observed, suggesting multiple and independent inter-species genetic exchange of drug-resistant determinants. The floR was found to be in the variable region containing various mobile genetic elements and other antibiotic resistance determinants; however, no evidence of HGT could be found. The floR gene identified in this study is chromosomal for all isolates. The study highlights a plausible impact of antimicrobials used in veterinary settings on human health. Ff shares cross-resistance with chloramphenicol, which is still in use in several countries. Furthermore, by selecting for floR-resistance genes, we may be selecting for and facilitating the zoonotic and reverse zoonotic exchange of other flanking resistance markers between human and animal pathogens or commensals with detrimental public health consequences.}, } @article {pmid38760381, year = {2024}, author = {Nguyen, Q and Nguyen, YTP and Ha, TT and Tran, DTN and Voong, PV and Chau, V and Nguyen, PLN and Le, NTQ and Nguyen, LPH and Nguyen, TTN and Trinh, TV and Carrique-Mas, JJ and Baker, S and Thwaites, G and Rabaa, MA and Choisy, M and Chung, HT and Pham, DT}, title = {Genomic insights unveil the plasmid transfer mechanism and epidemiology of hypervirulent Klebsiella pneumoniae in Vietnam.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4187}, pmid = {38760381}, issn = {2041-1723}, support = {222983/Z/21/Z//Wellcome Trust (Wellcome)/ ; 0010734//Oxford University | John Fell Fund, University of Oxford (John Fell OUP Research Fund)/ ; }, mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/isolation & purification ; Vietnam/epidemiology ; Humans ; *Plasmids/genetics ; *Klebsiella Infections/epidemiology/microbiology ; *Phylogeny ; *Whole Genome Sequencing ; Virulence/genetics ; Adult ; Female ; Gene Transfer, Horizontal ; Male ; Genome, Bacterial ; Middle Aged ; Anti-Bacterial Agents/pharmacology ; Child ; Genomics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Hypervirulent Klebsiella pneumoniae (hvKp) is a significant cause of severe invasive infections in Vietnam, yet data on its epidemiology, population structure and dynamics are scarce. We screened hvKp isolates from patients with bloodstream infections (BSIs) at a tertiary infectious diseases hospital in Vietnam and healthy individuals, followed by whole genome sequencing and plasmid analysis. Among 700 BSI-causing Kp strains, 100 (14.3%) were hvKp. Thirteen hvKp isolates were identified from 350 rectal swabs of healthy adults; none from 500 rectal swabs of healthy children. The hvKp isolates were genetically diverse, encompassing 17 sequence types (STs), predominantly ST23, ST86 and ST65. Among the 113 hvKp isolates, 14 (12.6%) carried at least one antimicrobial resistance (AMR) gene, largely mediated by IncFII, IncR, and IncA/C plasmids. Notably, the acquisition of AMR conjugative plasmids facilitated horizontal transfer of the non-conjugative virulence plasmid between K. pneumoniae strains. Phylogenetic analysis demonstrated hvKp isolates from BSIs and human carriage clustered together, suggesting a significant role of intestinal carriage in hvKp transmission. Enhanced surveillance is crucial to understand the factors driving intestinal carriage and hvKp transmission dynamics for informing preventive measures. Furthermore, we advocate the clinical use of our molecular assay for diagnosing hvKp infections to guide effective management.}, } @article {pmid38756985, year = {2024}, author = {Roughgarden, J}, title = {Lytic/Lysogenic Transition as a Life-History Switch.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae028}, pmid = {38756985}, issn = {2057-1577}, abstract = {The transition between lytic and lysogenic life cycles is the most important feature of the life-history of temperate viruses. To explain this transition, an optimal life-history model is offered based a discrete-time formulation of phage/bacteria population dynamics that features infection of bacteria by Poisson sampling of virions from the environment. The time step is the viral latency period. In this model, density-dependent viral absorption onto the bacterial surface produces virus/bacteria coexistence and density dependence in bacterial growth is not needed. The formula for the transition between lytic and lysogenic phases is termed the 'fitness switch'. According to the model, the virus switches from lytic to lysogenic when its population grows faster as prophage than as virions produced by lysis of the infected cells, and conversely for the switch from lysogenic to lytic. A prophage that benefits the bacterium it infects automatically incurs lower fitness upon exiting the bacterial genome, resulting in its becoming locked into the bacterial genome in what is termed here as a 'prophage lock'. The fitness switch qualitatively predicts the ecogeographic rule that environmental enrichment leads to microbialization with a concomitant increase in lysogeny, fluctuating environmental conditions promote virus-mediated horizontal gene transfer, and prophage-containing bacteria can integrate into the microbiome of a eukaryotic host forming a functionally integrated tripartite holobiont. These predictions accord more with the 'Piggyback-the-Winner' hypothesis than with the 'Kill-the-Winner' hypothesis in virus ecology.}, } @article {pmid38756231, year = {2024}, author = {Pobeguts, OV and Galaymina, MA and Sikamov, KV and Urazaeva, DR and Avshalumov, AS and Mikhailycheva, MV and Babenko, VV and Smirnov, IP and Gorbachev, AY}, title = {Unraveling the adaptive strategies of Mycoplasma hominis through proteogenomic profiling of clinical isolates.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1398706}, pmid = {38756231}, issn = {2235-2988}, mesh = {Humans ; *Mycoplasma hominis/genetics/metabolism ; *Proteogenomics ; *Mycoplasma Infections/microbiology ; *Adaptation, Physiological ; Biofilms/growth & development ; Genome, Bacterial ; Phenotype ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/genetics ; }, abstract = {INTRODUCTION: Mycoplasma hominis (M. hominis) belongs to the class Mollicutes, characterized by a very small genome size, reduction of metabolic pathways, including transcription factors, and the absence of a cell wall. Despite this, they adapt well not only to specific niches within the host organism but can also spread throughout the body, colonizing various organs and tissues. The adaptation mechanisms of M. hominis, as well as their regulatory pathways, are poorly understood. It is known that, when adapting to adverse conditions, Mycoplasmas can undergo phenotypic switches that may persist for several generations.

METHODS: To investigate the adaptive properties of M. hominis related to survival in the host, we conducted a comparative phenotypic and proteogenomic analysis of eight clinical isolates of M. hominis obtained from patients with urogenital infections and the laboratory strain H-34.

RESULTS: We have shown that clinical isolates differ in phenotypic features from the laboratory strain, form biofilms more effectively and show resistance to ofloxacin. The comparative proteogenomic analysis revealed that, unlike the laboratory strain, the clinical isolates possess several features related to stress survival: they switch carbon metabolism, activating the energetically least advantageous pathway of nucleoside utilization, which allows slowing down cellular processes and transitioning to a starvation state; they reconfigure the repertoire of membrane proteins; they