@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.},
}

*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

@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.},
}

Animals
*Gastropoda/genetics
*Molecular Sequence Annotation
*Genome
*Chromosomes/genetics
Genomics/methods

@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.},
}

*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

@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.},
}

*Genome, Mitochondrial
*Lavandula/genetics
*Phylogeny
RNA, Transfer/genetics
Organelles/genetics
Gene Transfer, Horizontal
RNA Editing
Molecular Sequence Annotation
Genome, Plant
Evolution, Molecular

@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.},
}

*Methanococcus/genetics/metabolism
Corrosion
*Adaptation, Physiological
*Hydrogenase/genetics/metabolism
Gene Transfer, Horizontal
Methane/metabolism
Iron/metabolism

@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.},
}

*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

@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 {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.},
}

*Gene Transfer, Horizontal
*DNA Transposable Elements/genetics
*Gene Expression Regulation, Bacterial
Bacterial Proteins/genetics/metabolism
Evolution, Molecular
Operon
Up-Regulation
Conjugation, Genetic

@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},
doi = {10.4142/jvs.24074},
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.},
}

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

@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.},
}

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

@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'.},
}

*Plants/metabolism/genetics
Biological Evolution
Metabolic Networks and Pathways/genetics
Evolution, Molecular

@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).},
}

*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

@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.},
}

*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

@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.},
}

*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

@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.},
}

*Escherichia coli/genetics
*Conjugation, Genetic
*DNA, Single-Stranded/chemistry
Click Chemistry
Gene Transfer, Horizontal
Oligonucleotides/chemistry

@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.},
}

*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

@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.},
}

*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

@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).},
}

*Plasmids/genetics/metabolism
*Gene Transfer, Horizontal
*Bacteria/genetics/metabolism
Conjugation, Genetic

@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.},
}

*Soil Microbiology
*Soil Pollutants
*Tetracycline Resistance/genetics
*Gene Transfer, Horizontal
Plants/microbiology
Humans
Bacteria/genetics/drug effects
Soil/chemistry
Tetracycline/pharmacology

@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.},
}

*Agriculture/methods
*Drug Resistance, Microbial/genetics
Artificial Intelligence
Anti-Bacterial Agents
Gene Transfer, Horizontal
Drug Resistance, Bacterial/genetics
Wastewater/microbiology
Animals

@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.},
}

*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

@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.},
}

*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

@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.},
}

*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

@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.},
}

*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

@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.},
}

*Prophages/genetics
Rhodobacter capsulatus/virology/genetics
Gene Transfer, Horizontal
Genome, Viral
Phylogeny
Evolution, Molecular
Methylobacterium/virology/genetics

@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.},
}

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

@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.},
}

*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

@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.},
}

*Triazoles/toxicity/pharmacology
*Gene Transfer, Horizontal
*Fungicides, Industrial/toxicity/pharmacology
*Biofilms/drug effects
Drug Resistance, Microbial/genetics
Plasmids/genetics
Genes, Bacterial

@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.},
}

*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

@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.},
}

*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

@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.},
}

*Asparagus Plant/genetics
*Genome, Mitochondrial
*Phylogeny
*Domestication
*Evolution, Molecular
RNA Editing
Gene Transfer, Horizontal
Genome, Chloroplast

@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.},
}

*CRISPR-Cas Systems/genetics
Humans
*Gastrointestinal Microbiome/genetics
Animals
Gene Editing
Probiotics/therapeutic use

@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 ; },
}

*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.},
}

*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

@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.},
}

*CRISPR-Cas Systems/genetics
Humans
*Bacterial Infections/microbiology/genetics
Gene Editing
Bacteria/genetics

@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.},
}

*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

@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.},
}

*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