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395800.9912Antimicrobial-Resistant Bacteria Carriage in Rodents According to Habitat Anthropization. It is increasingly suggested that the dynamics of antimicrobial-resistant bacteria in the wild are mostly anthropogenically driven, but the spatial and temporal scales at which these phenomena occur in landscapes are only partially understood. Here, we explore this topic by studying antimicrobial resistance in the commensal bacteria from micromammals sampled at 12 sites from a large heterogenous landscape (the Carmargue area, Rhone Delta) along a gradient of anthropization: natural reserves, rural areas, towns, and sewage-water treatment plants. There was a positive relationship between the frequency of antimicrobial-resistant bacteria and the level of habitat anthropization. Although low, antimicrobial resistance was also present in natural reserves, even in the oldest one, founded in 1954. This study is one of the first to support the idea that rodents in human-altered habitats are important components of the environmental pool of resistance to clinically relevant antimicrobials and also that a "One Health" approach is required to assess issues related to antimicrobial resistance dynamics in anthropized landscapes.202337140742
906810.9910TnCentral: a Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis. We describe here the structure and organization of TnCentral (https://tncentral.proteininformationresource.org/ [or the mirror link at https://tncentral.ncc.unesp.br/]), a web resource for prokaryotic transposable elements (TE). TnCentral currently contains ∼400 carefully annotated TE, including transposons from the Tn3, Tn7, Tn402, and Tn554 families; compound transposons; integrons; and associated insertion sequences (IS). These TE carry passenger genes, including genes conferring resistance to over 25 classes of antibiotics and nine types of heavy metal, as well as genes responsible for pathogenesis in plants, toxin/antitoxin gene pairs, transcription factors, and genes involved in metabolism. Each TE has its own entry page, providing details about its transposition genes, passenger genes, and other sequence features required for transposition, as well as a graphical map of all features. TnCentral content can be browsed and queried through text- and sequence-based searches with a graphic output. We describe three use cases, which illustrate how the search interface, results tables, and entry pages can be used to explore and compare TE. TnCentral also includes downloadable software to facilitate user-driven identification, with manual annotation, of certain types of TE in genomic sequences. Through the TnCentral homepage, users can also access TnPedia, which provides comprehensive reviews of the major TE families, including an extensive general section and specialized sections with descriptions of insertion sequence and transposon families. TnCentral and TnPedia are intuitive resources that can be used by clinicians and scientists to assess TE diversity in clinical, veterinary, and environmental samples. IMPORTANCE The ability of bacteria to undergo rapid evolution and adapt to changing environmental circumstances drives the public health crisis of multiple antibiotic resistance, as well as outbreaks of disease in economically important agricultural crops and animal husbandry. Prokaryotic transposable elements (TE) play a critical role in this. Many carry "passenger genes" (not required for the transposition process) conferring resistance to antibiotics or heavy metals or causing disease in plants and animals. Passenger genes are spread by normal TE transposition activities and by insertion into plasmids, which then spread via conjugation within and across bacterial populations. Thus, an understanding of TE composition and transposition mechanisms is key to developing strategies to combat bacterial pathogenesis. Toward this end, we have developed TnCentral, a bioinformatics resource dedicated to describing and exploring the structural and functional features of prokaryotic TE whose use is intuitive and accessible to users with or without bioinformatics expertise.202134517763
669620.9908The Role of Gulls as Reservoirs of Antibiotic Resistance in Aquatic Environments: A Scoping Review. The role of wildlife with long-range dispersal such as gulls in the global dissemination of antimicrobial resistance (AMR) across natural and anthropogenic aquatic environments remains poorly understood. Antibiotic-resistant bacteria have been detected in resident and migratory gulls worldwide for more than a decade, suggesting gulls as either sentinels of AMR pollution from anthropogenic sources or independent reservoirs that could maintain and disperse AMR across aquatic environments. However, confirming either of these roles remains challenging and incomplete. In this review, we present current knowledge on the geographic regions where AMR has been detected in gulls, the molecular characterization of resistance genes, and the evidence supporting the capacity of gulls to disperse AMR across regions or countries. We identify several limitations of current research to assess the role of gulls in the spread of AMR including most studies not identifying the source of AMR, few studies comparing bacteria isolated in gulls with other wild or domestic species, and almost no study performing longitudinal sampling over a large period of time to assess the maintenance and dispersion of AMR by gulls within and across regions. We suggest future research required to confirm the role of gulls in the global dispersion of AMR including the standardization of sampling protocols, longitudinal sampling using advanced satellite tracking, and whole-genome sequencing typing. Finally, we discuss the public health implications of the spread of AMR by gulls and potential solutions to limit its spread in aquatic environments.202134367104
871430.9907Tales from the tomb: the microbial ecology of exposed rock surfaces. Although a broad diversity of eukaryotic and bacterial taxa reside on rock surfaces where they can influence the weathering of rocks and minerals, these communities and their contributions to mineral weathering remain poorly resolved. To build a more comprehensive understanding of the diversity, ecology and potential functional attributes of microbial communities living on rock, we sampled 149 tombstones across three continents and analysed their bacterial and eukaryotic communities via marker gene and shotgun metagenomic sequencing. We found that geographic location and climate were important factors structuring the composition of these communities. Moreover, the tombstone-associated microbial communities varied as a function of rock type, with granite and limestone tombstones from the same cemeteries harbouring taxonomically distinct microbial communities. The granite and limestone-associated communities also had distinct functional attributes, with granite-associated bacteria having more genes linked to acid tolerance and chemotaxis, while bacteria on limestone were more likely to be lichen associated and have genes involved in photosynthesis and radiation resistance. Together these results indicate that rock-dwelling microbes exhibit adaptations to survive the stresses of the rock surface, differ based on location, climate and rock type, and seem pre-disposed to different ecological strategies (symbiotic versus free-living lifestyles) depending on the rock type.201829235707
669440.9907Interconnected microbiomes and resistomes in low-income human habitats. Antibiotic-resistant infections annually claim hundreds of thousands of lives worldwide. This problem is exacerbated by exchange of resistance genes between pathogens and benign microbes from diverse habitats. Mapping resistance gene dissemination between humans and their environment is a public health priority. Here we characterized the bacterial community structure and resistance exchange networks of hundreds of interconnected human faecal and environmental samples from two low-income Latin American communities. We found that resistomes across habitats are generally structured by bacterial phylogeny along ecological gradients, but identified key resistance genes that cross habitat boundaries and determined their association with mobile genetic elements. We also assessed the effectiveness of widely used excreta management strategies in reducing faecal bacteria and resistance genes in these settings representative of low- and middle-income countries. Our results lay the foundation for quantitative risk assessment and surveillance of resistance gene dissemination across interconnected habitats in settings representing over two-thirds of the world's population.201627172044
669550.9906'Disperse abroad in the land': the role of wildlife in the dissemination of antimicrobial resistance. Antimicrobial resistance (AMR) has been detected in the microbiota of many wildlife species, including long-distance migrants. Inadequately treated wastes from humans and livestock dosed with antimicrobial drugs are often assumed to be the main sources of AMR to wildlife. While wildlife populations closely associated with human populations are more likely to harbour clinically important AMR related to that found in local humans and livestock, AMR is still common in remote wildlife populations with little direct human influence. Most reports of AMR in wildlife are survey based and/or small scale, so researchers can only speculate on possible sources and sinks of AMR or the impact of wildlife AMR on clinical resistance. This lack of quantitative data on the flow of AMR genes and AMR bacteria across the natural environment could reflect the numerous AMR sources and amplifiers in the populated world. Ecosystems with relatively simple and well-characterized potential inputs of AMR can provide tractable, but realistic, systems for studying AMR in the natural environment. New tools, such as animal tracking technologies and high-throughput sequencing of resistance genes and mobilomes, should be integrated with existing methodologies to understand how wildlife maintains and disperses AMR.201627531155
378360.9906Ecology drives a global network of gene exchange connecting the human microbiome. Horizontal gene transfer (HGT), the acquisition of genetic material from non-parental lineages, is known to be important in bacterial evolution. In particular, HGT provides rapid access to genetic innovations, allowing traits such as virulence, antibiotic resistance and xenobiotic metabolism to spread through the human microbiome. Recent anecdotal studies providing snapshots of active gene flow on the human body have highlighted the need to determine the frequency of such recent transfers and the forces that govern these events. Here we report the discovery and characterization of a vast, human-associated network of gene exchange, large enough to directly compare the principal forces shaping HGT. We show that this network of 10,770 unique, recently transferred (more than 99% nucleotide identity) genes found in 2,235 full bacterial genomes, is shaped principally by ecology rather than geography or phylogeny, with most gene exchange occurring between isolates from ecologically similar, but geographically separated, environments. For example, we observe 25-fold more HGT between human-associated bacteria than among ecologically diverse non-human isolates (P = 3.0 × 10(-270)). We show that within the human microbiome this ecological architecture continues across multiple spatial scales, functional classes and ecological niches with transfer further enriched among bacteria that inhabit the same body site, have the same oxygen tolerance or have the same ability to cause disease. This structure offers a window into the molecular traits that define ecological niches, insight that we use to uncover sources of antibiotic resistance and identify genes associated with the pathology of meningitis and other diseases.201122037308
378570.9906A network approach to decipher the dynamics of Lysobacteraceae plasmid gene sharing. Plasmids provide an efficient vehicle for gene sharing among bacterial populations, playing a key role in bacterial evolution. Network approaches are particularly suitable to represent multipartite relationships and are useful tools to characterize plasmid-mediated gene sharing events. The bacterial family Lysobacteraceae includes plant commensal, plant pathogenic and opportunistic human pathogens for which plasmid-mediated adaptation has been reported. We searched for homologues of plasmid gene sequences from this family in the entire diversity of available bacterial genome sequences and built a network of plasmid gene sharing from the results. While plasmid genes are openly shared between the bacteria of the family Lysobacteraceae, taxonomy strongly defined the boundaries of these exchanges, which only barely reached other families. Most inferred plasmid gene sharing events involved a few genes only, and evidence of full plasmid transfers were restricted to taxonomically closely related taxa. We detected multiple plasmid-chromosome gene transfers, including the known sharing of a heavy metal resistance transposon. In the network, bacterial lifestyles shaped substructures of isolates colonizing specific ecological niches and harbouring specific types of resistance genes. Genes associated with pathogenicity or antibiotic and metal resistance were among those that most importantly structured the network, highlighting the imprints of human-mediated selective pressure on pathogenic populations. A massive sequencing effort on environmental Lysobacteraceae is therefore required to refine our understanding of how this reservoir fuels the emergence and the spread of genes among this family and its potential impact on plant, animal and human health.202335593155
773780.9906Distinctive signatures of pathogenic and antibiotic resistant potentials in the hadal microbiome. BACKGROUND: Hadal zone of the deep-sea trenches accommodates microbial life under extreme energy limitations and environmental conditions, such as low temperature, high pressure, and low organic matter down to 11,000 m below sea level. However, microbial pathogenicity, resistance, and adaptation therein remain unknown. Here we used culture-independent metagenomic approaches to explore the virulence and antibiotic resistance in the hadal microbiota of the Mariana Trench. RESULTS: The results indicate that the 10,898 m Challenger Deep bottom sediment harbored prosperous microbiota with contrasting signatures of virulence factors and antibiotic resistance, compared with the neighboring but shallower 6038 m steep wall site and the more nearshore 5856 m Pacific basin site. Virulence genes including several famous large translocating virulence genes (e.g., botulinum neurotoxins, tetanus neurotoxin, and Clostridium difficile toxins) were uniquely detected in the trench bottom. However, the shallower and more nearshore site sediment had a higher abundance and richer diversity of known antibiotic resistance genes (ARGs), especially for those clinically relevant ones (e.g., fosX, sul1, and TEM-family extended-spectrum beta-lactamases), revealing resistance selection under anthropogenic stresses. Further analysis of mobilome (i.e., the collection of mobile genetic elements, MGEs) suggests horizontal gene transfer mediated by phage and integrase as the major mechanism for the evolution of Mariana Trench sediment bacteria. Notably, contig-level co-occurring and taxonomic analysis shows emerging evidence for substantial co-selection of virulence genes and ARGs in taxonomically diverse bacteria in the hadal sediment, especially for the Challenger Deep bottom where mobilized ARGs and virulence genes are favorably enriched in largely unexplored bacteria. CONCLUSIONS: This study reports the landscape of virulence factors, antibiotic resistome, and mobilome in the sediment and seawater microbiota residing hadal environment of the deepest ocean bottom on earth. Our work unravels the contrasting and unique features of virulence genes, ARGs, and MGEs in the Mariana Trench bottom, providing new insights into the eco-environmental and biological processes underlying microbial pathogenicity, resistance, and adaptative evolution in the hadal environment.202235468809
377690.9905FARME DB: a functional antibiotic resistance element database. Antibiotic resistance (AR) is a major global public health threat but few resources exist that catalog AR genes outside of a clinical context. Current AR sequence databases are assembled almost exclusively from genomic sequences derived from clinical bacterial isolates and thus do not include many microbial sequences derived from environmental samples that confer resistance in functional metagenomic studies. These environmental metagenomic sequences often show little or no similarity to AR sequences from clinical isolates using standard classification criteria. In addition, existing AR databases provide no information about flanking sequences containing regulatory or mobile genetic elements. To help address this issue, we created an annotated database of DNA and protein sequences derived exclusively from environmental metagenomic sequences showing AR in laboratory experiments. Our Functional Antibiotic Resistant Metagenomic Element (FARME) database is a compilation of publically available DNA sequences and predicted protein sequences conferring AR as well as regulatory elements, mobile genetic elements and predicted proteins flanking antibiotic resistant genes. FARME is the first database to focus on functional metagenomic AR gene elements and provides a resource to better understand AR in the 99% of bacteria which cannot be cultured and the relationship between environmental AR sequences and antibiotic resistant genes derived from cultured isolates.Database URL: http://staff.washington.edu/jwallace/farme.201728077567
7666100.9904Antibiotic resistance genes allied to the pelagic sediment microbiome in the Gulf of Khambhat and Arabian Sea. Antibiotics have been widely spread in the environments, imposing profound stress on the resistome of the residing microbes. Marine microbiomes are well established large reservoirs of novel antibiotics and corresponding resistance genes. The Gulf of Khambhat is known for its extreme tides and complex sedimentation process. We performed high throughput sequencing and applied bioinformatics techniques on pelagic sediment microbiome across four coordinates of the Gulf of Khambhat to assess the marine resistome, its corresponding bacterial community and compared with the open Arabian Sea sample. We identified a total of 2354 unique types of resistance genes, with most abundant and diverse gene profile in the area that had anthropogenic activities being carried out on-shore. The genes with >1% abundance in all samples included carA, macB, sav1866, tlrC, srmB, taeA, tetA, oleC and bcrA which belonged to the macrolides, glycopeptides and peptide drug classes. ARG enriched phyla distribution was quite varying between all the sites, with Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes among the dominant phyla. Based on the outcomes, we also propose potential biomarker candidates Desulfovibrio, Thermotaga and Pelobacter for antibiotic monitoring in the two of the Gulf samples probable contamination prone environments, and genera Nitrosocccus, Marinobacter and Streptomyces in the rest of the three studied samples. Outcomes support the concept that ARGs naturally originate in environments and human activities contribute to the dissemination of antibiotic resistance.201930412889
7478110.9904Global analysis of the metaplasmidome: ecological drivers and spread of antibiotic resistance genes across ecosystems. BACKGROUND: Plasmids act as vehicles for the rapid spread of antibiotic resistance genes (ARGs). However, few studies of the resistome at the community level distinguish between ARGs carried by mobile genetic elements and those carried by chromosomes, and these studies have been limited to a few ecosystems. This is the first study to focus on ARGs carried by the metaplasmidome on a global scale. RESULTS: This study shows that only a small fraction of the plasmids reconstructed from 27 ecosystems representing 9 biomes are catalogued in public databases. The abundance of ARGs harboured by the metaplasmidome was significantly explained by bacterial richness. Few plasmids with or without ARGs were shared between ecosystems or biomes, suggesting that plasmid distribution on a global scale is mainly driven by ecology rather than geography. The network linking plasmids to their hosts shows that these mobile elements have thus been shared between bacteria across geographically distant environmental niches. However, certain plasmids carrying ARGs involved in human health were identified as being shared between multiple ecosystems and hosted by a wide variety of hosts. Some of these mobile elements, identified as keystone plasmids, were characterised by an enrichment in antibiotic resistance genes (ARGs) and CAS-CRISPR components which may explain their ecological success. The ARGs accounted for 9.2% of the recent horizontal transfers between bacteria and plasmids. CONCLUSIONS: By comprehensively analysing the plasmidome content of ecosystems, some key habitats have emerged as particularly important for monitoring the spread of ARGs in relation to human health. Of particular note is the potential for air to act as a vector for long-distance transport of ARGs and accessory genes across ecosystems and continents. Video Abstract.202540108678
3073120.9903A watershed impacted by anthropogenic activities: Microbial community alterations and reservoir of antimicrobial resistance genes. Water is the main resource for maintaining life. Anthropic activities influence the microbial epidemiological chain in watersheds, which can act as ways of disseminating microorganisms resistant to antimicrobial drugs, with impacts on human, animal, and environmental health. Here, we characterized aquatic microbial communities and their resistomes in samples collected along Rio das Ostras watershed during two seasons. Surface water samples were collected at eleven sites from the Jundiá, Iriry, and Rio das Ostras rivers in two seasons (dry and wet season). Microbial DNA was extracted, high-throughput sequenced and screened for antimicrobial resistance genetic (ARG) markers. The physicochemical characteristics and the microbiota data confirmed that Rio das Ostras watershed can be divided into three well defined portions: rural, urban, and marine. Rural areas were enriched by bacteria typically found in limnic environments and Patescibacteria phyla. The urban portion was characterized by sites with low pH and groups associated with iron oxidation. Some genera of clinical relevance were also identified, though in relatively low abundance. The marine site was enriched mainly by Cyanobacteria and bacteria that showed strong correlation with conductivity, salinity, and chloride. Twenty-six ARG markers were identified on the resistome, being found most frequently in the urban area, despite being present in rural sites. Among them were some related to classes of great clinical concern, such as genes coding for extended-spectrum beta-lactamase (bla(CTX-M) and bla(TEM)), resistance to carbapenems (bla(KPC)) and to methicillin by Staphylococcus aureus (mecA). These results broaden our understanding of the microbial community of a watershed impacted by anthropogenic actions. The large number of ARGs detected along the Rio das Ostras watershed contrasts with the small number of microorganisms of clinical relevance observed, suggesting that antimicrobial resistance has arisen from non-clinical environments and microbes. Our results corroborate that freshwater acts as a reservoir of antimicrobial resistance genes.202134328962
9067130.9903PIPdb: a comprehensive plasmid sequence resource for tracking the horizontal transfer of pathogenic factors and antimicrobial resistance genes. Plasmids, as independent genetic elements, carrying resistance or virulence genes and transfer them among different pathogens, posing a significant threat to human health. Under the 'One Health' approach, it is crucial to control the spread of plasmids carrying such genes. To achieve this, a comprehensive characterization of plasmids in pathogens is essential. Here we present the Plasmids in Pathogens Database (PIPdb), a pioneering resource that includes 792 964 plasmid segment clusters (PSCs) derived from 1 009 571 assembled genomes across 450 pathogenic species from 110 genera. To our knowledge, PIPdb is the first database specifically dedicated to plasmids in pathogenic bacteria, offering detailed multi-dimensional metadata such as collection date, geographical origin, ecosystem, host taxonomy, and habitat. PIPdb also provides extensive functional annotations, including plasmid type, insertion sequences, integron, oriT, relaxase, T4CP, virulence factors genes, heavy metal resistance genes and antibiotic resistance genes. The database features a user-friendly interface that facilitates studies on plasmids across diverse host taxa, habitats, and ecosystems, with a focus on those carrying antimicrobial resistance genes (ARGs). We have integrated online tools for plasmid identification and annotation from assembled genomes. Additionally, PIPdb includes a risk-scoring system for identifying potentially high-risk plasmids. The PIPdb web interface is accessible at https://nmdc.cn/pipdb.202539460620
3786140.9903Complex interactions between diverse mobile genetic elements drive the evolution of metal-resistant bacterial genomes. In this study, we compared the genomes of three metal-resistant bacteria isolated from mercury-contaminated soil. We identified diverse and novel MGEs with evidence of multiple LGT events shaping their genomic structure and heavy metal resistance. Among the three metal-resistant strains, Sphingobium sp SA2 and Sphingopyxis sp SE2 were resistant to multiple metals including mercury, cadmium, copper, zinc and lead. Pseudoxanthomonas sp SE1 showed resistance to mercury only. Whole genome sequencing by Illumina and Oxford Nanopore technologies was undertaken to obtain comprehensive genomic data. The Sphingobium and Sphingopyxis strains contained multiple chromosomes and plasmids, whereas the Pseudoxanthomonas strain contained one circular chromosome. Consistent with their metal resistance profiles, the strains of Sphingobium and Sphingopyxis contained a higher quantity of diverse metal resistance genes across their chromosomes and plasmids compared to the single-metal resistant Pseudoxanthomonas SE1. In all three strains, metal resistance genes were principally associated with various novel MGEs including genomic islands (GIs), integrative conjugative elements (ICEs), transposons, insertion sequences (IS), recombinase in trio (RIT) elements and group II introns, indicating their importance in facilitating metal resistance adaptation in a contaminated environment. In the Pseudoxanthomonas strain, metal resistance regions were largely situated on a GI. The chromosomes of the strains of Sphingobium and Sphingopyxis contained multiple metal resistance regions, which were likely acquired by several GIs, ICEs, numerous IS elements, several Tn3 family transposons and RIT elements. Two of the plasmids of Sphingobium were impacted by Tn3 family transposons and ISs likely integrating metal resistance genes. The two plasmids of Sphingopyxis harboured transposons, IS elements, an RIT element and a group II intron. This study provides a comprehensive annotation of complex genomic regions of metal resistance associated with novel MGEs. It highlights the critical importance of LGT in the evolution of metal resistance of bacteria in contaminated environments.202337915109
3261150.9903A global metagenomic map of urban microbiomes and antimicrobial resistance. We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.202134043940
9650160.9903Plasmid-Encoded Traits Vary across Environments. Plasmids are key mobile genetic elements in bacterial evolution and ecology as they allow the rapid adaptation of bacteria under selective environmental changes. However, the genetic information associated with plasmids is usually considered separately from information about their environmental origin. To broadly understand what kinds of traits may become mobilized by plasmids in different environments, we analyzed the properties and accessory traits of 9,725 unique plasmid sequences from a publicly available database with known bacterial hosts and isolation sources. Although most plasmid research focuses on resistance traits, such genes made up <1% of the total genetic information carried by plasmids. Similar to traits encoded on the bacterial chromosome, plasmid accessory trait compositions (including general Clusters of Orthologous Genes [COG] functions, resistance genes, and carbon and nitrogen genes) varied across seven broadly defined environment types (human, animal, wastewater, plant, soil, marine, and freshwater). Despite their potential for horizontal gene transfer, plasmid traits strongly varied with their host's taxonomic assignment. However, the trait differences across environments of broad COG categories could not be entirely explained by plasmid host taxonomy, suggesting that environmental selection acts on the plasmid traits themselves. Finally, some plasmid traits and environments (e.g., resistance genes in human-related environments) were more often associated with mobilizable plasmids (those having at least one detected relaxase) than others. Overall, these findings underscore the high level of diversity of traits encoded by plasmids and provide a baseline to investigate the potential of plasmids to serve as reservoirs of adaptive traits for microbial communities. IMPORTANCE Plasmids are well known for their role in the transmission of antibiotic resistance-conferring genes. Beyond human and clinical settings, however, they disseminate many other types of genes, including those that contribute to microbially driven ecosystem processes. In this study, we identified the distribution of traits genetically encoded by plasmids isolated from seven broadly categorized environments. We find that plasmid trait content varied with both bacterial host taxonomy and environment and that, on average, half of the plasmids were potentially mobilizable. As anthropogenic activities impact ecosystems and the climate, investigating and identifying the mechanisms of how microbial communities can adapt will be imperative for predicting the impacts on ecosystem functioning.202336629415
7722170.9903Genome-resolving metagenomics reveals wild western capercaillies (Tetrao urogallus) as avian hosts for antibiotic-resistance bacteria and their interactions with the gut-virome community. The gut microbiome is a critical component of avian health, influencing nutrient uptake and immune functions. While the gut microbiomes of agriculturally important birds have been studied, the microbiomes of wild birds still need to be explored. Filling this knowledge gap could have implications for the microbial rewilding of captive birds and managing avian hosts for antibiotic-resistant bacteria (ARB). Using genome-resolved metagenomics, we recovered 112 metagenome-assembled genomes (MAGs) from the faeces of wild and captive western capercaillies (Tetrao urogallus) (n = 8). Comparisons of bacterial diversity between the wild and captive capercaillies suggest that the reduced diversity in the captive individual could be due to differences in diet. This was further substantiated through the analyses of 517,657 clusters of orthologous groups (COGs), which revealed that gene functions related to amino acids and carbohydrate metabolisms were more abundant in wild capercaillies. Metagenomics mining of resistome identified 751 antibiotic resistance genes (ARGs), of which 40.7 % were specific to wild capercaillies suggesting that capercaillies could be potential reservoirs for hosting ARG-associated bacteria. Additionally, the core resistome shared between wild and captive capercaillies indicates that birds can acquire these ARG-associated bacteria naturally from the environment (43.1 % of ARGs). The association of 26 MAGs with 120 ARGs and 378 virus operational taxonomic units (vOTUs) also suggests a possible interplay between these elements, where putative phages could have roles in modulating the gut microbiota of avian hosts. These findings can have important implications for conservation and human health, such as avian gut microbiota rewilding, identifying the emerging threats or opportunities due to phage-microbe interactions, and monitoring the potential spread of ARG-associated bacteria from wild avian populations.202337018898
7358180.9902Global dispersal and potential sources of antibiotic resistance genes in atmospheric remote depositions. Antibiotic resistance has become a major Global Health concern and a better understanding on the global spread mechanisms of antibiotic resistant bacteria (ARB) and intercontinental ARB exchange is needed. We measured atmospheric depositions of antibiotic resistance genes (ARGs) by quantitative (q)PCR in rain/snow collected fortnightly along 4 y. at a remote high mountain LTER (Long-Term Ecological Research) site located above the atmospheric boundary layer (free troposphere). Bacterial composition was characterized by 16S rRNA gene sequencing, and air mass provenances were determined by modelled back trajectories and rain/snow chemical composition. We hypothesize that the free troposphere may act as permanent reservoir and vector for ARB and ARGs global dispersal. We aimed to i) determine whether ARGs are long-range intercontinental and persistently dispersed through aerosols, ii) assess ARGs long-term atmospheric deposition dynamics in a remote high mountain area, and iii) unveil potential diffuse ARGs pollution sources. We showed that the ARGs sul1 (resistance to sulfonamides), tetO (resistance to tetracyclines), and intI1 (a proxy for horizontal gene transfer and anthropogenic pollution) were long-range and persistently dispersed in free troposphere aerosols. Major depositions of tetracyclines resistance matched with intensification of African dust outbreaks. Potential ARB mostly traced their origin back into agricultural soils. Our study unveils that air masses pathways are shaping ARGs intercontinental dispersal and global spread of antibiotic resistances, with potential predictability for interannual variability and remote deposition rates. Because climate regulates aerosolization and long-range air masses movement patterns, we call for a more careful evaluation of the connections between land use, climate change and ARB long-range intercontinental dispersal.202235016024
7477190.9902Importance of mobile genetic elements for dissemination of antimicrobial resistance in metagenomic sewage samples across the world. We are facing an ever-growing threat from increasing antimicrobial resistance (AMR) in bacteria. To mitigate this, we need a better understanding of the global spread of antimicrobial resistance genes (ARGs). ARGs are often spread among bacteria by horizontal gene transfer facilitated by mobile genetic elements (MGE). Here we use a dataset consisting of 677 metagenomic sequenced sewage samples from 97 countries or regions to study how MGEs are geographically distributed and how they disseminate ARGs worldwide. The ARGs, MGEs, and bacterial abundance were calculated by reference-based read mapping. We found systematic differences in the abundance of MGEs and ARGs, where some elements were prevalent on all continents while others had higher abundance in separate geographic areas. Different MGEs tended to be localized to temperate or tropical climate zones, while different ARGs tended to separate according to continents. This suggests that the climate is an important factor influencing the local flora of MGEs. MGEs were also found to be more geographically confined than ARGs. We identified several integrated MGEs whose abundance correlated with the abundance of ARGs and bacterial genera, indicating the ability to mobilize and disseminate these genes. Some MGEs seemed to be more able to mobilize ARGs and spread to more bacterial species. The host ranges of MGEs seemed to differ between elements, where most were associated with bacteria of the same family. We believe that our method could be used to investigate the population dynamics of MGEs in complex bacterial populations.202337856515