Exploring antibiotic resistance genes, mobile gene elements, and virulence gene factors in an urban freshwater samples using metagenomic analysis. - Related Documents




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326901.0000Exploring antibiotic resistance genes, mobile gene elements, and virulence gene factors in an urban freshwater samples using metagenomic analysis. Antibiotic resistance genes (ARGs) and antimicrobial resistance elements (AMR) are novel environmental contaminants that pose a significant risk to human health globally. Freshwater contains a variety of microorganisms that might affect human health; its quality must be assessed before use. However, the dynamics of mobile genetic elements (MGEs) and ARG propagation in freshwater have rarely been studied in Singapore. Therefore, this study used metagenomics to compare diversity, virulence factor composition, and ARG and MGE co-occurrence with bacterial communities in paired (n = 8) environmental freshwater samples. KneadData, FMAP, and Kraken2 were used for bioinformatics analysis and R (v4.1.1) for statistical analysis. Sequence reads with a total of 9043 species were taxonomically classified into 66 phyla, 130 classes, 261 orders, 584 families, and 2477 genera. Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes were found the Phyla in all samples. Analysis of QIIME output by PICRUSt and ß-diversity showed unique clusters and functional microbial community structures. A total of 2961 ARGs were found that conferred resistance to multidrug, aminoglycosides, tetracyclines, elfamycins, and more. The classified ARG mechanism revealed significant distribution of virulence factors in bacterial cells. Transposes and transposon were highly correlated to ARG gene transfer. Co-occurrence network analysis showed several MGEs appear to use the same ARGs (intI and rho) and were dominant in all samples. Furthermore, ARGs are also highly correlated with bacteria like Campylobacter and Escherichia. This study enhances the understanding of antibiotic risk assessment and provides a new perspective on bacterial assembly contamination and the functional prevalence of ARGs and MGEs with antibiotic resistance bacteria. Moreover, it raises public awareness because these contaminants put people's lives at risk of acquiring bacterial infections. In addition, it can also help propose hybrid water treatment approaches.202335939194
686810.9998Rare resistome rather than core resistome exhibited higher diversity and risk along the Yangtze River. As important freshwater ecosystems, the occurrence and distribution of antibiotic resistance genes (ARGs) in rivers are relevant to public health. However, studies investigating ARGs of different environmental media in river ecosystems are limited. In this study, we analyzed the ARGs of microbes in free-living setting, particle-associated setting, sediment and bank soil of the Yangtze River using metagenomics. Twenty-six ARGs were found in all samples regardless of media (core resistome) with a diversity of 8.6 %-34.7 %, accounting for 22.7 %-89.2 % of the relative abundance of the overall ARGs. The core resistome of the Yangtze River was dominated by multidrug resistance genes consisting mainly of efflux pumps and bacitracin resistance genes. The rare resistome was dominated by multidrug, sulfonamide, and aminoglycoside resistance genes. The core resistome was more prevalent in chromosomes, implying that these ARGs with low diversity and high relative abundance may be intrinsic to microbes in the Yangtze River. The rare resistome was more prevalent in plasmids, suggesting these ARGs with high diversity and low relative abundance were acquired under environmental stresses and had transfer potential. Additionally, we found that core and rare resistome were mainly carried by specific bacteria. Noteworthily, twenty-two ARGs of high clinical concern were identified in rare resistome, especially aac(6')-I, sul1, and tetM, which were plasmid-borne and hosted by clinically relevant pathogens. Both core and rare resistome hosts showed the highest niche breadths in particle-associated setting compared to other media, and particle-associated setting could provide more stable and ideal conditions for resistome hosts to survive. This study elucidated the genetic locations of ARGs and the community assembly mechanisms of ARG hosts in freshwater environments.202438039820
686720.9998Comparative analysis of characteristics of antibiotic resistomes between Arctic soils and representative contaminated samples using metagenomic approaches. Antibiotic resistance is one of the most concerned global health issues. However, comprehensive profiles of antibiotic resistance genes (ARGs) in various environmental settings are still needed to address modern antibiotic resistome. Here, Arctic soils and representative contaminated samples from ARG pollution sources were analyzed using metagenomic approaches. The diversity and abundance of ARGs in Arctic soils were significantly lower than those in contaminated samples (p < 0.01). ARG profiles in Arctic soils were featured with the dominance of vanF, ceoB, and bacA related to multidrug and bacitracin, whereas those from ARG pollution sources were characterized by prevalent resistance to anthropogenic antibiotics such as sulfonamides, tetracyclines, and beta-lactams. Mobile genetic elements (MGEs) were found in all samples, and their abundance and relatedness to ARGs were both lower in Arctic soils than in polluted samples. Significant relationships between bacterial communities and ARGs were observed (p < 0.01). Cultural bacteria in Arctic soils had clinically-concerned resistance to erythromycin, vancomycin, ampicillin, etc., but ARGs relevant to those antibiotics were undetectable in their genomes. Our results suggested that Arctic environment could be an important reservoir of novel ARGs, and antibiotic stresses could cause ARG pollution via horizontal gene transfer and enrichment of resistant bacteria.202438452676
686930.9998Contaminant-degrading bacteria are super carriers of antibiotic resistance genes in municipal landfills: A metagenomics-based study. Municipal landfills are hotspot sources of antimicrobial resistance (AMR) and are also important habitats of contaminant-degrading bacteria. However, high diversity of antibiotic resistance genes (ARGs) in landfills hinders assessing AMR risks in the affected environment. More concerned, whether there is co-selection or enrichment of antibiotic-resistant bacteria and contaminant-degrading bacteria in these extremely polluted environments is far less understood. Here, we collected metagenomic datasets of 32 raw leachate and 45 solid waste samples in 22 municipal landfills of China. The antibiotic resistome, antibiotic-resistant bacteria and contaminant-degrading bacteria were explored, and were then compared with other environmental types. Results showed that the antibiotic resistome in landfills contained 1,403 ARG subtypes, with the total abundance over the levels in natural environments and reaching the levels in human feces and sewage. Therein, 49 subtypes were listed as top priority ARGs for future surveillance based on the criteria of enrichment in landfills, mobilizable and present in pathogens. By comparing to those in less contaminated river environments, we elucidated an enrichment of antibiotic-resistant bacteria with contaminant-degrading potentials in landfills. Bacteria in Pseudomonadaceae, Moraxellaceae, Xanthomonadaceae and Enterobacteriaceae deserved the most concerns since 72.2 % of ARG hosts were classified to them. Klebsiella pneumoniae, Acinetobacter nosocomialis and Escherichia coli were abundant multidrug-resistant pathogenic species in raw leachate (∼10.2 % of total microbiomes), but they rarely carried contaminant-degradation genes. Notably, several bacterial genera belonging to Pseudomonadaceae had the most antibiotic-resistant, pathogenic, and contaminant-degrading potentials than other bacteria. Overall, the findings highlight environmental selection for contaminant-degrading antibiotic-resistant pathogens, and provide significant insights into AMR risks in municipal landfills.202539729867
321540.9998Prevalence of antibiotic resistance genes its association with microbiota in raw milk of northwest Xinjiang. The issue of antibiotic resistance caused by antibiotic resistance genes (ARGs) has become a significant concern in environmental research in recent years, while raw milk is an important link in the food chain and has become one of the carriers and reservoirs of ARGs, which has not been taken seriously. This research employed high-throughput quantitative PCR and Illumina sequencing techniques targeting the 16S rRNA gene. These methods were used to examine the bacterial community composition and genes associated with antibiotic resistance in raw milk samples collected from the northwestern area of Xinjiang. An aggregate of 31 distinct resistance alleles were identified, with their abundance reaching as high as 3.70 × 10(5) copies per gram in the analyzed raw milk samples. Microorganisms harboring ARGs that confer resistance to beta-lactams, tetracyclines, aminoglycosides, and chloramphenicol derivatives were prevalent in raw milk. Procrustes analysis revealed a certain degree of correlation between the microbial community and the antibiotic resistance gene (ARG) profiles. Furthermore, network analysis demonstrated that Actinobacteria and Firmicutes were the predominant phyla exhibiting co-occurrence relationships with specific ARGs. Combining the findings from Variance Partitioning Analysis (VPA), the distribution of ARGs was mainly driven by three factors: the combined effect of physicochemical properties and mobile genetic elements (MGEs) (33.5%), the interplay between physicochemical parameters and microbial communities (31.8%), and the independent contribution of physicochemical factors (20.7%). The study demonstrates that the overall abundance of ARGs correlates with physicochemical parameters, bacterial community composition, and the presence of MGEs. Furthermore, understanding these associations facilitates the evaluation of antibiotic resistance risks, thereby contributing to enhanced farm management practices and the assurance of food safety.202540718809
327750.9998Airborne antibiotic resistome and human health risk in railway stations during COVID-19 pandemic. Antimicrobial resistance is recognized as one of the greatest public health concerns. It is becoming an increasingly threat during the COVID-19 pandemic due to increasing usage of antimicrobials, such as antibiotics and disinfectants, in healthcare facilities or public spaces. To explore the characteristics of airborne antibiotic resistome in public transport systems, we assessed distribution and health risks of airborne antibiotic resistome and microbiome in railway stations before and after the pandemic outbreak by culture-independent and culture-dependent metagenomic analysis. Results showed that the diversity of airborne antibiotic resistance genes (ARGs) decreased following the pandemic, while the relative abundance of core ARGs increased. A total of 159 horizontally acquired ARGs, predominantly confering resistance to macrolides and aminoglycosides, were identified in the airborne bacteria and dust samples. Meanwhile, the abundance of horizontally acquired ARGs hosted by pathogens increased during the pandemic. A bloom of clinically important antibiotic (tigecycline and meropenem) resistant bacteria was found following the pandemic outbreak. 251 high-quality metagenome-assembled genomes (MAGs) were recovered from 27 metagenomes, and 86 genera and 125 species were classified. Relative abundance of ARG-carrying MAGs, taxonomically assigned to genus of Bacillus, Pseudomonas, Acinetobacter, and Staphylococcus, was found increased during the pandemic. Bayesian source tracking estimated that human skin and anthropogenic activities were presumptive resistome sources for the public transit air. Moreover, risk assessment based on resistome and microbiome data revealed elevated airborne health risks during the pandemic.202336731187
686460.9998Metagenomics analysis revealing the occurrence of antibiotic resistome in salt lakes. Although antimicrobial resistance genes (ARGs) in dozens of environments have been well documented, the distribution of ARGs in salt lake ecosystems has been less intensively investigated. In this study, the broad-spectrum ARG profiles, microbial community composition and the comprehensive associations between microbiome and antimicrobial resistome in four salt lakes were investigated using a metagenomic approach. A total of 175 ARG subtypes affiliated with 19 ARG types were detected, and ARGs conferring resistance to multidrug, bacitracin, and macrolide-lincosamide-streptogramin (MLS) accounted for 71.2% of the total ARG abundance. However, the abundance of ARGs significantly decreased with the increasing salinity in the lakes. Both ARG profiles and microbial community structure presented remarkable discrepancies in different lakes, as well as in different sample types. Microbes such as genera Azoarcus, Aeromonas, Pseudomonas, and Kocuria, significantly co-occurred with multiple ARGs, indicating that these bacteria are potential ARG hosts in salt lake ecosystems. Collectively, this work provides new insights into the occurrence and distribution of ARGs in salt lake ecosystems.202134380279
686670.9998Deciphering the antibiotic resistome in stratified source water reservoirs in China: Distribution, risk, and ecological drive. The proliferation and dissemination of antibiotic resistance genes (ARGs) in source water reservoirs may pose a threat to human health. This study investigated the antibiotic resistance in stratified reservoirs in China across different seasons and spatial locations. In total, 120 ARG subtypes belonging to 15 ARG types were detected with an abundance ranging from 171.06 to 793.71 × /Gb. Multidrug, tetracycline, aminoglycoside, and bacitracin resistance genes were dominant in the reservoirs. The abundance and transfer potential of ARGs were notably higher, especially during the stratified period, with markedly elevated levels in the bottom layer compared to the surface layer. Metagenomic assembly yielded 1357 ARG-carrying contigs, belonging to 83 resistant bacterial species, of which 13 were identified as human pathogen bacteria (HPB). HPB hosts (Sphingomonas sp., Burkholderiales sp., and Ralstonia sp., etc.) were super carriers of ARGs. Genes including ompR, bacA, golS, and ugd carried on HPB plasmids exhibited higher abundance in the water, warranting attention to the risk of resistance transmission. Environmental pressures have caused a shift in the assembly mechanism of ARGs, transitioning from a random process in surface water to a deterministic process in bottom water. The results of this study will deepen people's understanding of the ARG risk in stratified reservoirs.202539673943
327180.9998Metagenomic characterization of bacterial community and antibiotic resistance genes found in the mass transit system in Seoul, South Korea. Mass transit systems, including subways and buses, are useful environments for studying the urban microbiome, as the vast majority of populations in urban areas use public transportation. Microbial communities in urban environments include both human- and environment-associated bacteria that play roles in health and pathogen transmission. In this study, we used shotgun metagenomic sequencing to profile microbial communities sampled from various surfaces found in subway stations and bus stops within the Seoul mass transit system. The metagenomic approach and network analysis were used to investigate broad-spectrum antibiotic resistance genes (ARGs) and their co-occurrence patterns. We uncovered 598 bacterial species in 76 samples collected from various surfaces within the Seoul mass transit system. All samples were dominated by the potential human pathogen Salmonella enterica (40 %) and the human skin bacterium Cutibacterium acnes (19 %). Significantly abundant biomarkers detected in subway station samples were associated with bacteria typically found in the human oral cavity and respiratory tract, whereas biomarkers detected in bus stop samples were associated with bacteria commonly found in soil, water, and plants. Temperature and location had significant effects on microbial community structure and diversity. In total, 41 unique ARG subtypes were identified, associated with single-drug or multidrug resistance to clinically important and extensively used antibiotics, including aminoglycosides, carbapenem, glycopeptide, and sulfonamides. We revealed that Seoul subway stations and bus stops possess unique microbiomes containing potential human pathogens and ARGs. These findings provide insights for refining location-specific responses to reduce exposure to potentially causative agents of infectious diseases, improving public health.202236257123
686590.9998A metagenomic analysis framework for characterization of antibiotic resistomes in river environment: Application to an urban river in Beijing. River is considered generally as a natural reservoir of antibiotic resistance genes (ARGs) in environments. For the prevention and control of ARG risks, it is critical to comprehensively characterize the antibiotic resistomes and their associations in riverine systems. In this study, we proposed a metagenomic framework for identifying antibiotic resistomes in river sediments from multiple categories, including ARG potential, ARG hosts, pathogenicity potential, co-selection potential and gene transfer potential, and applied it to understand the presence, hosts, and co-occurrence of ARGs in the sediments of an urban river in Beijing. Results showed that a total of 203 ARG subtypes belonging to 21 ARG types were detected in the river sediments with an abundance range of 107.7-1004.1×/Gb, dominated by multidrug, macrolide-lincosamide-streptogramin, bacitracin, quinolone and sulfonamide resistance genes. Host-tracking analysis identified Dechloromonas, Pseudoxanthomonas, Arenimonas, Lysobacter and Pseudomonas as the major hosts of ARGs. A number of ARG-carrying contigs (ACCs) were annotated as fragments of pathogenic bacteria and carried multiple multidrug-ARGs. In addition, various biocide/metal resistance genes (B/MRGs) and mobile genetic elements (MGEs), including prophages, plasmids, integrons and transposons, were detected in the river sediments. More importantly, the co-occurrence analysis via ACCs showed a strong association of ARGs with B/MRGs and MGEs, indicating high potential of co-selection and active horizontal transmission for ARGs in the river environment, likely driven by the frequent impact of anthropogenic activities in that area.201930453138
3092100.9998Potential reservoirs of antimicrobial resistance in livestock waste and treated wastewater that can be disseminated to agricultural land. Livestock manure, dairy lagoon effluent, and treated wastewater are known reservoirs of antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and virulence factor genes (VFGs), and their application to agricultural farmland could be a serious public health threat. However, their dissemination to agricultural lands and impact on important geochemical pathways such as the nitrogen (N) cycle have not been jointly explored. In this study, shotgun metagenomic sequencing and analyses were performed to examine the diversity and composition of microbial communities, ARGs, VFGs, and N cycling genes in different livestock manure/lagoon and treated wastewater collected from concentrated animal feeding operations (CAFOs) and a municipal wastewater treatment plant along the west coast of the United States. Multivariate analysis showed that diversity indices of bacterial taxa from the different microbiomes were not significantly different based on InvSimpson (P = 0.05), but differences in ARG mechanisms were observed between swine manure and other microbiome sources. Comparative resistome profiling showed that ARGs in microbiome samples belonged to four core resistance classes: aminoglycosides (40-55 %), tetracyclines (30-45 %), beta-lactam-resistance (20-35 %), macrolides (18-30 %), and >50 % of the VFGs that the 24 microbiomes harbored were phyletically affiliated with two bacteria, Bacteroidetes fragilis and Enterobacter aerogenes. Network analysis based on Spearman correlation showed co-occurrence patterns between several genes such as transporter-gene and regulator, efflux pump and involved-in-polymyxin- resistance, aminoglycoside, beta-lactam, and macrolide with VFGs and bacterial taxa such as Firmicutes, Candidatus Themoplasmatota, Actinobacteria, and Bacteroidetes. Metabolic reconstruction of metagenome-assembled genome (MAGs) analysis showed that the most prevalent drug resistance mechanisms were associated with carbapenem resistance, multidrug resistance (MDR), and efflux pump. Bacteroidales was the main taxa involved in dissimilatory nitrate reduction (DNRA) in dairy lagoon effluent. This study demonstrates that the dissemination of waste from these sources can increase the spread of ARGs, ARB, and VFGs into agricultural lands, negatively impacting both soil and human health.202336781130
3098110.9998Bacterial Communities and Resistance and Virulence Genes in Hospital and Community Wastewater: Metagenomic Analysis. Metagenomic studies have made it possible to deepen the analysis of the abundance of bacterial populations that carry resistance and virulence determinants in the wastewater environment. In this study, a longitudinal collection of samples of community and hospital wastewater from August 2021 to September 2022 was obtained. Shotgun metagenomic sequencing and bioinformatic analysis were performed to characterize the bacterial abundance, antimicrobial resistance genes (ARGs), plasmids, and virulence factor genes (VFGs) contained in the wastewater. The microbial composition of the community and hospital wastewater showed that the most abundant bacterial phyla detected in all samples were: Proteobacteria, Bacteroides, Firmicutes, Campylobacterota, and Actinobacteria. Seasonal differences in the relative abundances of species, ARGs, plasmids, and VFGs were observed. In this study, a total of 270 ARGs were detected, and it was found that the absolute abundance of ARGs only showed a 39% reduction in the treated wastewater. Furthermore, the ARGs detected in this study were found to encode resistance to antibiotics of the last choice. Our results showed that plasmids carrying resistance genes were more abundant in raw wastewater, and 60% more abundant in hospital wastewater compared to community wastewater. Several of the VFGs detected in this study encode for adhesion, motility, and biofilm formation, which likely allows bacteria to remain and persist in the wastewater environment and survive WWTP treatment systems, thus managing to escape into the environment via treated wastewater.202540076673
3169120.9998Plastispheres as reservoirs of antimicrobial resistance: Insights from metagenomic analyses across aquatic environments. Evidence suggests that plastic particles from various environments can accumulate harmful microorganisms and carry bacteria with antimicrobial resistance genes (ARGs). The so-called "plastisphere" might facilitate the spread of pathogens and antimicrobial resistance across environments, posing risks to human and animal health. This study aimed to analyze the diversity and abundance of ARGs found in plastispheres from various aquatic environments, identify clinically relevant pathogenic species, and ascertain bacterial hosts carrying ARGs. We present data from 36 metagenomes collected from plastispheres in different environments (freshwater, raw wastewater, and treated wastewater). The diversity and abundance of ARGs in the resistome of the plastispheres were analyzed through metagenomic methods. A total of 537 high-quality metagenomic-assembled genomes (MAGs) were constructed to identify clinically relevant pathogens and to link the detected ARGs to their bacterial hosts. The results show that the environment has the greatest influence on the abundance and diversity of ARGs in the plastispheres resistome, with the wastewater plastisphere containing a resistome with the highest diversity of ARGs. Resistance to beta-lactams, aminoglycosides, and tetracyclines were the most abundant resistance mechanisms detected in the different plastispheres. The construction of MAGs identified potential pathogens and environmental bacteria that confer resistance to one or several drug classes, with beta-lactams being the most pervasive form of AMR detected. This work enhances our understanding of the plastisphere's role in antimicrobial resistance dissemination and its ecological and public health risks.202540901934
3176130.9997Comprehensive profiling and risk assessment of antibiotic resistance genes in a drinking water watershed by integrated analysis of air-water-soil. The prevalence of antibiotic resistance genes (ARGs) in diverse habitats threatens public health. Watersheds represent critical freshwater ecosystems that interact with both the soil and atmosphere. However, a holistic understanding of ARGs distribution across these environmental media is currently inadequate. We profiled ARGs and bacterial communities in air-water-soil in the same watershed area during four seasons using high-throughput qPCR and 16S rRNA gene sequencing. Our findings demonstrated that aminoglycoside resistance genes (58.5%) were dominant in water, and multidrug resistance genes (55.2% and 54.2%) were dominant in soil and air. Five ARGs and nineteen bacterial genera were consistently detected in all samples, were named as shared genes or bacteria. Co-occurrence Network analysis revealed the co-occurrence module of resistance genes, mobile genetic elements (MGEs), and potential bacterial hosts, indicating that shared genes and bacteria may persist and co-spread across different environmental media. The risk assessment framework, based on ARGs' abundance, detection rate, and mobility, identified 33 high-risk ARGs. This is essential to evaluate the health risks of ARGs and to develop strategies to limit the threat of antibiotic resistance. Our study offers new insights into the risks associated with ARGs in the environment and suggests that ARGs may depend on specific bacterial cohabitants that co-exist with MGEs to facilitate their spread across environmental interfaces.202337742410
3232140.9997Metagenome-Based Analysis of the Microbial Community Structure and Drug-Resistance Characteristics of Livestock Feces in Anhui Province, China. We analyzed metagenome data of feces from sows at different physiological periods reared on large-scale farms in Anhui Province, China, to provide a better understanding of the microbial diversity of the sow intestinal microbiome and the structure of antibiotic-resistance genes (ARGs) and virulence genes it carries. Species annotation of the metagenome showed that in the porcine intestinal microbiome, bacteria were dominant, representing >97% of the microorganisms at each physiological period. Firmicutes and Proteobacteria dominated the bacterial community. In the porcine gut microbiome, the viral component accounted for an average of 0.65%, and the species annotation results indicated that most viruses were phages. In addition, we analyzed the microbiome for ARGs and virulence genes. Multidrug-like, MLS-like, and tetracycline-like ARGs were most abundant in all samples. Evaluation of the resistance mechanisms indicated that antibiotic inactivation was the main mechanism of action in the samples. It is noteworthy that there was a significant positive correlation between ARGs and the total microbiome. Moreover, comparative analysis with the Virulence Factor Database showed that adhesion virulence factors were most abundant.202438393105
6887150.9997Horizontal gene transfer in activated sludge enhances microbial antimicrobial resistance and virulence. Activated sludge (AS) plays a vital role in removing organic pollutants and nutrients from wastewater. However, the risks posed by horizontal gene transfer (HGT) between bacteria in AS are still unclear. Here, a total of 478 high-quality non-redundant metagenome-assembled genomes (MAGs) were obtained. >50 % and 5 % of MAGs were involved in at least one HGT and recent HGT, respectively. Most of the transfers (82.4 %) of antimicrobial resistance genes (ARGs) occurred among the classes of Alphaproteobacteria and Gammaproteobacteria. The bacteria involved in the transfers of virulence factor genes (VFGs) mainly include Alphaproteobacteria (42.3 %), Bacteroidia (19.2 %), and Gammaproteobacteria (11.5 %). Moreover, the number of ARGs and VFGs in the classes of Alphaproteobacteria and Gammaproteobacteria was higher than that in other bacteria (P < 0.001). Mobile genetic elements were important contributors to ARGs and VFGs in AS bacteria. These results have implications for the management of antimicrobial resistance and virulence in activated sludge microorganisms.202438013098
3233160.9997A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants. The concentration of viruses in sewage sludge is significantly higher (10-1000-fold) than that found in natural environments, posing a potential risk for human and animal health. However, the composition of these viruses and their role in the transfer of pathogenic factors, as well as their role in the carbon, nitrogen, and phosphorus cycles remain poorly understood. In this study, we employed a shotgun metagenomic approach to investigate the pathogenic bacteria and viral composition and function in two wastewater treatment plants located on a campus. Our analysis revealed the presence of 1334 amplicon sequence variants (ASVs) across six sludge samples, with 242 ASVs (41.22% of total reads) identified as pathogenic bacteria. Arcobacter was found to be the most dominant pathogen accounting for 6.79% of total reads. The virome analysis identified 613 viral genera with Aorunvirus being the most abundant genus at 41.85%. Approximately 0.66% of these viruses were associated with human and animal diseases. More than 60% of the virome consisted of lytic phages. Host prediction analysis revealed that the phages primarily infected Lactobacillus (37.11%), Streptococcus (21.11%), and Staphylococcus (7.11%). Furthermore, our investigation revealed an abundance of auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and phosphorus cycling within the virome. We also detected a total of 113 antibiotic resistance genes (ARGs), covering major classes of antibiotics across all samples analyzed. Additionally, our findings indicated the presence of virulence factors including the clpP gene accounting for approximately 4.78%, along with toxin genes such as the RecT gene representing approximately 73.48% of all detected virulence factors and toxin genes among all samples analyzed. This study expands our understanding regarding both pathogenic bacteria and viruses present within sewage sludge while providing valuable insights into their ecological functions.202438675877
6885170.9997Abundant bacteria shaped by deterministic processes have a high abundance of potential antibiotic resistance genes in a plateau river sediment. Recent research on abundant and rare bacteria has expanded our understanding of bacterial community assembly. However, the relationships of abundant and rare bacteria with antibiotic resistance genes (ARGs) remain largely unclear. Here, we investigated the biogeographical patterns and assembly processes of the abundant and rare bacteria from river sediment at high altitudes (Lhasa River, China) and their potential association with the ARGs. The results showed that the abundant bacteria were dominated by Proteobacteria (55.4%) and Cyanobacteria (13.9%), while the Proteobacteria (33.6%) and Bacteroidetes (18.8%) were the main components of rare bacteria. Rare bacteria with a large taxonomic pool can provide function insurance in bacterial communities. Spatial distribution of persistent abundant and rare bacteria also exhibited striking differences. Strong selection of environmental heterogeneity may lead to deterministic processes, which were the main assembly processes of abundant bacteria. In contrast, the assembly processes of rare bacteria affected by latitude were dominated by stochastic processes. Abundant bacteria had the highest abundance of metabolic pathways of potential drug resistance in all predicted functional genes and a high abundance of potential ARGs. There was a strong potential connection between these ARGs and mobile genetic elements, which could increase the ecological risk of abundant taxa and human disease. These results provide insights into sedimental bacterial communities and ARGs in river ecosystems.202236406442
6852180.9997Distribution and co-occurrence patterns of antibiotic resistance genes in black soils in Northeast China. Black soils (Mollisols) are among the most important soil resources for crop production and food security. In China, they are mainly distributed in the northeastern region. To investigate soil antibiotic resistance distribution patterns and monitor soil quality, we randomly chose nine corn fields in Northeast China and analyzed the antibiotic resistance gene (ARG) distribution and co-occurrence patterns on the basis of high-throughput approaches and network analyses. High genetic diversity (136 unique genes) and low ARG abundances (10(-5)-10(-2) copies/16S rRNA gene copy) were detected, with relatively few interactions among ARGs. Type I integron genes were prevalent in the soil and were positively correlated with ARGs, which may increase the risk of ARG transmission. Most ARGs were strongly associated with microorganisms. Moreover, several ARGs were significantly correlated with antibiotics, nutrients, and metal elements. The generation and dissemination of ARGs, which were most likely mediated by mobile genetic elements (MGEs) and bacteria, were affected by environmental conditions. These results provide insights into the widespread co-occurrence patterns in soil resistomes.202235809539
6870190.9997Antibiotic resistome in landfill leachate and impact on groundwater. Landfill leachate is a hotspot in antibiotic resistance development. However, little is known about antibiotic resistome and host pathogens in leachate and their effects on surrounding groundwater. Here, metagenomic sequencing was used to explore profiles, host bacteria, environmental risks and influencing factors of antibiotic resistome in raw and treated leachate and surrounding groundwater of three landfills. Results showed detection of a total of 324 antibiotic resistance genes (ARGs). The ARGs conferring resistance to multidrug (8.8 %-25.7 %), aminoglycoside (13.1 %-39.2 %), sulfonamide (10.0 %-20.9 %), tetracycline (5.7 %-34.4 %) and macrolide-lincosamide-streptogramin (MLS, 5.3 %-29.5 %) were dominant in raw leachate, while multidrug resistance genes were the major ARGs in treated leachate (64.1 %-83.0 %) and groundwater (28.7 %-76.6 %). Source tracking analysis suggests non-negligible influence of leachate on the ARGs in groundwater. The pathogens including Acinetobacter pittii, Pseudomonas stutzeri and P. alcaligenes were the major ARG-carrying hosts. Variance partitioning analysis indicates that the microbial community, abiotic variables and their interaction contributed most to the antibiotic resistance development. Our results shed light on the dissemination and driving mechanisms of ARGs from leachate to the groundwater, indicating that a comprehensive risk assessment and efficient treatment approaches are needed to deal with ARGs in landfill leachate and nearby groundwater. ENVIRONMENTAL IMPLICATIONS: Antibiotic resistance genes are found abundant in the landfill sites, and these genes could be disseminated into groundwater via leaching of wastewater and infiltration of leachate. This results in deterioration of groundwater quality and human health risks posed by these ARGs and related pathogens. Thus measures should be taken to minimize potential negative impacts of landfills on the surrounding environment.202438547976