Integrative metagenomic dissection of last-resort antibiotic resistance genes and mobile genetic elements in hospital wastewaters. - Related Documents




#
Rank
Similarity
Title + Abs.
Year
PMID
012345
327401.0000Integrative metagenomic dissection of last-resort antibiotic resistance genes and mobile genetic elements in hospital wastewaters. Hospital wastewater is a critical source of antimicrobial resistance (AMR), which facilitates the proliferation and spread of clinically significant antimicrobial resistance genes (ARGs) and pathogenic bacteria. This study utilized metagenomic approaches, including advanced binning techniques, such as MetaBAT2, MaxBin2, and CONCOCT, which offer significant improvements in accuracy and completeness over traditional binning methods. These methods were used to comprehensively assess the dynamics and composition of resistomes and mobilomes in untreated wastewater samples taken from two general hospitals and one cancer hospital. This study revealed a diverse bacterial landscape, largely consisting of Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with notable variations in microbial composition among hospitals. Analysis of the top 15 genera showed unique microbial pattern distribution in each hospital: Aeromonas was predominant in 1stHWTS (49.39 %), Acidovorax in the CAHWTS at 16.85 %, and Escherichia and Bacteroides in the 2ndHWTS at 11.44 % and 11.33 %, respectively. A total of 114 pathogenic bacteria were identified, with drug-resistant Aeromonas caviae and Escherichia coli being the most prevalent. The study identified 34 types and 1660 subtypes of ARGs, including important last-resort antibiotic resistance genes (LARGs), such as bla(NDM), mcr, and tet(X). Using metagenomic binning, this study uncovered distinct patterns of host-resistance associations, particularly with Proteobacteria and Firmicutes. Network analysis highlighted the complex interactions among ARGs, mobile genetic elements (MGEs), and bacterial species, all contributing to the dissemination of AMR. These findings emphasize the intricate nature of AMR in hospital wastewater and the influence of hospital-specific factors on microbial resistance patterns. This study provides support for implementing integrated management strategies, including robust surveillance, advanced wastewater treatment, and strict antibiotic stewardship, to control the dissemination of AMR. Understanding the interplay among bacterial communities, ARGs, and MGEs is important for developing effective public health measures against AMR.202439067608
327310.9998Integrating metagenomic and isolation strategies revealed high contamination of pathogenies and resistome in market shrimps. This study employs a comprehensive approach combining metagenomic analysis and bacterial isolation to elucidate the microbial composition, antibiotic resistance genes (ARGs), and virulence factors (VFGs) present in shrimps from market and supermarket. Metagenomic analysis of shrimps revealed a dominance of Proteobacteria and Bacteroidetes with Firmicutes notably enriched in some samples. On the other hand, the dominant bacteria isolated included Citrobacter portucalensis, Escherichia coli, Salmonella enterica, Vibrio species and Klebsiella pneumonaie. Metagenomic analysis unveiled a diverse spectrum of 23 main types and 380 subtypes of ARGs in shrimp samples including many clinical significant ARGs such as bla(KPC), bla(NDM), mcr, tet(X4) etc. Genomic analysis of isolated bacterial strains identified 14 ARG types with 109 subtype genes, which complemented the metagenomic data. Genomic analysis also allowed us to identify a rich amount of MDR plasmids, which provided further insights into the dissemination of resistance genes in different species of bacteria in the same samples. Examination of VFGs and mobile genetic elements (MGEs) in both metagenomic and bacterial genomes revealed a complex landscape of factors contributing to bacterial virulence and genetic mobility. Potential co-occurrence patterns of ARGs and VFGs within human pathogenic bacteria underlined the intricate interplay between antibiotic resistance and virulence. In conclusion, this integrated analysis for the first time provides a comprehensive view and sheds new light on the potential hazards associated with shrimp products in the markets. The findings underscore the necessity of ongoing surveillance and intervention strategies to mitigate risks posed by antibiotic-resistant bacteria in the food supply chain using the novel comprehensive approaches.202438522537
731720.9997Metagenomic surveillance of microbial community and antibiotic resistant genes associated with Malaysian wastewater during the COVID-19 pandemic. Wastewater is a reservoir of pathogens and hotspots for disseminating antibiotic resistance genes across species. The metagenomic surveillance of wastewater provides insight into the native microbial community, antibiotic-resistance genes (ARGs) and mobile genetic elements. t. The COVID-19 pandemic has caused wider dissemination of ARGs and resistant bacteria in wastewater. Although immensely significant, no research has been performed on the Malaysian wastewater microbial community and ARGs or their correlation with COVID-19 infections. This study utilised a 16S metagenomics approach to characterise the microbial community in Malaysian wastewater during high and low-case phases of the pandemic. Bacteria belonging to Bacteriodales, Bacillales, Actinomycetales and opportunistic pathogens-Arcobacters, Flavobacteria, and Campylobacterales, Neisseriales, were enriched during higher COVID-19 pandemic (active cases). Additionally, copy number profiling of ARGs in water samples showed the prevalence of elements conferring resistance to antibiotics like sulphonamides, cephalosporins, and colistin. The high prevalence of intI1 and other ion-based transporters in samples highlights an extensive risk of horizontal gene transfer to previously susceptible species. Our study emphasises the importance of wastewater surveillance in understanding microbial community dynamics and ARG dissemination, particularly during public health crises like the COVID-19 pandemic.202439724227
318330.9997The microbiome, resistome, and their co-evolution in sewage at a hospital for infectious diseases in Shanghai, China. The emergence of antibiotic-resistant bacteria (ARB) caused by the overuse of antibiotics severely threatens human health. Hospital sewage may be a key transmission hub for ARB. However, the complex link between the microbiome and resistomeresistance in hospital sewage remains unclear. In this study, metagenomic assembly and binning methods were used to investigate the microbial community, resistome, and association of antibiotic resistance genes (ARGs) with ARB in sewage from 10 representative sites (outpatient building, surgery building, internal medicine buildings [IMB1-4], staff dormitory, laboratory animal building, tuberculosis building [TBB], and hospital wastewater treatment plant) of a hospital in Shanghai from June 2021 to February 2022. A total of 252 ARG subtypes, belonging to 17 antibiotic classes, were identified. The relative abundance of KPC-2 was higher at IMBs and TBB than at other sites. Of the ARG-carrying contigs, 47.3%-62.6% were associated with mobile genetic elements, and the proportion of plasmid-associated ARGs was significantly higher than that of chromosome-associated ARGs. Although a similar microbiome composition was shared, certain bacteria were enriched at different sites. Potential pathogens Enterococcus B faecium and Klebsiella pneumoniae were primarily enriched in IMB2 and IMB4, respectively. The same ARGs were identified in diverse bacterial hosts (especially pathogenic bacteria), and accordingly, the latter possessed multiple ARGs. Furthermore, gene flow was frequently observed in the sewage of different buildings. The results provide crucial information on the characterization profiles of resistomes in hospital sewage in Shanghai.IMPORTANCEEnvironmental antibiotic resistance genes (ARGs) play a critical role in the emergence and spread of antimicrobial resistance, which poses a global health threat. Wastewater from healthcare facilities serves as a significant reservoir for ARGs. Here, we characterized the microbial community along with the resistome (comprising all antibiotic resistance genes) in wastewater from a specialized hospital for infectious diseases in Shanghai. Potential pathogenic bacteria (e.g., Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Enterococcus B faecium) were frequently detected in hospital wastewater and carried multiple ARGs. A complex link between microbiome and resistome was observed in the wastewater of this hospital. The monitoring of ARGs and antibiotic-resistant bacteria (ARB) in hospital wastewater might be of great significance for preventing the spread of ARB.202438132570
327740.9997Airborne 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
320850.9997Effects of Antibiotic Residues on Fecal Microbiota Composition and Antimicrobial Resistance Gene Profiles in Cattle from Northwestern China. Grazing is a free-range farming model commonly practiced in low-external-input agricultural systems. The widespread use of veterinary antibiotics in livestock farming has led to significant environmental accumulation of antibiotic residues and antibiotic resistance genes (ARGs), posing global health risks. This study investigated the antibiotic residues, bacterial community, ARG profiles, and mobile genetic elements (MGEs) in cattle feces from three provinces in western China (Ningxia, Xinjiang, and Inner Mongolia) under grazing modes. The HPLC-MS detection showed that the concentration of tetracycline antibiotics was the highest in all three provinces. Correlation analysis revealed a significant negative correlation between antibiotic residues and the diversity and population abundance of intestinal microbiota. However, the abundance of ARGs was directly proportional to antibiotic residues. Then, the Sankey analysis revealed that the ARGs in the cattle fecal samples were concentrated in 15 human pathogenic bacteria (HPB) species, with 9 of these species harboring multiple drug resistance genes. Metagenomic sequencing revealed that carbapenemase-resistant genes (bla(KPC) and bla(VIM)) were also present in considerable abundance, accounting for about 10% of the total ARGs detected in three provinces. Notably, Klebsiella pneumoniae strains carrying bla(CTX-M-55) were detected, which had a possibility of IncFII plasmids harboring transposons and IS19, indicating the risk of horizontal transfer of ARGs. This study significantly advances the understanding of the impact of antibiotic residues on the fecal microbiota composition and ARG profiles in grazing cattle from northwestern China. Furthermore, it provides critical insights for the development of rational antibiotic usage strategies and comprehensive public health risk assessments.202540732167
326860.9997Resistomic features and novel genetic element identified in hospital wastewater with short- and long-read metagenomics. The global spread of antimicrobial resistance (AMR) poses a serious threat to public health, with hospital wastewater treatment plants (WWTPs) recognized as a key hotspot for resistant pathogens and antibiotic resistance genes (ARGs). This study employed advanced hybrid sequencing platforms to provide a comprehensive resistomic analysis of a Qingdao WWTP in China, revealing previously uncovered AMR transmission risks. We identified 175 ARG subtypes conferring resistance to 38 antimicrobials, including the last-resort antibiotics, highlighting the extensive and concerning resistance reservoir within this environment. Multidrug resistance genes predominated, followed by ARGs targeting aminoglycoside, β-lactam, tetracycline, glycopeptide, and macrolide classes, reflecting clinically relevant resistance patterns. Co-occurrence analysis revealed ARGs were strongly associated with mobile genetic elements, especially for ARGs targeting sulfonamide, glycopeptide, macrolide, tetracycline, aminoglycoside, and β-lactam classes, providing concrete evidence of their high dissemination potential. A striking 85 % of 131 metagenome-assembled genomes (MAGs) carried ARGs, demonstrating prevalent resistance in the wastewater microbiome. Furthermore, the identification of several rarely studied genomic islands (GIs), including those conferring resistance to antibiotics and heavy metals, and notably, the novel variant GIAS409 carrying transposases and heavy metal resistance operons, reveals a significant and previously neglected mechanism for co-selection and dissemination. This study significantly advances our understanding of AMR dynamics in hospital WWTPs, demonstrating that current treatment approaches (42 % ARG removal) have limited efficacy and that WWTP may serve as potential hotspots for multidrug resistance development. Collectively, these findings emphasize the urgent need for improved wastewater management to safeguard public health.202540915207
327670.9997Deciphering risks of resistomes and pathogens in intensive laying hen production chain. Antimicrobial resistance (AMR) and pathogens derived from food animals and their associated environments have emerged as challenging threats to humans from a health perspective, but our understanding of these risks and their key prevention and control points in the current intensive breeding industry remains poor. By creating an integral composition and risk profile of the resistome and microbiome through metagenomics in feces, flies, dust, sewage, and soil along the four-stage laying hen production chain, we found that the whole production chain is a hotspot for antimicrobial resistance genes (ARGs) with 374 known subtypes and pathogens, including 157 human pathogenic bacteria (HPB). Feces and flies were identified as major risk sources for these contaminations. Also, we confirmed a twin-risk of AMR and pathogenicity prevailing throughout the chain, but with different frequencies in each stage; thus, high-risk ARGs in the young chicken stage and highly prioritized HPB in the chick stage contributed 37.33 % to the total AMR risk and 36.36 % to the pathogenic risks, respectively, thus rendering the two stages to be the key prevention points. Moreover, the prevalence of 112 binned ARG supercarriers (for example, Klebsiella pneumoniae harboring 20 ARGs) was unraveled along the production chain, especially in feces, flies, and dust, and 87 potential hosts exhibited high pathogenic risk, high-risk AMR, or both, with 262 ARGs and 816 virulence factor genes. Overall, this study provides first-hand comprehensive data on high-risk ARGs and their pathogenic hosts in the intensive laying hen production chain, and thus is fundamentally important for developing new measures to help control the global AMR crisis induced through the animal-environment-human pathway.202336702267
319180.9997Profiling of Bacterial Communities of Hospital Wastewater Reveals Clinically Relevant Genera and Antimicrobial Resistance Genes. In Mexico, hospital wastewater (HWW) is a source of chemical and microbiological contamination, and it is released into the municipal sewage system without prior treatment. This water may contain pathogenic bacteria and antimicrobial resistance genes, which represent a risk to Public Health and the environment. So far, there are no studies that analyse this problem comprehensively, relating bacterial population structures, chemical contaminants, and seasonality. The aim of this work was to seasonally characterise the bacterial communities of HWW, including clinically relevant bacteria and resistance genes in Hospital Juárez de México (HJM), and to evaluate the impact of physicochemical factors on their composition. A one-year observational, cross-sectional study was conducted at five HWW discharge points of HJM. Fourteen physicochemical parameters were determined by using standard methodologies, and statistical differences between discharges and seasons were evaluated. Bacterial communities were analysed by targeted amplicon sequencing of the V3-V4 region of the 16S rRNA gene. In addition, the presence of eight antimicrobial resistance genes of local epidemiological importance was assessed. Data were analysed using alpha and beta diversity indices, principal component analysis, and multivariate statistical tests. HWW showed high taxonomic diversity, with Proteobacteria, Firmicutes, and Bacteroidetes standing out. Clinically relevant bacteria were identified in 73.3% of the analyses, with Enterobacter and Escherichia-Shigella predominating. Total and dissolved solids, temperature, nitrate, and pH significantly influenced the bacterial composition of HWW. Seven out of the eight genes evaluated were identified, with bla(KPC), bla(OXA-40), and mcr-1 being the most frequent, showing significant seasonal differences. This study underlines the microbiological and chemical complexity of HWW, highlighting the impact of clinically relevant bacteria and antimicrobial resistance genes on Public Health. The findings emphasise the need to implement hospital waste management programmes and ideally specific treatment plants to minimise the associated risks and protect the environment and human health.202540572204
258190.9997Evaluation of the resistome and gut microbiome composition of hospitalized patients in a health unit of southern Brazil coming from a high animal husbandry production region. INTRODUCTION: Antimicrobial resistance (AMR) poses a significant threat to global public health. The One Health approach, which integrates human, animal, and environmental health, highlights the roles of agricultural and hospital settings in the propagation of AMR. This study aimed to analyze the resistome and gut microbiome composition of individuals from a high-intensity animal husbandry area in the western region of Santa Catarina, Southern Brazil, who were subsequently admitted to the University Hospital in the city of Florianopolis, located in the eastern part of the same state. METHODS: Rectal swab samples were collected upon admission and discharge. Metagenomic sequencing and resistome analysis were employed to identify antimicrobial resistance genes (ARGs) and their associated bacterial taxa. Additionally, the impact of the hospital environment on the resistome and microbiome profiles of these patients was assessed. RESULTS: A total of 247 genetic elements related to AMR were identified, with 66.4% of these elements present in both admission and discharge samples. Aminoglycoside resistance genes were the most prevalent, followed by resistance genes for tetracyclines and lincosamides. Notably, unique resistance genes, including dfrF and mutations in gyrB, were identified at discharge. ARGs were associated with 55 bacterial species, with Lactobacillus fermentum, harboring the ermB gene. (MLSB), detected in both admission and discharge samples. The most prevalent bacterial families included Mycobacteriaceae, Enterobacteriaceae, and Bacteroidaceae. Among these, Mycobacteriaceae was the most abundant, with ARGs primarily associated with mutations in the 16S rRNA gene, RNA polymerase subunits, and gyrases. DISCUSSION: The study revealed a high prevalence of genes related to aminoglycoside and tetracycline resistance, with a notable increase in certain resistance determinants at discharge, likely influenced by extended antimicrobial use. The presence of mcr genes, associated with colistin resistance, in both admission and discharge samples from a single patient highlights a concerning trend in AMR, particularly in relation to animal husbandry. These findings underscore the substantial impact of antimicrobial use on resistance development and the complex dynamics of the resistome in hospital settings. They also emphasize the influence of local factors, such as intensive animal production, on resistance patterns and advocate for ongoing surveillance and policy development to manage multidrug-resistant bacteria eVectively.202439896720
3184100.9997Comparative assessment of microbiome and resistome of influent and effluent of sewage treatment plant and common effluent treatment plant located in Delhi, India using shotgun approach. Antimicrobial resistance (AMR) is a significant threat that demands surveillance to identify and analyze trends of the emerging antibiotic resistance genes (ARGs) and potential microbial carriers. The influent of the wastewater treatment plants (WWTPs) reflects the microbes derived from the population and effluent being the source of dissemination of potential pathogenic microbes and AMR. The present study aimed to monitor microbial communities and antibiotic resistance genes in WWTPs employing a whole metagenome shotgun sequencing approach. The samples were collected from a sewage treatment plant (STP) and a common effluent treatment plant (CETP) in Delhi, India. The results showed the influent of STP to be rich in Bifidobacterium, Bacteroides, Escherichia, Arcobacter, and Pseudomonas residents of gut microbiota and known to cause diseases in humans and animals; whereas the CETP sample was abundant in Aeromonas, Escherichia, and Shewanella known to be involved in the degradation of different compounds. Interestingly, the effluent samples from both STPs and CETP were rich in microbial diversity, comprising organic and xenobiotic compound degrading and disease-causing bacteria, indicating the effluent being the source of dissemination of concerning bacteria to the environment. The functional profile at both sites displayed similarity with an abundance of housekeeping function genes as analyzed by Clusters of Orthologous Genes (COG), KEGG Orthology (KO), and subsystem databases. Resistome profiling by MEGARes showed the dominance of ARGs corresponding to beta-lactams having relative abundance ranging from 16% to 34% in all the metagenome datasets, followed by tetracycline (8%-16%), aminoglycosides (7%-9%), multi-drug (5%-9%), and rifampin (3%-9%). Also, AMR genes oxa, ant3-DPRIME, and rpoB, which are of clinical importance were predominantly and most prevalently present in all the samples. The presence of AMR in effluents from both types of treatment plants indicates that wastewater from both sources contributes to the spread of pathogenic bacteria and resistance genes, increasing the environmental AMR burden and therefore requires tertiary treatment before discharge. This work will facilitate further research towards the identification of suitable biomarkers for monitoring antibiotic resistance.202439232318
3226110.9997Metagenomic profiles of the antimicrobial resistance in traditional Chinese fermented meat products: Core resistome and co-occurrence patterns. Antimicrobial resistance (AMR) poses a significant challenge to global health, and the presence of antibiotic resistance genes (ARGs) in food poses a potential threat to public health. Traditional Chinese fermented meat products (FMPs) are highly favored because of their unique flavors and cultural value. However, microbial safety and the potential distribution and composition of AMR in these products remain unclear. In this study, a comprehensive analysis of bacterial composition and antibiotic-resistant populations in 216 samples of traditional fermented meat products from different regions of China was conducted using a metagenomic approach. Staphylococcus was the most abundant genus in the samples, accounting for an average abundance of 29.9 %, followed by Tetragenococcus (17.1 %), and Latilactobacillus (3.6 %). A core resistome of FMP samples was constructed for the first time using co-occurrence network analysis, which revealed the distribution and interrelationships of ARGs and bio/metal-resistant genes (BMRGs). Random forest analysis identified the lincosamide nucleotidyltransferase lnuA and the multidrug and toxic compound extrusion (MATE) transporter abeM as potential indicators for assessing the overall abundance of the core resistome. Additionally, Staphylococcus, Acinetobacter, and Pseudomonas were identified as hosts constituting the core resistome. Despite their low abundance, the latter two still serve as major reservoirs of antibiotic resistance genes. Notably, Lactococcus cremoris was identified as the key host for tetracycline resistance genes in the samples, highlighting the need for enhanced resistance monitoring in lactic acid bacteria. Based on our findings, in the microbial safety assessment of fermented meat products, beyond common foodborne pathogens, attention should be focused on detecting and controlling coagulase-negative Staphylococcus, Acinetobacter, and Pseudomonas, and addressing bacterial resistance. The quantitative detection of lnuA and abeM could provide a convenient and rapid method for assessing the overall abundance of the core resistome. Our findings have important implications for the control of bacterial resistance and prevention of pathogenic bacteria in fermented meat products.202438754174
3185120.9997Differences in co-selection and localization of antimicrobial resistance and virulence genes among Acinetobacter isolates from patients, pig waste, and the environment. Acinetobacter species are indigenous bacteria in water environments, whereas in clinical settings, they can pose a serious risk of nosocomial infection as opportunistic pathogens harboring multidrug-resistance genes. Understanding the similarities and differences in pathogenicity and drug resistance among Acinetobacter strains isolated from animals, humans, and the environment through a One Health approach is essential for mitigating their infection risk. We explored the resistome and virulome of 38 Acinetobacter isolates obtained from pigs' waste, patients, wastewater, and wastewater-impacted environments, including river and coastal area which receives wastewater effluent. Hybrid genome assemblies demonstrated distinct difference in the composition and location of antibiotic resistance genes (ARGs). Patient- and environment-associated isolates demonstrated chromosomally integrated ARGs and genes encoding efflux pumps, whereas pig waste-associated isolates exhibited a diverse range of ARG types predominantly located on plasmid replicons. Additionally, an analysis of virulence genes (VGs) across all Acinetobacter isolates revealed that VGs are more prevalent in patient- and environment-associated isolates compared to pig waste-associated isolates. Notably, a positive correlation between the number of ARGs and VGs located on the chromosome was observed in environment-associated isolates, which may imply co-selection of ARGs and VGs. Overall, this study highlights differences in the localization and co-selection of ARGs and VGs among patient-, pig waste-, and environment- associated isolates, suggesting that Acinetobacter spp. adapted to the human body tend to possess VGs and ARGs together, while those derived from animals may preferentially harbor transferable ARGs.202541039664
3467130.9997Epidemiological characteristics of antibiotic resistance genes in various bacteria worldwide. OBJECTIVES: This study aims to investigate the epidemiological characteristics of various bacteria carrying ARGs on a global scale over extended time periods. METHODS: A total of 25,285 globally isolated bacteria's genomes were analyzed to explore ARGs. The analysis focused on temporal, geographic, and species distribution, including pathogenic and non-pathogenic bacteria, intracellular parasitic states, ARG types, and their association with MGEs. Multiple linear regression was employed to identify ARG risk factors in bacteria. RESULTS: The overall prevalence of bacteria with ARGs was 64.2%, indicating that at least one ARG was present in 64.2% (16,243/25,285) of the included bacterial, with an average of 14.4 ARGs per bacterium. ARGs have been increasing globally, averaging one additional ARG every three years, closely linked to rising antibiotic consumption. Pathogenic bacteria harbored more ARGs than non-pathogenic ones. Intracellular parasitic bacteria still carry specific types of ARGs despite being less likely to generate ARGs. Clinical and human-associated bacteria showed higher ARG counts, and bacteria isolated from humans had the highest number of disinfectant-resistant genes. The average number of ARGs in bacteria isolated from high-middle-income and lower-middle-income countries is higher. Factors like motility, non-sporulation, Gram-positive staining, extracellular parasitism, and human pathogenicity are linked to higher ARGs levels. CONCLUSIONS: An increasing number of bacteria carrying ARGs pose a significant challenge to the control of antibiotics-resistant pathogens worldwide. The issue of bacteria carrying more ARGs requires greater global attention.202540147137
3215140.9997Prevalence 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
3186150.9997Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics. Efficient sewage treatment is critical for limiting environmental transmission of antibiotic-resistant bacteria. In many low and middle income countries, however, large proportions of sewage are still released untreated into receiving water bodies. In-depth knowledge of how such discharges of untreated urban waste influences the environmental resistome is largely lacking. Here, we highlight the impact of uncontrolled discharge of partially treated and/or untreated wastewater on the structure of bacterial communities and resistome of sediments collected from Mutha river flowing through Pune city in India. Using shotgun metagenomics, we found a wide array (n = 175) of horizontally transferable antibiotic resistance genes (ARGs) including carbapenemases such as NDM, VIM, KPC, OXA-48 and IMP types. The relative abundance of total ARGs was 30-fold higher in river sediments within the city compared to upstream sites. Forty four ARGs, including the tet(X) gene conferring resistance to tigecycline, OXA-58 and GES type carbapenemases, were significantly more abundant in city sediments, while two ARGs were more common at upstream sites. The recently identified mobile colistin resistance gene mcr-1 was detected only in one of the upstream samples, but not in city samples. In addition to ARGs, higher abundances of various mobile genetic elements were found in city samples, including integron-associated integrases and ISCR transposases, as well as some biocide/metal resistance genes. Virulence toxin genes as well as bacterial genera comprising many pathogens were more abundant here; the genus Acinetobacter, which is often associated with multidrug resistance and nosocomial infections, comprised up to 29% of the 16S rRNA reads, which to our best knowledge is unmatched in any other deeply sequenced metagenome. There was a strong correlation between the abundance of Acinetobacter and the OXA-58 carbapenemase gene. Our study shows that uncontrolled discharge of untreated urban waste can contribute to an overall increase of the abundance and diversity of ARGs in the environment, including those conferring resistance to last-resort antibiotics.201728780361
3164160.9997Variations in Bacterial Communities and Antibiotic Resistance Genes Across Diverse Recycled and Surface Water Irrigation Sources in the Mid-Atlantic and Southwest United States: A CONSERVE Two-Year Field Study. Reduced availability of agricultural water has spurred increased interest in using recycled irrigation water for U.S. food crop production. However, there are significant knowledge gaps concerning the microbiological quality of these water sources. To address these gaps, we used 16S rRNA gene and metagenomic sequencing to characterize taxonomic and functional variations (e.g., antimicrobial resistance) in bacterial communities across diverse recycled and surface water irrigation sources. We collected 1 L water samples (n = 410) between 2016 and 2018 from the Mid-Atlantic (12 sites) and Southwest (10 sites) U.S. Samples were filtered, and DNA was extracted. The V3-V4 regions of the 16S rRNA gene were then PCR amplified and sequenced. Metagenomic sequencing was also performed to characterize antibiotic, metal, and biocide resistance genes. Bacterial alpha and beta diversities were significantly different (p < 0.001) across water types and seasons. Pathogenic bacteria, such as Salmonella enterica, Staphylococcus aureus, and Aeromonas hydrophilia were observed across sample types. The most common antibiotic resistance genes identified coded against macrolides/lincosamides/streptogramins, aminoglycosides, rifampin and elfamycins, and their read counts fluctuated across seasons. We also observed multi-metal and multi-biocide resistance across all water types. To our knowledge, this is the most comprehensive longitudinal study to date of U.S. recycled water and surface water used for irrigation. Our findings improve understanding of the potential differences in the risk of exposure to bacterial pathogens and antibiotic resistance genes originating from diverse irrigation water sources across seasons and U.S. regions.202236194536
6593170.9997Metagenomic analysis of human, animal, and environmental samples identifies potential emerging pathogens, profiles antibiotic resistance genes, and reveals horizontal gene transfer dynamics. Antimicrobial resistance (AMR) poses a significant threat to global health. The indiscriminate use of antibiotics has accelerated the emergence and spread of drug-resistant bacteria, compromising our ability to treat infectious diseases. A One Health approach is essential to address this urgent issue, recognizing the interconnectedness of human, animal, and environmental health. This study investigated the prevalence and transmission of AMR in a temporary settlement in Kathmandu, Nepal. By employing shotgun metagenomics, we analyzed a diverse range of samples, including human fecal samples, avian fecal samples, and environmental samples. Our analysis revealed a complex interplay of pathogenic bacteria, virulence factors (VF), and antimicrobial resistance genes (ARGs) across these different domains. We identified a diverse range of bacterial species, including potential pathogens, in both human and animal samples. Notably, Prevotella spp. was the dominant gut bacterium in human samples. Additionally, we detected a wide range of phages and viruses, including Stx-2 converting phages, which can contribute to the virulence of Shiga toxin-producing E. coli (STEC) strains. Our analysis revealed the presence of 72 virulence factor genes and 53 ARG subtypes across the studied samples. Poultry samples exhibited the highest number of ARG subtypes, suggesting that the intensive use of antibiotics in poultry production may contribute to the dissemination of AMR. Furthermore, we observed frequent horizontal gene transfer (HGT) events, with gut microbiomes serving as key reservoirs for ARGs. This study underscores the critical role of a One Health approach in addressing AMR. By integrating human, animal, and environmental health perspectives, we can better understand the complex dynamics of AMR and develop effective strategies for prevention and control. Our findings highlight the urgent need for robust surveillance systems, judicious antibiotic use, and improved hygiene practices to mitigate the impact of AMR on public health.202540204742
3180180.9997Residential urban stormwater runoff: A comprehensive profile of microbiome and antibiotic resistance. Non-point stormwater runoff is a major contamination source of receiving waterbodies. Heightened incidence of waterborne disease outbreaks related to recreational use and source water contamination is associated with extreme rainfall events. Such extreme events are predicted to increase in some regions due to climate change. Consequently, municipal separate storm sewer systems (MS4s) conveying pathogens to receiving waters are a growing public health concern. In addition, the spread of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria in various environmental matrices, including urban runoff, is an emerging threat. The resistome and microbiota profile of MS4 discharges has yet to be fully characterized. To address this knowledge gap, we first analyzed the relationship between rainfall depth and intensity and E. coli densities (fecal indicator) in stormwater from four MS4 outflows in Columbus, Ohio, USA during the spring and summer of 2017. Microbial source tracking (MST) was conducted to examine major fecal contamination sources in the study sewersheds. A subset of samples was analyzed for microbial and resistome profiles using a metagenomic approach. The results showed a significant positive relationship between outflow E. coli density and rainfall intensity. MST results indicate prevalent fecal contamination from ruminant populations in the study sites (91% positive among the samples tested). Protobacteria and Actinobacteria were two dominant bacteria at a phylum level. A diverse array of ARGs and potentially pathogenic bacteria (e.g. Salmonella enterica Typhimurium), fungi (e.g. Scedosporium apiospermum), and protists (e.g. Acanthamoeba palestinensis) were found in urban stormwater outflows that discharge into adjacent streams. The most prevalent ARGs among samples were β-lactam resistance genes and the most predominant virulence genes within bacterial community were related with Staphylococcus aureus. A comprehensive contamination profile indicates a need for sustainable strategies to manage urban stormwater runoff amid increasingly intense rainfall events to protect public and environmental health.202032392682
6594190.9997An omics-based framework for assessing the health risk of antimicrobial resistance genes. Antibiotic resistance genes (ARGs) are widespread among bacteria. However, not all ARGs pose serious threats to public health, highlighting the importance of identifying those that are high-risk. Here, we developed an 'omics-based' framework to evaluate ARG risk considering human-associated-enrichment, gene mobility, and host pathogenicity. Our framework classifies human-associated, mobile ARGs (3.6% of all ARGs) as the highest risk, which we further differentiate as 'current threats' (Rank I; 3%) - already present among pathogens - and 'future threats' (Rank II; 0.6%) - novel resistance emerging from non-pathogens. Our framework identified 73 'current threat' ARG families. Of these, 35 were among the 37 high-risk ARGs proposed by the World Health Organization and other literature; the remaining 38 were significantly enriched in hospital plasmids. By evaluating all pathogen genomes released since framework construction, we confirmed that ARGs that recently transferred into pathogens were significantly enriched in Rank II ('future threats'). Lastly, we applied the framework to gut microbiome genomes from fecal microbiota transplantation donors. We found that although ARGs were widespread (73% of genomes), only 8.9% of genomes contained high-risk ARGs. Our framework provides an easy-to-implement approach to identify current and future antimicrobial resistance threats, with potential clinical applications including reducing risk of microbiome-based interventions.202134362925