Research Note: The structure and diversity of antibiotic resistance genes in animal house environment. - Related Documents




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321101.0000Research Note: The structure and diversity of antibiotic resistance genes in animal house environment. In recent years, a series of public health issues caused by the spread of antibiotic resistance have been widely concerned. The indoor air of livestock and poultry houses is considered to be one of the main sources of environmental contamination of ARGs. This study characterized the micro-organisms and ARGs in the air particulate matter of chicken houses using metagenomics. The study successfully detected 761 different subtypes of resistance genes including aminoglycosides, tetracyclines, MLSB etc., 4 types of mobile genetic elements, and various pathogenic microorganisms from the aerosols in the chicken coop environment. The results showed that the abundance of ARGs in the air of the chicken coop was at a relatively high level, correlation network analysis showed that multiple types of ARGs could promote the emergence of antibiotic-resistant bacteria.202438889568
710610.9998The swine waste resistome: Spreading and transfer of antibiotic resistance genes in Escherichia coli strains and the associated microbial communities. The overuse of antimicrobials in livestock farming has led to the development of resistant bacteria and the spread of antibiotic-resistant genes (ARGs) among animals. When manure containing these antibiotics is applied to agricultural fields, it creates a selective pressure that promotes the acquisition of ARGs by bacteria, primarily through horizontal gene transfer. Most research on ARGs focuses on their role in clinical antibiotic resistance and their transfer from environmental sources to bacteria associated with humans, such as Escherichia coli. The study investigates the spread of antibiotic-resistant genes (ARGs) through class 1 integrons in 27 Escherichia coli strains from pig manure. It focuses on six common ARGs (ermB, cmlA, floR, qnrS, tetA, and TEM) and the class 1 integron gene, assessing their prevalence in manure samples from three pig farms. The study found correlations and anticorrelations among these genes, indicating a predisposition of the integron in spreading certain ARGs. Specifically, cmlA and tetA genes were positively correlated with each other and negatively with int1, suggesting they are not transferred via Int1. Farm B had the highest int1 counts and a higher abundance of the TEM gene, but lower levels of cmlA and tetA genes. The results underscore the complexity of predicting ARG spread in agricultural environments and the associated health risks to humans through the food chain. The study's results offer valuable insights into the antibiotic-resistant genes (ARGs) profile in swine livestock, potentially aiding in the development of methods to trace ARGs in the environment.202439053184
729320.9998Prevalence and transmission of antibiotic resistance and microbiota between humans and water environments. The transmission routes for antibiotic resistance genes (ARGs) and microbiota between humans and water environments is poorly characterized. Here, we used high-throughput qPCR analyses and 16S rRNA gene sequencing to examine the occurrence and abundance of antibiotic resistance genes and microbiota in both healthy humans and associated water environments from a Chinese village. Humans carried the most diverse assemblage of ARGs, with 234 different ARGs being detected. The total abundance of ARGs in feces, on skin, and in the effluent from domestic sewage treatment systems were approximately 23, 2, and 7 times higher than their abundance in river samples. In total, 53 ARGs and 28 bacteria genera that were present in human feces could also be found in the influent and effluent of rural sewage treatment systems, and also downstream of the effluent release point. We identified the bacterial taxa that showed a significant association with ARGs (P < 0.01, r > 0.8) by network analysis, supporting the idea that these bacteria could carry some ARGs and transfer between humans and the environment. Analysis of ARGs and microbiota in humans and in water environments helps to define the transmission routes and dynamics of antibiotic resistance within these environments. This study highlights human contribution to the load of ARGs into the environment and suggests means to prevent such dissemination.201830420129
736530.9998A case study on the distribution of the environmental resistome in Korean shrimp farms. Hundreds of tons of antibiotics are widely used in aquaculture to prevent microbial infections and promote fish growth. However, the overuse of antibiotics and chemical products can lead to the selection and spreading of antibiotic-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs), which are of great concern considering the threat to public health worldwide. Here, in-depth metagenome sequencing was performed to explore the environmental resistome and ARB distribution across farming stages in shrimp farms and examine anthropogenic effects in nearby coastal waters. A genome-centric analysis using a metagenome binning approach allowed us to accurately investigate the distribution of pathogens and ARG hosts in shrimp farms. The diversity of resistomes was higher in shrimp farms than in coastal waters, and the distribution of resistomes was dependent on the farming stage. In particular, the tetracycline resistance gene was found mainly at the early post-larval stage regardless of the farm. The metagenome-assembled genomes of Vibrio spp. were dominant at this stage and harbored tet34, which is known to confer resistance to oxytetracycline. In addition, opportunistic pathogens such as Francisella, Mycoplasma, Photobacterium, and Vibrio were found in abundance in shrimp farms, which had multiple virulence factors. This study highlights the increased resistance diversity and environmental selection of pathogens in shrimp farms. The use of environmental pollutants on farms may cause an increase in resistome diversity/abundance and the transmission of pathogens to the surrounding environment, which may pose future risks to public health and aquatic organisms.202134653940
729440.9998The Sources and Potential Hosts Identification of Antibiotic Resistance Genes in the Yellow River, Revealed by Metagenomic Analysis. The fate of antibiotic resistance genes (ARGs) has been revealed in various environmental media in recent years. Namely, the emergence of genes that resist colistin and carbapenems has attracted wide attention. However, the pollution condition of ARGs and sources in the Yellow River is still little understood, despite the river being the second longest in China. The present study determined the levels of ARG pollution in the Henan section of the Yellow River and evaluated the role of the aquaculture industry in the spread of ARGs. As revealed by the results, a total of 9 types of ARGs were detected in the sediments of the Yellow River, and the total ARG content in the Yellow River ranges from 7.27 to 245.45 RPKM. Sul1 and sul2 are the dominant ARGs, and the huge usage of sulfonamides, horizontal gene transfer, and wide bacteria host contribute to the prevalence of these two genes. The results of Spearman correlation analysis indicate that the breeding industry has little influence on ARGs in the Yellow River. Network analysis reveals that the opportunistic pathogen Pseudomonas is the potential host of sul1, tetG, and ANT(3'')-IIa, which can pose a risk to human health.202236012061
710850.9998Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems. It has been proposed that livestock production effluents such as wastewater, airborne dust and manure increase the density of antimicrobial resistant bacteria and genes in the environment. The public health risk posed by this proposed outcome has been difficult to quantify using traditional microbiological approaches. We utilized shotgun metagenomics to provide a first description of the resistome of North American dairy and beef production effluents, and identify factors that significantly impact this resistome. We identified 34 mechanisms of antimicrobial drug resistance within 34 soil, manure and wastewater samples from feedlot, ranch and dairy operations. The majority of resistance-associated sequences found in all samples belonged to tetracycline resistance mechanisms. We found that the ranch samples contained significantly fewer resistance mechanisms than dairy and feedlot samples, and that the resistome of dairy operations differed significantly from that of feedlots. The resistome in soil, manure and wastewater differed, suggesting that management of these effluents should be tailored appropriately. By providing a baseline of the cattle production waste resistome, this study represents a solid foundation for future efforts to characterize and quantify the public health risk posed by livestock effluents.201627095377
321960.9998Airborne bacterial contaminations in typical Chinese wet market with live poultry trade. Chinese wet markets with live poultry trade have been considered as major sources of pathogen dissemination, and sites for horizontal transfer of bacterial and viral pathogens. In this study, the pathogenic bacteria and antibiotic resistant genes (ARGs) in air samples collected at a typical Chinese wet market had been analysis and quantified. Corynebacterium minutissimum and other pathogenic bacteria accounted for 0.81-8.02% of the whole microbial community in different air samples. The four ARGs quantified in this study showed a comparable relative concentration (copies/ng_DNA) with municipal wastewater. Poultry manures were demonstrated to be important microbial contamination source in wet market, which was supported by both microbial composition based source tracking and the quantification of airborne microbial density. A series of Firmicutes and Bacteroidetes indicators of poultry area contamination were successfully screened, which will be useful for the more convenient monitoring of airborne poultry area contamination. Our results indicate bioaerosols acted as important route for the transmissions of pathogens and ARGs. Continued surveillance of airborne microbial contamination is required in poultry trade wet market. PRACTICAL IMPLICATIONS: Urban live poultry markets are important sources of pathogen dissemination, and sites for horizontal transfer of viral and bacterial pathogens. In the present field-study, pathogenic bacteria and antibiotic resistance genes were focused to provide quantitative information on the levels of microbial contaminations at the indoor air of wet markets. Results demonstrated that poultry manures were important microbial contamination source in wet market, and in the meanwhile bioaerosols were identified as important route for the transmissions of microbial contaminants. A series of Firmicutes and Bacteroidetes indicators of poultry area contamination were successfully screened, which will be useful for the more convenient monitoring of airborne poultry area contamination.201627503629
686770.9998Comparative 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
685280.9998Distribution 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
741490.9998Structure of the manure resistome and the associated mobilome for assessing the risk of antimicrobial resistance transmission to crops. In this study, the impact of bovine and poultry manure on the quantitative and qualitative composition of antibiotic resistance genes (ARGs) and the environmental mobilome associated with antimicrobial resistance in soil and crops was determined with the use of next generation sequencing methods. The aim of the study was to perform a metagenomic analysis of manure to estimate the risk of the transmission of ARGs and bacterial drug resistance carriers to fertilized soil and crops. The total copy number of ARGs was nearly four times higher in poultry manure (555 ppm) than in bovine manure (140 ppm), and this relationship was also noted in fertilized soil. Poultry manure induced a much greater increase in the concentrations of ARGs in the soil environment (196.4 ppm) than bovine manure (137.8 ppm) immediately after supplementation. The application of poultry manure led to the highest increase in the abundance of genes encoding resistance to tetracyclines (9%), aminoglycosides (3.5%), sulfonamides (3%), bacitracin (2%), chloramphenicol (2%), and macrolide-lincosamide-streptogramin antibiotics (1%). Heavy metals were stronger promoters of antibiotic resistance in the environment than antibiotics. Antibiotics exerted a greater influence on maintaining the diversity of ARGs than on increasing their abundance in soil. Large quantities of insertion sequences (IS), including those associated with the mobility of ARGs in the population of ESKAPEE pathogens, are introduced to soil with manure. These IS remain stable for up to several months, which indicates that manure, in particular poultry manure, significantly increases the risk of rapid ARG transfer to the environment. Manure also largely contributes to an increase in the diversity of the resistome and mobilome in the metagenome of bacteria isolated from crops. Bacteria of the phylum Proteobacteria appear to play a major role in the transmission of multiple ARGs in crops grown for human and animal consumption.202234864022
3169100.9998Plastispheres 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
3212110.9998Distribution and driving factors of antibiotic resistance genes in treated wastewater from different types of livestock farms. Treated wastewater from livestock farms is an important reservoir for antibiotic resistance genes (ARGs), and is a main source of ARGs in the environment. However, the distribution and driving factors of ARGs in treated wastewater from different types of livestock farms are rarely reported. In this study, treated wastewater from 69 large-scale livestock farms of different types, including broiler, layer, and pig farms, was collected, and 11 subtypes of ARGs, 2 mobile genetic elements (MGEs) and bacterial community structure were analyzed. The results revealed detection rates of NDM-1 and mcr-1 of 90 % and 43 %, respectively, and the detection rates of other ARGs were 100 %. The relative abundance of ARGs, such as tetA, tetX and strB, in broiler farms was significantly higher than that in layer farms, but the bacterial α diversity was significantly lower than that in other farm types. Furthermore, although the treatment process had a greater impact on the physicochemical properties of the treated wastewater than the livestock type, livestock type was the main factor affecting the bacterial community in the treated wastewater. The analysis of potential host bacteria of ARGs revealed significant differences in the host bacteria of ARGs in treated wastewater from different types of livestock farms. The host bacteria of ARGs in broiler farms mainly belonged to Actinobacteria, layer farms mainly belonged to Proteobacteria, and pig farms mainly belonged to Firmicutes. Additionally, redundancy analysis showed that the distribution of ARGs may have resulted from the combination of multiple driving factors in different types of livestock farms, among which tnpA and NH(4)(+)-N were the main influencing factors. This study revealed multiple driving factors for the distribution of typical ARGs in treated wastewater from different types of livestock farms, providing basic data for the prevention and control of ARG pollution in agricultural environments.202235934031
6853120.9998Occurrence and distribution of antibiotics and antibiotic resistance genes in the guts of shrimp from different coastal areas of China. With the continuous increase in shrimp (Litopenaeus vannamei) aquaculture production, the widespread use of antibiotics as a means of preventing and treating diseases has adversely affected the environment, animal health and symbiotic microorganisms in gut environments. At the same time, antibiotic resistance genes (ARGs) are widespread in aquaculture and pose a great threat to aquatic organisms and humans. Therefore, in the present study, the occurrence and distribution of 17 antibiotics, ARGs and mobile genetic elements (MGEs) were detected in the guts of shrimp collected from 12 coastal regions of China. The results showed that sulfadiazine, ciprofloxacin and norfloxacin were detectable in the guts of L. vannamei at all sampling sites. Sul1, sul2, floR and intI-1 were also detected in the guts of L. vannamei at all sampling sites. The total relative abundances of ARGs and MGEs were significantly positively correlated according to Pearson correlation analysis. Sulfonamide resistance genes (sul1 and sul2) were significantly positively correlated with intI-1. These results indicated that MGEs could increase the risk of horizontal gene transfer of ARGs in a gut environment. MGEs are the most important factors promoting the spread of ARGs. Correlation analysis showed that sulfadiazine was significantly positively correlated with sul1 and sul2 and that fluoroquinolone antibiotics were significantly positively correlated with floR, indicating that antibiotics could induce the production of ARGs. Network analysis indicated that Iamia and Alkaliphilus species may harbor the most antibiotic resistance genes, and these bacteria were closely related to the proliferation and spread of ARGs in a gut environment. Antibiotic use and the spread of ARGs in mariculture systems may have negative effects on shrimp and human health. The use of antibiotics should be strictly regulated to control contaminants in mariculture systems, including pathogens and ARGs, thereby reducing potential risks to human health.202234990667
7107130.9998A Comprehensive Study of the Microbiome, Resistome, and Physical and Chemical Characteristics of Chicken Waste from Intensive Farms. The application of chicken waste to farmland could be detrimental to public health. It may contribute to the dissemination of antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) from feces and their subsequent entry into the food chain. The present study analyzes the metagenome and resistome of chicken manure and litter obtained from a commercial chicken farm in Poland. ARB were isolated, identified, and screened for antibiogram fingerprints using standard microbiological and molecular methods. The physicochemical properties of the chicken waste were also determined. ARGs, integrons, and mobile genetic elements (MGE) in chicken waste were analyzed using high-throughput SmartChip qPCR. The results confirm the presence of many ARGs, probably located in MGE, which can be transferred to other bacteria. Potentially pathogenic or opportunistic microorganisms and phytopathogens were isolated. More than 50% of the isolated strains were classified as being multi-drug resistant, and the remainder were resistant to at least one antibiotic class; these pose a real risk of entering the groundwater and contaminating the surrounding environment. Our results indicate that while chicken manure can be sufficient sources of the nutrients essential for plant growth, its microbiological aspects make this material highly dangerous to the environment.202236009027
3176140.9998Comprehensive 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
3170150.9998A review of antibiotic resistance genes in major river basins in China: Distribution, drivers, and risk. Antibiotic resistance genes (ARGs) have complex transmission pathways and are prone to form multi-drug-resistant bacteria, threatening the ecological environment and human health. This paper elucidates the distribution and dissemination of ARGs across seven major river basins in China through a comprehensive analysis of relevant literature from the past decade. It presents a comprehensive catalog of pertinent risk assessment methodologies and potential management strategies aimed at mitigating the threat posed by antibiotic resistance due to ARGs. The analysis results showed that the pollution abundance of ARGs showed a decreasing trend from east to west, with the estuarine environment and economically developed areas standing out, with sulfonamides and tetracyclines, among others, as the main types of pollution. Human activities are closely related to the occurrence and spread of ARGs. Mobile genetic factors and microbial communities act as the main drivers to promote the proliferation of ARGs among different microorganisms through horizontal transfer and other pathways. The exhibition of ARGs assessment methods was comparatively analyzed, while Chinese river basins are at medium-high risk and need to be managed rationally. This review can provide a reference for the distribution, spread and management of ARGs in Chinese river basin.202540010590
3215160.9998Prevalence 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
7363170.9998Occurrence of antibiotics and antibiotic resistance genes at various stages of different aquaculture modes surrounding Tai Lake, China. INTRODUCTION: Aquaculture is an important source of antibiotics and ARGs in environmental waters. However, the occurrence of antibiotics and ARGs under different modes and stages of aquaculture has rarely been systematically studied. METHODS: This paper uses qPCR, LC-MS, and High-Throughput sequencing across different culture modes and stages to investigate antibiotics, resistance genes, and microbial communities in the water bodies, and analyze contamination differences between these modes. RESULTS: The quinolone and chloramphenicol were the main antibiotics, and the highest absolute abundance genes were quinolone resistance genes (qnrB) and quinolone resistance genes (sul1), with the mobile genetic element (MGE) intI1, both of which exhibited a gradual seasonal increase. Microbial diversity also varies seasonally, especially with a gradual increase in the abundance of some pathogenic bacteria (Flavobacterium). Antibiotics and resistance genes were found at higher levels in fish ponds compared to shrimp and crab ponds, while they were lower in shrimp and crab ponds that utilized the ecological mode ponds than in the traditional culture mode ponds. CONCLUSION: Our study presents a comprehensive characterization of antibiotics and ARGs in aquaculture waters from various perspectives. Ecological aquaculture modes contribute to reducing antibiotic and resistance gene pollution in water bodies. These findings will support the optimization of aquaculture mode and antibiotic usage to the green and sustainable development of aquaculture finally.202539959160
7292180.9998Class 1 integron and related antimicrobial resistance gene dynamics along a complex freshwater system affected by different anthropogenic pressures. The risk for human health posed by polluted aquatic environments, and especially those carrying antibiotic resistance genes (ARGs) of clinical interest, is still debated. This is because of our limited knowledge of the dynamics of antimicrobial resistance in the environment, the selection mechanisms underlying the spread of ARGs, and the ecological factors potentially favoring their return to humans. The Class 1 integron is one of the most effective platforms for the dissemination of ARGs. In this study we investigated a freshwater system consisting of a lake-river-lake continuum, determining the abundance of class 1 integrons and their associated ARGs by a modulated metagenomic approach. Bacterial abundance and community composition were used to identify the potential carriers of class 1 integrons and their associated ARGs over a period of six months. Class 1 integrons and their ARG cargoes were significantly more abundant in riverine sampling sites receiving treated wastewater. Further, class 1 integrons carried ARGs ranked at the highest risk for human health (e.g., catB genes), in particular, genes encoding resistance to aminoglycosides. Genera of potential pathogens, such as Pseudomonas and Escherichia-Shigella, were correlated with class 1 integrons. The lake-river-lake system demonstrated a clear relationship between the integrase gene of class 1 integrons (intI1) and anthropogenic impact, but also a strong environmental filtering that favored the elimination of intI1 once the human derived stressors were reduced. Overall, the results of this study underline the role class 1 integrons as proxy of anthropogenic pollution and suggest this genetic platform as an important driver of aminoglycoside resistance genes, including high risk ARGs, of potential concern for human health.202336351483
3207190.9998Dissemination of antibiotic resistance genes from aboveground sources to groundwater in livestock farms. Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are prevalent in various environments on livestock farms, including livestock waste, soil, and groundwater. Contamination of groundwater by ARB and ARGs in livestock farms is a growing concern as it may have potentially huge risks to human health. However, the source of groundwater-borne ARB and ARGs in animal farms remains largely unknown. In this study, different types of samples including groundwater and its potential contamination sources from aboveground (pig feces, wastewater, and soil) from both working and abandoned swine feedlots in southern China were collected and subjected to metagenomic sequencing and ARB isolation. The source tracking based on metagenomic analysis revealed that 56-95 % of ARGs in groundwater was attributable to aboveground sources. Using metagenomic assembly, we found that 45 ARGs predominantly conferring resistance to aminoglycosides, sulfonamides, and tetracyclines could be transferred from the aboveground sources to groundwater, mostly through plasmid-mediated horizontal gene transfer. Furthermore, the full-length nucleotide sequences of sul1, tetA, and TEM-1 detected in ARB isolates exhibited the close evolutionary relationships between aboveground sources and groundwater. Some isolated strains of antibiotic-resistant Pseudomonas spp. from aboveground sources and groundwater had the high similarity (average nucleotide identity > 99 %). Notably, the groundwater-borne ARGs were identified as mainly carried by bacterial pathogens, potentially posing risks to human and animal health. Overall, this study underscores the dissemination of ARGs from aboveground sources to groundwater in animal farms and associated risks.202438598950