A metagenomic study of antibiotic resistance genes in a hypereutrophic subtropical lake contaminated by anthropogenic sources. - Related Documents




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349201.0000A metagenomic study of antibiotic resistance genes in a hypereutrophic subtropical lake contaminated by anthropogenic sources. Antibiotic resistance genes (ARGs) are a major threat to human and environmental health. This study investigated the occurrence and distribution of ARGs in Lake Cajititlán, a hypereutrophic subtropical lake in Mexico contaminated by anthropogenic sources (urban wastewater and runoff from crop and livestock production). ARGs (a total of 475 genes) were detected in 22 bacterial genera, with Pseudomonas (144 genes), Stenotrophomonas (88 genes), Mycobacterium (54 genes), and Rhodococcus (27 genes) displaying the highest frequencies of ARGs. Among these, Pseudomonas aeruginosa and Stenotrophomonas maltophilia showed the highest number of ARGs. The results revealed a diverse array of ARGs, including resistance to macrolides (11.55 %), aminoglycosides (8.22 %), glycopeptides (6.22 %), tetracyclines (4 %), sulfonamides (4 %), carbapenems (1.11 %), phenicols (0.88 %), fluoroquinolones (0.44 %), and lincosamides (0.22 %). The most frequently observed ARGs were associated with multidrug resistance (63.33 %), with MexF (42 genes), MexW (36 genes), smeD (31 genes), mtrA (25 genes), and KHM-1 (22 genes) being the most common. Lake Cajititlán is a recreational area for swimming, fishing, and boating, while also supporting irrigation for agriculture and potentially acting as a drinking water source for some communities. This raises concerns about the potential for exposure to antibiotic-resistant bacteria through these activities. The presence of ARGs in Lake Cajititlán poses a significant threat to both human and environmental health. Developing strategies to mitigate the risks of antibiotic resistance, including improving wastewater treatment, and promoting strategic antibiotic use and disposal, is crucial. This study represents a significant advancement in the understanding of antibiotic resistance dynamics in a hypereutrophic subtropical lake in a developing country, providing valuable insights for the scientific community and policymakers.202438583614
535710.9996Occurrence and diversity of antibiotic resistance in untreated hospital wastewater. Antibiotics, antibiotic-resistant bacteria (ARB), antibiotic-resistance genes (ARGs), and mobile genetic elements (MGEs) have been reported in many environments. However, the investigation of their occurrence and diversity in untreated hospital wastewater is still insufficient. High concentrations of antibiotic residues were found in hospital wastewater using solid-phase extraction and UPLC-MS/MS analysis. The concentrations of six of 14 antibiotics reached μg/L levels in the hospital wastewater, which is higher than reported in other aquatic environments. Results of high-throughput sequencing analysis indicated that sequences affiliated to genera Escherichia and Acinetobacter were the predominant in the cultivable multiple-antibiotic-resistant bacteria (CMARB) recovered from the wastewater of three hospitals in China, with compositions of 34%-74%. Notably, several genera containing clinically pathogenic or opportunistic CMARB (e.g., Escherichia, Acinetobacter, Aeromonas, Myroides, Enterococcus, Proteus, Pseudomonas, and Streptococcus) were detected at high relative abundances in the wastewaters of the three hospitals. High-capacity quantitative PCR showed that 131-139 unique ARGs of the 178 targeted genes were detected in the hospital wastewaters. The high prevalence of five MGEs and 12 ARGs was confirmed with qPCR, and some positive correlations between ARGs and MGEs were identified, such as between intI1 and qnrD, intI2 and sul3, intI3 and tetX, Tn916/Tn1545 and sul2, and ISCR1 and sul3. These results suggest that highly abundant antibiotic-resistant pathogens and highly mobile ARGs already exist in the human body, and that their release from hospitals without effective treatment poses high risks to environments and human health.201829054666
535820.9996Abundance of antibiotics, antibiotic resistance genes and bacterial community composition in wastewater effluents from different Romanian hospitals. Antimicrobial resistance represents a growing and significant public health threat, which requires a global response to develop effective strategies and mitigate the emergence and spread of this phenomenon in clinical and environmental settings. We investigated, therefore, the occurrence and abundance of several antibiotics and antibiotic resistance genes (ARGs), as well as bacterial community composition in wastewater effluents from different hospitals located in the Cluj County, Romania. Antibiotic concentrations ranged between 3.67 and 53.05 μg L(-1), and the most abundant antibiotic classes were β-lactams, glycopeptides, and trimethoprim. Among the ARGs detected, 14 genes confer resistance to β-lactams, aminoglycosides, chloramphenicol, macrolide-lincosamide-streptogramin B (MLSB) antibiotics, sulfonamides, and tetracyclines. Genes encoding quaternary ammonium resistance and a transposon-related element were also detected. The sulI and qacEΔ1 genes, which confer resistance to sulfonamides and quaternary ammonium, had the highest relative abundance with values ranging from 5.33 × 10(-2) to 1.94 × 10(-1) and 1.94 × 10(-2) to 4.89 × 10(-2) copies/16 rRNA gene copies, respectively. The dominant phyla detected in the hospital wastewater samples were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Among selected hospitals, one of them applied an activated sludge and chlorine disinfection process before releasing the effluent to the municipal collector. This conventional wastewater treatment showed moderate removal efficiency of the studied pollutants, with a 55-81% decrease in antibiotic concentrations, 1-3 order of magnitude lower relative abundance of ARGs, but with a slight increase of some potentially pathogenic bacteria. Given this, hospital wastewaters (raw or treated) may contribute to the spread of these emerging pollutants in the receiving environments. To the best of our knowledge, this study quantified for the first time the abundance of antibiotics and ARGs in wastewater effluents from different Romanian hospitals.201728347610
534030.9996Hospital wastewaters: A reservoir and source of clinically relevant bacteria and antibiotic resistant genes dissemination in urban river under tropical conditions. The occurrence and dissemination of antibiotic resistant genes (ARGs) that are associated with clinical pathogens and the evaluation of associated risks are still under-investigated in developing countries under tropical conditions. In this context, cultivable and molecular approaches were performed to assess the dissemination of bacteria and the antibiotic resistance genes in aquatic environment in Kinshasa, Democratic Republic of the Congo. Cultivable approach quantified β-lactam, carbapenem resistant, and total Escherichia coli and Enterobacteriaceae in river sediments and surface waters that receive raw hospital effluents. The molecular approach utilized Quantitative Polymerase Chain Reaction (qPCR) to quantify the total bacteria and the richness of relevant bacteria (Escherichia coli, Enterococcus, and Pseudomonas), and antibiotic resistance genes (ARGs: bla(OXA-48), bla(CTX-M), bla(IMP), bla(TEM)) in sediment samples. Statistical analysis were employed to highlight the significance of hospital contribution and seasonal variation of bacteria and ARGs into aquatic ecosystems in suburban municipalities of Kinshasa, Democratic Republic of the Congo. The contribution of hospitals to antibiotic resistance proliferation is higher in the dry season than during the wet season (p < 0.05). Hospital similarly contributed Escherichia coli, Enterococcus, and Pseudomonas and ARGs significantly to the sediments in both seasons (p < 0.05). The organic matter content correlated positively with E. coli (r = 0.50, p < 0.05). The total bacterial load correlated with Enterococcus, and Pseudomonas (0.49 < r < 0.69, p < 0.05). Each ARG correlated with the total bacterial load or at least one relevant bacteria (0.41 < r < 0.81, p < 0.05). Our findings confirm that hospital wastewaters contributed significantly to antibiotic resistance profile and the significance of this contribution increased in the dry season. Moreover, our analysis highlights this risk from untreated hospital wastewaters in developing countries, which presents a great threat to public health.202032470679
320440.9996Spread of airborne antibiotic resistance from animal farms to the environment: Dispersal pattern and exposure risk. Animal farms have been considered as the critical reservoir of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB). Spread of antibiotic resistance from animal farms to the surrounding environments via aerosols has become a growing concern. Here we investigated the dispersal pattern and exposure risk of airborne ARGs (especially in zoonotic pathogens) in the environment of chicken and dairy farms. Aerosol, dust and animal feces samples were collected from the livestock houses and surrounding environments (upwind and downwind areas) for assessing ARG profiles. Antibiotic resistance phenotype and genotype of airborne Staphylococcus spp. was especially analyzed to reveal the exposure risk of airborne ARGs. Results showed that airborne ARGs were detected from upwind (50 m/100 m) and downwind (50 m/100 m/150 m) air environment, wherein at least 30% of bacterial taxa dispersed from the animal houses. Moreover, atmospheric dispersion modeling showed that airborne ARGs can disperse from the animal houses to a distance of 10 km along the wind direction. Clinically important pathogens were identified in airborne culturable bacteria. Genus of Staphylococcus, Sphingomonas and Acinetobacter were potential bacterial host of airborne ARGs. Airborne Staphylococcus spp. were isolated from the environment of chicken farm (n = 148) and dairy farm (n = 87). It is notable that all isolates from chicken-related environment were multidrug-resistance (>3 clinical-relevant antibiotics), with more than 80% of them carrying methicillin resistance gene (mecA) and associated ARGs and MGEs. Presence of numerous ARGs and diverse pathogens in dust from animal houses and the downwind residential areas indicated the accumulation of animal feces origin ARGs in bioaerosols. Employees and local residents in the chick farming environment are exposed to chicken originated ARGs and multidrug resistant Staphylococcus spp. via inhalation. This study highlights the potential exposure risks of airborne ARGs and antibiotic resistant pathogens to human health.202234673316
534850.9996Characterization of microbial community and antibiotic resistome in intra urban water, Wenzhou China. The present study investigated the water quality index, microbial composition and antimicrobial resistance genes in urban water habitats. Combined chemicals testing, metagenomic analyses and qualitative PCR (qPCR) were conducted on 20 locations, including rivers from hospital surrounds (n = 7), community surrounds (n = 7), and natural wetlands (n = 6). Results showed that the indexes of total nitrogen, phosphorus, and ammonia nitrogen of hospital waters were 2-3 folds high than that of water from wetlands. Bioinformatics analysis revealed a total of 1,594 bacterial species from 479 genera from the three groups of water samples. The hospital-related samples had the greatest number of unique genera, followed by those from wetlands and communities. The hospital-related samples contained a large number of bacteria associated with the gut microbiome, including Alistipes, Prevotella, Klebsiella, Escherichia, Bacteroides, and Faecalibacterium, which were all significantly enriched compared to samples from the wetlands. Nevertheless, the wetland waters enriched bacteria from Nanopelagicus, Mycolicibacterium and Gemmatimonas, which are typically associated with aquatic environments. The presence of antimicrobial resistance genes (ARGs) that were associated with different species origins in each water sample was observed. The majority of ARGs from hospital-related samples were carried by bacteria from Acinetobacter, Aeromonas and various genera from Enterobacteriaceae, which each was associated with multiple ARGs. In contrast, the ARGs that were exclusively in samples from communities and wetlands were carried by species that encoded only 1 to 2 ARGs each and were not normally associated with human infections. The qPCR showed that water samples of hospital surrounds had higher concentrations of intI1 and antimicrobial resistance genes such as tetA, ermA, ermB, qnrB, sul1, sul2 and other beta-lactam genes. Further genes of functional metabolism reported that the enrichment of genes associated with the degradation/utilization of nitrate and organic phosphodiester were detected in water samples around hospitals and communities compared to those from wetlands. Finally, correlations between the water quality indicators and the number of ARGs were evaluated. The presence of total nitrogen, phosphorus, and ammonia nitrogen were significantly correlated with the presence of ermA and sul1. Furthermore, intI1 exhibited a significant correlation with ermB, sul1, and bla(SHV), indicating a prevalence of ARGs in urban water environments might be due to the integron intI1's diffusion-promoting effect. However, the high abundance of ARGs was limited to the waters around the hospital, and we did not observe the geographical transfer of ARGs along with the river flow. This may be related to water purifying capacity of natural riverine wetlands. Taken together, continued surveillance is required to assess the risk of bacterial horizontal transmission and its potential impact on public health in the current region.202337396356
530160.9996High levels of antibiotic resistance genes and opportunistic pathogenic bacteria indicators in urban wild bird feces. This study analyzed fresh feces from three common bird species that live in urban environments and interact with human communities. Antibiotic resistance genes (ARGs) encoding resistance to three major classes of antibiotics (i.e., tetracyclines, β-lactams, and sulfonamides) and the mobile genetic element integrase gene (intI1) were abundant (up to 10(9), 10(8), 10(9), and 10(10) copies/g dry feces for tetW, bla(TEM), sul1, and intI1, respectively), with relative concentrations surprisingly comparable to that in poultry and livestock that are occasionally fed antibiotics. Biomarkers for opportunistic pathogens were also abundant (up to 10(7) copies/g dry feces) and the dominant isolates (i.e., Enterococcus spp. and Pseudomonas aeruginosa) harbored both ARGs and virulence genes. ARGs in bird feces followed first-order attenuation with half-lives ranging from 1.3 to 11.1 days in impacted soil. Although residual antibiotics were detected in the feces, no significant correlation was observed between fecal antibiotic concentrations and ARG relative abundance. Thus, other unaccounted factors likely contributed selective pressure for ARG maintenance. These findings highlight the contribution of wild urban bird feces to the maintenance and dissemination of ARGs, and the associated health risks.202032663725
534270.9996Prevalence of antibiotic resistance genes in drinking and environmental water sources of the Kathmandu Valley, Nepal. Antibiotic-resistant bacteria-associated infections are responsible for more than 1.2 million annual deaths worldwide. In low- and middle-income countries (LMICs), the consumption of antibiotics for human and veterinary uses is not regulated effectively. Overused and misused antibiotics can end up in aquatic environments, which may act as a conduit for antibiotic resistance dissemination. However, data on the prevalence of antibiotic resistance determinants in aquatic environments are still limited for LMICs. In this study, we evaluated the prevalence and concentration of antibiotic resistance genes (ARGs) in different drinking and environmental water sources collected from the Kathmandu Valley, Nepal, using droplet digital polymerase chain reaction to understand the current situation of ARG contamination. River water and shallow dug well water sources were the most contaminated with ARGs. Almost all samples contained sul1 (94%), and intI1 and tet(A) were detected in 83 and 60% of the samples, respectively. Maximum ARG concentration varied between 4.2 log(10) copies/100 ml for mecA and 9.3 log(10) copies/100 ml for sul1. Significant positive correlations were found between ARGs (r > 0.5, p < 0.01), except for mecA, qnrS, and vanA. As sul1 and intI1 were detected in almost all samples, the presence of these genes in a given sample may need to be considered as background antibiotic resistance in LMICs. Therefore, monitoring of ARGs, such as β-lactam ARGs, quinolone resistance genes, and vancomycin resistance genes, may provide a better picture of the antibiotic resistance determinants in aquatic environments of LMICs.202236071971
320680.9996High pollution and health risk of antibiotic resistance genes in rural domestic sewage in southeastern China: A study combining national-scale distribution and machine learning. Rural domestic sewage has emerged as an important reservoir of antibiotic resistance genes (ARGs) under rapid urbanization, while the national-scale geographical patterns and risks of ARGs remaining unclear. We investigated ARG pollution in rural domestic sewage across 39 sites in 22 Chinese provinces using metagenomic sequencing, identifying 702 ARG subtypes across 21 types. Multidrug resistance genes were predominant in the shared ARGs, accounting for 58.96 % of the total ARG abundance. Host bacteria analysis revealed Klebsiella pneumoniae and Escherichia coli were the main pathogenic-resistant bacteria. Southeastern China exhibited the highest level of ARG pollution in rural domestic sewage, followed by south-central, northern, and western. This ARG pollution was primarily caused by human/animal feces based on ARG indicators. Partial least-squares path model and partial redundancy analysis highlighted antibiotics as the primary driver, explaining 24.16 % of ARG variation, with sulfamethazine, norfloxacin, and ofloxacin identified as priority control targets. Risk assessment by calculating the risk index indicated 24.58 % of detected ARGs posed potential health threats, particularly multidrug resistance. Machine learning models predicted higher ARG risks in rural domestic sewage from southeastern China with intensive human activity. This study underscores the crucial impact of antibiotics in ARG proliferation and risk in rural domestic sewage.202540701495
534190.9996Occurrence of Bacterial Markers and Antibiotic Resistance Genes in Sub-Saharan Rivers Receiving Animal Farm Wastewaters. Antibiotic resistant bacteria and genes which confer resistance to antibiotics from human/animal sources are currently considered a serious environmental and a public health concern. This problem is still little investigated in aquatic environment of developing countries according to the different climatic conditions. In this research, the total bacterial load, the abundance of relevant bacteria (Escherichia coli (E. coli), Enterococcus (Ent), and Pseudomonas), and antibiotic resistance genes (ARGs: bla(OXA-48), bla(CTX-M), sul1, sul2, sul3, and tet(B)) were quantified using Quantitative Polymerase Chain Reaction (qPCR) in sediments from two rivers receiving animal farming wastewaters under tropical conditions in Kinshasa, capital city of the Democratic Republic of the Congo. Human and pig host-specific markers were exploited to examine the sources of contamination. The total bacterial load correlated with relevant bacteria and genes bla(OXA-48), sul3, and tet(B) (P value < 0.01). E. coli strongly correlated with 16s rDNA, Enterococcus, Pseudomonas spp., bla(OXA-48), sul3, and tet(B) (P value < 0.01) and with bla(CTX-M), sul1, and sul2 at a lower magnitude (P value < 0.05). The most abundant and most commonly detected ARGs were sul1, and sul2. Our findings confirmed at least two sources of contamination originating from pigs and anthropogenic activities and that animal farm wastewaters didn't exclusively contribute to antibiotic resistance profile. Moreover, our analysis sheds the light on developing countries where less than adequate infrastructure or lack of it adds to the complexity of antibiotic resistance proliferation with potential risks to the human exposure and aquatic living organisms. This research presents useful tools for the evaluation of emerging microbial contaminants in aquatic ecosystems which can be applied in the similar environment.201931619758
3283100.9996Prevalence of diverse antimicrobial resistance genes and bacteria in sewage treatment plant-derived sludge environment. Antimicrobial resistance (AMR) contamination in the environment is one of the most significant worldwide threats of the 21(st) century. Since sludge is heavily exposed to diverse contaminants, including pharmaceuticals, the inhabitant bacterial population is expected to exhibit resistance to antimicrobial agents. In this study, sewage treatment plant (STP) sludge samples were analyzed to assess the antibiotic-resistant bacterial population, abundance of AMR genes (ermF, qnrS, Sul1, blaGES, blaCTX-M, and blaNDM), and mobile genetic elements (intl1 and IS26). Out of 16, six bacterial isolates exhibited resistance to 13 antibiotics with a high multiple antibiotic resistance index (MARI) (0.93) and high metal tolerance. Quantitative polymerase chain reaction showed the abundance of target genes ranging from 6.6 × 10(3) to 6.5 × 10(8) copies g(-1) sludge. The overall outcome reveals that STP sludge comprised varied multidrug-resistant bacterial populations. It will give insights into the functions of heavy metals and biofilm development in the selection and spread of AMR genes and the associated bacteria. Therefore, the application of sludge needs proper screening for AMR and metal contamination prior to its countless applications. This study will contribute immensely to the risk analysis of STP effluents on environmental health, including control of AMR transmission.202438463555
3493110.9996Studies on the airborne bacterial communities and antimicrobial resistance genes in duck houses based on metagenome and PCR analysis. The threat of antimicrobial resistance (AMR) is on the rise globally, especially with the development of animal husbandry and the increased demand for antibiotics. Livestock and poultry farms, as key sites for prevalence of antibiotic-resistant bacteria (ARB), can spread antimicrobial resistance genes (ARGs) through microbial aerosols and affect public health. In this study, total suspended particulate matter (TSP) and airborne culturable microorganisms were collected from duck houses in Tai'an, Shandong Province, and the bacterial communities and airborne ARGs were analyzed using metagenomics and PCR methods. The results showed that the bacterial communities in the air of duck houses were mainly Actinobacteria, Firmicutes, Proteobactria, Chlamydia, and Bcateroidetes at the phylum level. At the genus level, the air was dominated by Corynebacterium, Jeotgalicoccus, Staphylococcus, Brevibacterium, and Megacoccus, and contained some pathogenic bacteria such as Staphylococcus aureus, Corynebacterium diphtheriae, Klebsiella oxytoca, Acinetobacter baumannii, and Pseudomonas aeruginosa, which were also potential hosts for ARGs. The airborne ARGs were mainly macrolides (10.97%), penicillins (10.73%), cephalosporins (8.91%), streptozotocin (8.91%), and aminoglycosides (8.02%). PCR detected 27 ARGs in airborne culturable microorganisms, and comparative analysis between PCR and the metagenomic data revealed that a total of 9 ARGs were found to the same, including macrolides ErmA, ErmF, tetracyclines tetG, tetX, methicarbamazepines dfrA12, dfrA15, aminoglycosides APH3-VI, ANT2-Ⅰ, and sulfonamides sul2. Moreover, inhalation exposure modeling showed that the workers in duck houses inhaled higher concentrations of ARB, human pathogenic bacteria (HPB) and human pathogenic antibiotic-resistant bacteria (HPARB) than hospital workers. These results provide new insights into airborne microorganisms and ARGs in animal farms and lay the foundation for further study.202438157791
3491120.9996Assessment of seasonal variations in antibiotic resistance genes and microbial communities in sewage treatment plants for public health monitoring. The spread of antimicrobial resistance (AMR) around the globe, especially in the urban cities with high population, is a major concern. Therefore, the current study aims at identifying antibiotic resistant bacteria, microbial community compositions and the quantification of antimicrobial resistant genes from six sewage treatment plants (STPs) across Pune city in Maharashtra, India. A total of 106 isolates obtained were tested against six antibiotics in which the highest resistance was observed against trimethoprim (24.53 %). The qPCR assays of seven antibiotic resistance genes revealed abundance of bla(imp-1) and mecA genes in the summer and monsoon seasons followed by bla(NDM-1) gene in the summer and winter seasons. The alpha diversity indices depicted highest microbial diversity of inlet samples during winter, followed by inlet samples during the summer and monsoon seasons. Comparative analysis revealed Bifidobacterium (51 %), Pseudomonas (28.7 %) and Zoogloea (17.6 %) as the most abundant genera in the inlet samples during the summer, monsoon and winter seasons respectively while Acinetobacter (31 %) and Flavobacterium (23 % in winter and 18.2 % in summer) dominated the outlet samples. The co-network analysis revealed positive and negative interactions in the winter and monsoon but only positive interactions in the summer season. Venn diagrams showed higher abundance of ASVs in the outlet samples than the inlet. The top genera correlated exactly opposite with the pH compared to BOD and COD. PICRUSt2-based functional prediction revealed a higher abundance of methicillin resistance, β-lactamase resistance and multidrug resistance genes in inlet samples while chloramphenicol resistance was found higher in outlet samples. Further, we observed that potential pathogens causing infectious disease such as pertussis, shigellosis and tuberculosis were present in all three seasons.202540320120
3208130.9996Effects 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
5343140.9996Discovery of sulfonamide resistance genes in deep groundwater below Patna, India. Global usage of pharmaceuticals has led to the proliferation of bacteria that are resistant to antimicrobial treatments, creating a substantial public health challenge. Here, we investigate the emergence of sulfonamide resistance genes in groundwater and surface water in Patna, a rapidly developing city in Bihar, India. We report the first quantification of three sulfonamide resistance genes (sulI, sulII and sulIII) in groundwater (12-107 m in depth) in India. The mean relative abundance of gene copies was found to be sulI (2.4 × 10(-2) copies/16S rRNA gene) > sulII (5.4 × 10(-3) copies/16S rRNA gene) > sulIII (2.4 × 10(-3) copies/16S rRNA gene) in groundwater (n = 15) and surface water (n = 3). A comparison between antimicrobial resistance (AMR) genes and wastewater indicators, particularly tryptophan:fulvic-like fluorescence, suggests that wastewater was associated with AMR gene prevalence. Urban drainage channels, containing hospital and domestic wastes, are likely a substantial source of antimicrobial resistance in groundwater and surface water, including the Ganges (Ganga) River. This study is a reference point for decision-makers in the fight against antimicrobial resistance because it quantifies and determines potential sources of AMR genes in Indian groundwater.202438797351
3192150.9996Metagenome-Wide Analysis of Rural and Urban Surface Waters and Sediments in Bangladesh Identifies Human Waste as a Driver of Antibiotic Resistance. In many low- and middle-income countries, antibiotic-resistant bacteria spread in the environment due to inadequate treatment of wastewater and the poorly regulated use of antibiotics in agri- and aquaculture. Here, we characterized the abundance and diversity of antibiotic-resistant bacteria and antibiotic resistance genes in surface waters and sediments in Bangladesh through quantitative culture of extended-spectrum beta-lactamase (ESBL)-producing coliforms and shotgun metagenomics. Samples were collected from highly urbanized settings (n = 7), rural ponds with a history of aquaculture-related antibiotic use (n = 11), and rural ponds with no history of antibiotic use (n = 6). ESBL-producing coliforms were found to be more prevalent in urban samples than in rural samples. Shotgun sequencing showed that sediment samples were dominated by the phylum Proteobacteria (on average, 73.8% of assigned reads), while in the water samples, Cyanobacteria were the predominant phylum (on average, 60.9% of assigned reads). Antibiotic resistance genes were detected in all samples, but their abundance varied 1,525-fold between sites, with the highest levels of antibiotic resistance genes being present in urban surface water samples. The abundance of antibiotic resistance genes was significantly correlated (R(2) = 0.73; P = 8.9 × 10(-15)) with the abundance of bacteria originating from the human gut, which suggests that the release of untreated sewage is a driver for the spread of environmental antibiotic resistance genes in Bangladesh, particularly in highly urbanized settings. IMPORTANCE Low- and middle-income countries (LMICs) have higher burdens of multidrug-resistant infections than high-income countries, and there is thus an urgent need to elucidate the drivers of the spread of antibiotic-resistant bacteria in LMICs. Here, we study the diversity and abundance of antibiotic resistance genes in surface water and sediments from rural and urban settings in Bangladesh. We found that urban surface waters are particularly rich in antibiotic resistance genes, with a higher number of them associated with plasmids, indicating that they are more likely to spread horizontally. The abundance of antibiotic resistance genes was strongly correlated with the abundance of bacteria that originate from the human gut, suggesting that uncontrolled release of human waste is a major driver for the spread of antibiotic resistance in the urban environment. Improvements in sanitation in LMICs may thus be a key intervention to reduce the dissemination of antibiotic-resistant bacteria.202134254820
5338160.9996Characterisation of microbial communities and quantification of antibiotic resistance genes in Italian wastewater treatment plants using 16S rRNA sequencing and digital PCR. The spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in humans, animals and environment is a growing threat to public health. Wastewater treatment plants (WWTPs) are crucial in mitigating the risk of environmental contamination by effectively removing contaminants before discharge. However, the persistence of ARB and ARGs even after treatment is a challenge for the management of water system. To comprehensively assess antimicrobial resistance dynamics, we conducted a one-year monitoring study in three WWTPs in central Italy, both influents and effluents. We used seasonal sampling to analyze microbial communities by 16S rRNA, as well as to determine the prevalence and behaviour of major ARGs (sul1, tetA, bla(TEM), bla(OXA-48), bla(CTX-M-1 group), bla(KPC)) and the class 1 Integron (int1). Predominant genera included in order: Arcobacter, Acinetobacter, Flavobacterium, Pseudarcobacter, Bacteroides, Aeromonas, Trichococcus, Cloacibacterium, Pseudomonas and Streptococcus. A higher diversity of bacterial communities was observed in the effluents compared to the influents. Within these communities, we also identified bacteria that may be associated with antibiotic resistance and pose a significant threat to human health. The mean concentrations (in gene copies per liter, gc/L) of ARGs and int1 in untreated wastewater (absolute abundance) were as follows: sul1 (4.1 × 10(9)), tetA (5.2 × 10(8)), bla(TEM) (1.1 × 10(8)), bla(OXA-48) (2.1 × 10(7)), bla(CTX-M-1 group) (1.1 × 10(7)), bla(KPC) (9.4 × 10(5)), and int1 (5.5 × 10(9)). The mean values in treated effluents showed reductions ranging from one to three log. However, after normalizing to the 16S rRNA gene (relative abundance), it was observed that in 37.5 % (42/112) of measurements, the relative abundance of ARGs increased in effluents compared to influents. Furthermore, correlations were identified between ARGs and bacterial genera including priority pathogens. This study improves our understanding of the dynamics of ARGs and provides insights to develop more effective strategies to reduce their spread, protecting public health and preserving the future efficacy of antibiotics.202438750766
3109170.9996Metagenomic characterization of bacterial community and antibiotic resistance genes in representative ready-to-eat food in southern China. Ready-to-eat (RTE) foods have been considered to be reservoirs of antibiotic resistance bacteria, which constitute direct threat to human health, but the potential microbiological risks of RTE foods remain largely unexplored. In this study, the metagenomic approach was employed to characterize the comprehensive profiles of bacterial community and antibiotic resistance gene (ARG) in 18 RTE food samples (8 RTE meat, 7 RTE vegetables and 3 RTE fruit) in southern China. In total, the most abundant phyla in RTE foods were Proteobacteria, Firmicutes, Cyanobacteria, Bacteroidetes and Actinobacteria. 204 ARG subtypes belonging to 18 ARG types were detected with an abundance range between 2.81 × 10(-5) and 7.7 × 10(-1) copy of ARG per copy of 16S rRNA gene. Multidrug-resistant genes were the most predominant ARG type in the RTE foods. Chloramphenicol, macrolide-lincosamide-streptogramin, multidrug resistance, aminoglycoside, bacitracin, tetracycline and β-lactam resistance genes were dominant, which were also associated with antibiotics used extensively in human medicine or veterinary medicine/promoters. Variation partitioning analysis indicated that the join effect of bacterial community and mobile genetic elements (MGEs) played an important role in the resistome alteration. This study further deepens the comprehensive understanding of antibiotic resistome and the correlations among the antibiotic resistome, microbiota, and MGEs in the RTE foods.202033093543
3213180.9996Investigating antibiotics, antibiotic resistance genes, and microbial contaminants in groundwater in relation to the proximity of urban areas. Groundwater is an essential public and drinking water supply and its protection is a goal for global policies. Here, we investigated the presence and prevalence of antibiotic residues, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and microbial contamination in groundwater environments at various distances from urban areas. Antibiotic concentrations ranged from below detection limit to 917 ng/L, being trimethoprim, macrolide, and sulfonamide the most abundant antibiotic classes. A total of eleven ARGs (aminoglycoside, β-lactam, chloramphenicol, Macrolide-Lincosamide-Streptogramin B - MLSB, sulfonamide, and tetracycline), one antiseptic resistance gene, and two MGEs were detected by qPCR with relative abundances ranging from 6.61 × 10(-7) to 2.30 × 10(-1) copies/16S rRNA gene copies. ARGs and MGEs were widespread in the investigated groundwater environments, with increased abundances not only in urban, but also in remote areas. Distinct bacterial community profiles were observed, with a higher prevalence of Betaproteobacteria and Bacteroidetes in the less-impacted areas, and that of Firmicutes in the contaminated groundwater. The combined characteristics of increased species diversity, distinct phylogenetic composition, and the possible presence of fecal and/or pathogenic bacteria could indicate different types of contamination. Significant correlations between ARGs, MGEs and specific taxa within the groundwater bacterial community were identified, revealing the potential hosts of resistance types. Although no universal marker gene could be determined, a co-selection of int1, qacEΔ1 and sulI genes, a proxy group for anthropogenic pollution, with the tetC, tetO, tetW resistance genes was identified. As the tet group was observed to follow the pattern of environmental contamination for the groundwater samples investigated in this study, our results strongly support the proposal of this group of genes as an environmental tracer of human impact. Overall, the present study investigated several emerging contaminants in groundwater habitats that may be included in monitoring programs to enable further regulatory and protection measures.201829454283
3490190.9996Monitoring and evaluation of antibiotic resistance genes in three rivers in northeast China. Antibiotic resistance genes (ARGs) have become an important public health problem. In this study, we used metagenomic sequencing to analyze the composition of ARGs in selected original habitats of northeast China, comprising three different rivers and riverbank soils of the Heilongjiang River, Tumen River, and Yalu River. Twenty types of ARG were detected in the water samples. The major ARGs were multidrug resistance genes, at approximately 0.5 copies/16S rRNA, accounting for 57.5% of the total ARG abundance. The abundance of multidrug, bacitracin, beta-lactam, macrolide-lincosamide-streptogramin, sulfonamide, fosmidomycin, and polymyxin resistance genes covered 96.9% of the total ARG abundance. No significant ecological boundary of ARG diversity was observed. The compositions of the resistance genes in the three rivers were very similar to each other, and 92.1% of ARG subtypes were shared by all water samples. Except for vancomycin resistance genes, almost all ARGs in riverbank soils were detected in the river water. About 31.05% ARGs were carried by Pseudomonas. Opportunistic pathogenic bacteria carrying resistance genes were mainly related to diarrhea and respiratory infections. Multidrug and beta-lactam resistance genes correlated positively with mobile genetic elements (MGEs), indicating a potential risk of diffusion. The composition of ARGs in three different rivers was similar, indicating that climate plays an important role in ARG occurrence. ARG subtypes in river water were almost completely the same as those in riverbank soil. ARGs had no significant geographical distribution characteristics. Many ARGs were carried by human pathogenic bacteria related to diarrhea and respiratory infections, such as Pseudomonas aeruginosa and Aeromonas caviae. In general, our results provide a valuable dataset of river water ARG distribution in northeast China. The related ecological and geographical distribution characteristics should be further explored.202235122641