The transferable resistome of biosolids-plasmid sequencing reveals carriage of clinically relevant antibiotic resistance genes. - Related Documents




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332901.0000The transferable resistome of biosolids-plasmid sequencing reveals carriage of clinically relevant antibiotic resistance genes. Biosolids, widely used as organic fertilizers due to their high nutrient content, are significant reservoirs for antimicrobial-resistant bacteria (ARB) carrying transferable antimicrobial resistance genes (ARGs). This study investigated the transferability of ARG-containing plasmids of bacteria from biosolids originating from 12 German wastewater treatment plants (WWTPs) of varying sizes. Using exogenous plasmid captures with the recipient strain Escherichia coli CV601 gfp+, we collected 103 plasmids from 11 WWTPs. Characterization through DNA-based methods, including real-time PCR and Southern blot hybridization, revealed that the highest proportion of transconjugants harbored IncP (57%) and IncN (20%) plasmids. Complete sequencing of representative plasmids identified IncPβ, IncPε, IncQ2, IncN, and IncU plasmids carrying ARGs linked to mobile genetic elements (MGEs), including class 1 integrons, transposons, and IS elements (e.g., Tn402, IS26, and IS6100). These ARG-MGE complexes were integrated into specific plasmid regions, and similar plasmids were found across WWTPs and diverse geographic locations. The results underscore the role of WWTPs as hotspots for horizontal gene transfer, with biosolids serving as reservoirs for multi-resistant bacteria and resistance plasmids. This highlights the urgent need for improved biosolid management strategies to mitigate the release of ARGs and ARB into agricultural environments. IMPORTANCE: This study emphasizes the critical role of wastewater treatment plants (WWTPs) in facilitating the horizontal transfer of ARGs through biosolids. As biosolids are routinely applied to agricultural soils, their load of clinically relevant ARG content and transferability pose risks to animal and human health through plant-associated bacteria or surface water. By identifying conserved ARG-MGE associations across diverse plasmid types and WWTPs, this work highlights the global and persistent nature of resistance dissemination. These findings underscore the urgent need for sustainable management practices to limit the spread of antimicrobial-resistant bacteria (ARB) and associated ARGs in agricultural ecosystems. Ensuring safe biosolid use will contribute to combating antimicrobial resistance gene connectivity from environmental to human- or animal-associated bacteria globally.202541104936
344510.9998Horizontal plasmid transfer promotes antibiotic resistance in selected bacteria in Chinese frog farms. The emergence and dissemination of antibiotic resistance genes (ARGs) in the ecosystem are global public health concerns. One Health emphasizes the interconnectivity between different habitats and seeks to optimize animal, human, and environmental health. However, information on the dissemination of antibiotic resistance genes (ARGs) within complex microbiomes in natural habitats is scarce. We investigated the prevalence of antibiotic resistant bacteria (ARB) and the spread of ARGs in intensive bullfrog (Rana catesbeiana) farms in the Shantou area of China. Antibiotic susceptibilities of 361 strains, combined with microbiome analyses, revealed Escherichia coli, Edwardsiella tarda, Citrobacter and Klebsiella sp. as prevalent multidrug resistant bacteria on these farms. Whole genome sequencing of 95 ARB identified 250 large plasmids that harbored a wide range of ARGs. Plasmid sequences and sediment metagenomes revealed an abundance of tetA, sul1, and aph(3″)-Ib ARGs. Notably, antibiotic resistance (against 15 antibiotics) highly correlated with plasmid-borne rather than chromosome-borne ARGs. Based on sequence similarities, most plasmids (62%) fell into 32 distinct groups, indicating a potential for horizontal plasmid transfer (HPT) within the frog farm microbiome. HPT was confirmed in inter- and intra-species conjugation experiments. Furthermore, identical mobile ARGs, flanked by mobile genetic elements (MGEs), were found in different locations on the same plasmid, or on different plasmids residing in the same or different hosts. Our results suggest a synergy between MGEs and HPT to facilitate ARGs dissemination in frog farms. Mining public databases retrieved similar plasmids from different bacterial species found in other environmental niches globally. Our findings underscore the importance of HPT in mediating the spread of ARGs in frog farms and other microbiomes of the ecosystem.202439089095
729220.9998Class 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
326830.9997Resistomic 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
326340.9997Short- and long-read metagenomics insight into the genetic contexts and hosts of mobile antibiotic resistome in Chinese swine farms. Antibiotic resistance genes (ARGs) are emerging environmental contaminants posing a threat to public health. Intensive swine farms are recognized as hotspots for antibiotic resistance genes (ARGs). However, antibiotic resistome and their genetic contexts, hosts, and transferability in Chinese swine farms remain largely unexplored. Here, we used Illumina and Oxford Nanopore metagenomics sequencing to investigate the antibiotic resistome context of 14 distantly located large-scale (10,000 animals per year) commercial swine farms in China. We identified high abundant and diverse ARGs (609,966.8 with 1433 types, belonging to 38 different antibiotic classes) in all samples, including those encoding resistance to clinically critical important antibiotics (such as mcr, tetX, optrA, poxtA, qnr and bla(CTX-M)). About 75% of the ARGs detected were carried by mobile genetic elements (mainly plasmids), suggesting their high transmission potential into receiving environments. Host-tracking analysis identified Clostridiales, Faecalibacterium prausnitzii and Escherichia coli as the predominant bacterial hosts of mobile ARGs. Notably, genome binning generated 246 high-completeness draft genomes. Genetic context analysis of the multiple resistant (MDR) genes in binned genomes showed the involvement of insertion sequences (ISs), integron and SGI2 genomic island, implying their importance role in promoting the development of MDR bacteria. Overall, these findings substantially expand our current knowledge of mobile antibiotic resistome in Chinese swine farms, and suggest reasonable management of animal wastes in swine farms to reduce the dissemination of antibiotic resistance to the environment.202235259381
320750.9997Dissemination 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
333160.9997Impact of Wastewater Treatment on the Prevalence of Integrons and the Genetic Diversity of Integron Gene Cassettes. The integron platform allows the acquisition, expression, and dissemination of antibiotic resistance genes within gene cassettes. Wastewater treatment plants (WWTPs) contain abundant resistance genes; however, knowledge about the impacts of wastewater treatment on integrons and their gene cassettes is limited. In this study, by using clone library analysis and high-throughput sequencing, we investigated the abundance of class 1, 2, and 3 integrons and their corresponding gene cassettes in three urban WWTPs. Our results showed that class 1 integrons were most abundant in WWTPs and that wastewater treatment significantly reduced the abundance of all integrons. The WWTP influents harbored the highest diversity of class 1 integron gene cassettes, whereas class 3 integron gene cassettes exhibited highest diversity in activated sludge. Most of the gene cassette arrays detected in class 1 integrons were novel. Aminoglycoside, beta-lactam, and trimethoprim resistance genes were highly prevalent in class 1 integron gene cassettes, while class 3 integrons mainly carried beta-lactam resistance gene cassettes. A core class 1 integron resistance gene cassette pool persisted during wastewater treatment, implying that these resistance genes could have high potential to spread into environments through WWTPs. These data provide new insights into the impact of wastewater treatment on integron pools and highlight the need for surveillance of resistance genes within both class 1 and 3 integrons.IMPORTANCE Wastewater treatment plants represent a significant sink and transport medium for antibiotic resistance bacteria and genes spreading into environments. Integrons are important genetic elements involved in the evolution of antibiotic resistance. To better understand the impact of wastewater treatment on integrons and their gene cassette contexts, we conducted clone library construction and high-throughput sequencing to analyze gene cassette contexts for class 1 and class 3 integrons during the wastewater treatment process. This study comprehensively profiled the distribution of integrons and their gene cassettes (especially class 3 integrons) in influents, activated sludge, and effluents of conventional municipal wastewater treatment plants. We further demonstrated that while wastewater treatment significantly reduced the abundance of integrons and the diversity of associated gene cassettes, a large fraction of integrons persisted in wastewater effluents and were consequentially discharged into downstream natural environments.201829475864
318570.9997Differences 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
346680.9997Behavior of last resort antibiotic resistance genes (mcr-1 and bla(NDM-1)) in a drinking water supply system and their possible acquisition by the mouse gut flora. Mcr-1 and bla(NDM-1) antibiotic resistance genes (ARGs) confer resistance to colistins and carbapenems, which are often antibiotics used as a last resort in tertiary care hospitals. Dissemination of these two ARGs in drinking water supply systems and their effect on healthy gut bacteria are poorly studied. In this study, the dissemination of mcr-1 and bla(NDM-1) in a drinking water supply system, and their effect on the antibiotic resistance of mouse gut bacteria are explored. Metagenome analysis revealed that source water (Taipu river and Jinze reservoir) was polluted with ARGs. Mcr-1 and bla(NDM-1) can be disseminated through the water distribution system. Even advanced water treatments (ozone and biological activated carbon (BAC)) could not effectively remove mcr-1 and bla(NDM-1). Low concentrations of chloramine disinfectants in the water distribution system were not effective at limiting ARG abundance. Mobile genetic elements were also found to play a major role in the dissemination of ARGs via horizontal gene transfer (HGT) throughout the water supply system. Statistical analysis revealed that there was no effect of temperature on the abundance of mcr-1 and bla(NDM-1) throughout the water supply system. A last resort ARG, mcr-1 can disseminate from drinking water to the healthy mouse gut. The presence of mcr-1 in a strain belonging to Enterococcus hirae, which is different from the strain belonging to the Bacillus cereus group isolated from drinking water, strongly supports the phenomena of HGT inside the gut. This research provides novel insights into the role of drinking water in disseminating ARGs to the gut and strongly suggests that drinking water may also play a major role apart from other factors known to be involved in the prevalence of last resort ARGs in the gut.202031896482
344690.9997Prevalence and transmission risk of colistin and multidrug resistance in long-distance coastal aquaculture. Due to the wide use of antibiotics, intensive aquaculture farms have been recognized as a significant reservoir of antibiotic resistomes. Although the prevalence of colistin resistance genes and multidrug-resistant bacteria (MDRB) has been documented, empirical evidence for the transmission of colistin and multidrug resistance between bacterial communities in aquaculture farms through horizontal gene transfer (HGT) is lacking. Here, we report the prevalence and transmission risk of colistin and multidrug resistance in 27 aquaculture water samples from 9 aquaculture zones from over 5000 km of subtropical coastlines in southern China. The colistin resistance gene mcr-1, mobile genetic element (MGE) intl1 and 13 typical antibiotic resistance genes (ARGs) were prevalent in all the aquaculture water samples. Most types of antibiotic (especially colistin) resistance are transmissible in bacterial communities based on evidence from laboratory conjugation and transformation experiments. Diverse MDRB were detected in most of the aquaculture water samples, and a strain with high-level colistin resistance, named Ralstonia pickettii MCR, was isolated. The risk of horizontal transfer of the colistin resistance of R. pickettii MCR through conjugation and transformation was low, but the colistin resistance could be steadily transmitted to offspring through vertical transfer. The findings have important implications for the future regulation of antibiotic use in aquaculture farms globally to address the growing threat posed by antibiotic resistance to human health.202337935916
3330100.9997Antibiotic-manufacturing sites are hot-spots for the release and spread of antibiotic resistance genes and mobile genetic elements in receiving aquatic environments. High antibiotic releases from manufacturing facilities have been identified as a risk factor for antibiotic resistance development in bacterial pathogens. However, the role of antibiotic pollution in selection and transferability of antibiotic resistance genes (ARGs) is still limited. In this study, we analyzed effluents from azithromycin-synthesis and veterinary-drug formulation facilities as well as sediments from receiving river and creek taken at the effluent discharge sites, upstream and downstream of discharge. Culturing showed that the effluent discharge significantly increased the proportion of antibiotic resistant bacteria in exposed sediments compared to the upstream ones. Quantitative real-time PCR revealed that effluents from both industries contained high and similar relative abundances of resistance genes [sul1, sul2, qacE/qacEΔ1, tet(A)], class 1 integrons (intI1) and IncP-1 plasmids (korB). Consequently, these genes significantly increased in relative abundances in receiving sediments, with more pronounced effects being observed for river than for creek sediments due to lower background levels of the investigated genes in the river. In addition, effluent discharge considerably increased transfer frequencies of captured ARGs from exposed sediments into Escherichia coli CV601 recipient as shown by biparental mating experiments. Most plasmids exogenously captured from effluent and polluted sediments belonged to the broad host range IncP-1ε plasmid group, conferred multiple antibiotic resistance and harbored class 1 integrons. Discharge of pharmaceutical waste from antibiotic manufacturing sites thus poses a risk for development and dissemination of multi-resistant bacteria, including pathogens.201931260930
3177110.9997Metagenomic investigation of antibiotic resistance genes and resistant bacteria contamination in pharmaceutical plant sites in China. Pharmaceutical plant sites play a significant role in the dissemination of antibiotic resistance genes (ARGs) into the environment. It is imperative to comprehensively monitor of ARGs across various environmental media at these sites. This study focused on three pharmaceutical plants, two located in North China and one in South China. Through metagenomic approaches, we examined the composition, mobility potential, and bacterial hosts of ARGs in diverse media such as process water, groundwater, topsoil, soil cores, and pharmaceutical fermentation residues across diverse environmental matrices, including topsoil, soil cores, process water, groundwater, and pharmaceutical fermentation residues. We identified a wide array of ARGs, comprising 21 types and 740 subtypes, with process water exhibiting the highest abundance and diversity. Treatment processes varied in their efficacy in eliminating ARGs, and the clinically relevant ARGs should also be considered when evaluating wastewater treatment plant efficiency. Geographical distinctions in groundwater ARG distribution between northern and southern regions were observed. Soil samples from the three sites showed minimal impact from pharmaceutical activity, with vancomycin-resistance genes being the most prevalent. High levels of ARGs in pharmaceutical fermentation residues underscore the necessity for improved waste management practices. Metagenomic assembly revealed that plasmid-mediated ARGs were more abundant than chromosome-mediated ARGs. Metagenome-assembled genomes (MAGs) analysis identified 166 MAGs, with 62 harboring multiple ARGs. Certain bacteria tended to carry specific types of ARGs, revealing distinct host-resistance associations. This study enhances our understanding of ARG dissemination across different environmental media within pharmaceutical plants and underscores the importance of implementing strict regulations for effluent and residue discharge to control ARG spread.202438960118
7106120.9997The 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
6594130.9997An 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
3447140.9997The Impact of Urban Pollution on Plasmid-Mediated Resistance Acquisition in Enterobacteria from a Tropical River. Background: The exposure of environmental bacteria to contaminants in aquatic ecosystems accelerates the dissemination of antibiotic-resistance genes (ARGs) through horizontal gene transfer (HGT). Methods: In this study, we sampled three locations along a contamination gradient of a polluted river, focusing on isolating Enterobacteria from the surface waters to investigate the relationship between urban pollution and antibiotic resistance. The genomes of 15 isolates (5 per site) were sequenced to identify plasmid-borne ARGs and their association with resistance phenotypes. Results: Isolates from the site with the highest contamination (Site 3) showeda larger number of ARGs, plasmids, and resistance phenotypes. Notably, one of the isolates analyzed, E. coli A231-12, exhibited phenotypic resistance to seven antibiotics, presumably conferred by a single plasmid carrying 12 ARGs. Comparative analysis of this plasmid revealed its close evolutionary relationship with another IncH plasmid hosted by Salmonella enterica, underscoring its high ARG burden in the aquatic environment. Other plasmids identified in our isolates carried sul and dfrA genes, conferring resistance to trimethoprim/sulfamethoxazole, a commonly prescribed antibiotic combination in clinical settings. Conclusions: These results highlight the critical need to expand research on the link between pollution and plasmid-mediated antimicrobial resistance in aquatic ecosystems, which can act as reservoirs of ARGs.202439596782
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
7317160.9997Metagenomic 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
3469170.9997Antibiotic resistance genes of emerging concern in municipal and hospital wastewater from a major Swedish city. The spread of antibiotic resistance among bacterial pathogens is to a large extent mediated by mobile antibiotic resistance genes (ARGs). The prevalence and geographic distribution of several newly discovered ARGs, as well as some clinically important ARGs conferring resistance to last resort antibiotics, are largely unknown. Targeted analysis of wastewater samples could allow estimations of carriage in the population connected to the sewers as well as release to the environment. Here we quantified ARGs conferring resistance to linezolid (optrA and cfr(A)) and colistin (mcr-1, -2, -3, -4 and -5) and the recently discovered gar (aminoglycoside ARG) and sul4 (sulphonamide ARG) in raw hospital and municipal wastewater as well as treated municipal wastewater during five years in a low antibiotic resistance prevalence setting (Gothenburg, Sweden). Additionally, variations in bacterial composition of the wastewaters characterized by 16S rRNA sequencing were related to the variations of the ARGs in an attempt to reveal if the presence of known or suspected bacterial host taxa could explain the presence of the ARGs in wastewater. The mcr-1, mcr-3, mcr-4, mcr-5, sul4 and gar genes were detected regularly in all types of wastewater samples while optrA and cfr(A) were detected only in hospital wastewater. The most abundant genes were mcr-3 and mcr-5, especially in municipal wastewater. The detection of optrA was restricted to a peak during one year. Most of the ARGs correlated with taxa previously described as bacterial hosts and associated with humans. Although some of the tentative hosts may include bacteria also thriving in wastewater environments, detection of the ARGs in the wastewaters could reflect their presence in the gut flora of the contributing populations. If so, they could already today or in the near future hinder treatment of bacterial infections in a setting where they currently are rarely targeted/detected during clinical surveillance.202234748849
3334180.9997Metagenomic profiling of antibiotic resistance genes in Red Sea brine pools. Antibiotic resistance (AR) is an alarming global health concern, causing an annual death rate of more than 35,000 deaths in the US. AR is a natural phenomenon, reported in several pristine environments. In this study, we report AR in pristine Red Sea deep brine pools. Antimicrobial resistance genes (ARGs) were detected for several drug classes with tetracycline and macrolide resistance being the most abundant. As expected, ARGs abundance increased in accordance with the level of human impact with pristine Red Sea samples having the lowest mean ARG level followed by estuary samples, while activated sludge samples showed a significantly higher ARG level. ARG hierarchical clustering grouped drug classes for which resistance was detected in Atlantis II Deep brine pool independent of the rest of the samples. ARG abundance was significantly lower in the Discovery Deep brine pool. A correlation between integrons and ARGs abundance in brine pristine samples could be detected, while insertion sequences and plasmids showed a correlation with ARGs abundance in human-impacted samples not seen in brine pristine samples. This suggests different roles of distinct mobile genetic elements (MGEs) in ARG distribution in pristine versus human-impacted sites. Additionally, we showed the presence of mobile antibiotic resistance genes in the Atlantis II brine pool as evidenced by the co-existence of integrases and plasmid replication proteins on the same contigs harboring predicted multidrug-resistant efflux pumps. This study addresses the role of non-pathogenic environmental bacteria as a silent reservoir for ARGs, and the possible horizontal gene transfer mechanism mediating ARG acquisition.202337061654
3458190.9997MinION Nanopore Sequencing Enables Correlation between Resistome Phenotype and Genotype of Coliform Bacteria in Municipal Sewage. Wastewater treatment plants (WWTPs) functioned as the intersection between the human society and nature environment, are receiving increasingly more attention on risk assessment of the acquisition of environmental antibiotic resistance genes (ARGs) by pathogenetic populations during treatment. However, because of the general lack of robust resistome profiling methods, genotype, and resistance phenotype is still poorly correlated in human pathogens of sewage samples. Here we applied MinION sequencing to quantify the resistance genes of multiple antibiotic resistant (MAR) coliform bacteria, a common indicator for human enteric pathogens in sewage samples. Our pipeline could deliver the results within 30 h from sample collection and the resistome quantification was consistent to that based on the Illumina platform. Additionally, the long nanopore reads not only enabled a simultaneous identification of the carrier populations of ARGs detected, but also facilitated the genome reconstruction of a representative MAR strain, from which we identified an instance of chromosomal integration of environmental resistance gene obtained by plasmid exchange with a porcine pathogen. This study demonstrated the utilization of MinION sequencing in quick monitoring and simultaneous phylogenetic tracking of environmental ARGs to address potential health risk associated with them.201729163399