Validated predictive modelling of the environmental resistome

Dissemination and persistence of antimicrobial resistance (AMR) along the wastewater-river continuum

Antimicrobial resistance (AMR) is a global health hazard. Although clinical and agricultural environments are well-established contributors to the evolution and dissemination of AMR, research on wastewater treatment works (WwTWs) has highlighted their potential role as disseminators of AMR in freshwater environments. Using metagenomic sequencing and analysis, we investigated the changes in resistomes and associated mobile genetic elements within untreated wastewater influents and treated effluents of five WwTWs, and sediments collected from corresponding river environments in Oxfordshire, UK, across three seasonal periods within a year. Our analysis demonstrated a high diversity and abundance of antimicrobial resistance genes (ARGs) in untreated wastewater influents, reflecting the varied anthropogenic and environmental origins of wastewater. WwTWs effectively reduced AMR in the final effluent, with an average 87 % reduction in normalised ARG abundance and an average 63 % reduction in richness. However, wastewater effluents significantly impacted the antimicrobial resistome of the receiving rivers, with an average 543 % increase in ARG abundance and a 164 % increase in richness from upstream sediments to downstream sediments. The normalised abundance of the human gut-associated bacteriophage crAssphage was highly associated with both ARG abundance and richness. We observed seasonal variation in the resistome of raw influent which was not found in the effluent-receiving sediments. We illustrate the potential of WwTWs as focal points for disseminating ARGs and resistance-selecting chemicals, contributing to the elevation of environmental AMR. Our study emphasises the need for a comprehensive understanding of the anthropogenic impacts on AMR evolution and dissemination in wastewater and river environments, informing efforts to mitigate this growing public health crisis.

Integron-associated genes are reliable indicators of antibiotic resistance in wastewater despite treatment- and seasonality-driven fluctuations

The present study aims to characterize the bacterial community, resistome and integron abundance of a municipal wastewater treatment plant (WWTP) over the course of 12 months and evaluate the year-long performance of integron-related genes as potential indicators of antibiotic resistance mechanisms in influents and effluents. For that, total DNA was extracted and subjected to 16S rRNA-targeted metabarcoding, high-throughput (HT) qPCR (48 targets) and standard qPCR (5 targets). Targets included integrase genes, antibiotic resistance genes (ARGs) and putative pathogenic groups. A total of 16 physicochemical parameters determined in the wastewater samples were also considered. Results revealed that the WWTP treatment significantly impacted the bacterial community, as well as the content in ARGs and integrase genes. Indeed, there was a relative enrichment from influent to effluent of 13 pathogenic groups (e.g., Legionella and Mycobacterium) and genes conferring resistance to sulphonamides, aminoglycosides and disinfectants. Effluent samples (n = 25) also presented seasonal differences, with an increase of the total ARGs' concentration in summer, and differences between winter and summer on relative abundance of sulphonamide and disinfectant resistance mechanisms. From the eight putative integron-related genes selected, all were positively correlated with the total ARGs' content in wastewater and the relative abundance of resistance to most of the specific antibiotic classes. The genes intI1, blaGES and qacE∆1 were the most strongly correlated with the total concentration of ARGs. Genes blaGES and blaVIM, were better correlated to resistance to beta-lactams, aminoglycosides and tetracyclines. This study supports the use of integron-related genes as powerful indicators of antibiotic resistance in wastewater, being robust despite the variability caused by wastewater treatment and seasonality.

Antimicrobial resistance in rural rivers: Comparative study of the Coquet (Northumberland) and Eden (Cumbria) River catchments

Many studies have characterised resistomes in river microbial communities. However, few have compared resistomes in parallel rural catchments that have few point-source inputs of antimicrobial genes (ARGs) and organisms (i.e., AMR) - catchments where one can contrast more nebulous drivers of AMR in rural rivers. Here, we used quantitative microbial profiling (QMP) to compare resistomes and microbiomes in two rural river catchments in Northern England, the Coquet and Eden in Northumberland and Cumbria, respectively, with different hydrological and geographical conditions. The Eden has higher flow rates, higher annual surface runoff, and longer periods of soil saturation, whereas the Coquet is drier and has lower flowrates. QMP analysis showed the Eden contained significantly more abundant microbes associated with soil sources, animal faeces, and wastewater than the Coquet, which had microbiomes like less polluted rivers (Wilcoxon test, p < 0.01). The Eden also had greater ARG abundances and resistome diversity (Kruskal Wallis, p < 0.05), and higher levels of potentially clinically relevant ARGs. The Eden catchment had greater and flashier runoff and more extensive agricultural land use in its middle reach, which explains higher levels of AMR in the river. Hydrological and geographic factors drive AMR in rural rivers, which must be considered in environmental monitoring programmes.

Linking antibiotic resistance gene patterns with advanced faecal pollution assessment and environmental key parameters along 2300 km of the Danube River

The global spread of antimicrobial resistance (AMR) in the environment is a growing health threat. Large rivers are of particular concern as they are highly impacted by wastewater discharge while being vital lifelines serving various human needs. A comprehensive understanding of occurrence, spread and key drivers of AMR along whole river courses is largely lacking. We provide a holistic approach by studying spatiotemporal patterns and hotspots of antibiotic resistance genes (ARGs) along 2311 km of the navigable Danube River, combining a longitudinal and temporal monitoring campaign. The integration of advanced faecal pollution diagnostics and environmental and chemical key parameters allowed linking ARG concentrations to the major pollution sources and explaining the observed patterns. Nine AMR markers, including genes conferring resistance to five different antibiotic classes of clinical and environmental relevance, and one integrase gene were determined by probe-based qPCR. All AMR targets could be quantified in Danube River water, with intI1 and sul1 being ubiquitously abundant, qnrS, tetM, blaTEM with intermediate abundance and blaOXA-48like, blaCTX-M-1 group, blaCTX-M-9 group and blaKPC genes with rare occurrence. Human faecal pollution from municipal wastewater discharges was the dominant factor shaping ARG patterns along the Danube River. Other significant correlations of specific ARGs were observed with discharge, certain metals and pesticides. In contrast, intI1 was not associated with wastewater but was already established in the water microbiome. Animal contamination was detected only sporadically and was correlated with ARGs only in the temporal sampling set. During temporal monitoring, an extraordinary hotspot was identified emphasizing the variability within natural waters. This study provides the first comprehensive baseline concentrations of ARGs in the Danube River and lays the foundation for monitoring future trends and evaluating potential reduction measures. The applided holistic approach proved to be a valuable methodological contribution towards a better understanding of the environmental occurrence of AMR.

Does Environmental Exposure to Pharmaceutical and Personal Care Product Residues Result in the Selection of Antimicrobial-Resistant Microorganisms, and is this Important in Terms of Human Health Outcomes?

The environment plays a critical role in the development, dissemination, and transmission of antimicrobial resistance (AMR). Pharmaceuticals and personal care products (PPCPs) enter the environment through direct application to the environment and through anthropogenic pollution. Although there is a growing body of evidence defining minimal selective concentrations (MSCs) of antibiotics and the role antibiotics play in horizontal gene transfer (HGT), there is limited evidence on the role of non-antibiotic PPCPs. Existing data show associations with the development of resistance or effects on bacterial growth rather than calculating selective endpoints. Research has focused on laboratory-based systems rather than in situ experiments, although PPCP concentrations found throughout wastewater, natural water, and soil environments are often within the range of laboratory-derived MSCs and at concentrations shown to promote HGT. Increased selection and HGT of AMR by PPCPs will result in an increase in total AMR abundance in the environment, increasing the risk of exposure and potential transmission of environmental AMR to humans. There is some evidence to suggest that humans can acquire resistance from environmental settings, with water environments being the most frequently studied. However, because this is currently limited, we recommend that more evidence be gathered to understand the risk the environment plays in regard to human health. In addition, we recommend that future research efforts focus on MSC-based experiments for non-antibiotic PPCPS, particularly in situ, and investigate the effect of PPCP mixtures on AMR. Environ Toxicol Chem 2024;43:623-636. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Beach sand plastispheres are hotspots for antibiotic resistance genes and potentially pathogenic bacteria even in beaches with good water quality

Massive amounts of microplastics are transported daily from the oceans and rivers onto beaches. The ocean plastisphere is a hotspot and a vector for antibiotic resistance genes (ARGs) and potentially pathogenic bacteria. However, very little is known about the plastisphere in beach sand. Thus, to describe whether the microplastics from beach sand represent a risk to human health, we evaluated the bacteriome and abundance of ARGs on microplastic and sand sampled at the drift line and supralittoral zones of four beaches of poor and good water quality. The bacteriome was evaluated by sequencing of 16S rRNA gene, and the ARGs and bacterial abundances were evaluated by high-throughput real-time PCR. The results revealed that the microplastic harbored a bacterial community that is more abundant and distinct from that of beach sand, as well as a greater abundance of potential human and marine pathogens, especially the microplastics deposited closer to seawater. Microplastics also harbored a greater number and abundance of ARGs. All antibiotic classes evaluated were found in the microplastic samples, but not in the beach sand ones. Additionally, 16 ARGs were found on the microplastic alone, including genes related to multidrug resistance (blaKPC, blaCTX-M, tetM, mdtE and acrB_1), genes that have the potential to rapidly and horizontally spread (blaKPC, blaCTX-M, and tetM), and the gene that confers resistance to antibiotics that are typically regarded as the ultimate line of defense against severe multi-resistant bacterial infections (blaKPC). Lastly, microplastic harbored a similar bacterial community and ARGs regardless of beach water quality. Our findings suggest that the accumulation of microplastics in beach sand worldwide may constitute a potential threat to human health, even in beaches where the water quality is deemed satisfactory. This phenomenon may facilitate the emergence and dissemination of bacteria that are resistant to multiple drugs.

Performance of sewage sludge treatment for the removal of antibiotic resistance genes: Status and prospects

Wastewater treatment plants (WWTPs) receive wastewater containing antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs), which are predominant contributors to environmental pollution in water and soil. Of these sources, sludge is a more significant contributor than effluent. Knowing how sludge treatment affects the fate of ARGs is vital for managing the risk of these genes in both human and natural environments. This review therefore discusses the sources and transmission of ARGs in the environment and highlights the risks of ARGs in sludge. The effects of co-existing constituents (heavy metals, microplastics, etc.) on sludge and ARGs during treatment are collated to highlight the difficulty of treating sludge with complex constituents in ARGs. The effects of various sludge treatment methods on the abundances of ARGs in sludge and in soil from land application of treated sludge are discussed, pointing out that the choice of sludge treatment method should take into account various potential factors, such as soil and soil biology in subsequent land application. This review offers significant insights and explores the abundances of ARGs throughout the process of sludge treatment and disposal. Unintentional addition of antibiotic residues, heavy metals, microplastics and organic matter in sludge could significantly increase the abundance and reduce the removal efficiency of ARGs during treatment, which undoubtedly adds a barrier to the removal of ARGs from sludge treatment. The complexity of the sludge composition and the diversities of ARGs have led to the fact that no effective sludge treatment method has so far been able to completely eliminate the ecological risk of ARGs. In order to reduce risks resulting by transmission of ARGs, technical and management measures need to be implemented.

Fate and transport modelling for evaluating antibiotic resistance in aquatic environments: Current knowledge and research priorities

Antibiotics have revolutionised medicine in the last century and enabled the prevention of bacterial infections that were previously deemed untreatable. However, in parallel, bacteria have increasingly developed resistance to antibiotics through various mechanisms. When resistant bacteria find their way into terrestrial and aquatic environments, animal and human exposures increase, e.g., via polluted soil, food, and water, and health risks multiply. Understanding the fate and transport of antibiotic resistant bacteria (ARB) and the transfer mechanisms of antibiotic resistance genes (ARGs) in aquatic environments is critical for evaluating and mitigating the risks of resistant-induced infections. The conceptual understanding of sources and pathways of antibiotics, ARB, and ARGs from society to the water environments is essential for setting the scene and developing an appropriate framework for modelling. Various factors and processes associated with hydrology, ecology, and climate change can significantly affect the fate and transport of ARB and ARGs in natural environments. This article reviews current knowledge, research gaps, and priorities for developing water quality models to assess the fate and transport of ARB and ARGs. The paper also provides inputs on future research needs, especially the need for new predictive models to guide risk assessment on AR transmission and spread in aquatic environments.

The scope of antimicrobial resistance in residential aged care facilities determined through analysis of Escherichia coli and the total wastewater resistome

IMPORTANCE

Antimicrobial resistance (AMR) is a global threat that imposes a heavy burden on our health and economy. Residential aged care facilities (RACFs), where frequent inappropriate antibiotic use creates a selective environment that promotes the development of bacterial resistance, significantly contribute to this problem. We used wastewater-based epidemiology to provide a holistic whole-facility assessment and comparison of antimicrobial resistance in two RACFs and a retirement village. Resistant Escherichia coli, a common and oftentimes problematic pathogen within RACFs, was isolated from the wastewater, and the phenotypic and genotypic AMR was determined for all isolates. We observed a high prevalence of an international high-risk clone, carrying an extended-spectrum beta-lactamase in one facility. Analysis of the entire resistome also revealed a greater number of mobile resistance genes in this facility. Finally, both facilities displayed high fluoroquinolone resistance rates-a worrying trend seen globally despite measures in place aimed at limiting their use.

Identifying sources of antibiotic resistance genes in the environment using the microbial Find, Inform, and Test framework

Introduction

Antimicrobial resistance (AMR) is an increasing public health concern for humans, animals, and the environment. However, the contributions of spatially distributed sources of AMR in the environment are not well defined.

Methods

To identify the sources of environmental AMR, the novel microbial Find, Inform, and Test (FIT) model was applied to a panel of five antibiotic resistance-associated genes (ARGs), namely, erm(B), tet(W), qnrA, sul1, and intI1, quantified from riverbed sediment and surface water from a mixed-use region.

Results

A one standard deviation increase in the modeled contributions of elevated AMR from bovine sources or land-applied waste sources [land application of biosolids, sludge, and industrial wastewater (i.e., food processing) and domestic (i.e., municipal and septage)] was associated with 34-80% and 33-77% increases in the relative abundances of the ARGs in riverbed sediment and surface water, respectively. Sources influenced environmental AMR at overland distances of up to 13 km.

Discussion

Our study corroborates previous evidence of offsite migration of microbial pollution from bovine sources and newly suggests offsite migration from land-applied waste. With FIT, we estimated the distance-based influence range overland and downstream around sources to model the impact these sources may have on AMR at unsampled sites. This modeling supports targeted monitoring of AMR from sources for future exposure and risk mitigation efforts.

Trimethoprim resistance in surface and wastewater is mediated by contrasting variants of the dfrB gene

Trimethoprim (TMP) is a low-cost, widely prescribed antibiotic. Its effectiveness is increasingly challenged by the spread of genes coding for TMP-resistant dihydrofolate reductases: dfrA, and the lesser-known, evolutionarily unrelated dfrB. Despite recent reports of novel variants conferring high level TMP resistance (dfrB10 to dfrB21), the prevalence of dfrB is still unknown due to underreporting, heterogeneity of the analyzed genetic material in terms of isolation sources, and limited bioinformatic processing. In this study, we explored a coherent set of shotgun metagenomic sequences to quantitatively estimate the abundance of dfrB gene variants in aquatic environments. Specifically, we scanned sequences originating from influents and effluents of municipal sewage treatment plants as well as river-borne microbiomes. Our analyses reveal an increased prevalence of dfrB1, dfrB2, dfrB3, dfrB4, dfrB5, and dfrB7 in wastewater microbiomes as compared to freshwater. These gene variants were frequently found in genomic neighborship with other resistance genes, transposable elements, and integrons, indicating their mobility. By contrast, the relative abundances of the more recently discovered variants dfrB9, dfrB10, and dfrB13 were significantly higher in freshwater than in wastewater microbiomes. Moreover, their direct neighborship with other resistance genes or markers of mobile genetic elements was significantly less likely. Our findings suggest that natural freshwater communities form a major reservoir of the recently discovered dfrB gene variants. Their proliferation and mobilization in response to the exposure of freshwater communities to selective TMP concentrations may promote the prevalence of high-level TMP resistance and thus limit the future effectiveness of antimicrobial therapies.

Integrons in the development of antimicrobial resistance: critical review and perspectives

Antibiotic resistance development and pathogen cross-dissemination are both considered essential risks to human health on a worldwide scale. Antimicrobial resistance genes (AMRs) are acquired, expressed, disseminated, and traded mainly through integrons, the key players capable of transferring genes from bacterial chromosomes to plasmids and their integration by integrase to the target pathogenic host. Moreover, integrons play a central role in disseminating and assembling genes connected with antibiotic resistance in pathogenic and commensal bacterial species. They exhibit a large and concealed diversity in the natural environment, raising concerns about their potential for comprehensive application in bacterial adaptation. They should be viewed as a dangerous pool of resistance determinants from the "One Health approach." Among the three documented classes of integrons reported viz., class-1, 2, and 3, class 1 has been found frequently associated with AMRs in humans and is a critical genetic element to serve as a target for therapeutics to AMRs through gene silencing or combinatorial therapies. The direct method of screening gene cassettes linked to pathogenesis and resistance harbored by integrons is a novel way to assess human health. In the last decade, they have witnessed surveying the integron-associated gene cassettes associated with increased drug tolerance and rising pathogenicity of human pathogenic microbes. Consequently, we aimed to unravel the structure and functions of integrons and their integration mechanism by understanding horizontal gene transfer from one trophic group to another. Many updates for the gene cassettes harbored by integrons related to resistance and pathogenicity are extensively explored. Additionally, an updated account of the assessment of AMRs and prevailing antibiotic resistance by integrons in humans is grossly detailed-lastly, the estimation of AMR dissemination by employing integrons as potential biomarkers are also highlighted. The current review on integrons will pave the way to clinical understanding for devising a roadmap solution to AMR and pathogenicity. Graphical AbstractThe graphical abstract displays how integron-aided AMRs to humans: Transposons capture integron gene cassettes to yield high mobility integrons that target res sites of plasmids. These plasmids, in turn, promote the mobility of acquired integrons into diverse bacterial species. The acquisitions of resistant genes are transferred to humans through horizontal gene transfer.

Effects of freeze-thaw dynamics and microplastics on the distribution of antibiotic resistance genes in soil aggregates

This is the first study investigating the effects of freeze-thaw (FT) and microplastics (MPs) on the distribution of antibiotic resistance genes (ARGs) in soil aggregates (i.e., soil basic constituent and functional unit) via microcosm experiments. The results showed that FT significantly increased the total relative abundance of target ARGs in different aggregates due to the increase in intI1 and ARG host bacteria. However, polyethylene MPs (PE-MPs) hindered the increase in ARG abundance caused by FT. The host bacteria carrying ARGs and intI1 varied with aggregate size, and the highest number of hosts was observed in micro-aggregates (<0.25 mm). FT and MPs altered host bacteria abundance by affecting aggregate physicochemical properties and bacterial community and enhanced multiple antibiotic resistance via vertical gene transfer. Although the dominant factors affecting ARGs varied with aggregate size, intI1 was a co-dominant factor in various-sized aggregates. Furthermore, other than ARGs, FT, PE-MPs, and their integration promoted the proliferation of human pathogenic bacteria in aggregates. These findings suggested that FT and its integration with MPs significantly affected ARG distribution in soil aggregates. They amplified antibiotic resistance environmental risks, contributing to a profound understanding of soil antibiotic resistance in the boreal region.

Emerging organic contaminants in the River Ganga and key tributaries in the middle Gangetic Plain, India: Characterization, distribution & controls

The presence and distribution of emerging organic contaminants (EOCs) in freshwater environments is a key issue in India and globally, particularly due to ecotoxicological and potential antimicrobial resistance concerns. Here we have investigated the composition and spatial distribution of EOCs in surface water along a ∼500 km segment of the iconic River Ganges (Ganga) and key tributaries in the middle Gangetic Plain of Northern India. Using a broad screening approach, in 11 surface water samples, we identified 51 EOCs, comprising of pharmaceuticals, agrochemicals, lifestyle and industrial chemicals. Whilst the majority of EOCs detected were a mixture of pharmaceuticals and agrochemicals, lifestyle chemicals (and particularly sucralose) occurred at the highest concentrations. Ten of the EOCs detected are priority compounds (e.g. sulfamethoxazole, diuron, atrazine, chlorpyrifos, perfluorooctane sulfonate (PFOS), perfluorobutane sulfonate, thiamethoxam, imidacloprid, clothianidin and diclofenac). In almost 50% of water samples, sulfamethoxazole concentrations exceeded predicted no-effect concentrations (PNECs) for ecological toxicity. A significant downstream reduction in EOCs was observed along the River Ganga between Varanasi (Uttar Pradesh) and Begusarai (Bihar), likely reflecting dilution effects associated with three major tributaries, all with considerably lower EOC concentrations than the main Ganga channel. Sorption and/or redox controls were observed for some compounds (e.g. clopidol), as well as a relatively high degree of mixing of EOCs within the river. We discuss the environmental relevance of the persistence of several parent compounds (notably atrazine, carbamazepine, metribuzin and fipronil) and associated transformation products. Associations between EOCs and other hydrochemical parameters including excitation emission matrix (EEM) fluorescence indicated positive, significant, and compound-specific correlations between EOCs and tryptophan-, fulvic- and humic-like fluorescence. This study expands the baseline characterization of EOCs in Indian surface water and contributes to an improved understanding of the potential sources and controls on EOC distribution in the River Ganga and other large river systems.

Exploring the abundance and influencing factors of antimicrobial resistance genes in manure plasmidome from swine farms

Plasmids play a critical role in the dissemination of antimicrobial resistance genes (ARGs), however, a systematical understanding of ARGs originated from plasmids in swine production is currently lacking. Herein, quantitative polymerase chain reaction was applied to determine the prevalence of ten ARGs and the class1 integron gene intI1 of plasmid source in swine manure from 44 farms in Sichuan, Hubei and Hebei provinces, China. All assayed ARGs were observed in plasmid DNA samples, and the average absolute abundance of aac(6')-Ib-cr, bla_NDM, bla_CTX-M, optrA, ermB, floR, mcr-1, qnrS, tetM, sul1 and intI1 were 7.09, 2.90, 4.67, 6.62, 7.55, 7.14, 4.08, 4.85, 7.16, 7.11 and 8.07 of 10 log copies/gram, respectively. IntI1 showed a high correlation (r > 0.8, P < 0.01) with the abundance of aac(6')-Ib-cr and sul1 in swine manure. Moreover, the farm scale (i.e., herd population) and geographical location were not found to be critical factors influencing the absolute abundance of ARGs of plasmid DNA in swine farms. However, the concentrations of florfenicol, Cu, Zn, Fe, total phosphorus (TP) and total potassium (TK) demonstrated a significant correlation with the abundance of several ARGs. Particularly, Cu and Zn had high correlations with optrA and bla_CTX-M, respectively. Our results demonstrated that antibiotics, heavy metals and environmental nutrients are likely jointly contributing to the long-term persistence of ARGs in swine production. This study provides insights into the abundance and influencing factors of ARGs from swine manure, which is of significance for assessing and reducing the public health risks in livestock production.

Industrial effluents boosted antibiotic resistome risk in coastal environments

Wastewater treatment plants (WWTPs) have been regarded as an important source of antibiotic resistance genes (ARGs) in environment, but out of municipal domestic WWTPs, few evidences show how environment is affected by industrial WWTPs. Here we chose Hangzhou Bay (HZB), China as our study area, where land-based municipal and industrial WWTPs discharged their effluent into the bay for decades. We adopted high-throughput metagenomic sequencing to examine the antibiotic resistome of the WWTP effluent and coastal sediment samples. And we proposed a conceptual framework for the assessment of antibiotic resistome risk, and a new bioinformatic pipeline for the evaluation of the potential horizontal gene transfer (HGT) frequency. Our results revealed that the diversity and abundance of ARGs in the WWTP's effluent were significantly higher than those in the sediment. Furthermore, the antibiotic resistome in the effluent-receiving area (ERA) showed significant difference from that in HZB. For the first time, we identified that industrial WWTP effluent boosted antibiotic resistome risk in coastal sediment. The crucial evidences included: 1) the proportion of ARGs derived from WWTP activated sludge (WA) was higher (14.3 %) and two high-risky polymyxin resistance genes (mcr-4 and mcr-5) were enriched in the industrial effluent receiving area; 2) the HGT potential was higher between resistant microbiome of the industrial effluent and its ERA sediment; and 3) the highest resistome risk was determined in the industrial effluent, and some biocide resistance genes located on high-risky contigs were related to long-term stress of industrial chemicals. These findings highlight the important effects of industrial activities on the development of environmental antimicrobial resistance.

Antibiotic Resistance Genes in River Biofilms: A Metagenomic Approach toward the Identification of Sources and Candidate Hosts

Treated wastewater is a major pathway by which antibiotic resistance genes (ARG) enter aquatic ecosystems. However, knowledge gaps remain concerning the dissemination of specific ARG and their association with bacterial hosts. Here, we employed shotgun metagenomics to track ARG and taxonomic markers in river biofilms along a gradient of fecal pollution depicted by crAssphage signatures. We found strong evidence for an impact of wastewater effluents on both community composition and resistomes. In the light of such simultaneity, we employed a model comparison technique to identify ARG-host relationships from nonassembled metagenomic DNA. Hereby, a major cause of spurious associations otherwise encountered in correlation-based ARG-host analyses was suppressed. For several families of ARG, namely those conferring resistance to beta-lactams, particular bacterial orders were identified as candidate hosts. The found associations of blaFOX and cphA with Aeromonadales or blaPER with Chromatiales support the outcome of independent evolutionary analyses and thus confirm the potential of the methodology. For other ARG families including blaIMP or tet, clusters of bacterial orders were identified which potentially harbor a major proportion of host species. For yet other ARG, like, for example, ant or erm, no particular host candidates were identifiable, indicating their spread across various taxonomic groups.

(Antibiotic-Resistant) E. coli in the Dutch-German Vecht Catchment─Monitoring and Modeling

Fecally contaminated waters can be a source for human infections. We investigated the occurrence of fecal indicator bacteria (E. coli) and antibiotic-resistant E. coli, namely, extended spectrum beta-lactamase (ESBL)-producing E. coli (ESBL-EC) and carbapenemase-producing E. coli (CP-EC) in the Dutch-German transboundary catchment of the Vecht River. Over the course of one year, bacterial concentrations were monitored in wastewater treatment plant (WWTP) influents and effluents and in surface waters with and without WWTP influence. Subsequently, the GREAT-ER model was adopted for the prediction of (antibiotic-resistant) E. coli concentrations. The model was parametrized and evaluated for two distinct scenarios (average flow scenario, dry summer scenario). Statistical analysis of WWTP monitoring data revealed a significantly higher (factor 2) proportion of ESBL-EC among E. coli in German compared to Dutch WWTPs. CP-EC were present in 43% of influent samples. The modeling approach yielded spatially accurate descriptions of microbial concentrations for the average flow scenario. Predicted E. coli concentrations exceed the threshold value of the Bathing Water Directive for a good bathing water quality at less than 10% of potential swimming sites in both scenarios. During a single swimming event up to 61 CFU of ESBL-EC and less than 1 CFU of CP-EC could be taken up by ingestion.

The Role of the Environment in Dynamics of Antibiotic Resistance in Humans and Animals: A Modelling Study

Antibiotic resistance is transmitted between animals and humans either directly or indirectly, through transmission via the environment. However, little is known about the contribution of the environment to resistance epidemiology. Here, we use a mathematical model to study the effect of the environment on human resistance levels and the impact of interventions to reduce antibiotic consumption in animals. We developed a model of resistance transmission with human, animal, and environmental compartments. We compared the model outcomes under different transmission scenarios, conducted a sensitivity analysis, and investigated the impacts of curtailing antibiotic usage in animals. Human resistance levels were most sensitive to parameters associated with the human compartment (rate of loss of resistance from humans) and with the environmental compartment (rate of loss of environmental resistance and rate of environment-to-human transmission). Increasing environmental transmission could lead to increased or reduced impact of curtailing antibiotic consumption in animals on resistance in humans. We highlight that environment-human sharing of resistance can influence the epidemiology of resistant bacterial infections in humans and reduce the impact of interventions that curtail antibiotic consumption in animals. More data on resistance in the environment and frequency of human-environment transmission is crucial to understanding antibiotic resistance dynamics.

Vertical distribution of antibiotics and antibiotic resistance genes in a representative municipal solid waste landfill, China

The vertical distribution of sulfonamides (SAs), tetracyclines (TCs), macrolides (MLs), and their related antibiotic resistance genes (ARGs) were comprehensively investigated and characterized in a representative municipal solid waste (MSW) landfill in China. The total concentrations of target antibiotics in the MSW landfill were SAs > TCs > MLs. The abundances of mexF (10.78 ± 0.65 log₁₀copies/g) and sul genes (9.15 ± 0.54 log₁₀copies/g) were relatively high, while the tet genes (7.19 ± 0.77 log₁₀copies/g) were the lowest. Both the abundance of antibiotics and genes fluctuated with landfill depth, and the ARGs of the same antibiotics were consistent with depth change. Intl1 and sul genes (sul1, sul2) were tightly connected, and a close relationship also existed between tet genes (tetM, tetQ) and MLs resistance genes (ermB, mefA). High-throughput sequencing showed the dominant genera were Sporosarcina (38%) and Thiobacillus (17%) at sampling points A and C, while the microbial community varied with depth increase at point B were Brevundimonas (20%), Sporosarcina (20%), Pseudomonas (24%), Lysobacter (28%), and Thioalkalimicrobium (14%), respectively. Network analysis further visualized the relationship among antibiotics, genes, and microbial communities and the results indicated the non-random connection among them and the possible host of the target gene. Even at 12.0 m below the landfill surface, the pollution of antibiotics resistance was still serious, which posed difficulties for subsequent landfill remediation and pollution control.

Linkage and driving mechanisms of antibiotic resistome in surface and ground water: Their responses to land use and seasonal variation

Antibiotic resistance in the environment, mostly mediated by antibiotic resistance genes (ARGs), has posed a threat to ecological and human health. Contamination of surface water and groundwater with ARGs has become a serious environmental concern. However, the distinctions and similarities across ARG profiles, the various ecological processes associated with ARGs, the driving mechanisms for ARG profiles in surface water and groundwater, and how they respond to land use and seasonal variation remain unknown. To tackle these issues, the contamination of ARGs in surface water and groundwater in central China was investigated using metagenomic technology. The results indicated that seasonal changes in ARG abundance and diversity were inconsistent across surface water and groundwater, and that the relationship between ARGs in surface water and groundwater was stronger during the rainy season. Land use had a greater effect on ARGs in surface water than in groundwater and was stronger during the dry season than during the rainy season. More interestingly, the ideal buffer zones with the greatest impact of land use on the ARGs of surface water and groundwater had distinct radii: 1500 m for both dry and rainy seasons in surface water, and 1000 m for dry season and 500 m for rainy season in groundwater. Furthermore, stochastic mechanisms mediated by mobile gene elements (MGEs) contribute significantly more to ARG assemblages than deterministic processes, particularly in groundwater. Furthermore, our results also showed that ARG enrichment in microbial communities was host- dependent, and the risk of ARGs in groundwater was greater both during the rainy season and dry season. In conclusion, the findings have improved our understanding of the relationship and driving mechanisms of ARGs in surface and ground water, as well as their responses to land use and seasonal variation, which may be beneficial for limiting ARG pollution in a watershed with high levels of anthropogenic activity.

Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map

BACKGROUND

Antimicrobial resistance (AMR) is predicted to become the leading cause of death by 2050 with antibiotic resistance being an important component. Anthropogenic pollution introduces antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) to the natural environment. Currently, there is limited empirical evidence demonstrating whether humans are exposed to environmental AMR and whether this exposure can result in measurable human health outcomes. In recent years there has been increasing interest in the role of the environment and disparate evidence on transmission of AMR to humans has been generated but there has been no systematic attempt to summarise this. We aim to create two systematic maps that will collate the evidence for (1) the transmission of antibiotic resistance from the natural environment to humans on a global scale and (2) the state of antibiotic resistance in the environment in the United Kingdom.

METHODS

Search strategies were developed for each map. Searches were undertaken in 13 bibliographic databases. Key websites were searched and experts consulted for grey literature. Search results were managed using EndNote X8. Titles and abstracts were screened, followed by the full texts. Articles were double screened at a minimum of 10% at both stages with consistency checking and discussion when disagreements arose. Data extraction occurred in Excel with bespoke forms designed. Data extracted from each selected study included: bibliographic information; study site location; exposure source; exposure route; human health outcome (Map 1); prevalence/percentage/abundance of ARB/antibiotic resistance elements (Map 2) and study design. EviAtlas was used to visualise outputs.

RESULTS

For Map 1, 40 articles were included, from 11,016 unique articles identified in searches, which investigated transmission of AMR from the environment to humans. Results from Map 1 showed that consumption/ingestion was the most studied transmission route. Exposure (n = 17), infection (n = 16) and colonisation (n = 11) being studied as an outcome a similar number of times, with mortality studied infrequently (n = 2). In addition, E. coli was the most highly studied bacterium (n = 16). For Map 2, we included 62 studies quantifying ARB or resistance elements in the environment in the UK, from 6874 unique articles were identified in the searches. The most highly researched species was mixed communities (n = 32). The most common methodology employed in this research question was phenotypic testing (n = 37). The most commonly reported outcome was the characterisation of ARBs (n = 40), followed by characterisation of ARGs (n = 35). Other genetic elements, such as screening for intI1 (n = 15) (which encodes a Class 1 integron which is used as a proxy for environmental ARGs) and point mutations (n = 1) were less frequently reported. Both maps showed that research was focused towards aquatic environments.

CONCLUSIONS

Both maps can be used by policy makers to show the global (Map 1) and UK (Map 2) research landscapes and provide an overview of the state of AMR in the environment and human health impacts of interacting with the environment. We have also identified (1) clusters of research which may be used to perform meta-analyses and (2) gaps in the evidence base where future primary research should focus.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s13750-022-00262-2.

Metagenomic profiles of the resistome in subtropical estuaries: Co-occurrence patterns, indicative genes, and driving factors

Estuaries are resistome hotspots owing to resistome accumulation and propagation at these locations from surrounding rivers, yet the large-scale biogeographic pattern of resistome, especially biocide and metal resistance genes (BMRGs) and its driving mechanisms in estuarine waters remains to be elucidated. Here, a metagenomics-based approach was firstly used to investigate resistome and mobilome profiles in waters from 30 subtropical estuaries, South China. The Pearl River estuaries had a higher diversity and abundance of antibiotic resistance genes (ARGs), BMRGs, and mobile genetic elements (MGEs) when compared with estuaries from east and west regions. Genes resistant to multiple antibiotics, metals, and biocides were the most abundant gene types in the resistome. The abundance of MGEs (e.g., intI1, IS91, and tnpA) was highly associated with the total abundance of resistance genes, suggesting their utility as potential indicators for quantitative estimations of the resistome contamination. Further, MGEs contributed more than bacterial communities in shaping the resistome in subtropical estuaries. Physicochemical factors (e.g., pH) regulated MGE composition and stochastic assembly, which mediated the co-selection of ARGs and BMRGs via horizontal gene transfer. Our findings have important implications and provide a reference on the management of ARGs and BMRGs in subtropical estuarine ecosystems.

Natural recreational waters and the risk that exposure to antibiotic resistant bacteria poses to human health

Antimicrobial resistance (AMR) is widely recognised as a considerable threat to human health, wellbeing and prosperity. Many clinically important antibiotic resistance genes are understood to have originated in the natural environment. However, the complex interactions between humans, animals and the environment makes the health implications of environmental AMR difficult to quantify. This narrative review focuses on the current state of knowledge regarding antibiotic resistant bacteria (ARB) in natural bathing waters and implications for human health. It considers the latest research focusing on the transmission of ARB from bathing waters to humans. The limitations of existing evidence are discussed, as well as research priorities. The authors are of the opinion that future studies should include faecally contaminated bathing waters and people exposed to these environments to accurately parameterise environment-to-human transmission.

High Prevalence and Factors Associated With the Distribution of the Integron intI1 and intI2 Genes in Scottish Cattle Herds

Integrons are genetic elements that capture and express antimicrobial resistance genes within arrays, facilitating horizontal spread of multiple drug resistance in a range of bacterial species. The aim of this study was to estimate prevalence for class 1, 2, and 3 integrons in Scottish cattle and examine whether spatial, seasonal or herd management factors influenced integron herd status. We used fecal samples collected from 108 Scottish cattle herds in a national, cross-sectional survey between 2014 and 2015, and screened fecal DNA extracts by multiplex PCR for the integrase genes intI1, intI2, and intI3. Herd-level prevalence was estimated [95% confidence interval (CI)] for intI1 as 76.9% (67.8-84.0%) and intI2 as 82.4% (73.9-88.6%). We did not detect intI3 in any of the herd samples tested. A regional effect was observed for intI1, highest in the North East (OR 11.5, 95% CI: 1.0-130.9, P = 0.05) and South East (OR 8.7, 95% CI: 1.1-20.9, P = 0.04), lowest in the Highlands. A generalized linear mixed model was used to test for potential associations between herd status and cattle management, soil type and regional livestock density variables. Within the final multivariable model, factors associated with herd positivity for intI1 included spring season of the year (OR 6.3, 95% CI: 1.1-36.4, P = 0.04) and watering cattle from a natural spring source (OR 4.4, 95% CI: 1.3-14.8, P = 0.017), and cattle being housed at the time of sampling for intI2 (OR 75.0, 95% CI: 10.4-540.5, P < 0.001). This study provides baseline estimates for integron prevalence in Scottish cattle and identifies factors that may be associated with carriage that warrant future investigation.

Knowledge gaps in the assessment of antimicrobial resistance in surface waters

The spread of antibiotic resistance in the water environment has been widely described. However, still many knowledge gaps exist regarding the selection pressure from antibiotics, heavy metals and other substances present in surface waters as a result of anthropogenic activities, as well as the extent and impact of this phenomenon on aquatic organisms and humans. In particular, the relationship between environmental concentrations of antibiotics and the acquisition of ARGs by antibiotic-sensitive bacteria as well as the impact of heavy metals and other selective agents on antimicrobial resistance (AMR) need to be defined. Currently, established safety values are based on the effects of antibiotic toxicity neglecting the question of AMR spread. In turn, risk assessment of antibiotics in waterbodies remains a complex question implicating multiple variables and unknowns reinforced by the lack of harmonized protocols and official guidelines. In the present review, we discussed current state-of-the-art and the knowledge gaps related to pressure exerted by antibiotics and heavy metals on aquatic environments and their relationship to the spread of AMR. Along with this latter, we reflected on (i) the risk assessment in surface waters, (ii) selective pressures contributing to its transfer and propagation and (iii) the advantages of metagenomics in investigating AMR. Furthermore, the role of microplastics in co-selection for metal and antibiotic resistance, together with the need for more studies in freshwater are highlighted.

Ecological insights into the elevational biogeography of antibiotic resistance genes in a pristine river: Metagenomic analysis along the Yarlung Tsangpo River on the Tibetan Plateau

Presently, the prevalence of antibiotic resistance genes (ARGs) is regarded as an emerging environmental issue, and many studies have illuminated biogeographical patterns of the antibiotic resistome. However, few studies have investigated elevational biogeography and associated assembly mechanisms of ARGs in natural river systems. Accordingly, in the present study, we used metagenomics approaches to analyze the biogeographical pattern of ARGs along the pristine Yarlung Tsangpo River on the Tibetan Plateau. Our study retrieved the baseline profiles of ARGs in the pristine river and showed that the ARGs were dominated by bacA, which was resistant to bacitracin and represented more than 91% of total ARGs. The diversity and abundance of ARGs in the pristine river were lower than those in the human-impacted area, suggesting that the antibiotic resistome evolved and was promoted in a human-impacted environment. Furthermore, an elevational distance-decay relationship of ARGs was observed along the pristine Yarlung Tsangpo River, which provided strong evidence of ARG dissimilarity under the elevational variation. Elevational gradients could lead to changes in environmental variables and spatial factors, and consequently alter ARG composition. Elevational gradients could influence the assembly processes of ARGs. The deterministic and stochastic assembly processes both played critical roles and equally participated in shaping ARG composition at the watershed scale along the Yarlung Tsangpo River, and with increasing elevational variation along the river, the ecological processes of ARG assembly shifted from deterministic to stochastic. Moreover, abundant and rare ARGs were tentatively separated to investigate the difference and similarity in their distributions. Although abundant and rare ARGs presented similar distance-decay relationships, rare ARGs were more diverse and vulnerable to the dispersal process and mutation. Overall, our study provides valuable ecological insights to profile the large-scale elevational patterns of ARGs in a pristine river system, thereby providing important information for public health and environmental management.

Diversity, abundance and expression of the antibiotic resistance genes in a Chinese landfill: Effect of deposit age

Landfills are the hotspots for the occurrence of antibiotic resistance genes (ARGs) in the environment. However, limited information is available on the profile of ARGs in response to the varying age of refuse in landfills. In this study, the diversity, abundance and expression of ARGs in a Chinese landfill were assessed by high-throughput quantitative PCR. A total of 154 ARGs were detected and 66% of them were transcriptionally active. The total abundance of ARG transcripts was one magnitude lower than that of ARGs. The ermT-01, tetX, sul2, aadA-02 and aadA2-03 genes were found to be the most abundant ARGs (ARG transcripts) and their sum abundance showed a linear relation with the total abundance of ARGs (ARG transcripts). The total abundance of ARGs (ARG transcripts) in young refuse was significantly higher than that in old refuse (p < 0.01) and the profile of ARGs (ARG transcripts) between the old and young refuse was distinct as revealed by the principal coordinates analysis. The variation partitioning analysis showed heavy metals (mainly Cr and Zn) were the major drivers that affect the profile of ARGs (ARG transcripts). These findings provided new insights into the ARGs in landfills and indicated their potential threats should not be neglected.

Microbial Find, Inform, and Test Model for Identifying Spatially Distributed Contamination Sources: Framework Foundation and Demonstration of Ruminant Bacteroides Abundance in River Sediments

Microbial pollution in rivers poses known ecological and health risks, yet causal and mechanistic linkages to sources remain difficult to establish. Host-associated microbial source tracking (MST) markers help to assess the microbial risks by linking hosts to contamination but do not identify the source locations. Land-use regression (LUR) models have been used to screen the source locations using spatial predictors but could be improved by characterizing transport (i.e., hauling, decay overland, and downstream). We introduce the microbial Find, Inform, and Test (FIT) framework, which expands previous LUR approaches and develops novel spatial predictor models to characterize the transported contributions. We applied FIT to characterize the sources of BoBac, a ruminant Bacteroides MST marker, quantified in riverbed sediment samples from Kewaunee County, Wisconsin. A 1 standard deviation increase in contributions from land-applied manure hauled from animal feeding operations (AFOs) was associated with a 77% (p-value <0.05) increase in the relative abundance of ruminant Bacteroides (BoBac-copies-per-16S-rRNA-copies) in the sediment. This is the first work finding an association between the upstream land-applied manure and the offsite bovine-associated fecal markers. These findings have implications for the sediment as a reservoir for microbial pollution associated with AFOs (e.g., pathogens and antibiotic-resistant bacteria). This framework and application advance statistical analysis in MST and water quality modeling more broadly.

Impact of sulfamethoxazole on a riverine microbiome

The continued emergence of bacterial pathogens presenting antimicrobial resistance is widely recognised as a global health threat and recent attention focused on potential environmental reservoirs of antibiotic resistance genes (ARGs). Freshwater environments such as rivers represent a potential hotspot for ARGs and antibiotic resistant bacteria as they are receiving systems for effluent discharges from wastewater treatment plants (WWTPs). Effluent also contains low levels of different antimicrobials including antibiotics and biocides. Sulfonamides are antibacterial chemicals widely used in clinical, veterinary and agricultural settings and are frequently detected in sewage sludge and manure in addition to riverine ecosystems. The impact of such exposure on ARG prevalence and diversity is unknown, so the aim of this study was to investigate the release of a sub-lethal concentration of the sulfonamide compound sulfamethoxazole (SMX) on the river bacterial microbiome using a flume system. This system was a semi-natural in vitro flume using river water (30 L) and sediment (6 kg) with circulation to mimic river flow. A combination of 'omics' approaches were conducted to study the impact of SMX exposure on the microbiomes within the flumes. Metagenomic analysis showed that the addition of low concentrations of SMX (<4 μg L^-1) had a limited effect on the bacterial resistome in the water fraction only, with no impact observed in the sediment. Metaproteomics did not show differences in ARGs expression with SMX exposure in water. Overall, the river bacterial community was resilient to short term exposure to sub-lethal concentrations of SMX which mimics the exposure such communities experience downstream of WWTPs throughout the year.

Responses of Coastal Marine Microbiomes Exposed to Anthropogenic Dissolved Organic Carbon

Coastal seawaters receive thousands of organic pollutants. However, we have little understanding of the response of microbiomes to this pool of anthropogenic dissolved organic carbon (ADOC). In this study, coastal microbial communities were challenged with ADOC at environmentally relevant concentrations. Experiments were performed at two Mediterranean sites with different impact by pollutants and nutrients: off the Barcelona harbor ("BCN"), and at the Blanes Bay ("BL"). ADOC additions stimulated prokaryotic leucine incorporation rates at both sites, indicating the use of ADOC as growth substrate. The percentage of "membrane-compromised" cells increased with increasing ADOC, indicating concurrent toxic effects of ADOC. Metagenomic analysis of the BCN community challenged with ADOC showed a significant growth of Methylophaga and other gammaproteobacterial taxa belonging to the rare biosphere. Gene expression profiles showed a taxon-dependent response, with significantly enrichments of transcripts from SAR11 and Glaciecola spp. in BCN and BL, respectively. Further, the relative abundance of transposon-related genes (in BCN) and transcripts (in BL) correlated with the number of differentially abundant genes (in BCN) and transcripts (in BLA), suggesting that microbial responses to pollution may be related to pre-exposure to pollutants, with transposons playing a role in adaptation to ADOC. Our results point to a taxon-specific response to low concentrations of ADOC that impact the functionality, structure and plasticity of the communities in coastal seawaters. This work contributes to address the influence of pollutants on microbiomes and their perturbation to ecosystem services and ocean health.

Plasmid-Mediated Antibiotic Resistant Escherichia coli in Sarawak Rivers and Aquaculture Farms, Northwest of Borneo

Background: The emergence of plasmid-mediated antibiotic resistance in Escherichia coli in water resources could pose a serious threat to public health. The study aims to investigate the dispersion of plasmid-mediated antibiotic-resistant E. coli from six rivers in Sarawak and two aquaculture farms in Borneo. Methods: A total of 74 water samples were collected for the determination of their bacteria colony count. An IMViC test identified 31 E. coli isolates and tested their susceptibility against twelve clinically important antibiotics. The extraction of plasmid DNA was done using alkali lysis SDS procedures. Characteristics, including plasmid copy number, molecular weight size, resistance rate and multiple antibiotic resistance (MAR), were assessed. Results: Our findings revealed that bacterial counts in rivers and aquaculture farms ranged from log 2.00 to 3.68 CFU/mL and log 1.70 to 5.48 cfu/mL, respectively. Resistance to piperacillin (100%) was observed in all E. coli; resistance to amoxicillin (100%) and ampicillin (100%) was observed in E. coli found in aquaculture farms; resistance to streptomycin (93%) was observed in E. coli found in rivers. All E. coli were resistant to ≥2 antibiotics and formed 26 MAR profiles, ranging from an index of 0.17 to 0.83, indicating that there are high risks of contamination. Some (48.4%) of the E. coli were detected with plasmids (1.2 to >10 kb), whereas 51.6% of the E. coli did not harbor any plasmids. The plasmid copy numbers reported were one plasmid (n = 7), two plasmids (n = 4), ≥ two plasmids (4). E. coli isolated from the Muara Tuang River showed the highest-molecular-weight plasmids. A statistical analysis revealed that there is no significant correlation (r = 0.21, p = 0.253) between the number of plasmids and the MAR index of the tested isolates. Conclusion: The distribution of MAR in E. coli from rivers is higher compared to the aquaculture environment. Our study suggests that MAR in isolates could be chromosome-mediated. Our results suggest that riverbed sediments could serve as reservoirs for MAR bacteria, including pathogens, under different climatic conditions, and their analysis could provide information for public health concerns.

Calculating expected effects of treatment effectivity and river flow rates on the contribution of WWTP effluent to the ARG load of a receiving river

Concentrations of genetic markers for antibiotic resistance genes (ARGs) were measured in the effluents of three Norwegian wastewater treatment plants (WWTPs) and in a receiving river upstream and downstream of the discharge point of one WWTP. Calculations based on mass balances were carried out to evaluate the impact of river flow rates and treatment effectivity on the WWTP's contribution to the load of genetic markers in the river. At average river flow rates, the WWTP effluent contributes 5-15% to the genetic marker load of the respective river. However, at minimum river flow rates, the WWTP effluent contributes 22-55% to the loads of different genetic markers. Scenarios of an improved or worsened removal of genetic markers in the WWTP showed that a further 1-log removal using additional treatment would be sufficient to improve considerably the river water quality with respect to genetic markers. Then, at an average flow rate, the contribution of the WWTP effluent to the load of the river would be less than 2%. However, in the case of low treatment effectivity or malfunction of the WWTP, the marker load of the river would increase dramatically. Even at average flow rate, 75-92% of the marker load would then originate from the WWTP. The results demonstrate the importance of considering the flow rates and hydrologic characteristics of the recipient water body when deciding on priorities regarding the upgrade of WWTPs for further removal of ARGs.

Antibiotic resistome from the One-Health perspective: understanding and controlling antimicrobial resistance transmission

The concept of the antibiotic resistome was introduced just over a decade ago, and since then, active resistome studies have been conducted. In the present study, we describe the previously established concept of the resistome, which encompasses all types of antibiotic resistance genes (ARGs), and the important findings from each One-Health sector considering this concept, thereby emphasizing the significance of the One-Health approach in understanding ARG transmission. Cutting-edge research methodologies are essential for deciphering the complex resistome structure in the microbiomes of humans, animals, and the environment. Based on the recent achievements of resistome studies in multiple One-Health sectors, future directions for resistome research have been suggested to improve the understanding and control of ARG transmission: (1) ranking the critical ARGs and their hosts; (2) understanding ARG transmission at the interfaces of One-Health sectors; (3) identifying selective pressures affecting the emergence, transmission, and evolution of ARGs; and (4) elucidating the mechanisms that allow an organism to overcome taxonomic barriers in ARG transmission.

An inventory of 44 qPCR assays using hydrolysis probes operating with a unique amplification condition for the detection and quantification of antibiotic resistance genes

Early antibiotic resistance determinants (ARDs) detection in humans or animals is crucial to counteract their propagation. The ARDs quantification is fundamental to understand the perturbation caused by disruptors, such as antibiotics, during therapies. Forty-three qPCRs on the most diffused ARDs and integrons among human and animal Enterobacterales, and one on the 16S rDNA for bacteria quantification, were developed. The qPCRs, using hydrolysis probes, operated with a unique amplification condition and were tested analytically and diagnostically performing 435 reactions on five positive and negative controls for each qPCR. Diagnostic sensitivity and specificity were confirmed by PCR and genome sequencing of control isolates, demonstrating 100% performance for all qPCRs. An easy and rapid discrimination method for the epidemiologically relevant bla_CTX-Ms is provided. This large, noncommercial qPCRs inventory could serve for precise quantification of ARDs, but also as a rapid screening tool for surveillance purposes, providing the basis for further high-throughput developments.

Emerging organic contaminants in groundwater under a rapidly developing city (Patna) in northern India dominated by high concentrations of lifestyle chemicals

Aquatic pollution from emerging organic contaminants (EOCs) is of key environmental importance in India and globally, particularly due to concerns of antimicrobial resistance, ecotoxicity and drinking water supply vulnerability. Here, using a broad screening approach, we characterize the composition and distribution of EOCs in groundwater in the Gangetic Plain around Patna (Bihar), as an exemplar of a rapidly developing urban area in northern India. A total of 73 EOCs were detected in 51 samples, typically at ng.L^-1 to low μg.L^-1 concentrations, relating to medical and veterinary, agrochemical, industrial and lifestyle usage. Concentrations were often dominated by the lifestyle chemical and artificial sweetener sucralose. Seventeen identified EOCs are flagged as priority compounds by the European Commission, World Health Organisation and/or World Organisation for Animal Health: namely, herbicides diuron and atrazine; insecticides imidacloprid, thiamethoxam, clothianidin and acetamiprid; the surfactant perfluorooctane sulfonate (and related perfluorobutane sulfonate, perfluorohexane sulfonate, perfluorooctanoic acid and perfluoropentane sulfonate); and medical/veterinary compounds sulfamethoxazole, sulfanilamide, dapson, sulfathiazole, sulfamethazine and diclofenac. The spatial distribution of EOCs varies widely, with concentrations declining with depth, consistent with a strong dominant vertical flow control. Groundwater EOC concentrations in Patna were found to peak within ∼10 km distance from the River Ganges, indicating mainly urban inputs with some local pollution hotspots. A heterogeneous relationship between EOCs and population density likely reflects confounding factors including varying input types and controls (e.g. spatial, temporal), wastewater treatment infrastructure and groundwater abstraction. Strong seasonal agreement in EOC concentrations was observed. Co-existence of limited transformation products with associated parent compounds indicate active microbial degradation processes. This study characterizes key controls on the distribution of groundwater EOCs across the urban to rural transition near Patna, as a rapidly developing Indian city, and contributes to the wider understanding of the vulnerability of shallow groundwater to surface-derived contamination in similar environments.

Homogeneous selection drives antibiotic resistome in two adjacent sub-watersheds, China

Rivers are a significant reservoir of antibiotic resistance genes (ARGs), yet the biogeographic pattern of riverine ARGs and its underlying driving forces remain poorly understood. Here, we used metagenomic approach to investigate the spatio-temporal variation of ARGs in two adjacent sub-watersheds viz. North River (NR) and West River (WR), China. The results demonstrated that Bacitracin (22.8 % of the total ARGs), multidrug (20.7 %), sulfonamide (15.2 %) and tetracycline (10.9 %) were the dominant ARG types. SourceTracker analysis indicated that sewage treatment plants as the main source of ARGs, while animal feces mainly contributed in spreading the ARGs in the upstream of NR. Random forest and network analyses confirmed that NR was under the influence of fecal pollution. PCoA analysis demonstrated that the composition of ARGs changed along with the anthropogenic gradients, while the Raup-Crick null model showed that homogenizing selection mediated by class 1 integron intI1 resulted in stable ARG communities at whole watershed scale. Structural equation models revealed that microbial community, grassland and several non-antibiotic micropollutants may also play certain roles in influencing the distribution of ARGs. Overall, the observed deterministic formation of ARGs in riverine systems calls effective management strategies to mitigate the risks of antibiotic resistance on public health.

Linkage of antibiotic resistance genes, associated bacteria communities and metabolites in the wheat rhizosphere from chlorpyrifos-contaminated soil

Rhizosphere is a crucial site for the proliferation of antibiotic resistance genes (ARGs) in agricultural soil. Pesticide contamination is ubiquitous in soil, such as chlorpyrifos as one of the most commonly used pesticides. However, limited knowledge is reported about ARGs profiles changes and the driving mechanism of ARGs prevalence in rhizosphere soil after adding pesticide. In this study, irrespective of chlorpyrifos presence, the abundances of ARGs (tetM, tetO, tetQ, tetW, tetX, sul1 and sul2) and intI1 in rhizosphere soil of wheat were obviously higher than those in bulk soil. 20.0 mg·kg^-1 chlorpyrifos significantly increased the abundance of total ARGs and intI1 in bulk soil, respectively, at day 50 and 100, but not in rhizosphere soil. Rhizosphere influence on ARGs was far greater than chlorpyrifos. ARGs and intI1 abundances were higher at day 50 than ones at day 100. C/N ratio and NO₃^--N content, which were affected by rhizosphere and cultivation time, significantly explained the increased ARGs. Compared to bulk soil, rhizosphere shifted host bacteria of tetracycline resistance genes (TRGs), intI1 at genus level, and host bacteria of sul1, sul2 at phylum level. Rhizosphere simplified the linkage of ARGs, host bacteria and metabolites. Bacterial communities played important roles in the variation of ARGs and intI1, and the difference in the distribution of potential hosts between bulk and rhizosphere soil was related to metabolites abundance and composition. These results provide valuable information for understanding the linkage of ARGs, associated bacteria communities and metabolites in the wheat rhizosphere soil.

Antibiotic Resistance in Recreational Waters: State of the Science

Ambient recreational waters can act as both recipients and natural reservoirs for antimicrobial resistant (AMR) bacteria and antimicrobial resistant genes (ARGs), where they may persist and replicate. Contact with AMR bacteria and ARGs potentially puts recreators at risk, which can thus decrease their ability to fight infections. A variety of point and nonpoint sources, including contaminated wastewater effluents, runoff from animal feeding operations, and sewer overflow events, can contribute to environmental loading of AMR bacteria and ARGs. The overall goal of this article is to provide the state of the science related to recreational exposure and AMR, which has been an area of increasing interest. Specific objectives of the review include (1) a description of potential sources of antibiotics, AMR bacteria, and ARGs in recreational waters, as documented in the available literature; (2) a discussion of what is known about human recreational exposures to AMR bacteria and ARGs, using findings from health studies and exposure assessments; and (3) identification of knowledge gaps and future research needs. To better understand the dynamics related to AMR and associated recreational water risks, future research should focus on source contribution, fate and transport-across treatment and in the environment; human health risk assessment; and standardized methods.

Source tracking of antibiotic resistance genes in the environment - Challenges, progress, and prospects

Antibiotic resistance has become a global public health concern, rendering common infections untreatable. Given the widespread occurrence, increasing attention is being turned toward environmental pathways that potentially contribute to antibiotic resistance gene (ARG) dissemination outside the clinical realm. Studies during the past decade have clearly proved the increased ARG pollution trend along with gradient of anthropogenic interference, mainly through marker-ARG detection by PCR-based approaches. However, accurate source-tracking has been always confounded by various factors in previous studies, such as autochthonous ARG level, spatiotemporal variability and environmental resistome complexity, as well as inherent method limitation. The rapidly developed metagenomics profiles ARG occurrence within the sample-wide genomic context, opening a new avenue for source tracking of environmental ARG pollution. Coupling with machine-learning classification, it has been demonstrated the potential of metagenomic ARG profiles in unambiguously assigning source contribution. Through identifying indicator ARG and recovering ARG-host genomes, metagenomics-based analysis will further increase the resolution and accuracy of source tracking. In this review, challenges and progresses in source-tracking studies on environmental ARG pollution will be discussed, with specific focus on recent metagenomics-guide approaches. We propose an integrative metagenomics-based framework, in which coordinated efforts on experimental design and metagenomic analysis will assist in realizing the ultimate goal of robust source-tracking in environmental ARG pollution.

An Environmental Escherichia coli Strain Is Naturally Competent to Acquire Exogenous DNA

The diffusion of antibiotic resistance determinants in different environments, e.g., soil and water, has become a public concern for global health and food safety and many efforts are currently devoted to clarify this complex ecological and evolutionary issue. Horizontal gene transfer (HGT) has an important role in the spread of antibiotic resistance genes (ARGs). However, among the different HGT mechanisms, the capacity of environmental bacteria to acquire naked exogenous DNA by natural competence is still poorly investigated. This study aimed to characterize the ability of the environmental Escherichia coli strain ED1, isolated from the crustacean Daphnia sp., to acquire exogenous DNA by natural competence. Transformation experiments were carried out varying different parameters, i.e., cell growth phase, amount of exogenous DNA and exposition to artificial lake water (ALW) and treated wastewater to mimic environmental-like conditions that may be encountered in the agri-food system. Results were compared with those showed by the laboratory E. coli strain DH5α. Our experimental data, supported by genomic sequencing, showed that, when exposed to pure water, ED1 strain was able to acquire exogenous DNA with frequencies (10^–8–10^–9) statistically higher than the ones observed for DH5α strain (10^–10). Interestingly, higher values were retrieved for ED1 than DH5α strains exposed to ALW (10^–7 vs. 10^–9, respectively) or treated wastewater (10^–8 vs. 10^–10, respectively). We tested, therefore, ED1 strain ability to colonize the rhizosphere of lettuce, a model plant representative of raw-consumed vegetables of high economic importance in the ready-to-eat food industry. Results showed that ED1 strain was able to efficiently colonize lettuce rhizosphere, revealing a stable colonization for 14 days-long period. In conclusion, ED1 strain ability to acquire exogenous DNA in environmental-like conditions by natural competence, combined with its ability to efficiently and stably colonize plant rhizosphere, poses the attention to food and human safety showing a possible route of diffusion of antibiotic resistance in the agri-food system, sustaining the “One Health” warnings related to the antibiotic spread.

Non-antibiotic pharmaceuticals enhance the transmission of exogenous antibiotic resistance genes through bacterial transformation

Antibiotic resistance is a serious global threat for public health. Considering the high abundance of cell-free DNA encoding antibiotic resistance genes (ARGs) in both clinical and environmental settings, natural transformation is an important horizontal gene transfer pathway to transmit antibiotic resistance. It is acknowledged that antibiotics are key drivers for disseminating antibiotic resistance, yet the contributions of non-antibiotic pharmaceuticals on transformation of ARGs are overlooked. In this study, we report that some commonly consumed non-antibiotic pharmaceuticals, at clinically and environmentally relevant concentrations, significantly facilitated the spread of antibiotic resistance through the uptake of exogenous ARGs. This included nonsteroidal anti-inflammatories, ibuprofen, naproxen, diclofenac, the lipid-lowering drug, gemfibrozil, and the β-blocker propranolol. Based on the results of flow cytometry, whole-genome RNA sequencing and proteomic analysis, the enhanced transformation of ARGs was affiliated with promoted bacterial competence, enhanced stress levels, over-produced reactive oxygen species and increased cell membrane permeability. In addition, a mathematical model was proposed and calibrated to predict the dynamics of transformation during exposure to non-antibiotic pharmaceuticals. Given the high consumption of non-antibiotic pharmaceuticals, these findings reveal new concerns regarding antibiotic resistance dissemination exacerbated by non-antibiotic pharmaceuticals.

Ecotoxicity and antibiotic resistance of wastewater during transport in an urban sewage network

Urban wastewater (UWW) management usually entails biological and physicochemical monitoring due to its potential impact on the quality of the receiving environment. A major component of a sewage system is the pipe network leading the water to the treatment plant. Up to now, few studies have been conducted on the diverse phenomena that may affect the characteristics of the water during its transportation. In this study, ecotoxicity and potential antibiotic resistance were used in a global method to assess the change of UWW quality in a sewage system and determine if sewer pipes can act as a bioreactor spread. Three bioassays were conducted to assess the ecotoxicity of the samples and the concentration and relative abundance of two classes of integrons (as a proxy for antibiotic resistance) were measured. The results of the bioassay battery do not show a pattern, despite the fact that differences were noticeable between upstream and downstream samples. Antibiotic resistance appeared to decrease during transport in the pipe as the concentration and relative abundance of integrons decreased during several campaigns. This result should be confirmed in other sewer networks but already provides useful information for the management of urban sewage system.

Urbanization drives riverine bacterial antibiotic resistome more than taxonomic community at watershed scale

Although the occurrence and distribution of antibiotic resistance genes (ARGs) in various aquatic ecosystems are well explored, understanding of the ecological processes and mechanisms governing the composition and dynamics of bacterial ARGs still remains limited across space and time. Here, we used high-throughput approaches to detect spatial patterns of bacterial ARGs and operational taxonomic units (OTUs) in an urbanizing subtropical watershed, Xiamen, southeast China over a five-year period. At watershed scale, the OTU profiles were undergoing a directional change, but the ARG profiles showed a high stability or stochastic change over time. Compared with the upstream and midstream, the richness, absolute abundance, normalized abundance and diversity of ARGs were significantly higher in the downstream waters. Our results revealed a clear rural-urban disparity in ARG and OTU profiles which were mainly governed by deterministic and stochastic assembly processes, respectively. With the increase of urban building area along the river, the ecological processes of ARG profiles shifted from stochastic to deterministic. In downstream waters, the bacterial ARG profiles were much more stable than bacterial OTUs. Further, our results indicated that both human-dominated environment (e.g., land use) and mobile genetic elements (MGEs) played an important role in shaping the ARG profiles and dynamics. Overall, this was a response to spatially extensive human-landscape interactions that included urban development in the river downstream region, which were common across subtropical coastal cities of China and can alter the ARG profile dynamics along rural-urban gradient. Therefore, watershed management actions aiming at reducing threats posed by ARGs in urbanizing watershed should first consider the surrounding urbanization level and the mode and intensity of human activity. Our findings also imply that due to the decoupling of bacterial function and taxonomy, both aspects should be studied separately.

Microbial assisted phytodepuration for water reclamation: Environmental benefits and threats

Climate changes push for water reuse as a priority to counteract water scarcity and minimize water footprint especially in agriculture, one of the highest water consuming human activities. Phytodepuration is indicated as a promising technology for water reclamation, also in the light of its economic and ecological sustainability, and the use of specific bacterial inocula for microbial assisted phytodepuration has been proposed as a further advance for its implementation. Here we provided an overview on the selection and use of plant growth promoting bacteria in Constructed Wetland (CW) systems, showing their advantages in terms of plant growth support and pollutant degradation abilities. Moreover, CWs are also proposed for the removal of emerging organic pollutants like antibiotics from urban wastewaters. We focused on this issue, still debated in the literature, revealing the necessity to deepen the knowledge on the antibiotic resistance spread into the environment in relation to treated wastewater release and reuse. In addition, given the presence in the plant system of microhabitats (e.g. rhizosphere) that are hot spot for Horizontal Gene Transfer, we highlighted the importance of gene exchange to understand if these events can promote the diffusion of antibiotic resistance genes and antibiotic resistant bacteria, possibly entering in the food production chain when treated wastewater is used for irrigation. Ideally, this new knowledge will lead to improve the design of phytodepuration systems to maximize the quality and safety of the treated effluents in compliance with the 'One Health' concept.

High-quality treated wastewater causes remarkable changes in natural microbial communities and intI1 gene abundance

We carry out a mesocosms experiment to assess the impact of high-quality treated wastewater intended for agricultural reuse (HQWR) on freshwater bacteria seldom exposed to anthropogenic pollution. Effects were assessed by comparing the abundance and composition of bacterial communities as well as their resistance profile under control (source water from an unpolluted lake) and treatment conditions (source water mixed 1:1 with HQWR, with and without 5 μg L^-1 of cefotaxime). We investigated the effect of the different conditions on the abundance of genes encoding resistance to β-lactams and carbapenems (bla_TEM, bla_CTX-M, bla_OXA, and bla_KPC), fluoroquinolones (qnrS), tetracyclines (tetA), sulfonamides (sul2), macrolides (ermB), arsenic and cadmium (arsB and czcA, respectively), and on the gene encoding the Class 1 integron integrase (intI1). Bacterial communities exposed to HQWR showed a significant higher abundance of tetA, arsB, czcA, and intI1 genes, whereas those exposed to Cefotaxime-amended HQWR did not. Genes conferring resistance to carbapenems, β-lactams, fluoroquinolones, and macrolides were below detection limit in all treatments. Besides, the higher availability of nutrients under treatment conditions favored bacterial growth in comparison to those exposed to control conditions. Particularly, Acinetobacter spp. and Pseudomonas spp. were significantly enriched after 22 days of treatment exposure. The presence of cefotaxime (a third generation cephalosporine) in the feeding medium caused an enrichment of bacterial communities in sequences affiliated to Acinetobacter thus suggesting that these resistant forms may possess resistance genes other than those studied here (bla_CTX-M, bla_OXA, and bla_KPC). Although derived from a mesocosm experiment in continuous cultures, our results call attention to the need of refined regulations regarding the use of reclaimed water in agriculture since even high-quality treated wastewater may lead to undesired effects on receiving bacterial communities in terms of composition and dissemination of antibiotic resistance genes.

Translating antibiotic prescribing into antibiotic resistance in the environment: A hazard characterisation case study

The environment receives antibiotics through a combination of direct application (e.g., aquaculture and fruit production), as well as indirect release through pharmaceutical manufacturing, sewage and animal manure. Antibiotic concentrations in many sewage-impacted rivers are thought to be sufficient to select for antibiotic resistance genes. Yet, because antibiotics are nearly always found associated with antibiotic-resistant faecal bacteria in wastewater, it is difficult to distinguish the selective role of effluent antibiotics within a 'sea' of gut-derived resistance genes. Here we examine the potential for macrolide and fluoroquinolone prescribing in England to select for resistance in the River Thames catchment, England. We show that 64% and 74% of the length of the modelled catchment is chronically exposed to putative resistance-selecting concentrations (PNEC) of macrolides and fluoroquinolones, respectively. Under current macrolide usage, 115 km of the modelled River Thames catchment (8% of total length) exceeds the PNEC by 5-fold. Similarly, under current fluoroquinolone usage, 223 km of the modelled River Thames catchment (16% of total length) exceeds the PNEC by 5-fold. Our results reveal that if reduced prescribing was the sole mitigating measure, that macrolide and fluoroquinolone prescribing would need to decline by 77% and 85%, respectively, to limit resistance selection in the catchment. Significant reductions in antibiotic prescribing are feasible, but innovation in sewage-treatment will be necessary for achieving substantially-reduced antibiotic loads and inactivation of DNA-pollution from resistant bacteria. Greater confidence is needed in current risk-based targets for antibiotics, particularly in mixtures, to better inform environmental risk assessments and mitigation.

Assessment of Antibiotic Levels, Multi-Drug Resistant Bacteria and Genetic Biomarkers in the Waters of the Rio Grande River Between the United States-Mexico Border

BACKGROUND

The worldwide emergence of multi-drug resistant bacteria has become a health crisis, as fewer or sometimes no antimicrobial agents are effective against these bacteria. The Rio Grande River is the natural boundary between the United States (US) and Mexico. It spans a border region between Texas, New Mexico and Mexico. Underserved populations on the Mexican side use the river for recreational purposes, while on the US side, the river is used for irrigation and as a source of drinking water.

OBJECTIVES

The purpose of the present study was to evaluate the concentration of antibiotic residues, to determine the presence of genetic elements conferring antibiotic resistance and to characterize multi-drug resistant bacteria in the waters of the Rio Grande River.

METHODS

Water samples were obtained from the Rio Grande River. Deoxyribonucleic acid (DNA) was extracted from both isolated bacteria and directly from the water. Amplification of selected genetic elements was accomplished by polymerase chain reaction. Identification and isolation of bacteria was performed through MicroScan autoSCAN-4. Fecal contamination was assessed by IDEXX Colilert. Antibiotic residues were determined by liquid chromatography and mass spectrometry.

RESULTS

Antibiotics were found in 92% of both water and sediment samples. Antibiotic concentrations ranged from 0.38 ng/L - 742.73 ng/L and 0.39 ng/l - 66.3 ng/g dry weight in water and sediment samples, respectively. Genetic elements conferring resistance were recovered from all collection sites. Of the isolated bacteria, 91 (64.08%) were resistant to at least two synergistic antibiotic combinations and 11 (14.79%) were found to be resistant to 20 or more individual antibiotics. Fecal contamination was higher during the months of April and July.

CONCLUSIONS

The 26 km segment of the Rio Grande River from Sunland Park NM to El Paso, TX and Juarez, Mexico is an area of concern due to poor water quality. The presence of multidrug resistant bacteria, antibiotics and mobile genetic elements may be a health hazard for the surrounding populations of this binational border region. Policies need to be developed for the appropriate management of the environmental natural resources in this border region.

COMPETING INTERESTS

The authors declare no competing financial interests.

Validated predictive modelling of sulfonamide and beta-lactam resistance genes in landfill leachates

The spread of antimicrobial resistance via landfill leachates jeopardizes millions of people's health, which can be exacerbated due to the unclear quantitative relationships between leachate characteristics and occurrences of antibiotic resistance genes (ARGs). Here, in parallel with sampling raw leachates from a real landfill, we constructed a lab-scale landfill and collected its leachates for 260 days. All leachate samples were analyzed for the abundance of integrons, sulfonamide resistance (sulR; sul1 and sul2) and beta-lactams resistance (blaR; bla_OXA, bla_CTX-M, and bla_TEM) genes. The enrichment of sulR subtypes was closely associated with the integrons' prevalence during the landfilling process (0.65-0.75 log₁₀(copies/mL)), which can be explained by the multiple linear regression that contained intl1, pH, and nitrogen compounds as variables. The predicted abundance of sulR genes (6.06 ± 0.6 log₁₀(copies/mL)) was statistically the same as the observed value in raw leachates (P = 0.73). The abundance of blaR genes decreased from 5.0 to 2.5 log₁₀(copies/mL) during the experiment (P < 0.001); and a locally weighted regression of blaR genes with integrons, COD and total nitrogen accurately predicted blaR genes abundance in raw leachate (Bootstrap = 10,000, P = 0.67). The partial least squares path modelling (PLS-PM) showed that variations of blaR genes in the lab and raw leachates shared an identical pattern (PLS-PM, Bootstrap = 10,000, P > 0.05), which was influenced by integrons and environmental factors with the coefficients of -0.11 and 0.39, respectively. We believe the validated models are highly useful tools to streamline the strategies for monitoring and prediction of ARGs.