Persistence of antibiotic resistance genes from river water to tap water in the Yangtze River Delta

Microbial communities and mobile genetic elements determine the variations of antibiotic resistance genes for a continuous year in the urban river deciphered by metagenome assembly

Antibiotic resistance genes (ARGs) have become emerging environmental contaminants influenced by intricate regulatory factors. However, there is a lack of comprehensive studies on the evolution and distribution of ARGs over a full year in urban rivers, which serve as significant reservoirs of ARGs due to dynamic human activities. In this study, we conducted a 12-month metagenomic assembly to explore the microbial communities, ARGs, mobile genetic elements (MGEs) coexisting with ARGs, ARGs hosts, and the impact of environmental factors. Bacitracin (32%-47%) and multidrug (13%-24%) were detected throughout the year, constituting over 60% of the total abundance, making them the primary ARGs types. The assembly mechanisms of microbial communities and ARGs were primarily driven by stochastic processes. Integrase, IntI1, recombinase, and transposase were identified as the main MGEs coexisting with ARGs. Procrustes analysis revealed a significant structural association, indicating that the composition of host communities likely plays crucial roles in the seasonal composition and distribution of ARGs. Human pathogenic bacteria (HPBs) were identified in the summer, autumn, and winter, with Escherichia coli, Klebsiella pneumoniae, Acinetobacter lwoffii, and Burkholderiales bacterium being the primary HPBs. Mantle tests and PLS-PM equation analysis indicated that microbial communities and MGEs are the most critical factors determining the distribution and composition of ARGs in the river. Environmental factors (including water properties and nutrients) and ARGs hosts influence the evolution and abundance of ARGs by directly regulating microbial communities and MGEs. This study provides critical insights into risk assessment and management of ARGs in urban rivers.

Distribution and driving mechanisms of antibiotic resistance genes in urbanized watersheds

Antibiotic resistance genes (ARGs) have emerged as a global concern, posing significant threats to human health and safety. Understanding the contamination levels and driving mechanisms behind ARG proliferation is urgently needed. Urban watersheds, influenced by human activities, serve as critical reservoirs for ARGs; however, the impact of urbanization on ARG spread of and the underlying driving mechanisms remain unclear. This study evaluates the diversity and abundance of ARGs in water and sediment samples from the Jialing River watershed in Chongqing City, China. The obtained results indicate that aminoglycoside and multidrug ARGs are the primary contributors to ARG presence in both sediments and water. Additionally, the diversity and abundance of ARGs are higher in water than in sediments. ARGs in watershed show a significant positive correlation with mobile genetic elements (MGEs). While environmental factors in urbanized watersheds affect ARG abundance and distribution to some extent, they are not the primary drivers. Urbanization itself emerges as a prominent factor influencing ARG diversity and abundance in river basins. Specifically, livestock, healthcare, and agriculture are identified as the main social factors influencing ARG proliferation in the highly urbanized areas of the Jialing River watershed. Further investigation into other contributing social factors, such as industrial development, is warranted. This study reveals the factors driving ARG distribution in urbanized watersheds, providing a foundation for future efforts to maintain ecological health in these environments.

Neglected contributors to the transmission of bacterial antibiotic resistance in drinking water: Extracellular antibiotic resistance genes and the natural transformation

Antibiotic resistance genes (ARGs) have increasingly gained recognition as an "emerging contaminant" that poses a threat to the biosafety of drinking water. However, previous researches have primarily focused on the intracellular state of ARGs and rarely investigated the ecological characteristics (e.g., distribution and origin), environmental behavior (spread), and risks of extracellular form (eARGs) within drinking water systems. Therefore, this review evaluated isolation strategies and extraction methods for recovering eARGs from drinking water, elucidated the distribution characteristics of eARGs, and examined their impact on the antibiotic resistome from source water to tap water. We emphasized that chlorination and biological treatments significantly contribute to the prevalence and persistence of eARGs in drinking water. Moreover, we highlighted the role of biological reactors (e.g., biofilter, biological activated carbon) and drinking water distribution systems in facilitating the natural transformation of eARGs while significantly contributing to bacterial antibiotic resistance (BAR) propagation. Finally, we summarized the current risk assessment systems for ARGs and critically address remaining challenging questions necessary for better forecasting health risks associated with eARGs in drinking water environments. Collectively, this review enhances the understanding of ecological characteristics and environmental behavior of eARGs in drinking water while providing important implications for controlling and reducing BAR contamination not only in drinking water but also in other aquatic environments.

Prevalence of antibiotic resistance genes in different drinking water treatment processes in a northwest Chinese city

Antibiotic resistance genes (ARGs) are an emerging issue which are receiving increasing concerns in drinking water safety. However, the factors (e.g. treatment processes and water quality) affecting the removal efficiency of ARGs in the drinking water treatment plants (DWTPs) is still unclear. This work investigated the ARG profiles in each treatment process of two DWTPs located in a northwest Chinese city. The results showed that tetracycline and sulfonamide resistance genes were predominant among the 14 targeted ARGs. After the treatment, the Z water treatment plant which demonstrated a higher removal rate of ARGs (ranging from 50 to 80%), compared to the S plant (50-75%). And the average removal rate of tetracycline resistance genes (tetA, tetG, tetQ, tetX) was about 49.18% (S plant) and 67.50% (Z plant), as well as the removal rate of 64.2% and 72.9% for sulfonamide resistance (sul1 and sul2) at S and Z water plants, respectively. It was found that the relative abundance of main microbial communities (such as Bacteroidota, Actinobacteria, Verrucomicrobiota, Roseomonas), α-diversity index, as well as the abundance of pathogenic bacteria were all significantly reduced after different treatment processes. Network co-occurrence analysis revealed that Methylocystis possibly was the potential host for most ARGs, and sul1 was found across a broad spectrum of microorganisms in the drinking water environment. Adonis analysis showed that heavy metals and microbial communities explain solely 44.1% and 35.7% of variances of ARGs within DWTPs. This study provides insights into the contamination status and removal efficiencies of ARGs in DWTPs, offering valuable references for future studies on ARG removal, propagation, and diffusion patterns in drinking water treatment.

High-throughput profiling of antibiotic resistance genes in the Yellow River of Henan Province, China

Profiling antibiotic resistance genes (ARGs) in the Yellow River of China's Henan Province is essential for understanding the health risks of antibiotic resistance. The profiling of ARGs was investigated using high-throughput qPCR from water samples in seven representative regions of the Yellow River. The absolute and relative abundances of ARGs and moble genetic elements (MGEs) were higher in summer than in winter (ANOVA, p < 0.001). The diversity and abundance of ARGs were higher in the Yellow River samples from PY and KF than the other sites. Temperature (r = 0.470 ~ 0.805, p < 0.05) and precipitation (r = 0.492 ~ 0.815, p < 0.05) positively influenced the ARGs, while pH had a negative effect (r = - 0.462 ~ - 0.849, p < 0.05). Network analysis indicated that the pathogenic bacteria Rahnella, Bacillus, and Shewanella were the possible hub hosts of ARGs, and tnpA1 was the potential MGE hub. These findings provide insights into the factors influencing ARG dynamics and the complex interaction among the MGEs, pathogenic bacteria and environmental parameters in enriching ARGs in the Yellow River of Henan Province.

Leaching of antibiotic resistance genes and microbial assemblages following poultry litter applications in karst and non-karst landscapes

Antibiotic resistance is increasingly recognized as a critical challenge affecting human, animal, and environmental health. Yet, environmental dynamics and transport of antibiotic resistance genes (ARGs) and microbial communities in karst and non-karst leachate following poultry litter land applications are not well understood. This study investigates impacts of broiler poultry litter application on the proliferation of ARGs (tetW, qnrS, ermB, sulI, and blaCTX-M-32), class 1 integron (intI1 i), and alterations in microbial communities (16S rRNA) within karst derived soils, which are crucial and under-researched systems in the global hydrological cycle, and non-karst landscapes. Using large, intact soil columns (45 cm diam. × 100 cm depth) from karst and non-karst landscapes, the role of preferential flow and ARG transport in leachate was enumerated following surface application of poultry litter and simulated rain events. This research demonstrated that in poultry litter amended karst soils, ARG (i.e., ermB and tetW) abundance in leachate increased 1.5 times compared to non-karst systems (p < 0.05), highlighting the influence of geological factors on ARG proliferation. Notably, microbial communities in karst soil leachate exhibited increased diversity and abundance, suggesting a potential linkage between microbial composition and ARG presence. Further, our correlation and network analyses identified relationships between leachate ARGs, microbial taxa, and physicochemical properties, underscoring the complex interplay in these environmentally sensitive areas. These findings illuminate the critical role of karst systems in shaping ARG abundance and pollutant dispersal and microbial community dynamics, thus emphasizing the need for landscape-specific approaches in managing ARG dissemination to the environment. This study provides a deeper understanding of hydrogeological ARG dynamics but also lays the groundwork for future research and strategies to mitigate ARG dissemination through targeted manure applications across agricultural landscapes.

Spread of antibiotic resistance genes in drinking water reservoirs: Insights from a deep metagenomic study using a curated database

The exploration of antibiotic resistance genes (ARGs) in drinking water reservoirs is an emerging field. Using a curated database, we enhanced the ARG detection and conducted a comprehensive analysis using 2.2 Tb of deep metagenomic sequencing data to determine the distribution of ARGs across 16 drinking water reservoirs and associated environments. Our findings reveal a greater diversity of ARGs in sediments than in water, underscoring the importance of extensive background surveys. Crucial ARG carriers-specifically Acinetobacter, Pseudomonas, and Mycobacterium were identified in drinking water reservoirs. Extensive analysis of the data uncovered a considerable concern for drinking water safety, particularly in regions reliant on river sources. Mobile genetic elements have been found to contribute markedly to the propagation of ARGs. The results of this research suggest that the establishment of drinking water reservoirs for supplying raw water may be an effective strategy for alleviating the spread of water-mediated ARGs.

Distribution of antibiotic resistance genes and antibiotic residues in drinking water production facilities: Links to bacterial community

There is a rapid spread of antibiotic resistance in the environment. However, the impact of antibiotic resistance in drinking water is relatively underexplored. Thus, this study aimed to quantify antibiotic resistance genes (ARGs) and antibiotic residues in two drinking water production facilities (NW-E and NW-C) in North West Province, South Africa and link these parameters to bacterial communities. Physicochemical and ARG levels were determined using standard procedures. Residues (antibiotics and fluconazole) and ARGs were quantified using ultra-high performance liquid chromatography (UHPLC) chemical analysis and real-time PCR, respectively. Bacterial community compositions were determined by high-throughput 16S rRNA sequencing. Data were analysed using redundancy analysis and pairwise correlation. Although some physicochemical levels were higher in treated than in raw water, drinking water in NW-E and NW-C was safe for human consumption using the South African Water Quality Guideline (SAWQG). ARGs were detected in raw and treated water. In NW-E, the concentrations of ARGs (sul1, intl1, EBC, FOX, ACC and DHA) were higher in treated water than in raw water. Regarding antimicrobial agents, antibiotic and fluconazole concentrations were higher in raw than in treated water. However, in NW-C, trimethoprim concentrations were higher in raw than in treated water. Redundancy analysis showed that bacterial communities were not significantly correlated (Monte Carlo simulations, p-value >0.05) with environmental factors. However, pairwise correlation showed significant differences (p-value <0.05) for Armatimonas, CL500-29 marine group, Clade III, Dickeya and Zymomonas genera with environmental factors. The presence of ARGs and antibiotic residues in the current study indicated that antibiotic resistance is not only a clinical phenomenon but also in environmental settings, particularly in drinking water niches. Consumption of NW-E and NW-C treated water may facilitate the spread of antibiotic resistance among consumers. Thus, regulating and monitoring ARGs and antibiotic residues in drinking water production facilities should be regarded as paramount.

Airborne antibiotic and metal resistance genes - A neglected potential risk at e-waste recycling facilities

Heavy metal-rich environments can promote the selection of metal-resistance genes (MRGs) in bacteria, often leading to the simultaneous selection of antibiotic-resistance genes (ARGs) through a process known as co-selection. To comprehensively evaluate the biological pollutants at electronic-waste (e-waste) recycling facilities, air, soil, and river samples were collected at four distinct Swiss e-waste recycling facilities and analyzed for ARGs, MRGs, mobile genetic elements (MGEs), endotoxins, and bacterial species, with correlations drawn to heavy metal occurrence. To our knowledge, the present work marks the first attempt to quantify these bio-pollutants in the air of e-waste recycling facilities, that might pose a significant health risk to workers. Although ARG and MRG's profiles varied among the different sample types, intl1 consistently exhibited high relative abundance rates, identifying it as the predominant MGE across all sample types and facilities. These findings underscore its pivol role in driving diverse bacterial adaptations to extreme heavy metal exposure by selection and dissemination of ARGs and MRGs. All air samples exhibited consistent profiles of ARGs and MRGs, with blaTEM emerging as the predominant ARG, alongside pbrT and nccA as the most prevalent MRGs. However, one facility, engaged in batteries recycling and characterized by exceptionally high concentrations of heavy metals, showcased a more diverse resistance gene profile, suggesting that bacteria in this environment required more complex resistance mechanisms to cope with extreme metal exposure. Furthermore, this study unveiled a strong association between gram-negative bacteria and ARGs and less with MRGs. Overall, this research emphasizes the critical importance of studying biological pollutants in the air of e-waste recycling facilities to inform robust safety measures and mitigate the risk of resistance gene dissemination among workers. These findings establish a solid foundation for further investigations into the complex interplay among heavy metal exposure, bacterial adaptation, and resistance patterns in such distinctive ecosystems.

Antibiotic resistance genes alterations in murine guts microbiome are associated with different types of drinking water

Antibiotic resistance genes (ARGs) are emerging contaminants threatening public health and commonly found in drinking water. However, the effect of different types of drinking water on ARG alterations in the gut microbiome is unclear. This study examines this issue in murine models in three phases (phase I: acclimation using ddH2O; phase II: treatment using different types of water, i.e. river water (RW), tap water (TW) and commercial bottled water (CBW); and phase III: recovery using ddH2O) using high-throughput qPCR and 16S rRNA amplicon sequencing. Results reveal that exposure to different types of drinking water could lead to significant changes in the gut microbiome, mobile genetic elements (MGEs), and ARGs. In phase II, treatment of RW and TW significantly increased the abundance of aminoglycoside and tetracycline resistance genes in mice guts (P < 0.01). In the recovery phase, consuming distilled water was found to restore ARG profiles to a certain extent in mice guts. Procrustes, network, redundancy and variation partitioning analysis indicated that ARG alterations in mice guts might relate to MGEs and bacterial communities. Our work suggests that the type of drinking water consumed may play a crucial role in shaping ARGs in gut microbiomes, emphasizing the urgent need for access to clean drinking water to mitigate the growing threat of antimicrobial resistance.

Wastewater surveillance for antibiotics and resistance genes in a river catchment: Spatiotemporal variations and the main drivers

Wastewater-based epidemiology (WBE) is used for mining information about public health such as antibiotics resistance. This study investigated the distribution profiles of six types of antibiotic resistance genes (ARGs) in wastewater and rivers in Wuhu City, China. The levels of ARGs found in the Qingyijiang River were significantly higher than other rivers, and were comparable to effluent levels. Among the ARGs, sulfonamides ARGs and intI1 were the predominant in both wastewaters and rivers. Additionally, the concentrations of ARGs were higher on weekends as opposed to weekdays. Their distribution patterns remained consistent inter-week and inter-season using linear regression analysis (p < 0.001). Interestingly, the occurrence levels of ARGs in wastewaters during spring were significantly higher than in autumn, although insignificant in rivers. The apparent removal rate of ARGs in domestic wastewater sources ranged from 61.52-99.29%, except for qepA (-1.91% to 81.09%), whereas the removal rates in mixed domestic and industrial wastewaters showed a marked decrease (-92.94% to 76.67%). A correlation network analysis revealed that azithromycin and erythromycin were key antibiotics, while blaNDM-1, tetM, tetB, and ermB were identified as key ARGs. Sulfonamide and fluoroquinolone antibiotics, and tetracycline and macrolide ARGs were the primary contributors. Linear mixed models demonstrated that socio-economic variables positively impacted the occurrence levels of ARGs, whereas wastewater flow and river runoff were the negative drivers for their concentrations in wastewaters and surface waters, respectively. Overall, this WBE study contributes to the understanding of spatiotemporal profiles and main drivers of the occurrence of ARGs in wastewater and receiving water.

Large-Scale Biogeographical Shifts of Abundance of Antibiotic Resistance Genes and Marine Bacterial Communities as Their Carriers along a Trophic Gradient

The role of marine environments in the global spread of antibiotic resistance still remains poorly understood, leaving gaps in the One Health-based research framework. Antibiotic resistance genes (ARGs) encoding resistance to five major antibiotic classes, including sulfonamides (sul1, sul2), tetracyclines (tetA, tetB), β-lactams (blaCTX-M, blaTEMblaVIM), macrolides (ermB, mphA), aminoglycosides (aac3-2), and integrase gene (intl1) were quantified by RT-qPCR, and their distribution was investigated in relation to environmental parameters and the total bacterial community in bottom layer and surface waters of the central Adriatic (Mediterranean), over a 68 km line from the wastewater-impacted estuary to coastal and pristine open sea. Seasonal changes (higher in winter) were observed for antibiotic resistance frequency and the relative abundances of ARGs, which were generally higher in eutrophic coastal areas. In particular, intl1, followed by blaTEM and blaVIM, were strongly associated with anthropogenic influence and Gammaproteobacteria as their predominant carriers. Water column stratification and geographic location had a significant influence on ARGs distribution in the oligotrophic zone, where the bacterial community exhibited a seasonal shift from Gammaproteobacteria in winter to Marine group II in summer.

Occurrence, fate and potential health risks of antibiotic resistomes in a constructed wetlands-reservoir ecosystem for drinking water source improvement

The development of effective and feasible engineering technologies to control the transmission of antibiotic resistance genes (ARGs) and pathogenic antibiotic-resistant bacteria (PARB) form drinking water sources is urgently needed for ensuring drinking water safety. In this study, metagenomic analysis was applied to systematically explore the full profiles, removal, and potential health risks of antibiotic resistomes in a large constructed wetlands-reservoir ecosystem (CWs-R) for drinking water source improvement. A total of 343 ARG subtypes belonging to 18 ARG types were identified from water and sediment samples in the CWs-R ecosystem, with an average abundance of 0.339 copies/cell, and bacitracin and multidrug resistance genes were the predominant ARG types in the water and sediment, respectively. The CWs-R ecosystem showed an excellent removal efficiency of ARGs and mobile genetic elements (MGEs) in water, with the total removal rate reaching 64.82 % and 77.09 %, respectively, among which the emergent plant zone and ecological storage unit played major roles. The metagenomic assembly tracked many mobile ARGs and opportunistic pathogens in the CWs-R ecosystem and identified 19 contigs as ARG-carrying pathogens, including Staphylococcus aureus, Salmonella enterica, Escherichia coli, and Klebsiella pneumonia. Overall, the CWs-R ecosystem has an important role in reducing the potential public health risks posed by antibiotic resistomes in drinking water sources but still cannot fully eliminate them. Therefore, we further classified water and sediment samples in the CWs-R ecosystem and identified potential ARGs and PARB indicators based on the metagenomic analysis results by considering the potential for horizontal transfer of ARGs to opportunistic pathogens. Taken together, this work demonstrates the CWs-R ecosystem as an economical and feasible engineering technology to reduce the dissemination of antibiotic resistomes in the drinking water source, provides useful information for monitoring and controlling antibiotic resistance in similar water sources, and ensures biosafety of drinking water.

pH drives the spatial variation of antibiotic resistance gene profiles in riparian soils at a watershed scale

Owing to convenient water access, riparian areas are often sites for intensive livestock breeding industries and agriculture, which can increase the spread of antibiotic resistance genes (ARGs). However, studies on ARG profiles in riparian soils are limited and there is little information regarding the factors influencing ARGs at a watershed scale. Here, we analyzed ARG profiles, bacterial communities, and soil properties in riparian soils under different land-use types. A total of 124 ARGs and 25 mobile genetic elements (MGEs) were detected in the riparian soils, which covered almost all major classes of antibiotics. Non-metric multidimensional scaling analysis showed that both the distance to the water reservoir and land-use types played important roles in shaping ARG profiles in riparian soils at a watershed scale. Downstream soils harbored three times the abundance of ARGs compared with upstream and midstream soils. Distance-decay analysis indicated that the similarity of ARG profiles and bacterial community composition decreased significantly with the increase of geographical distance (p < 0.001). When taking the land-use type into consideration, the relative abundance and diversity of ARGs and MGEs in orchard and farmland soils were significantly higher than those in wasteland soils. This indicated that anthropogenic activities can also affect ARG patterns in riparian soils. MGE abundance was identified as major driving factors of ARG profiles. In addition, among all the examined soil properties, soil pH was found to be more important than nutrients and organic carbon in shaping ARG profiles. Our findings provide valuable data on ARG distribution in riparian soils in a reservoir catchment and highlight downstream soils is crucial for ensuring water source security.

Differential dose-response patterns of intracellular and extracellular antibiotic resistance genes under sub-lethal antibiotic exposure

Although antibiotics are one of the most significant factors contributing to the propagation of antibiotic resistance genes (ARGs), studies on the dose-response relationship at sub-lethal concentrations of antibiotics remain scarce, despite their importance for assessing the risks of antibiotics in the environment. In this study, we constructed a series of microcosms to investigate the propagation of intracellular (iARGs) and extracellular (eARGs) ARGs in both water and biofilms when exposed to antibiotics at various concentrations (1-100 μg/L) and frequencies. Results showed that eARGs were more abundant than iARGs in water, while iARGs were the dominant ARGs form in biofilms. eARGs showed differentiated dose-response relationships from iARGs. The abundance of iARGs increased with the concentration of antibiotics as enhanced selective pressure overcame the metabolic burden of antibiotic-resistant bacteria carrying ARGs. However, the abundance of eARGs decreased with increasing antibiotic concentrations because less ARGs were secreted from bacterial hosts at higher concentrations (100 μg/L). Furthermore, combined exposure to two antibiotics (tetracycline & imipenem) showed a synergistic effect on the propagation of iARGs, but an antagonistic effect on the propagation of eARGs compared to exposure to a single antibiotic. When exposed to antibiotic at a fixed total dose, one-time dosing (1 time/10 d) favored the propagation of iARGs, while fractional dosing (5 times /10 d) favored the propagation of eARGs. This study sheds light on the propagation of antibiotic resistance in the environment and can help in assessing the risks associated with the use of antibiotics.

A global perspective on compositions, risks, and ecological genesis of antibiotic resistance genes in biofilters of drinking water treatment plants

Antibiotic resistance genes (ARGs) in biofilters of drinking water treatment plants (DWTPs) are regarded to be a remarkable potential health risk to human. A global survey on ARGs in biofilters may help evaluate their risk features as a whole. This study aims to explore the compositions, risks, and ecological genesis of ARGs in the biofilters of DWTPs. In total, 98 metagenomes of DWTP biofilters were collected from Sequence Read Archive  (SRA)  of National center for Biotechnology Information (NCBI), and the main ARG types were recognized, with multidrug, bacitracin, and beta-lactam as the first three types. Source water types (surface water vs. groundwater) were found to significantly influence antibiotic resistome, overpassing biofilter media and locations. Although ARG abundances of surface water biofilters were approximately five times higher than that of groundwater biofilters, the risk pattern of ARGs was highly similar between surface water biofilters and groundwater biofilters, and up to 99.61% of the ARGs on average belong to the least risk and unassessed ranks, and only 0.23% the highest risk rank. Monobactam biosynthesis pathway and prodigiosin biosynthesis pathway, two antibiotics biosynthesis pathways, were observed to be positively correlated with several ARG types and total ARG abundance in samples of surface water and groundwater biofilters, respectively, suggesting their potential roles in ecological genesis of ARGs. Overall, the results of this study would deepen our understanding of the ARG risks in biofilters of DWTPs and shed light on their ecological genesis inside.

Antibiotic resistome alteration along a full-scale drinking water supply system deciphered by metagenome assembly: Regulated by seasonality, mobile gene elements and antibiotic resistant gene hosts

Both drinking water treatment processes and distribution can lead to antibiotic resistome variation, yet the variation of antibiotic resistome in the whole drinking water supply system (DWSS) combined with seasonality remains unknown. In this study, microbial community, antibiotic resistome, mobile genetic elements (MGEs) co-existing with antibiotic resistance genes (ARGs) and ARG hosts would be explored along a DWSS for four seasons with metagenome assembly. Multidrug and bacitracin ARGs were dominant ARGs in DWSS. Integrase, plasmids, recombinase and transposase were major MGEs co-existing with ARGs. Filtration and disinfection treatments could alter the ARG relative abundance, mainly via changing the abundance of ARG hosts (Limnohabitans and Polynucleobacter), which was influenced by water total organic carbon (TOC) content. When TOC was relatively high, filtration could proliferate ARGs via promoting antibiotic resistance bacteria (ARB) but chlorine dioxide could decrease ARGs via killing ARB. Filtration played an important role in controlling ARGs by reducing ARB when TOC was relatively low. The stimulation effect of disinfection on ARGs existed in more oligotrophic environment. Distribution could enrich ARGs in higher temperature by increasing MGEs co-occurring with ARGs and diversifying ARG hosts. MGEs co-occurring with ARGs became more abundant and diverse in disinfected water in warmer seasons. Microbial community was the most important factor determining the antibiotic resistome along a DWSS. These findings extend the knowledge about how and why water treatment processes and pipe distribution shape drinking water antibiotic resistome in different seasons.

Occurrence of antibiotic-resistant bacteria and resistance genes in the urban water cycle

This study investigates the antibiotic resistance fate in the urban water cycle, evaluating the dynamics of antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) in three different full-scale wastewater treatment plants (WWTPs) and two drinking water treatment plants (DWTPs) located in the same geographical area (North-West of Italy). ARB (tetracycline-, ampicillin-, and sulfonamide-resistant bacteria) were quantified by plate counting and the abundances of selected ARGs (i.e., tetA, bla_TEM, and sulII) and intI1 gene were measured using quantitative real-time PCR (qPCR). Higher concentrations of ARB and ARGs were observed in the WWTPs with respect to the DWTPs identifying the WWTP as hotspot for the spread of antibiotic resistances. Although a significant reduction of ARB and ARGs was observed in WWTPs and DWTPs after the treatment, none of the detected ARB or ARGs was completely removed in drinking water. The stability of the antibiotic-resistant rates between inlet and outlet associated with the reduction of relative ARG abundances underlined that both the treatments (WWTs and DWTs) did not apply any selective pressure. The overall results highlighted the importance to investigate the antibiotic resistance dynamics in aquatic ecosystems involved in urban water cycle integrating the information obtained by culture-dependent method with the culture-independent one and the need to monitor the presence of ARB and ARGs mainly in drinking water that represents a potential route of transmission to human.

Antimicrobial resistomes in food chain microbiomes

The safety and integrity of the global food system is in a constant state of flux with persistent chemical and microbial risks. While chemical risks are being managed systematically, microbial risks pose extra challenges. Antimicrobial resistant microorganism and persistence of related antibiotic resistance genes (ARGs) in the food chain adds an extra dimension to the management of microbial risks. Because the food chain microbiome is a key interface in the global health system, these microbes can affect health in many ways. In this review, we systematically summarize the distribution of ARGs in foods, describe the potential transmission pathway and transfer mechanism of ARGs from farm to fork, and discuss potential food safety problems and challenges. Modulating antimicrobial resistomes in the food chain facilitates a sustainable global food production system.

Tertiary Wastewater Treatment Processes Can Be a Double-Edged Sword for Water Quality Improvement in View of Mitigating Antimicrobial Resistance and Pathogenicity

Despite the high removal efficiency for chemical pollutants by tertiary wastewater treatment processes (TWTPs), there is no definite conclusion in terms of microbial risk mitigation yet. This study utilized metagenomic approaches to reveal the alterations of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), their co-occurrence, and potential hosts during multiple TWTPs. Results showed that the TWTPs reduced chemical pollutants in wastewater, but the denitrifying biofilter (DB) significantly increased the absolute abundances of selected antibiotic-resistant bacteria and ARGs, and simultaneously elevated the relative abundances of ARGs and VFGs through the enrichment of multidrug resistance and offensive genes, respectively. Moreover, the co-occurrence of ARGs and VFGs (e.g., bacA-tapW, mexF-adeG) was only identified after the DB treatment and all carried by Pseudomonas. Then, the ultraviolet and constructed wetland treatment showed good complementarity for microbial risk reduction through mitigating antibiotic resistance and pathogenicity. Network and binning analyses showed that the shift of key operational taxonomic units affiliating to Pseudomonas and Acinetobacter may contribute to the dynamic changes of ARGs and VFGs during the TWTPs. Overall, this study sheds new light on how the TWTPs affect the antibiotic resistome and VFG profiles and what TWTPs should be selected for microbial risk mitigation.

Gut microbiota links with cognitive impairment in amyotrophic lateral sclerosis: a multi-omics study

Recently, cognitive impairments (CI) and behavioral abnormalities in patients with amyotrophic lateral sclerosis (ALS) have been reported. However, the underlying mechanisms have been poorly understood. In the current study, we explored the role of gut microbiota in CI of ALS patients. We collected fecal samples from 35 ALS patients and 35 healthy controls. The cognitive function of the ALS patients was evaluated using the Edinburgh Cognitive and Behavioral ALS Screen. We analyzed these samples by using 16S rRNA gene sequencing as well as both untargeted and targeted (bile acids) metabolite mapping between patients with CI and patients with normal cognition (CN). We found altered gut microbial communities and a lower ratio of Firmicutes/ Bacteroidetes in the CI group, compared with the CN group. In addition, the untargeted metabolite mapping revealed that 26 and 17 metabolites significantly increased and decreased, respectively, in the CI group, compared with the CN group. These metabolites were mapped to the metabolic pathways associated with bile acids. We further found that cholic acid and chenodeoxycholic acid were significantly lower in the CI group than in the CN group. In conclusion, we found that the gut microbiota and its metabolome profile differed between ALS patients with and without CI and that the altered bile acid profile in fecal samples was significantly associated with CI in ALS patients. These results need to be replicated in larger studies in the future.

Antibiotic resistance genes in Chishui River, a tributary of the Yangtze River, China: Occurrence, seasonal variation and its relationships with antibiotics, heavy metals and microbial communities

The large-scale use and release of antibiotics may create selective pressure on antibiotic resistance genes (ARGs), causing potential harm to human health. River ecosystems have long been considered repositories of antibiotics and ARGs. Therefore, the distribution characteristics and seasonal variation in antibiotics and ARGs in the surface water of the main stream and tributaries of the Chishui River were studied. The concentrations of antibiotics in the dry season and rainy season were 54.18-425.74 ng/L and 66.57-256.40 ng/L, respectively, gradually decreasing along the river direction. The results of antibiotics in the dry season and rainy season showed that livestock and poultry breeding were the main sources in the surface water of the Chishui River basin. Risk assessments indicated high risk levels of OFL in both seasons. In addition, analysis of ARGs and microbial community diversity showed that sul1 and sul3 were the main ARGs in the two seasons. The highest abundance of ARGs was 7.70 × 10⁷ copies/L, and intl1 was significantly positively correlated with all resistance genes (p< 0.01), indicating that it can significantly promote the transmission of ARGs. Proteobacteria were the dominant microorganisms in surface water, with a higher average abundance in the dry season (60.64 %) than in the rainy season (39.53 %). Finally, correlation analyses were performed between ARGs and antibiotics, microbial communities and heavy metals. The results showed that there was a significant positive correlation between ARGs and most microorganisms and heavy metals (p< 0.01), indicating that occurrence and transmission in the environment are influenced by various environmental factors and cross-selection. In conclusion, the persistent residue and transmission of ARGs and their transfer to pathogens are a great threat to human health and deserve further study and attention.

Metagenomic binning and assembled genome analysis revealed the distinct composition of resistome and mobilome in the Ili River

Rivers play an important role in receiving and transporting the resistome among different environmental compartments. However, the difference in resistome and mobilome between the water and sediment and their underlying mechanisms were still poorly understood. In this study, the Ili River, an important water source in the arid area of Central Asia, was selected as the studied target. The comprehensive profile of resistome and mobilome and their host in water and sediment were studied based on metagenomic binning and assembled genome (MAG) analysis. The relative abundance of resistome and mobilome in sediment were 28.0 - 67.8 × /Gb and 46.5 - 121.1 × /Gb, respectively, which were significantly higher than those in water (23.1 - 52.8 ×/Gb and 25.3 - 67.7 ×/Gb). Multidrug and macrolides-lincosamides-streptogramin (MLS) resistance genes were the main ARG types in both water and sediment from relative abundance. Transposases dominated the relative abundance of mobilome, followed by insert elements and integrases. Strong correlations were found between the relative abundance of resistome and mobilome (r > 0.6 and p < 0.01) in both water and sediment, indicating the mobilome played an important role in the propagation of resistome in the Ili River. The main hosts for multidrug resistance genes via MAG analysis differed in water (Alphaproteobacteria and Gammaproteobacteria) and sediment (Gammaproteobacteria). Distinct compositions of resistome and mobilome existed between water and sediment in the Ili River. Specificity-occupancy analysis of the differential resistome and mobilome showed that occurrence frequencies and habitat selections of the differential ARGs shaped the resistome of water and sediment. In contrast, habitat was the main driver that shaped the mobilome in the Ili River.

Electrochemical degradation of antibiotics using flow-through graphene sponge electrodes

Graphene sponge electrodes doped with atomic boron and nitrogen were employed for electrochemical degradation of antibiotics sulfamethoxazole, trimethoprim, ofloxacin, and erythromycin. The removal of antibiotics that displayed strong π-π interactions (i.e., ofloxacin) with reduced graphene oxide (RGO) coating was less limited by the mass transfer and removal efficiencies > 80% were observed for the investigated range of electrolyte flowrates. At the highest applied flowrate (700 LMH), increase in the anodic current significantly worsened the removal of trimethoprim and erythromycin due to the detrimental impact of the evolving gas bubbles. Increase in current at 700 LMH led to a stepwise increase in the removal efficiency of sulfamethoxazole due to its enhanced electrosorption. Electrochemical degradation was achieved via ozone, hydrogen peroxide and hydroxyl radical (^•OH). Extraction of the employed graphene sponges confirmed the degradation of the strongly adsorbing antibiotics. Identified electrochemical transformation products of erythromycin confirmed the participation of ^•OH, through N-demethylation of the dimethylamine group. In real tap water, removal efficiencies were lower for all target antibiotics. Lower electric conductivity of tap water and thus increased thickness of the electric double layer likely limited their interaction with the graphene sponge surface, in addition to the presence of low amounts of organic matter.

Monitoring and evaluation of antibiotic resistance genes in three rivers in northeast China

Antibiotic resistance genes (ARGs) have become an important public health problem. In this study, we used metagenomic sequencing to analyze the composition of ARGs in selected original habitats of northeast China, comprising three different rivers and riverbank soils of the Heilongjiang River, Tumen River, and Yalu River. Twenty types of ARG were detected in the water samples. The major ARGs were multidrug resistance genes, at approximately 0.5 copies/16S rRNA, accounting for 57.5% of the total ARG abundance. The abundance of multidrug, bacitracin, beta-lactam, macrolide-lincosamide-streptogramin, sulfonamide, fosmidomycin, and polymyxin resistance genes covered 96.9% of the total ARG abundance. No significant ecological boundary of ARG diversity was observed. The compositions of the resistance genes in the three rivers were very similar to each other, and 92.1% of ARG subtypes were shared by all water samples. Except for vancomycin resistance genes, almost all ARGs in riverbank soils were detected in the river water. About 31.05% ARGs were carried by Pseudomonas. Opportunistic pathogenic bacteria carrying resistance genes were mainly related to diarrhea and respiratory infections. Multidrug and beta-lactam resistance genes correlated positively with mobile genetic elements (MGEs), indicating a potential risk of diffusion. The composition of ARGs in three different rivers was similar, indicating that climate plays an important role in ARG occurrence. ARG subtypes in river water were almost completely the same as those in riverbank soil. ARGs had no significant geographical distribution characteristics. Many ARGs were carried by human pathogenic bacteria related to diarrhea and respiratory infections, such as Pseudomonas aeruginosa and Aeromonas caviae. In general, our results provide a valuable dataset of river water ARG distribution in northeast China. The related ecological and geographical distribution characteristics should be further explored.

Antimicrobial Resistance in Rivers: A Review of the Genes Detected and New Challenges

River ecosystems are very important parts of the water cycle and an excellent habitat, food, and drinking water source for many organisms, including humans. Antibiotics are emerging contaminants which can enter rivers from various sources. Several antibiotics and their related antibiotic resistance genes (ARGs) have been detected in these ecosystems by various research programs and could constitute a substantial problem. The presence of antibiotics and other resistance cofactors can boost the development of ARGs in the chromosomes or mobile genetic elements of natural bacteria in rivers. The ARGs in environmental bacteria can also be transferred to clinically important pathogens. However, antibiotics and their resistance genes are both not currently monitored by national or international authorities responsible for controlling the quality of water bodies. For example, they are not included in the contaminant list in the European Water Framework Directive or in the US list of Water-Quality Benchmarks for Contaminants. Although ARGs are naturally present in the environment, very few studies have focused on non-impacted rivers to assess the background ARG levels in rivers, which could provide some useful indications for future environmental regulation and legislation. The present study reviews the antibiotics and associated ARGs most commonly measured and detected in rivers, including the primary analysis tools used for their assessment. In addition, other factors that could enhance antibiotic resistance, such as the effects of chemical mixtures, the effects of climate change, and the potential effects of the coronavirus disease 2019 pandemic, are discussed. Environ Toxicol Chem 2022;41:687-714. © 2022 SETAC.

A TbPO4-based capturer for environmental extracellular antibiotic genes by interrogating lanthanide phosphates nanoneedles

Accurate determination of antibiotic resistance genes (ARGs) in environmental DNA molecules (eDNA) is challenging owing to its low abundance in the aquatic environment. Here we report a facile and cost-efficient approach to extract trace amount of eDNAs in the aquatic environment using LnPO₄ nanomaterials. Among the nanomaterials, less crystalline TbPO₄ nanoneedles was identified as the most prominent candidate for long stranded DNA and short stranded DNA with adsorption efficiency above 97%. The adsorbed DNA was washed off from TbPO₄ nanoneedles by optimized eluant (85% PBS, 15% EtOH, 4 g/L glycine, pH 10.0) with an optimal DNA recovery of 78.83%. Our approach showed a comparable or better eDNA extraction efficiency than a commercial extraction method for different environmental samples, but 89% less cost. The high purity of the extracted eDNA was demonstrated by a high A_260/280 ratio. Using qPCR experiment, the occurrence of six common ARGs in the eDNA were detected with abundance ranging from 4.06 × 10³ to 3.51 × 10⁹ copies/L in river samples. This specific DNA capturer is valuable for the evaluation of spatial and temporal dynamic of ARGs pollution to provide insight into the potential risk with regard to the human health.

Sheet-on-sheet TiO2/Bi2MoO6 heterostructure for enhanced photocatalytic amoxicillin degradation

Developing sheet-on-sheet (2D/2D) heterostructure with built-in electric field (BIEF) is effective in boosting the performance of photocatalysts for emerging contaminants degradation. Herein, the 2D/2D microtopography and (-)TiO₂/(+)Bi₂MoO₆ BIEF were precisely integrated into hierarchical nanosheets, which can provide the basis and driving force for charge transfer both in in-plane and interface of heterojunction. The prepared photocatalyst (TiO₂/Bi₂MoO₆) showed high-efficiency and stable performance for photocatalytic amoxicillin (AMX) degradation, which was 18.2 and 5.7 times higher than TiO₂ and Bi₂MoO₆, respectively. More importantly, TiO₂/Bi₂MoO₆ showed more efficient photocatalytic activity and photogenerated charge separation than TiO₂@Bi₂MoO₆ (different morphology). Besides, four possible pathways of AMX degradation were proposed depending on Gaussian calculations and intermediates analysis by GC-MS and HPLC-TOFMS. This work sheds light on the design and construction of unique 2D/2D heterostructure photocatalysts for AMX degradation.

Risks of antibiotic resistance genes and antimicrobial resistance under chlorination disinfection with public health concerns

As a widely used disinfection technology, the effects of chlorination on antibiotic resistome and bacterial community received great scientific concerns, while the pathogens associated health risks kept largely unknown. With this concern, the present study used metagenomic analysis combined with culture method to reveal chlorination effects on antibiotic resistance genes (ARGs) and their bacterial hosts (total microbes and Escherichia coli) through simulating the chlorination dosage with human health concerns (drinking water and swimming pool). The resistome profiling showed that chlorination process could significantly decrease both abundance and diversity of total ARGs, while with limited removal rates of 6.0-8.7% for opportunistic pathogens E. coli isolates. Of all the observed 515 ARG subtypes, 105 core subtypes were identified and persistent during chlorination for both total microbes and E. coli. Antibiotic susceptibility test showed that chlorination treatment could efficiently remove multi-resistant E. coli isolates but select for tetracycline resistant isolates. Five ARG-carrying genomes (assigned to Bacteroidetes, Firmicutes, Actinobacteria) enriched by 18.1-102% after chlorination were retrieved by using metagenomic binning strategies. Bray-Curtis dissimilarity, network and procrustes analyses all indicated the remained antibiotic resistome and bacterial community were mainly chlorination-driven. Furthermore, a systematic pipeline for monitoring chlorination-associated antimicrobial resistance risks was proposed. These together enhance our knowledge of chlorination treatment associated public concerns, as important reference and guidance for surveillance and control of antibiotic resistance.

Pharmaceuticals in drinking water sources and tap water in a city in the middle reaches of the Yangtze River: occurrence, spatiotemporal distribution, and risk assessment

The occurrence of ten target pharmaceuticals was investigated in drinking water sources and tap water in a city in the middle reaches of the Yangtze River, including erythromycin (ERY), roxithromycin (RTM), ciprofloxacin (CPX), ofloxacin (OFX), sulfadiazine (SDZ), sulfamethoxazole (SMX), oxytetracycline (OTC), tetracycline (TC), ibuprofen (IBF), and naproxen (NPX). And the corresponding ecological risk for three classes of aquatic organisms and human health risk for different life stages were estimated. Results demonstrated that nine pharmaceuticals except for TC were detected with the frequencies of 20-100% and the concentrations of <LOQ-118.60 ng/L in drinking water sources. Only SMX and IBF were detected quantitatively with the highest concentrations of 0.69 ng/L and 1.28 ng/L in tap water, respectively. The concentrations of the target pharmaceuticals were lower than or comparable with those in other drinking water systems. The spatiotemporal variations of the target pharmaceuticals might be mainly attributed to their usage object, emission amount, and natural attenuation. The overall discrepancy of concentrations between drinking water sources and tap water might indicate the purification effect of drinking water treatment system. Individual pharmaceutical in drinking water resources posed negligible risks to invertebrate and fish; however, ERY, CPX, OFX, and SMX posed high risk to algae. Moreover, pharmaceutical exposure by tap water caused no risk to human health. Nevertheless, the long-term, chronic, and mixed risks of pharmaceuticals and the potential risk of antibiotic-resistant genes should be concerned. This study enriches environmental monitoring data of pharmaceuticals in drinking water sources and tap water, and provides scientific information for emerging pollutants management in drinking water system.

Whole-Genomic Analysis of NDM-5-Producing Enterobacteriaceae Recovered from an Urban River in China

Purpose

Three NDM-5-producing Enterobacteriaceae (Escherichia coli, Klebsiella pneumoniae, and Citrobacter braakii, one each) were isolated during a screening study for the presence of carbapenemase-producing Enterobacteriaceae (CPE) strains in urban rivers in China. The aim of the present study was to characterize these NDM-5-producing isolates by using whole-genome analysis.

Methods

In vitro susceptibility testing was performed using the broth microdilution method. Conjugation assay was carried out to investigate the transferability of bla_NDM-5-harboring plasmids. Whole-genome sequencing was performed using an Illumina HiSeq combined with the PacBio RSII system. The genetic characteristics of the bla_NDM-5-harboring plasmids were analyzed. Antimicrobial resistance genes and virulence genes were identified from the genome sequences. Phylogenetic analysis was performed based on core genome.

Results

Antimicrobial susceptibility testing showed that all three isolates were resistant to carbapenems, cephalosporins, quinolones, and aminoglycosides, and susceptible to colistin. Whole-genome sequencing showed that each isolate carried multiple antibiotic resistance genes mediating multidrug resistance, and harbored numerous virulence genes, some of which were located on plasmids. In these isolates, bla_NDM-5 was carried by an IncX3 plasmid in K. pneumoniae and C. braakii, and on an IncR/IncX1 plasmid in E. coli. Conjugation experiments showed that these bla_NDM-5-haboring plasmids were successfully transferred to E. coli J53. Phylogenetic analysis revealed that E. coli SCLZR49 was present in a cluster with isolates of different origin, K. pneumoniae SCLZR50 was mainly clustered with clinical isolates, and C. braakii SCLZR53 had closely genetic relationship with environmental isolates.

Conclusion

This study revealed contamination of the urban river ecosystems by clinically significant carbapenemase gene bla_NDM-5, raising the possibility of plasmid transmission into the environmental from humans and highlighting the need for a constant surveillance of CPE in the environment under the “One-Health” perspective.

Annual trends and health risks of antibiotics and antibiotic resistance genes in a drinking water source in East China

The extensive pollution of antibiotics and antibiotic resistance genes (ARGs) in drinking water has aroused worldwide concern. Successive monitoring of these pollutants has noteworthy significance for drinking water safety. Accordingly, this study conducted successive monitoring of antibiotics and ARGs from 2015 to 2017 in a drinking water source in East China. The total antibiotic concentration ranged from 19.68 ng/L to 497.00 ng/L, and decreased slightly from 2015 to 2017. Eighteen out of forty-one ARG subtypes showing resistance to six antibiotic classes and one class I integrase gene intI1, were detected in the drinking water source at concentrations ranging from 6.5 × 10⁴ copies/mL to 1.6 × 10⁶ copies/mL. Importantly, the total ARG concentration increased on an annual basis from 2015 to 2017 with an average annual increment of 0.25 orders of magnitude, which was mainly attributed to the increase in specific ARG subtypes, such as sul1, sul2, sul3, tetA, qnrB, and ermB. Most ARGs was positively correlated with the intI1 genes (r = 0.47-0.55, P < 0.01). Furthermore, the variation of antibiotics and ARGs appeared to be related to the water indices, particularly of the values of COD, BOD_5, NO₂-N (P < 0.05). This study provides basic data on antibiotic and ARG pollution in the studied drinking water source. Importantly, the findings expound that although the residual antibiotics in this drinking water source decreased slightly from 2015 to 2017, while its biological effect, the antibiotic resistance, increased annually, which give a warning of the antibiotic resistance pollution in the drinking water source.

The impact of microplastic-microbe interactions on animal health and biogeochemical cycles: A mini-review

Microplastic (MP) pollution has attracted global attention due to the extensive use of plastic products. The hydrophobic MP surface provides a habitat for multiple microorganisms. Although there have been several studies on the impact of plastic particles on microbial communities, there are few reviews that have systematically summarized the interaction between MPs and microbes and their effects on human health and biochemical circulation. The discussions in this review will take place under the following topics: (1) MPs prompt colonization, biofilm generation, and transfer of environmental microbes; (2) the microbial communities can cause the morphological alterations and biodegradation of MPs; (3) MP-microbe combinations can induce the alteration of intestinal flora and hazard animal health; (4) the biogeochemical cycles affected by MP-microbe interactions. This review will highlight the close interactions between MPs and microorganisms, and provide suggestions for future studies.

Prevalence of Antibiotic Resistance Genes, Heavy Metal Resistance Genes and the Class 1 Integron Gene in Well Water and Tap Water Samples from Four Cities in Henan Province, China

The presence of multi-resistance to both antibiotics and heavy metals in drinking water poses a significant risk to human health. Herein, we utilized qPCR to assess patterns of antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRGs), and class 1 integron (intI1) gene expression levels in well and tap water samples from four cities in Henan Province, China. The relative abundance of most index values was higher in well water relative to tap water, or was highest in Shangqiu City and lowest in Puyang City on average. The expression of ARG was closely correlated with that of intI1 and HMRG in both well and tap water. Overall, our data highlighted the health threat posed by ARGs in the drinking water supply and underscore the potential for the transfer of these genes between bacteria with the aid of intI1 under selective pressure associated with human activity and heavy metal stress.