Metagenomic exploration of antibiotic resistome in treated wastewater effluents and their receiving water

Occurrence and distribution of antibiotic resistance genes in urban rivers with black-odor water of Harbin, China

Antibiotic resistance gene contamination in polluted rivers remains a widely acknowledged environmental issue. This study focused on investigating the contamination conditions of antibiotic resistance genes (ARGs) in Harbin's urban black-odor rivers, specifically Dongfeng Ditch and Hejia Ditch. The research employed a SmartChip Real-Time PCR System to explore the types, abundance, and distribution of ARGs in diverse habitats, such as surface water and sediment. Additionally, the study examined the correlation of ARGs with mobile genetic elements (MGEs) and various environmental factors. It was found that antibiotic resistance genes were prevalent in both water and sediment within the black-odor ditches. The dominant types of ARGs identified included aminoglycoside, sulfonamide, multidrug-resistant, and β-lactam ARGs. Notably, the top four ARGs, in terms of relative abundance, were sul1, fox5, qacEdelta1-01 and aadA1. Most categories of ARGs have significant positive connections with MGEs, indicating that the enrichment and spreading of ARGs in rivers are closely related to MGEs. Based on the correlation analysis, it is found that environmental factors such as dissolved oxygen (DO), ammonia nitrogen (NH4-N), and phosphate (PO4-P) played a substantial role in influencing the variations observed in ARGs. By employing a risk assessment framework based on the human association, host pathogenicity, and mobility of ARGs, the identification of seven high-risk ARGs was achieved. In addition, it is important to assess the environmental risk of ARGs from multiple perspectives (abundance,detection rateand mobility). This study provides a significant reference regarding the presence of ARGs contamination in urban inland black-odor rivers, essential for assessing the health risks associated with ARGs and devising strategies to mitigate the threat of antibiotic resistance.

Metagenomic profiling of raw wastewater in Portugal highlights microbiota and resistome signatures of public health interest beyond the usual suspects

In response to the rapid emergence and dissemination of antimicrobial resistant bacteria (ARB) and genes (ARGs), integrated surveillance systems are needed to address antimicrobial resistance (AMR) within the One Health Era. Wastewater analyses enable biomarker monitoring at the sewershed level, offering timely insights into pathogen circulation and ARB/ARGs trends originating from different compartments. During two consecutive epidemic waves of the COVID-19 pandemic in Portugal, taxonomic and functional composition of raw urban wastewater from two wastewater treatment plants (WWTPs) representing one million in equivalent population, located in the main urban areas of the country, were profiled by shotgun metagenomics. Hospital wastewater from two central hospitals located in the WWTPs catchment areas were also sequenced. The resistome and virulome were profiled using metagenomic assemblies without taxonomic constraint, and then specifically characterized for ESKAPE pathogens. Urban and hospital wastewater exhibited specific microbiota signatures, Pseudomonadota dominated in the first and Bacteroidota in the latter. Correlation network analyses highlighted 85 (out of top 100) genera co-occurring across samples. The most frequent ARGs were classified in the multidrug, tetracyclines, and Macrolides, Lincosamides, Streptogramins (MLS) classes. Links established between AMR determinants and bacterial hosts evidenced that the diversity and abundance of ARGs is not restricted to ESKAPE, being also highly predominant among emergent enteropathogens, like Aeromonas and Aliarcobacter, or in the iron (II) oxidizer Acidovorax. The Aliarcobacter genus accumulated high abundance of sulphonamides and polymyxins ARGs, while Acinetobacter and Aeromonas hosted the highest abundance of ARGs against beta-lactams. Other bacteria (e.g. Clostridioides, Francisella, Vibrio cholerae) and genes (e.g. vanA-type vancomycin resistance) of public health interest were detected, with targeted monitoring efforts being needed to establish informative baseline data. Altogether, results highlight that wastewater monitoring is a valuable component of pathogen and AMR surveillance in healthy populations, providing a community-representative snapshot of public health trends beyond priority pathogens.

Strain-level multidrug-resistant pathogenic bacteria in urban wastewater treatment plants: Transmission, source tracking and evolution

Wastewater treatment plants (WWTPs) serve as reservoirs for various pathogens and play a pivotal role in safeguarding environmental safety and public health by mitigating pathogen release. Pathogenic bacteria, known for their potential to cause fatal infections, present a significant and emerging threat to global health and remain poorly understood regarding their origins and transmission in the environment. Using metagenomic approaches, we identified a total of 299 pathogens from three full-scale WWTPs. We comprehensively elucidated the occurrence, dissemination, and source tracking of the pathogens across the WWTPs, addressing deficiencies in traditional detection strategies. While indicator pathogens in current wastewater treatment systems such as Escherichia coli are effectively removed, specific drug-resistant pathogens, including Pseudomonas aeruginosa, Pseudomonas putida, and Aeromonas caviae, persist throughout the treatment process, challenging complete eradication efforts. The anoxic section plays a predominant role in controlling abundance but significantly contributes to downstream pathogen diversity. Additionally, evolution throughout the treatment process enhances pathogen diversity, except for upstream transmission, such as A. caviae str. WP8-S18-ESBL-04 and P. aeruginosa PAO1. Our findings highlight the necessity of expanding current biomonitoring indicators for wastewater treatment to optimize treatment strategies and mitigate the potential health risks posed by emerging pathogens. By addressing these research priorities, we can effectively mitigate risks and safeguard environmental safety and public health.

Diverse bacterial hosts and potential risk of antibiotic resistomes in ship ballast water revealed by metagenomic binning

Ship ballast water promoting the long-range migration of antibiotic resistance genes (ARGs) has raised a great concern. This study attempted to reveal ARGs profile in ballast water and decipher their hosts and potential risk using metagenomic approaches. In total, 710 subtypes across 26 ARG types were identified among the ballast water samples from 13 ships of 11 countries and regions, and multidrug resistance genes were the most dominant ARGs. The composition of ARGs were obviously different across samples, and only 5% of the ARG subtypes were shared by all samples. Procrustes analysis showed the bacterial community contributed more than the mobile genetic elements (MGEs) in shaping the antibiotic resistome. Further, 79 metagenome-assembled genomes (46 genera belong to four phyla) were identified as ARG hosts, with predominantly affiliated with the Proteobacteria. Notably, potential human pathogens (Alcaligenes, Mycolicibacterium, Rhodococcus and Pseudomonas) were also recognized as the ARG hosts. Above 30% of the ARGs hosts contained the MGEs simultaneously, supporting a pronounced horizontal gene transfer capability. A total of 43 subtypes (six percent of overall ARGs) of ARGs were assessed with high-risk, of which 23 subtypes belonged to risk Rank I (including rsmA, ugd, etc.) and 20 subtypes to the risk Rank II (including aac(6)-I, sul1, etc.). In addition, antibiotic resistance risk index indicated the risk of ARGs in ballast water from choke points of maritime trade routes was significantly higher than that from other regions. Overall, this study offers insights for risk evaluation and management of antibiotic resistance in ballast water.

Metagenomic Investigation of the Short-Term Temporal and Spatial Dynamics of the Bacterial Microbiome and the Resistome Downstream of a Wastewater Treatment Plant in the Iskar River in Bulgaria

Waste Water Treatment Plants (WWTP) aim to reduce contamination in effluent water; however, studies indicate antimicrobial resistance genes (ARGs) persist post-treatment, potentially leading to their spread from human populated areas into the environment. This study evaluated the impact of a large WWTP serving 125,000 people on the Iskar River in Bulgaria, by characterizing the spatial and short-term temporal dynamics in bacterial community dynamics and resistance profiles of the surface water. Pairs of samples were collected biweekly on four dates from two different locations, one about 800 m after the WWTP effluents and the other 10 km downstream. Taxonomic classification revealed the dominance of Pseudomonodota and Bacteriodota, notably the genera Flavobacterium, Aquirufa, Acidovorax, Polynucleobacter, and Limnohabitans. The taxonomic structure corresponded with both lentic and lotic freshwater habitats, with Flavobacterium exhibiting a significant decrease over the study period. Principal Coordinate Analysis revealed statistically significant differences in bacterial community composition between samples collected on different dates. Differential abundance analysis identified notable enrichment of Polynucleobacter and Limnohabitans. There were shifts within the enriched or depleted bacterial taxa between early and late sampling dates. High relative abundance of the genes erm(B), erm(F), mph(E), msr(E) (macrolides); tet(C), tet(O), tet(W), tet(Q) and tet(X) (tetracyclines); sul1 and sul2 (sulphonamides); and cfxA3, cfxA6 (beta-lactams) were detected, with trends of increased presence in the latest sampling dates and in the location closer to the WWTP. Of note, genes conferring resistance to carbapenems blaOXA-58 and blaIMP-33-like were identified. Co-occurrence analysis of ARGs and mobile genetic elements on putative plasmids showed few instances, and the estimated human health risk score (0.19) according to MetaCompare2.0 was low. In total, 29 metagenome-assembled genomes were recovered, with only a few harbouring ARGs. This study enhances our understanding of freshwater microbial community dynamics and antibiotic resistance profiles, highlighting the need for continued ARGs monitoring.

Metagenome sequencing reveals shifts in phage-associated antibiotic resistance genes from influent to effluent in wastewater treatment plants

Antibiotic resistance poses a significant threat to global health, and the microbe-rich activated sludge environment may contribute to the dissemination of antibiotic resistance genes (ARGs). ARGs spread across various bacterial populations via multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages (phages). However, the potential role of phages in spreading ARGs in wastewater treatment systems remains unclear. This study characterized the core resistome, mobile genetic elements (MGEs), and virus-associated ARGs (vir_ARGs) in influents (Inf) and effluents (Eff) samples from nine WWTPs in eastern China. The abundance of ARGs in the Inf samples was higher than that in the Eff samples. A total of 21 core ARGs were identified, accounting for 38.70 %-83.70 % of the different samples. There was an increase in MGEs associated with phage-related processes from influents to effluents (from 12.68 % to 21.10 %). These MGEs showed strong correlations in relative abundance and composition with the core ARGs in the Eff samples. Across the Inf and Eff samples, 58 unique vir_ARGs were detected, with the Eff samples exhibiting higher diversity of vir_ARGs than the Inf samples. Statistical analyses indicated a robust relationship between core ARG profile, MGEs associated with phage-related processes, and vir_ARG composition in the Eff samples. Additionally, the co-occurrence of MGEs and ARGs in viral genomes was observed, ranging from 22.73 % to 68.75 %. This co-occurrence may exacerbate the persistence and spread of ARGs within WWTPs. The findings present new information on the changes in core ARGs, MGEs, and phage-associated ARGs from influents to effluents in WWTPs and provide new insights into the role of phage-associated ARGs in these systems.

Effects of wastewater treatment plant effluent on microbial risks of pathogens and their antibiotic resistance in the receiving river

The increase in effluent discharge from wastewater treatment plants (WWTPs) into urban rivers has raised concerns about the potential effects on pathogen risks. This study utilized metagenomic sequencing combined with flow cytometry to analyze pathogen concentrations and antibiotic resistance in a typical effluent-receiving river. Quantitative microbial risk assessment (QMRA) was employed to assess the microbial risks of pathogens. The results indicated obvious spatial-temporal differences (i.e., summer vs. winter and effluent vs. river) in microbial composition. Microcystis emerged as a crucial species contributing to these variations. Pathogen concentrations were found to be higher in the river than in the effluent, with the winter exhibiting higher concentrations compared to the summer. The effluent discharge slightly increased the pathogen concentrations in the river in summer but dramatically reduced them in winter. The combined effects of cyanobacterial bloom and high temperature were considered key factors suppressing pathogen concentrations in summer. Moreover, the prevalence of antibiotic resistance of pathogens in the river was inferior to that in the effluent, with higher levels in winter than in summer. Three high-concentration pathogens (Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa) were selected for QMRA. The results showed that the risks of pathogens exceeded the recommended threshold value. Escherichia coli posed the highest risks. And the fishing scenario posed significantly higher risks than the walking scenario. Importantly, the effluent discharge helped reduce the microbial risks in the receiving river in winter. The study contributes to the management and decision-making regarding microbial risks in the effluent-receiving river.

Mapping the spread and mobility of antibiotic resistance in wastewater due to COVID-19 surge

Large amounts of antibiotics have been discharged into wastewater during the COVID-19 pandemic due to overuse and misuse of antibiotics to treat patients. Wastewater-based surveillance can be used as an early warning for antibiotic resistance (AR) emergence. The present study analyzed municipal wastewater corresponding to the major pandemic waves (WW1, WW2, and WW3) in India along with hospital wastewater (Ho) taken as a benchmark for AR. Commonly prescribed antibiotics during a pandemic, azithromycin and cefixime residues, were found in the range of 2.1-2.6 μg/L in Ho and WW2. Total residual antibiotic concentration was less in WW2; however, the total antibiotic resistance gene (ARG) count was 1065.6 ppm compared to 85.2 ppm in Ho. Metagenome and RT-qPCR analysis indicated a positive correlation between antibiotics and non-corresponding ARGs (blaOXA, aadA, cat, aph3, and ere), where 7.2-7.5% was carried by plasmid in the bacterial community of WW1 and WW2. Moreover, as the abundance of the dfrA and int1 genes varied most among municipal wastewater, they can be suggested as AR markers for the pandemic. The common pathogens Streptococcus, Escherichia, Shigella, and Aeromonas were putative ARG hosts in metagenome-assembled genomes. The ARG profile and antibiotic levels varied between municipal wastewaters but were fairly similar for WW2 and Ho, suggesting the impact of the pandemic in shaping the resistome pattern. The study provides insights into the resistome dynamic, AR markers, and host-ARG association in wastewater during the COVID-19 surge. Continued surveillance and identification of intervention points for AR beyond the pandemic are essential to curbing the environmental spread of ARGs in the near future.

Application of high-throughput sequencing technologies and analytical tools for pathogen detection in urban water systems: Progress and future perspectives

The ubiquitous presence of pathogenic microorganisms, such as viruses, bacteria, fungi, and protozoa, in urban water systems poses a significant risk to public health. The emergence of infectious waterborne diseases mediated by urban water systems has become one of the leading global causes of mortality. However, the detection and monitoring of these pathogenic microorganisms have been limited by the complexity and diversity in the environmental samples. Conventional methods were restricted by long assay time, high benchmarks of identification, and narrow application sceneries. Novel technologies, such as high-throughput sequencing technologies, enable potentially full-spectrum detection of trace pathogenic microorganisms in complex environmental matrices. This review discusses the current state of high-throughput sequencing technologies for identifying pathogenic microorganisms in urban water systems with a concise summary. Furthermore, future perspectives in pathogen research emphasize the need for detection methods with high accuracy and sensitivity, the establishment of precise detection standards and procedures, and the significance of bioinformatics software and platforms. We have compiled a list of pathogens analysis software/platforms/databases that boast robust engines and high accuracy for preference. We highlight the significance of analyses by combining targeted and non-targeted sequencing technologies, short and long reads technologies, sequencing technologies, and bioinformatic tools in pursuing upgraded biosafety in urban water systems.

Wastewater treatment plant effluents exert different impacts on antibiotic resistome in water and sediment of the receiving river: Metagenomic analysis and risk assessment

Wastewater treatment plants (WWTPs) are considered as hotspots for the spread of antibiotic resistome into the environment. However, the differential contributions of WWTPs to the antibiotic resistome in the receiving river water and sediment are poorly understood. Here, based on metagenomic analysis, we found that the WWTP effluents significantly elevated the diversities and abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in the receiving river water from the Qinghai-Tibet Plateau, but showed less interference with the antibiotic resistome in sediment. Estimated by SourceTracker, WWTPs contributed 60.691.8% of ARGs in downstream river water, much higher than those for sediment (7.7568.0%). A holistic comparison of ARG risks based on analysis of ARG combination, mobility risk, ARG hosts and ARG-carrying pathogens further revealed the great impacts of WWTP effluents on downstream river water rather than sediment. Among various MGEs, tnpA exhibited the greatest potential for the dissemination of ARGs, and displayed highest co-occurrence frequency with multiple ARGs. P. aeruginosa, E. cloacae, and E. coli were identified as the critical-priority pathogens of ARG hosts. This study demonstrated the much greater impacts of WWTP effluents on the downstream water compared with sediment, which is significant for developing effective strategies to mitigate ARG risks.

Comparison of antibiotic-resistant Escherichia coli and extra-intestinal pathogenic E. coli from main river basins under different levels of the sewer system development

Antimicrobial-resistant Escherichia coli in the aquatic environments is considered a strong indicator of sewage or animal waste contamination and antibiotic pollution. Sewer construction and wastewater treatment plant (WWTP) infrastructure may serve as concentrated point sources of contamination of antibiotic-resistant bacteria and antibiotic resistance genes. In this study, we focused on the distribution of antimicrobial-resistant E. coli in two rivers with large drainage areas and different urbanisation levels. E. coli from Kaoping River with drainage mainly from livestock farming had higher resistance to antibiotics (e.g. penicillins, tetracyclines, phenicols, aminoglycosides, and sulpha drugs) and presented more positive detection of antibiotic-resistance genes (e.g. ampC, blaTEM, tetA, and cmlA1) than that from Tamsui River. In Kaoping River with a lower percentage of sewer construction nearby (0-30%) in contrast to a higher percentage of sewer construction (55-92%) in Tamsui River, antimicrobial-resistant E. coli distribution was related to livestock farming waste. In Tamsui River, antimicrobial resistant E. coli isolates were found more frequently in the downstream drainage area of WWTPs with secondary water treatment than that of WWTPs with tertiary water treatment. The Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR showed that the fingerprinting group was significantly related to the sampling site (p < 0.01) and sampling date (p < 0.05). By utilising ERIC-PCR in conjunction with antibiotic susceptibility and antibiotic-resistance gene detection, the relationship among different strains of E. coli could be elucidated. Furthermore, we identified the presence of six extra-intestinal pathogenic E. coli isolates and antibiotic-resistant E. coli isolates near drinking water sources, posing a potential risk to public health through community transmission. In conclusion, this study identified environmental factors related to antibiotic-resistant bacteria and antibiotic-resistance gene contamination in rivers during urban development. The results facilitate the understanding of specific management of different waste streams across different urban areas. Periodic surveillance of the effects of WWTPs and livestock waste containing antibiotic-resistant bacteria and antibiotic-resistance genes on river contamination is necessary.

Antimicrobial resistome and mobilome in the urban river affected by combined sewer overflows and wastewater treatment effluent

The dissemination of antimicrobial resistance in the environment is an emerging global health problem. Wastewater treatment effluent and combined sewer overflows (CSOs) are major sources of antimicrobial resistance in urban rivers. This study aimed to clarify the effect of municipal wastewater treatment effluent and CSO on antimicrobial resistance genes (ARGs), mobile gene elements, and the microbial community in an urban river. The ARG abundance per 16S-based microbial population in the target river was 0.37-0.54 and 0.030-0.097 during the CSO event and dry weather, respectively. During the CSO event, the antimicrobial resistome in the river shifted toward a higher abundance of ARGs to clinically important drug classes, including macrolide, fluoroquinolone, and β-lactam, whereas ARGs to sulfonamide and multidrug by efflux pump were relatively abundant in dry weather. The abundance of intI1 and tnpA genes were highly associated with the total ARG abundance, suggesting their potential application as an indicator for estimating resistome contamination. Increase of prophage during the CSO event suggested that impact of CSO has a greater potential for horizontal gene transfer (HGT) via transduction. Consequently, CSO not only increases the abundance of ARGs to clinically important antimicrobials but also possibly enhances potential of HGT in urban rivers.

Ecotoxicity and resistance genes induction changing of antibiotic tetracycline degradation products dominated by differential free radicals

Studying the ecological risks of antibiotics and their degradation products is of great importance to water environment security and advanced oxidation processes (AOPs) development. This work studied the changes and internal influencing mechanisms of ecotoxicity and the capacity for inducing antibiotic resistance genes (ARGs) shown by the tetracycline (TC) degradation products generated in AOPs with differential free radicals. Under the action of superoxide radicals and singlet oxygen in the ozone system, and sulfate and hydroxyl radicals in the thermally activated potassium persulfate system, TC exhibited differential degradation pathways and resulted in the differential growth inhibition trends on the determined strains. Microcosm experiments combined with metagenomics were also performed to analyze the remarkable changes in the TC resistance genes tetA (60), tetT, and otr(B) induced by the degradation products and ARG hosts in the natural water environment. Microcosm experiments exhibited that the microbial community in actual water have changed significantly with the addition of TC and degradation intermediates. Furthermore, the richness of genes related to oxidative stress was investigated to discuss the effect on reactive oxygen species production and SOS response caused by TC and its intermediates.

Metagenomic surveillance of antibiotic resistome in influent and effluent of wastewater treatment plants located on the Qinghai-Tibetan Plateau

As hotspots for the dissemination of antibiotic resistance genes (ARGs), wastewater treatment plants (WWTPs) have attracted global attention. However, there lacks a sufficient metagenomic surveillance of antibiotic resistome in the WWTPs located on the Qinghai-Tibet Plateau. Here, metagenomic approaches were used to comprehensively investigate the occurrence, mobility potential, and bacterial hosts of ARGs in influent and effluent of 18 WWTPs located on the Qinghai-Tibet Plateau. The total ARG relative abundances and diversity were significantly decreased from influent to effluent across the WWTPs. Multidrug, bacitracin, sulfonamide, aminoglycoside, and beta-lactam ARGs generally consisted of the main ARG types in effluent samples, which were distinct from influent samples. A group of 72 core ARGs accounting for 61.8-95.8 % of the total ARG abundances were shared by all samples. Clinically relevant ARGs mainly conferring resistance to beta-lactams were detected in influent (277 ARGs) and effluent (178 ARGs). Metagenomic assembly revealed that the genetic location of an ARG on a plasmid or a chromosome was related to its corresponding ARG type, demonstrating the distinction in the mobility potential of different ARG types. The abundance of plasmid-mediated ARGs accounted for a much higher proportion than that of chromosome-mediated ARGs in both influent and effluent. Moreover, the ARGs co-occurring with diverse mobile genetic elements in the effluent exhibited a comparable mobility potential with the influent. Furthermore, 137 metagenome-assembled genomes (MAGs) assigned to 13 bacterial phyla were identified as the ARG hosts, which could be effectively treated in most WWTPs. Notably, 46 MAGs were found to carry multiple ARG types and the potential pathogens frequently exhibited multi-antibiotic resistance. Some ARG types tended to be carried by certain bacteria, showing a specific host-resistance association pattern. This study highlights the necessity for metagenomic surveillance and will facilitate risk assessment and control of antibiotic resistome in WWTPs located on the vulnerable area.

Variations in antibiotic resistance genes and microbial community in sludges passing through biological nutrient removal and anaerobic digestion processes in municipal wastewater treatment plants

Antimicrobial resistance (AMR) represents a relentless, silent pandemic. Contributing to this are wastewater treatment plants (WWTPs), a potential source of antibiotic resistance genes' (ARGs) transmission to the environment, threatening public health. The presence of ARGs in pathogenic bacteria and their release into the environment by WWTPs threatens the public health. The current study investigated changes in ARGs' abundance in biological nutrient removal (BNR) processes and anaerobic digestion (AD) reactors of two WWTPs. Also, microbial community structure, which is known to shape the distribution and abundance of ARGs, was also analyzed. The relative abundance of eight ARGs (tetX, tetA, tetM, TEM, sul1, sul2, ermB and qnrD) was quantified as ARGs' copies/16 S rRNA gene copies using quantitative polymerase chain reaction (qPCR). Microbial community composition was assessed by 16 S rRNA microbiome sequencing analysis. TetX was prevalent among the eight ARGs, followed by TEM and sul1. However, its abundance was decreased in the AD sludges compared to BNR sludges. Proteobacteria was the major bacterial phylum found in all the sludge samples, while Arcobacter, 12up and Acidovorax were the predominant genera. Acinetobacter and Flavobacterium were significantly more abundant in the BNR sludges, while 12up and Aeromonas were predominant in AD sludges. Principal component analysis (PCA) revealed a clear difference in dominant ARGs and bacteria between the sludges in the processes of BNR and AD of the two WWTPs. Clinically relevant bacterial genera, Klebsiella and Enterococcus, found in both the BNR and AD sludges, were significantly correlated with the tetX gene. Throughout this study, the relationship between microbial communities and specific ARGs was revealed, illustrating that the composition of the microbial community could play a vital role in the abundance of ARGs. These results will better inform future studies aimed at controlling the spread of ARGs and their potential hosts from WWTPs.

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.

Urban monitoring of antimicrobial resistance during a COVID-19 surge through wastewater surveillance

During the early phase of the COVID-19 pandemic, infected patients presented with symptoms similar to bacterial pneumonias and were treated with antibiotics before confirmation of a bacterial or fungal co-infection. We reasoned that wastewater surveillance could reveal potential relationships between reduced antimicrobial stewardship, specifically misprescribing antibiotics to treat viral infections, and the occurrence of antimicrobial resistance (AMR) in an urban community. Here, we analyzed microbial communities and AMR profiles in sewage samples from a wastewater treatment plant (WWTP) and a community shelter in Las Vegas, Nevada during a COVID-19 surge in December 2020. Using a respiratory pathogen and AMR enrichment next-generation sequencing panel, we identified four major phyla in the wastewater, including Actinobacteria, Firmicutes, Bacteroidetes and Proteobacteria. Consistent with antibiotics that were reportedly used to treat COVID-19 infections (e.g., fluoroquinolones and beta-lactams), we also measured a significant spike in corresponding AMR genes in the wastewater samples. AMR genes associated with colistin resistance (mcr genes) were also identified exclusively at the WWTP, suggesting that multidrug resistant bacterial infections were being treated during this time. We next compared the Las Vegas sewage data to local 2018-2019 antibiograms, which are antimicrobial susceptibility profile reports about common clinical pathogens. Similar to the discovery of higher levels of beta-lactamase resistance genes in sewage during 2020, beta-lactam antibiotics accounted for 51 ± 3 % of reported antibiotics used in antimicrobial susceptibility tests of 2018-2019 clinical isolates. Our data highlight how wastewater-based epidemiology (WBE) can be leveraged to complement more traditional surveillance efforts by providing community-level data to help identify current and emerging AMR threats.

How multi-walled carbon nanotubes in wastewater influence the fate of coexisting antibiotic resistant genes in the subsequent disinfection process

Wastewater treatment plants (WWTPs) are important hubs for the spread of antibiotic resistance genes (ARGs). Engineered nanoparticles, which was inevitably released to WWTPs, could change environmentally sensitive of antibiotic resistant bacteria (ARB). This would influence the fate of ARGs in subsequent disinfection process and consequent health risk. In this study, the ARGs fate of the effluent in conventional sodium hypochlorite (NaClO) disinfection process was investigated as multi-walled carbon nanotubes (MWCNTs) existed in sequencing batch reactor (SBR). The results showed the existence of MWCNTs in SBR could enhance the removal efficiency of intracellular 16S rRNA gene and intI1, extracellular intI1, sul2 and tetX in the effluent by NaClO. This is mainly due to the variation of bacterial physiological status, bacterial population structure and the activation of NaClO under the role of MWCNTs. MWCNTs in SBR could increase in membrane permeability of bacterial cells, which would be conducive to the penetration of chlorination to cytoplasm. MWCNTs in SBR also could change the bacterial population structure and induce the chlorine-sensitive bacteria; thus the potential hosts of ARGs in the effluent would be more easily inactivated by NaClO. Moreover, the residual MWCNTs in the effluent could activate NaClO to generate various free radical, which would enhance the oxidizing capacity of chlorination.

Spatial and temporal effects of fish feed on antibiotic resistance in coastal aquaculture farms

For the first time, both spatial and temporal effects of fish feed on changes in abundance of antibiotic resistance genes (ARGs) were investigated in South Korea via quantifying ARGs and analyzing physicochemical parameters in the influent (IN) and effluent before (BF) and 30 min after (AF) the fish feeding time of sixteen flow-through fish farms. The absolute abundance of ARGs in AF samples was 5 times higher than in BF and 12 times higher than in IN samples. Values of physicochemical parameters such as ammonia, total nitrogen, suspended solids and turbidity in the effluent significantly increased by 21.6, 4.2, 2.6 and 1.65 times, respectively, after fish feeding. Spatially, the fish farms on Jeju Island exhibited higher relative abundance (3.02 × 10^-4 - 6.1 × 10^-2) of ARGs compared to the farms in nearby Jeollanam-do (3.4 × 10^-5 - 8.3 × 10^-3). Seasonally, samples in summer and autumn showed a higher abundance of ARGs than in winter and spring. To assess risk to the food chain as well as public health, further studies are warranted to explore the pathogenic potential of these ARGs.

Anthropogenic impacts on antibiotic resistance genes and their hosts from pristine to urban river using metagenomic and binning approaches

Driven by anthropogenic pressure, Antibiotic resistance genes (ARGs) could transfer from the environmental resistome into human commensals or even pathogens. The transport of ARGs through aquatic ecosystems is crucial and has attracted attention. Here, we employed metagenomic and binning to compare ARGs profiles, their co-occurrence with metal resistance genes (MRGs) and mobile genetic elements (MGEs), and their hosts between pristine and anthropogenic influenced rivers and explore the ecological mechanisms underlying the dissemination of ARGs induced by anthropogenic activities. The significantly increased relative abundance of macrolide-lincosamide-streptogramins, vancomycin, β-lactam and sulfonamide resistance genes along the environmental gradient from pristine to polluted sediments implied that anthropogenic impact aided the emergence and dissemination of certain ARGs. At the lower reach of the Ba River, the higher ratios for contigs carrying more than one ARG suggested that anthropogenic pollution favored the co-occurrence of multiple ARGs. Anthropogenic pressures also increased the relative abundance of advantaged hosts, including Chloroflexi, Firmicutes and Euryarchaeota. At the lower reach of Ba River, Romboutsia timonensis carrying multiple ARGs and ICEs were successfully recovered, posing a serious threat to human health by affecting the metabolism of gut microbiomes. And Methanothrix soehngenii affiliated to archaea carrying multiple ARGs, MRGs and ICEs were also recovered from the lower Ba River. The partial least squares path modeling revealed that MGEs were the most predominant factors inducing the ARG profiles, and the antibiotic resistance could be enriched by co-transfer with MRGs. Furthermore, environmental factors could impact the ARG profiles indirectly by first influencing the ARGs' hosts.

The balance between treatment efficiency and receptor quality determines wastewater impacts on the dissemination of antibiotic resistance

This study investigated the balance between treatment efficiency and impact caused by urban wastewater treatment plants (UWTPs) on the dissemination of antibiotic resistance. Four full-scale UWTPs (PT1-PT4) and the receiving river were sampled over four campaigns. The 16 S rRNA gene, two mobile genetic elements (MGEs), eight antibiotic resistance genes (ARGs), and culturable bacteria were monitored over different treatment stages and in hospital effluent. The bacterial and antibiotic resistance load was not significantly different in the inflow of the four UWTPs (p > 0.01). Biological treatment promoted ARGs reduction values up to 2.5 log-units/mL, while UV (PT1, PT2) or sand filtration/ozonation (PT3) led to removal values < 0.6 log-units/mL. The final effluent of PT3, with the highest removal rates and significantly lower ARGs abundance, was not significantly different from the receiving water body. Emerging ARGs (e.g., bla_VIM, bla_OXA-48, and bla_KPC) were sporadically detected in the river, although more frequent downstream. Hospital effluent might contribute for the occurrence of some, but not all these ARGs in the river. A major conclusion was that the impact of the UWTPs on the river was not only determined by treatment efficiency and final effluent quality, but also by the background contamination of the river and/or dilution rate.

Metagenomics analysis of probable transmission of determinants of antibiotic resistance from wastewater to the environment - A case study

During mechanical-biological treatment, wastewater droplets reach the air with bioaerosols and pose a health threat to wastewater treatment plant (WWTP) employees and nearby residents. Microbiological pollutants and antimicrobial resistance determinants are discharged to water bodies with treated wastewater (TWW), which poses a potential global epidemiological risk. In the present study, the taxonomic composition of microorganisms was analyzed, and the resistome profile and mobility of genes were determined by metagenomic next-generation sequencing in samples of untreated wastewater (UWW), wastewater collected from an activated sludge (AS) bioreactor, TWW, river water collected upstream and downstream from the wastewater discharge point, and in upper respiratory tract swabs collected from WWTP employees. Wastewater and the emitted bioaerosols near WWTP's facilities presumably contributed to the transmission of microorganisms, in particular bacteria of the phylum Actinobacteria and the associated antibiotic resistance genes (ARGs) (including ermB, ant(2″)-I, tetM, penA and cfxA2) to the upper respiratory tract of WWTP employees. The discharged wastewater increased the taxonomic diversity of microorganisms and the concentrations of various ARGs (including bacA, emrE, sul1, sul2 and tetQ) in river water. This study fills in the knowledge gap on the health risks faced by WWTP employees. The study has shown that microbiological pollutants and antimicrobial resistance determinants are also in huge quantities discharged to rivers with TWW, posing a potential global epidemiological threat.

Bacterial Hosts and Genetic Characteristics of Antibiotic Resistance Genes in Wastewater Treatment Plants of Xinjiang (China) Revealed by Metagenomics

Antibiotic resistance genes (ARGs) pose a widespread concern for human health and wastewater treatment plants (WWTPs) are considered to be a major source of ARG transmission. In this paper, the potential hosts and genetic characteristics of ARGs in the influent, activated sludge and effluent of WWTPs in Xinjiang were studied by metagenomics. Bacitracin resistance gene (bacA), beta-lactamase gene (class A beta-lactamase), multidrug resistance genes (mexD, qacEdelta1), and sulfonamide resistance genes (sul1, and sul2) are persistent antibiotic resistance genes (PARGs). The potential hosts of ARGs were mainly pathogens, with Escherichia coli (12.9%), Acinetobacter johnsonii (8.94%), and Klebsiella pneumoniae (5.30%) accounting for the highest proportions. Chromosomal sequences and plasmid sequences accounted for 42.0% and 22.6% of ARG-carrying contigs (ACCs) in the influent, respectively. Meanwhile, the effluent contained 58.3% of ACCs in plasmids and 8.30% in chromosomes. Bacitracin resistance genes and multidrug resistance genes were mainly carried by chromosomes, while resistance genes for macrolide–lincosamide–streptogramin (MLS), vancomycin, sulfonamide, beta-lactam, tetracycline, chloramphenicol, and aminoglycoside were mainly carried by plasmids. ICEPae690-sul1-qacEdelta1 and ICEPmiChn3-sul2 were stable coexistence structures and heighten the transfer potential of ARGs in the environment. This study provided a clearer picture of host bacterial sources and genetic context of ARGs in the environment.

Effect of ozonation-based disinfection methods on the removal of antibiotic resistant bacteria and resistance genes (ARB/ARGs) in water and wastewater treatment: a systematic review

Antibiotic resistance is considered a universal health threat of the 21st century which its distribution and even development are mainly mediated by water-based media. Disinfection processes with the conventional methods are still the most promising options to combat such crises in aqueous matrices especially wastewater. Knowing that the extent of effectiveness and quality of disinfection is of great importance, this paper aimed to systematically review and discuss ozonation (as one of the main disinfectants with large scale application) effect on removing antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) from aqueous solutions, for which no study has been reported. For this, a comprehensive literature survey was performed within the international databases using appropriate keywords which yielded several studies involving different aspects and the effectiveness extent of ozonation on ARB & ARGs. The results showed that no definite conclusion could be drawn about the superiority of ozone alone or in a hybrid form. Mechanism of action was carefully evaluated and discussed although it is still poorly understood. Evaluation of the studies from denaturation and repairment perspectives showed that regrowth cannot be avoided after ozonation, especially for some ARB & ARGs variants. In addition, the comparison of the effectiveness on ARB & ARGs showed that ozonation is more effective for resistant bacteria than their respective genes. The degradation efficiency was found to be mainly influenced by operational parameters of CT (i.e. ozone dose & contact time), solids, alkalinity, pH, and type of pathogens and genes. Moreover, the correlation between ARB & ARGs removal and stressors (such as antibiotic residuals, heavy metals, aromatic matters, microcystins, opportunistic pathogens, etc.) has been reviewed to give the optimal references for further in-depth studies. The future perspectives have also been reported.

Higher abundance of core antimicrobial resistant genes in effluent from wastewater treatment plants

Wastewater treatment plants (WWTPs) receive sewage water from a variety of sources, including livestock farms, hospitals, industries, and households, that contain antimicrobial resistant bacteria (ARB) and antimicrobial resistant genes (ARGs). Current treatment technologies are unable to completely remove ARB and ARGs, which are eventually released into the aquatic environment. This study focused on the core resistome of urban WWTPs that are persistent through wastewater treatment processes. We adopted the Hiseq-based metagenomic sequencing approach to identify the core resistome, their genetic context, and pathogenic potential of core ARGs in the influent (IN) and effluent (EF) samples of 12 urban WWTPs in South Korea. In this study, the abundance of ARGs ranged from 0.32 to 3.5 copies of ARGs per copy of the 16S rRNA gene, where the IN samples were relatively higher than the EF samples, especially for the macrolide-lincosamide-streptogramin (MLS)- and tetracycline- resistant genes. On the other hand, there were 43 core ARGs sharing up to 90% of the total, among which the relative abundance of sul1, APH(3'')-lb, and RbpA was higher in EF than in IN (p < 0.05). Moreover, tetracycline and sulfonamide-related core ARGs in both EF and IN were significantly more abundant on plasmids than on chromosomes (p < 0.05). We also found that the majority of core ARGs were carried by opportunistic pathogens such as Acinetobacter baumannii, Enterobacter cloacae, and Pseudomonas aeruginosa in both IN and EF. In addition, phages were the only mobile elements whose abundance correlated with that of core ARGs in EF, suggesting that transduction may play a major role in disseminating ARGs in the receiving water environment of the urban WWTP. The persistent release of core ARGs with pathogenic potential into environmental water is of immediate concern. The mobility of ARGs and ARBs in the environment is a major public health concern. These results should be taken into consideration when developing policy to mitigate environmental dissemination of ARG by WWTPs.

Metagenomic analysis of MWWTP effluent treated via solar photo-Fenton at neutral pH: Effects upon microbial community, priority pathogens, and antibiotic resistance genes

The effectiveness of advanced technologies on eliminating antibiotic resistant bacteria (ARB) and resistance genes (ARGs) from wastewaters have been recently investigated. Solar photo-Fenton has been proven effective in combating ARB and ARGs from Municipal Wastewater Treatment Plant effluent (MWWTPE). However, most of these studies have relied solely on cultivable methods to assess ARB removal. This is the first study to investigate the effect of solar photo-Fenton upon ARB and ARGs in MWWTPE by high throughput metagenomic analysis (16S rDNA sequencing and Whole Genome Sequencing). Treatment efficiency upon priority pathogens and resistome profile were also investigated. Solar photo-Fenton (30 mg L-1 of Fe2+ intermittent additions and 50 mg L-1 of H2O2) reached 76-86% removal of main phyla present in MWWTPE. An increase in Proteobacteria abundance was observed after solar photo-Fenton and controls in which H2O2 was present as an oxidant (Fenton, H2O2 only, solar/H2O2). Hence, tolerance mechanisms presented by this group should be further assessed. Solar photo-Fenton achieved complete removal of high priority Staphylococcus and Enterococcus, as well as Klebsiella pneumoniae and Pseudomonas aeruginosa. Substantial reduction of intrinsically multi-drug resistant bacteria was detected. Solar photo-Fenton removed nearly 60% of ARGs associated with sulfonamides, macrolides, and tetracyclines, and complete removal of ARGs related to β-lactams and fluoroquinolones. These results indicate the potential of using solar-enhanced photo-Fenton to limit the spread of antimicrobial resistance, especially in developing tropical countries.

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.

Diversity of Multidrug-Resistant Bacteria in an Urbanized River: A Case Study of the Potential Risks from Combined Sewage Overflows

Wastewater contamination and urbanization contribute to the spread of antibiotic resistance in aquatic environments. This is a particular concern in areas receiving chronic pollution of untreated waste via combined sewer overflow (CSO) events. The goal of this study was to expand knowledge of CSO impacts, with a specific focus on multidrug resistance. We sampled a CSO-impacted segment of the James River (Virginia, USA) during both clear weather and an active overflow event and compared it to an unimpacted upstream site. Bacteria resistant to ampicillin, streptomycin, and tetracycline were isolated from all samples. Ampicillin resistance was particularly abundant, especially during the CSO event, so these isolates were studied further using disk susceptibility tests to assess multidrug resistance. During a CSO overflow event, 82% of these isolates were resistant to five or more antibiotics, and 44% were resistant to seven or more. The latter statistic contrasts starkly with the upstream reference site, where only 4% of isolates displayed resistance to more than seven antibiotics. DNA sequencing (16S rRNA gene) revealed that ~35% of our isolates were opportunistic pathogens, comprised primarily of the genera Stenotrophomonas, Pseudomonas, and Chryseobacterium. Together, these results demonstrate that CSOs can be a significant source of viable clinically-relevant bacteria to the natural environment and that multidrug resistance is an important understudied component of the environmental spread of antibiotic resistance.