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Background: Hadal zone of the deep-sea trenches accommodates microbial life under extreme energy limitations and environmental conditions, such as low temperature, high pressure, and low organic matter down to 11,000 m below sea level. However, microbial pathogenicity, resistance, and adaptation therein remain unknown. Here we used culture-independent metagenomic approaches to explore the virulence and antibiotic resistance in the hadal microbiota of the Mariana Trench. Results: The results indicate that the 10,898 m Challenger Deep bottom sediment harbored prosperous microbiota with contrasting signatures of virulence factors and antibiotic resistance, compared with the neighboring but shallower 6038 m steep wall site and the more nearshore 5856 m Pacific basin site. Virulence genes including several famous large translocating virulence genes (e.g., botulinum neurotoxins, tetanus neurotoxin, and Clostridium difficile toxins) were uniquely detected in the trench bottom. However, the shallower and more nearshore site sediment had a higher abundance and richer diversity of known antibiotic resistance genes (ARGs), especially for those clinically relevant ones (e.g., fosX, sul1, and TEM-family extended-spectrum beta-lactamases), revealing resistance selection under anthropogenic stresses. Further analysis of mobilome (i.e., the collection of mobile genetic elements, MGEs) suggests horizontal gene transfer mediated by phage and integrase as the major mechanism for the evolution of Mariana Trench sediment bacteria. Notably, contig-level co-occurring and taxonomic analysis shows emerging evidence for substantial co-selection of virulence genes and ARGs in taxonomically diverse bacteria in the hadal sediment, especially for the Challenger Deep bottom where mobilized ARGs and virulence genes are favorably enriched in largely unexplored bacteria. Conclusions: This study reports the landscape of virulence factors, antibiotic resistome, and mobilome in the sediment and seawater microbiota residing hadal environment of the deepest ocean bottom on earth. Our work unravels the contrasting and unique features of virulence genes, ARGs, and MGEs in the Mariana Trench bottom, providing new insights into the eco-environmental and biological processes underlying microbial pathogenicity, resistance, and adaptative evolution in the hadal environment. [ABSTRACT FROM AUTHOR]

Metagenomic analysis reveals that antibiotic-resistance genes (ARGs) are widely distributed in both human-associated and non-human-associated habitats. However, it is difficult to equally compare ARGs between samples without a standard method. Here, we constructed a comprehensive profile of the distribution of potential ARGs in bacterial tree of life and global habitats by investigating ARGs in 55 000 bacterial genomes, 16 000 bacterial plasmid sequences, 3000 bacterial integron sequences and 850 metagenomes using a standard pipeline. We found that >80% of all known ARGs are not carried by any plasmid or integron sequences. Among potential mobile ARGs, tetracycline and beta-lactam resistance genes (such as tetA , tetM and class A beta-lactamase gene) distribute in multiple pathogens across bacterial phyla, indicating their clinical relevance and importance. We showed that class 1 integrases (intI1) display a poor linear relationship with total ARGs in both non-human-associated and human-associated environments. Furthermore, both total ARGs and intI1 genes show little correlation with the degree of anthropogenicity. These observations highlight the need to differentiate ARGs of high clinical relevance. This profile is published on an online platform (ARGs-OSP, http://args-osp.herokuapp.com/) as a valuable resource for the most challenging topics in this field, i.e. the risk, evolution and emergence of ARGs. [ABSTRACT FROM AUTHOR]

Water and sanitation represent a key battlefront in combatting the spread of antimicrobial resistance (AMR). Basic water sanitation infrastructure is an essential first step towards protecting public health, thereby limiting the spread of pathogens and the need for antibiotics. AMR presents unique human health risks, meriting new risk assessment frameworks specifically adapted to water and sanitation-borne AMR. There are numerous exposure routes to AMR originating from human waste, each of which must be quantified for its relative risk to human health. Wastewater treatment plants play a vital role in centralized collection and treatment of human sewage, but there are numerous unresolved issues in terms of the microbial ecological processes occurring within them and the extent to which they attenuate or amplify AMR. Research is needed to advance understanding of the fate of resistant bacteria and antibiotic resistance genes in various waste management systems, depending on the local constraints and intended reuse applications. World Health Organization and national AMR action plans would benefit from a more holistic 'One Water' understanding. In this article we provide a framework for research, policy, practice and public engagement aimed at limiting the spread of AMR from water and sanitation in low-, medium- and high-income countries. This perspective synthesizes the roundtable discussion focused on water and sanitation aspects of antimicrobial resistance that took place at the 4th Environmental Dimension of Antibiotic Resistance conference. [ABSTRACT FROM AUTHOR]

Although dairy manure is widely applied to land, it is relatively understudied compared to other livestock as a potential source of antibiotic resistance genes (ARGs) to the environment and ultimately to human pathogens. Ceftiofur, the most widely used antibiotic used in U.S. dairy cows, is a 3rd generation cephalosporin, a critically important class of antibiotics to human health. The objective of this study was to evaluate the effect of typical ceftiofur antibiotic treatment on the prevalence of ARGs in the fecal microbiome of dairy cows using a metagenomics approach. β-lactam ARGs were found to be elevated in feces from Holstein cows administered ceftiofur (n = 3) relative to control cows (n = 3). However, total numbers of ARGs across all classes were not measurably affected by ceftiofur treatment, likely because of dominance of unaffected tetracycline ARGs in the metagenomics libraries. Functional analysis via MG-RAST further revealed that ceftiofur treatment resulted in increases in gene sequences associated with “phages, prophages, transposable elements, and plasmids”, suggesting that this treatment also enriched the ability to horizontally transfer ARGs. Additional functional shifts were noted with ceftiofur treatment (e.g., increase in genes associated with stress, chemotaxis, and resistance to toxic compounds; decrease in genes associated with metabolism of aromatic compounds and cell division and cell cycle), along with measureable taxonomic shifts (increase in Bacterioidia and decrease in Actinobacteria). This study demonstrates that ceftiofur has a broad, measureable and immediate effect on the cow fecal metagenome. Given the importance of 3rd generation cephalospirins to human medicine, their continued use in dairy cattle should be carefully considered and waste treatment strategies to slow ARG dissemination from dairy cattle manure should be explored. [ABSTRACT FROM AUTHOR]

In the present study, a newly developed metagenomic analysis approach was applied to investigate the abundance and diversity of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in aquaculture farm sediments, activated sludge, biofilm, anaerobic digestion sludge, and river water. BLASTX analysis against the Comprehensive Antibiotic Resistance Database was conducted for the metagenomic sequence data of each sample and then the ARG-like sequences were sorted based on structured sub-database using customized scripts. The results showed that freshwater fishpond sediment had the highest abundance (196 ppm), and anaerobic digestion sludge possessed the highest diversity (133 subtypes) of ARGs among the samples in this study. Significantly, rifampin resistance genes were universal in all the diverse samples and consistently accounted for 26.9~38.6 % of the total annotated ARG sequences. Furthermore, a significant linear correlation ( R = 0.924) was found between diversities (number of subtypes) of ARGs and diversities of plasmids in diverse samples. This work provided a wide spectrum scan of ARGs and MGEs in different environments and revealed the prevalence of rifampin resistance genes and the strong correlation between ARG diversity and plasmid diversity for the first time. [ABSTRACT FROM AUTHOR]

Abstract: The chlorination behaviours of 12 antibiotics belonging to six classes at environmentally relevant concentrations were systematically examined under typical conditions relevant to municipal wastewater chlorination. Cefotaxime, cefalexin, ampicillin and tetracycline were completely removed under all three initial free chlorine dosages (5 mg/L, 10 mg/L, and 15 mg/L). The removal efficiencies of sulphamethoxazole, sulphadiazine, roxithromycin, anhydro-erythromycin, ofloxacin, and trimethoprim were closely correlated to the residual free chlorine concentration, and no further significant mass removal was observed after the residual free chlorine concentration decreased to less than ∼0.75 mg/L. Ammonia plays a critical role during chlorination because of its competition with antibiotics for free chlorine to form combined chlorine, which reacts slowly with these antibiotics. Except for norfloxacin and ciprofloxacin, the removal behaviours of the 10 other target antibiotics under ammonia nitrogen concentrations ranging from 2 to 15 mg/L were characterised by a rapid initial removal rate upon contact with free chlorine during the first 5 s–1 min (depending on the specific antibiotic and ammonia nitrogen concentration) and then a much slower removal rate. Free chlorine was responsible for the reaction with antibiotics during the rapid stage (first 5 s–1 min), whereas combined chlorine reacted with antibiotics in the subsequent slow stage. Combined chlorine can remove norfloxacin and ciprofloxacin at a relatively faster rate. The presence of suspended solids at 30 mg/L slightly decreased the antibiotic removal rate. The kinetic rate constants decreased by 2.1–13.9%, while the half-lives increased by 2.0–15.0% compared to those of a 0 mg/L suspended solid for the target antibiotics. [Copyright &y& Elsevier]

Understanding the removal mechanisms and kinetics of trace tetracycline by activated sludge is critical to both evaluation of tetracycline elimination in sewage treatment plants and risk assessment/management of tetracycline released to soil environment due to the application of biosolids as fertilizer. Adsorption is found to be the primary removal mechanism while biodegradation, volatilization, and hydrolysis can be ignored in this study. Adsorption kinetics was well described by pseudo-second-order model. Faster adsorption rate ( k = 2.04 × 10 g min μg) and greater adsorption capacity ( q = 38.8 μg g) were found in activated sludge treating freshwater sewage. Different adsorption rate and adsorption capacity resulted from chemical properties of sewage matrix rather than activated sludge surface characteristics. The decrease of tetracycline adsorption in saline sewage was mainly due to Mg which significantly reduced adsorption distribution coefficient ( K) from 12,990 ± 260 to 4,690 ± 180 L kg. Species-specific adsorption distribution coefficients followed the order of $$ K_{\mathrm{d}}^{{ + 00}} \gg K_{\mathrm{d}}^{{ + - 0}} > K_{\mathrm{d}}^{{ + - - }} $$. Contribution of zwitterionic tetracycline to the overall adsorption was >90 % in the actual pH range in aeration tank. Adsorption of tetracycline in a wide range of temperature (10 to 35 °C) followed the Freundlich adsorption isotherm well. [ABSTRACT FROM AUTHOR]

Abstract: The effect of pH on chlorination behaviors of 12 antibiotics, including β-lactams, sulfonamides, fluoroquinolones, tetracyclines, macrolides, and others at environmentally relevant concentrations was systematically examined in the effluent matrix of activated sludge process. The removal of most antibiotics (except cefalexin and tetracycline) significantly depended on pH in the range of 5.5–8.5. The elimination rates of ciprofloxacin, norfloxacin, anhydro-erythromycin, and roxithromycin increased while that of sulfamethoxazole decreased significantly with the increase of pH. Sulfadiazine, ofloxacin, and trimethoprim exhibited the highest reactivity with free available chlorine under the pH of 6–7, 7, and 7.5, respectively. Not only the free available chlorine species (HOCl and OCl−), but also the antibiotics species (cationic, neutral and anionic) affected the overall reaction rate. Anionic antibiotic species are usually much more reactive (1–3 orders of magnitude greater) than cationic antibiotic species toward free available chlorine. Although OCl− is a weaker oxidant than HOCl, chlorination of sulfadiazine, sulfamethoxazole, ciprofloxacin, norfloxacin, and trimethoprim with OCl− became significant at pH>7.5. The observed kinetics rate constants calculated from species-specific rate constants could accurately (0.91< R 2 <0.99) predict the antibiotic removal in chlorination of activated sludge effluent with similar DOC and ammonia concentration to this study at a given pH value. [Copyright &y& Elsevier]

Occurrence, transformation, and fate of antibiotics in municipal wastewater treatment plants (WWTPs) are becoming an emerging environmental research area. As pseudopersistent pollutants, antibiotics belonging to 6 classes (i.e., β-lactams, sulfonamides, quinolones, tetracyclines, macrolides, and others) have been frequently detected in sewage, activated sludge, digested sludge, and effluents. The authors summarized the latest information on occurrence, transformation, and fate of antibiotics in WWTPs based on more than 90 papers published in the past 8 years. The results show that extensive researches on antibiotics occurrence have been conducted mainly in East Asia, North America, Europe, and Australia. Adsorption, biodegradation, disinfection, and membrane separation were the dominant removal routes for antibiotic in different wastewater treatment processes of WWTPs. Many antibiotics cannot be removed completely in wastewater treatment processes and would enter into environment via effluent and sludge. [ABSTRACT FROM AUTHOR]

Abstract: The mass flows and removal of 20 antibiotics of seven classes in two wastewater treatment plants (WWTPs) of Hong Kong were investigated in different seasons of a whole year, using bihourly 24h flow proportional composite samples. Antibiotics were detected at concentrations of 3.2–1718, 1.3–1176 and 1.1–233ngL−1 in influents, secondary and disinfection effluents. Total daily discharges of all the detected antibiotics from effluents of Shatin and Stanley WWTPs were 470–710 and 3.0–5.2gd−1, respectively. Ampicillin, cefalexin, sulfamethoxazole, sulfadiazine, sulfamethazine, chlortetracycline and vancomycin were effectively (52–100%) eliminated by activated sludge process while ampicillin and cefalexin were effectively (91–99%) eliminated by disinfection. Bihourly variation analysis showed that concentrations of the major antibiotics in influents varied more significantly in Stanley WWTP which served small communities. [Copyright &y& Elsevier]

Abstract: In this study, solid phase extraction (SPE) and ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) were utilized to develop a rapid, sensitive and reliable method for trace analysis of 21 antibiotics belonging to 7 classes in influent and effluent of municipal wastewater treatment plant. Detection parameters for SPE preconcentration and UPLC-MS/MS analysis were optimized, including sample pH, eluant, mobile phase (solvent and formic acid concentration), column temperature, and flow rate. Under the optimal conditions, the recoveries for different antibiotics ranged from 60.5% to 109.7% and all analytes were detected within 10.0min by UPLC-MS/MS. The validation study indicated that the method detection limits (MDLs) for the 21 antibiotics were from 0.3 to 60.0ngL−1 for effluent, while higher MDLs (0.5–84.0ngL−1) for influent. Accuracy and precision for both within-run (−11.6 to 14.3% and 0.2 to 15.6%) and between-run tests (−7.2 to 8.7% and 1.9 to 16.4%) were acceptable. The analysis of influent and effluent samples of two municipal wastewater treatment plants in Hong Kong revealed the presence of 11 antibiotics, including ampicillin, cefalexin, sulfamethoxazole, sulfadiazine, norfloxacin, ciprofloxacin, ofloxacin, tetracycline, roxithromycin, erythromycin-H2O, and trimethoprim. Their concentration ranged from 3.5 to 720.0ngL−1 in influent and from 2.1 to 556.4ngL−1 in effluent. [Copyright &y& Elsevier]

The use of antibiotics may accelerate the development of antibiotic resistance genes (ARGs) and bacteria which shade health risks to humans and animals. The emerging of ARGs in the water environment is becoming an increasing worldwide concern. Hundreds of various ARGs encoding resistance to a broad range of antibiotics have been found in microorganisms distributed not only in hospital wastewaters and animal production wastewaters, but also in sewage, wastewater treatment plants, surface water, groundwater, and even in drinking water. This review summarizes recently published information on the types, distributions, and horizontal transfer of ARGs in various aquatic environments, as well as the molecular methods used to detect environmental ARGs, including specific and multiplex PCR (polymerase chain reaction), real-time PCR, DNA sequencing, and hybridization based techniques. [ABSTRACT FROM AUTHOR]

Abstract The proliferation of antibiotic resistance genes (ARGs) in drinking water and their potential horizontal transfer to pathogenic microbes may cause failure of antibiotics. However, antimicrobial resistome monitoring in drinking water is not currently routine. The bacterial hosts of ARGs, especially small-sized microbes in drinking water, may not be effectively removed by membrane filtration disinfection and thus pose threats to human health. In the present study, using metagenomic based approach, we investigated antibiotic resistome of small-sized microbes (0.2–0.45 μm) in 20 household drinking water samples from 12 cities in Mainland China, Hong Kong and Singapore. A total of 265 ARG subtypes belonging to 17 ARG types were detected at abundances ranging from 4.0 × 10−2 to 1.0 × 100 copies/cell. Multidrug, bacitracin and aminoglycoside resistance genes are dominant, and 43 ARG subtypes were specifically carried by small-size microbes. Metagenomic assembly strategy revealed fragments of three opportunistic pathogen, i.e. Pseudomonas alcaligenes , Pseudomonas aeruginosa and Mycobacterium gordonae , carried mex W, aph (3′)-I and aac (2′)-I, respectively. Drinking water samples were classified into three groups based on the presence of ARG, pathogen and ARG-carrying pathogen. These new insights into the antibiotic resistome of small microbes in drinking water over a broad scale indicate the need for more comprehensive ARGs monitoring and surveillance of drinking water supplies. These findings, together with the perspectives and strategies proposed in this study, could support initiatives to improve drinking water safety. Graphical abstract Image 1 Highlights • Potential risks of small-sized microbial resistome in drinking water to human health. • Antibiotic resistome monitoring and host identification (pathogen/non-pathogen). • 43 ARG subtypes specifically carried by small-sized microbes. • Classification of drinking water samples based on the presence of ARG and pathogen. [ABSTRACT FROM AUTHOR]

Carbon-based nanozymes have recently received enormous concern, however, there is still a huge challenge for inexpensive and large-scale synthesis of magnetic carbon-based "Two-in-One" mimics with both peroxidase (POD)-like and laccase-like activities, especially their potential applications in multi-mode sensing of antibiotics and neurotransmitters in biofluids. Although some progresses have been made in this field, the feasibility of biomass-derived carbon materials with both POD-like and laccase-like activities by polyatomic doping strategy is still unclear. In addition, multi-mode sensing platform can provide a more reliable result because of the self-validation, self-correction and mutual agreement. Nevertheless, the use of magnetic carbon-based nanozyme sensors for the multi-mode detection of antibiotics and neurotransmitters have not been investigated. We herein report a shrimp shell-derived N, O-codoped porous carbon confined magnetic CuFe 2 O 4 nanosphere with outstanding laccase-like and POD-like activities for triple-mode sensing of antibiotic d -penicillamine (D-PA) and chloramphenicol (CPL), as well as colorimetric detection of neurotransmitters in biofluids. The magnetic CuFe 2 O 4 /N, O-codoped porous carbon (MCNPC) armored mimetics was successfully fabricated using a combined in-situ coordination and high-temperature crystallization method. The synthesized MCNPC composite with superior POD-like activity can be used for colorimetric/temperature/smartphone-based triple-mode detection of D-PA and CPL in goat serum. Importantly, the MCNPC nanozyme can also be used for colorimetric analysis of dopamine and epinephrine in human urine. This work not only offered a novel strategy to large-scale, cheap synthesize magnetic carbon-based "Two-in-One" armored mimetics, but also established the highly sensitive and selective platforms for triple-mode monitoring D-PA and CPL, as well as colorimetric analysis of neurotransmitters in biofluids without any tanglesome sample pretreatment. [Display omitted] • Magnetic CuFe 2 O 4 /N, O co-doped porous carbon (MCNPC) was prepared using shrimp shell. • MCNPC had excellent peroxidase-like and laccase-like activities. • MCNPC can be used for triple-mode sensing of d -penicillamine and chloramphenicol. • MCNPC can be successfully used for colorimetric detection of neurotransmitters. [ABSTRACT FROM AUTHOR]

• We developed a device for rapid MRSA detection, which can detect two genes in SA or MRSA simultaneously for 30~40 min. • After simple sample processing, the mixture can be directly loaded onto the chip device. • The results can be directly determined by a color change, without special instrument. This device can be widely applied in many fields. Staphylococcus aureus (SA) is one of the most common pathogenic bacteria, and methicillin-resistant SA (MRSA) is an equally common drug-resistant bacteria. MRSA detection is of great significance for clinical diagnosis, medication guidance, and prevention of antibiotic abuse. Traditional MRSA detection using the culture method is time-consuming, laborious, and difficult to conduct rapid on-site detection. In this research, we developed a device for rapid MRSA detection, which can detect the nuc gene in SA and mecA gene in MRSA simultaneously for 30–40 min. After simple sample processing, the mixture can be directly loaded onto the chip device. The detection results can be directly determined by a color change, with a limitation of approximately 102 copies. This isothermal amplification chip device can be widely applied in many fields, with simple operation and low contamination. [ABSTRACT FROM AUTHOR]

The risk associated with antibiotic resistance disseminating from animal and human feces is an urgent public issue. In the present study, we sought to establish a pipeline for annotating antibiotic resistance genes (ARGs) based on metagenomic assembly to investigate ARGs and their co-occurrence with associated genetic elements. Genetic elements found on the assembled genomic fragments include mobile genetic elements (MGEs) and metal resistance genes (MRGs). We then explored the hosts of these resistance genes and the shared resistome of pig, chicken and human fecal samples. High levels of tetracycline, multidrug, erythromycin, and aminoglycoside resistance genes were discovered in these fecal samples. In particular, significantly high level of ARGs (7762 ⨰/Gb) was detected in adult chicken feces, indicating higher ARG contamination level than other fecal samples. Many ARGs arrangements (e.g., macA-macB and tetA-tetR) were discovered shared by chicken, pig and human feces. In addition, MGEs such as the aadA5-dfrA17-carrying class 1 integron were identified on an assembled scaffold of chicken feces, and are carried by human pathogens. Differential coverage binning analysis revealed significant ARG enrichment in adult chicken feces. A draft genome, annotated as multidrug resistant Escherichia coli, was retrieved from chicken feces metagenomes and was determined to carry diverse ARGs (multidrug, acriflavine, and macrolide). The present study demonstrates the determination of ARG hosts and the shared resistome from metagenomic data sets and successfully establishes the relationship between ARGs, hosts, and environments. This ARG annotation pipeline based on metagenomic assembly will help to bridge the knowledge gaps regarding ARG-associated genes and ARG hosts with metagenomic data sets. Moreover, this pipeline will facilitate the evaluation of environmental risks in the genetic context of ARGs. [ABSTRACT FROM AUTHOR]

• We collected time-series influent, AS and effluent for metagenomic sequencing. • Prevalence of ARGs and MGEs was examined in effluents from global cities. • An online platform integrating the resistome risk ranking scheme was developed. • ARG variants with high risk were characterized in effluents. Wastewater treatment plants (WWTPs) are regarded as critical points in disseminating antibiotic resistance genes (ARGs). In particular, the discharging effluents from WWTPs generally bring downstream catchment areas exogenous ARGs and resistant bacteria. However, there lacks a sufficient assessment of the resistome and mobilome in effluents. In this study, a consecutive monthly sampling was conducted over 13 months in three Hong Kong (HK) WWTPs for metagenomic sequencing. Prevalence information of ARGs and mobile genetic elements (MGEs) was compared with counterparts in effluents from cities of North America, South America, Europe, and Asia. Moreover, a publicly accessible platform integrating the exposure ranking scheme, which was based on the global archive of ARG abundance, and a readily implementable online pipeline was developed to benefit communication in academia and government consultancy. Results demonstrated HK WWTPs were featured high ARG removal efficiency of 2.34–2.43 log reduction rate, and effluents were ranked in moderate levels of Level 2 and Level 3 in the exposure prioritizing scheme based on total ARG abundance. Moreover, absolute quantification of temporal variations of effluent resistome disclosed distinct changes over time among varied ARG types which were associated with prevalently used antibiotics, including quinolone and sulfonamide. This reinforces the need for real-time management of WWTP systems. Notably, ARGs of anthropogenic prevalence, high mobility, and potential pathogenicity were found to be present in HK effluents, drawing attention to the necessity for improved risk management. In addition, source tracking of effluent resistome and structural equation model analysis was conducted to explore the disparity in ARG abundance and diversity in different samples. The discovery of this study and the recommendation of a comprehensive exposure assessment will facilitate decision-making in resistome management in WWTPs to reduce the ARG and antibiotic resistant bacteria (ARB) contamination in the receiving environments. [Display omitted] [ABSTRACT FROM AUTHOR]

Abstract: Antibiotic resistance genes (ARGs) are increasingly a focus of concern because they pose a potential health risk. The Pearl River (PR) and Pearl River Estuary (PRE) show a distinct gradient in anthropogenic impacts, in particular associated with the use of antibiotics, from the river, to the estuary, and on to the coast. In this study, two surveys were conducted in the PR and PRE areas during the winter and summer of 2011, respectively. Seven tet genes consisting of efflux pump (tetA, tetC, and tetH) and ribosomal protection proteins (tetB, tetM, tetO, and tetW) were analyzed using the polymerase chain reaction (PCR) technique. The tet genes, with the exception of tetA and tetH, were widely detected in the PR and PRE environments. The tet genes exhibited a trend of an increase in total concentration and diversity with the degree of anthropogenic impacts from the river to the coast, indicating that riverine input was the main source of ARGs in the region. Significant correlations were observed between tet genes and antibiotic concentrations, as well as among different environmental compartments (water and sediments). The distribution patterns of tet genes were similar between the potential sources of pollution and the highly-impacted sites, but were significantly different between less-impacted sites and highly-impacted ones or pollution sources. The results suggest that ARGs and antibiotics may be released from identical sources, and transported in a similar manner in estuary/coastal environments close to sources of pollution. [Copyright &y& Elsevier]

Abstract: This study aimed to investigate the chlorination effects on microbial antibiotic resistance in a drinking water treatment plant. Biochemical identification, 16S rRNA gene cloning and metagenomic analysis consistently indicated that Proteobacteria were the main antibiotic resistant bacteria (ARB) dominating in the drinking water and chlorine disinfection greatly affected microbial community structure. After chlorination, higher proportion of the surviving bacteria was resistant to chloramphenicol, trimethoprim and cephalothin. Quantitative real-time PCRs revealed that sulI had the highest abundance among the antibiotic resistance genes (ARGs) detected in the drinking water, followed by tetA and tetG. Chlorination caused enrichment of ampC, aphA2, bla TEM-1, tetA, tetG, ermA and ermB, but sulI was considerably removed (p < 0.05). Metagenomic analysis confirmed that drinking water chlorination could concentrate various ARGs, as well as of plasmids, insertion sequences and integrons involved in horizontal transfer of the ARGs. Water pipeline transportation tended to reduce the abundance of most ARGs, but various ARB and ARGs were still present in the tap water, which deserves more public health concerns. The results highlighted prevalence of ARB and ARGs in chlorinated drinking water and this study might be technologically useful for detecting the ARGs in water environments. [Copyright &y& Elsevier]

• Antibiotics affect the dynamics of ammonia oxidizers in activated sludge • Four antibiotics (AMP, KAN, LIN, and TMP) could selectively enrich comammox • Different antibiotics select phylogenetically distant comammox Nitrospira • Comammox in wastewater treatment systems show high metabolic versatility While the ubiquitous presence of comammox in engineered systems provides the foundation of developing a novel biological nitrogen removal process, factors contributing to the comammox dynamics in engineered systems have not been well resolved. Here, we investigate the long-term effects of ten different antibiotics on microbial community dynamics in activated sludge and the results show that both types and concentrations of antibiotics affect the taxonomic composition of nitrifiers, including comammox, ammonia-oxidizing bacteria, and canonical nitrite-oxidizing bacteria. Specifically, phylogenetically different comammox Nitrospira were selectively enriched by four types of antibiotics (i.e., ampicillin, kanamycin, lincomycin, and trimethoprim). Comparative genomic analysis of the four newly identified comammox clade A Nitrospira revealed that the comammox enriched by antibiotics shared the conserved key metabolic potentials, such as carbon fixation, complete ammonia oxidation, and utilization of hydrogen as alternative electron donors, among the known comammox organisms. Comammox strains enriched in this study also encoded genes involved in formate and cyanate metabolism that were recently reported in comammox clade A organisms from wastewater treatment systems. Our findings highlight that the comammox in activated sludge ecosystems possess high metabolic versatility than previously recognized and could be selectively enriched by some antibiotics. [Display omitted] [ABSTRACT FROM AUTHOR]