Wastewater discharge drives ARGs spread in the coastal area: A case study in Hangzhou Bay, China

Occurrence and distribution of antibiotics and antibiotic resistance genes from the land to ocean in Daliao River-Liaodong Bay, China

In this study, the pollution status of antibiotics and ARGs in sediments from the land-sea intersection of Liaodong Bay was analyzed. The results showed that the level of antibiotic pollution ranged from ND to 433.27 ng/kg, with quinolones and tetracycline as the dominant antibiotics. The relative abundance of ARGs ranged from 3.62 × 10-3 to 1.32 × 10-1 copies/16SrRNA copies, with aminoglycoside and MLSB resistance genes being dominant. Regarding spatial distribution, the land and estuary areas showed higher antibiotic pollution levels than the offshore areas. Similarly, the land and estuary areas exhibited higher antibiotic diversity than the offshore areas. The ARGs were widely distributed on land, and their abundance gradually decreased to the downstream estuary area. Land and coastal areas exhibited higher ARG diversity than estuary areas. Analysis of environmental factors revealed a significant correlation between ARGs and non-corresponding antibiotics, and some ARGs were affected by heavy metals Cu and Pb.

Comparison of qPCR and metagenomic sequencing methods for quantifying antibiotic resistance genes in wastewater

Surveillance methods of circulating antibiotic resistance genes (ARGs) are of utmost importance in order to tackle what has been described as one of the greatest threats to humanity in the 21st century. In order to be effective, these methods have to be accurate, quickly deployable, and scalable. In this study, we compare metagenomic shotgun sequencing (TruSeq DNA sequencing) of wastewater samples with a state-of-the-art PCR-based method (Resistomap HT-qPCR) on four wastewater samples that were taken from hospital, industrial, urban and rural areas. ARGs that confer resistance to 11 antibiotic classes have been identified in these wastewater samples using both methods, with the most abundant observed classes of ARGs conferring resistance to aminoglycoside, multidrug-resistance (MDR), macrolide-lincosamide-streptogramin B (MLSB), tetracycline and beta-lactams. In comparing the methods, we observed a strong correlation of relative abundance of ARGs obtained by the two tested methods for the majority of antibiotic classes. Finally, we investigated the source of discrepancies in the results obtained by the two methods. This analysis revealed that false negatives were more likely to occur in qPCR due to mutated primer target sites, whereas ARGs with incomplete or low coverage were not detected by the sequencing method due to the parameters set in the bioinformatics pipeline. Indeed, despite the good correlation between the methods, each has its advantages and disadvantages which are also discussed here. By using both methods together, a more robust ARG surveillance program can be established. Overall, the work described here can aid wastewater treatment plants that plan on implementing an ARG surveillance program.

Metagenomics reveals the influence of small microplastics on microbial communities in coastal sediments

The ecological impact of microplastics (MPs) in coastal environments has been widely studied. However, the influence of small microplastics in the actual environment is often overlooked due to measurement challenges. In this study, Hangzhou Bay (HZB), China, was selected as our study area. High-throughput metagenomic sequencing and micro-Raman spectrometry were employed to analyze the microbial communities and microplastics of coastal sediment samples, respectively. We aimed to explore the ecological impact of MPs with small sizes (≤ 100 μm) in real coastal sediment environments. Our results revealed that as microplastic size decreased, the environmental behavior of MPs underwent alterations. In the coastal sediments, no significant correlations were observed between the detected MPs and the whole microbial communities, but small MPs posed potential hazards to eukaryotic communities. Moreover, these small MPs were more prone to microbial degradation and significantly affected carbon metabolism in the habitat. This study is the first to reveal the comprehensive impact of small MPs on microbial communities in a real coastal sediment environment.

Distribution characteristics of antibiotic resistance genes and microbial diversity in the inshore aquaculture area of Wenchang, Hainan, China

The rapid development of marine aquaculture has led to the increased use and release of antibiotics into the marine environment, consequently contributing to the emergence of antibiotic resistance. Information on antibiotic resistance in nearshore marine aquaculture areas remains limited, and research on the microbial composition and potential hosts of antibiotic resistance genes (ARGs) in marine aquaculture areas is scarce. This study used SmartChip real-time fluorescent quantitative PCR and qPCR to quantitatively analyze 44 ARGs and 10 mobile genetic elements (MGEs) genes in 12 sampling points in the nearshore aquaculture area of Wenchang. High-throughput sequencing of 16S rRNA was used to study microbial diversity in the study area, to clarify the correlation between ARGs, MGEs, and microbial diversity, and to determine the possible sources and potential hosts of ARGs. The results showed that a total of 37 ARGs and 8 MGEs were detected in the study area. The detection rate of 9 ARGs (aac(6')-Ib(aka aacA4)-02, catA1, cmlA, cfr, sul1, sul2, sulA/folP-01, tetC, tetX) was 100 %. The absolute abundance of ARGs in the 12 sampling points ranged from 2.75 × 107 to 3.79 × 1010 copies·L-1, and the absolute abundance of MGEs was 1.30 × 105 to 2.54 × 107 copies·L-1, which was relatively high compared to other research areas. ARGs and MGEs were significantly correlated, indicating that MGEs play an important role as a mediator in the spread of ARGs. At the phylum level, Proteobacteria and Cyanobacteria were the dominant bacteria in the study area, with HIMB11 and unidentifiedChloroplast being the dominant levels, respectively. Network analysis of ARGs and microorganisms (genus level) revealed that Cognatishimia, Thalassobius, Aestuariicoccus, Thalassotalea, and Vibrio were significantly correlated with multiple ARGs and were the main potential hosts of ARGs in the nearshore waters of Wenchang.

Distribution of bacterial community structures and spread of antibiotic resistome at industrially polluted sites of Mini River, Vadodara, Gujarat, India

The influence of anthropogenic pollution on the distribution of bacterial diversity, antibiotic-resistant bacteria (ARBs), and antibiotic resistance genes (ARGs) was mapped at various geo-tagged sites of Mini River, Vadodara, Gujarat, India. The high-throughput 16S rRNA gene amplicon sequencing analysis revealed a higher relative abundance of Planctomycetota at the polluted sites, compared to the pristine site. Moreover, the relative abundance of Actinobacteriota increased, whereas Chloroflexi decreased in the water samples of polluted sites than the pristine site. The annotation of functional genes in the metagenome samples of Mini River sites indicated the presence of genes involved in the defence mechanisms against bacitracin, aminoglycosides, cephalosporins, chloramphenicol, streptogramin, streptomycin, methicillin, and colicin. The analysis of antibiotic resistome at the polluted sites of Mini River revealed the abundance of sulfonamide, beta-lactam, and aminoglycoside resistance. The presence of pathogens and ARB was significantly higher in water and sediment samples of polluted sites compared to the pristine site. The highest resistance of bacterial populations in the Mini River was recorded against sulfonamide (≥ 7.943 × 103 CFU/mL) and ampicillin (≥ 8.128 × 103 CFU/mL). The real-time PCR-based quantification of ARGs revealed the highest abundance of sulfonamide resistance genes sul1 and sul2 at the polluted sites of the Mini River. Additionally, the antimicrobial resistance genes aac(6')-Ib-Cr and blaTEM were also found abundantly at polluted sites of the Mini River. The findings provide insights into how anthropogenic pollution drives the ARG and ARB distribution in the riverine ecosystem, which may help with the development of antimicrobial resistance mitigation strategies.

Mass-immigration shapes the antibiotic resistome of wastewater treatment plants

Wastewater treatment plants (WWTPs) are the hotspots for the spread of antibiotic resistance genes (ARGs) into the environment. Nevertheless, a comprehensive assessment of the city-level and short-term daily (inter-day) variations of ARG profiles in the whole process (influent-INF, activated sludge-AS and effluent-EF) of WWTPs is still lacking. Here, 285 ARGs and ten mobile gene elements were monitored in seven WWTPs in Xiamen for seven days via high-throughput qPCR. The average daily load of ARGs to WWTPs was about 1.32 × 1020 copies/d, and a total of 1.56 × 1018 copies/d was discharged to the environment across the entire city. Stochastic processes were the main force determining the assembly of ARG communities during sampling campaign, with their relative importance ranked in the order of INF > EFF > AS. There're little daily variations in ARG richness, abundance, β-diversity composition as well as assembly mechanisms. The results of SourceTracker, variation partitioning analysis, and hierarchical partitioning analysis indicated that bacteria and ARGs from upstream treatment processes played an increasingly dominant role in shaping ARG communities in AS and EFF, respectively, suggesting the importance of mass-immigration of bacteria and ARGs from the source on ARG transport in wastewater treatment processes. This emphasizes the need to revise the way we mitigate ARG contamination but focus on the source of ARGs in urban wastewater.

Unraveling the interplay between antibiotic resistance genes and microbial communities in water and sediments of the intensive tidal flat aquaculture

Tidal flats are formed valuably resources by the interaction of terrestrial and marine processes. Aquaculture on tidal flats has brought significant economic profits, but the over usage of antibiotics has resulted in the prevalence antibiotic resistance genes (ARGs) which pose serious threats to ecosystems. However, ARG abundances and bacterial community assemblies in the overlying water and sediments of tidal flat aquaculture areas have not been fully explored. Thus, antibiotic concentrations, ARG abundances, microbial communities and the influences of environmental factors in the Jiangsu tidal flat aquaculture ponds were investigated using high-throughput sequencing and qPCR. The concentrations of antibiotics at sampling ranged from not detectable to 2322.4 ng g-1, and sulfamethazine and ciprofloxacin were the dominant antibiotics. The sul1 and sul2 abundances were highest and the ARG abundances were higher in sediment than in water. Meanwhile, bacterial community diversities and structures were significantly different (P < 0.05) between water and sediment samples. Network analysis identified Sphingomonadacear, Pseudomonas, and Xanthobacteraceae as potential ARG-carrying pathogens. A positive correlation between ARGs and intI1 indicated that horizontal gene transfer occurred in water, while antibiotics and TN significantly influenced ARG abundances in sediment. Neutral modeling showed that deterministic and stochastic processes contributed most to the bacterial community assemblies of water and sediment samples, respectively. This study comprehensively illustrates the prevalence of ARGs in intensive tidal flat aquaculture regions and provides an effective foundation for the management of antibiotics usage.

Wastewater treatment plants: The missing link in global One-Health surveillance and management of antibiotic resistance

INTRODUCTION

As a global public health crisis, antibiotic resistance (AR) should be monitored and managed under the One-Health concept according to the World Health Organization (WHO), considering the interconnection between humans, animals, and the environment. But this approach often remains focused on human health and rarely on the environment and its compartments, especially wastewater as the main AR receptor. Wastewater treatment plants (WWTPs) not only are not designed for reliving AR but also provide appropriate conditions for enhancing AR through different mechanisms.

METHODS

By reviewing the research-based statistics on the inclusion of WWTPs in the One-Health/AR program crisis, this paper highlights the importance of paying attention to these hotspots, at first. Also, the importance and technical roadmap for the application of WWTPs in both surveillance and management of AR were provided. The current position of these facilities was also evaluated using strengths, weaknesses, opportunities, and threats (SWOT) analysis. In the end, the concluding knowledge gaps and research needs for future investigations were presented.

RESULTS

Despite the fact that wastewater matrices are the hotspot for AR dissemination, WWTPs appear under-represented in One-Health/AR literature. So, of the 414434 articles retrieved for One-Health only 1.5% (n = 6321) focused on AR and about 0.04% (n = 158) on WWTPs. The potential of WWTPs inclusion in AR surveillance has been confirmed by several studies, however, when it comes to its inclusion for management of AR, more evidence should be presented, which confirmed by SWOT results.

DISCUSSION

As such, WWTPs simultaneously provide opportunities for AR surveillance as it is assumed that this medium can reflect the reality of the corresponding society, and for managing unexpected crises which could impact the public. Nonetheless, there are still numerous considerations to change WWTPs role from Achilles' heel to Ajax' shield, including strengthening the research-based knowledge and conducting both surveillance and management strategies of AR under One-Health concept (One-Health/AR) in a clear straightforward framework.

Efficient Degradation of Intracellular Antibiotic Resistance Genes by Photosensitized Erythrosine-Produced 1O2

Intracellular antibiotic resistance genes (iARGs) constitute the important part of wastewater ARGs and need to be efficiently removed. However, due to the dual protection of intracellular DNA by bacterial membranes and the cytoplasm, present disinfection technologies are largely inefficient in iARG degradation. Herein, we for the first time found that erythrosine (ERY, an edible dye) could efficiently degrade iARGs by producing abundant 1O2 under visible light. Seven log antibiotic-resistant bacteria were inactivated within only 1.5 min, and 6 log iARGs were completely degraded within 40 min by photosensitized ERY (5.0 mg/L). A linear relationship was established between ARG degradation rate constants and 1O2 concentrations in the ERY photosensitizing system. Surprisingly, a 3.2-fold faster degradation of iARGs than extracellular ARGs was observed, which was attributed to the unique indirect oxidation of iARGs induced by 1O2. Furthermore, ERY photosensitizing was effective for iARG degradation in real wastewater and other photosensitizers (including Rose Bengal and Phloxine B) of high 1O2 yields could also achieve efficient iARG degradation. The findings increase our knowledge of the iARG degradation preference by 1O2 and provide a new strategy of developing technologies with high 1O2 yield, like ERY photosensitizing, for efficient iARG removal.

Characterization of microbial community and antibiotic resistome in intra urban water, Wenzhou China

The present study investigated the water quality index, microbial composition and antimicrobial resistance genes in urban water habitats. Combined chemicals testing, metagenomic analyses and qualitative PCR (qPCR) were conducted on 20 locations, including rivers from hospital surrounds (n = 7), community surrounds (n = 7), and natural wetlands (n = 6). Results showed that the indexes of total nitrogen, phosphorus, and ammonia nitrogen of hospital waters were 2-3 folds high than that of water from wetlands. Bioinformatics analysis revealed a total of 1,594 bacterial species from 479 genera from the three groups of water samples. The hospital-related samples had the greatest number of unique genera, followed by those from wetlands and communities. The hospital-related samples contained a large number of bacteria associated with the gut microbiome, including Alistipes, Prevotella, Klebsiella, Escherichia, Bacteroides, and Faecalibacterium, which were all significantly enriched compared to samples from the wetlands. Nevertheless, the wetland waters enriched bacteria from Nanopelagicus, Mycolicibacterium and Gemmatimonas, which are typically associated with aquatic environments. The presence of antimicrobial resistance genes (ARGs) that were associated with different species origins in each water sample was observed. The majority of ARGs from hospital-related samples were carried by bacteria from Acinetobacter, Aeromonas and various genera from Enterobacteriaceae, which each was associated with multiple ARGs. In contrast, the ARGs that were exclusively in samples from communities and wetlands were carried by species that encoded only 1 to 2 ARGs each and were not normally associated with human infections. The qPCR showed that water samples of hospital surrounds had higher concentrations of intI1 and antimicrobial resistance genes such as tetA, ermA, ermB, qnrB, sul1, sul2 and other beta-lactam genes. Further genes of functional metabolism reported that the enrichment of genes associated with the degradation/utilization of nitrate and organic phosphodiester were detected in water samples around hospitals and communities compared to those from wetlands. Finally, correlations between the water quality indicators and the number of ARGs were evaluated. The presence of total nitrogen, phosphorus, and ammonia nitrogen were significantly correlated with the presence of ermA and sul1. Furthermore, intI1 exhibited a significant correlation with ermB, sul1, and bla_SHV, indicating a prevalence of ARGs in urban water environments might be due to the integron intI1's diffusion-promoting effect. However, the high abundance of ARGs was limited to the waters around the hospital, and we did not observe the geographical transfer of ARGs along with the river flow. This may be related to water purifying capacity of natural riverine wetlands. Taken together, continued surveillance is required to assess the risk of bacterial horizontal transmission and its potential impact on public health in the current region.

Hypoxia triggers the proliferation of antibiotic resistance genes in a marine aquaculture system

The transmission of antibiotic resistance genes (ARGs) affects the safety of aquaculture animals. Dissolved oxygen (DO) can affect the transmission of ARGs, but its mechanism of action in this process is unclear. We conducted laboratory breeding experiment with low and control DO groups. Combined quantitative PCR and 16S rRNA sequencing to study the effect of DO on the spread of ARGs. Hypoxia treatment significantly increased the accumulation of ammonium and nitrite in aquaculture water, and it increased the relative abundances of ARGs and mobile genetic elements (MGEs), especially the ARGs resistant to drugs in the categories of sulfonamide, (flor)/(chlor)/(am)phenicol, and MLSB (macrolide, lincosamide and streptogramin B) and the MGE intI-1(clinic), by 2.39-95.69 % in 28 days relative to the control DO treatment. Though the abundance of ARG carries, especially the Rhodocyclaceae, Caldilineaceae, Cyclobacteriaceae, Saprospiraceae, Enterobacteriaceae, Sphingomonadaceae families, showed higher abundance in low DO groups, relating to the vertical transmission of ARGs. Hypoxia treatment is more likely to promote the horizontal gene transfer (HGT)-related pathways, including ABC transporters, two component system, and quorum sensing, thus to induce the HGT of ARGs. The changed bacterial proliferation also altered the abundance of MGEs, especially intI-1(clinic), which induced HGT of ARGs as well. Additionally, pearson correlation results revealed that the succession of bacterial community function played the strongest role in ARG proliferation, followed by bacterial community structure and MGEs. Our results highlight the importance of suitable DO concentration in controlling the spread of ARGs especially the HGT of ARGs. In the context of global attention to food safety, our results provide important information for ensuring the safety of aquatic products and the sustainable development of aquaculture.

The reasons for the spatial and media distribution variations of ARGs in a typical semi-enclosed bay

Antibiotic resistance genes (ARGs) are considered a newly emerging contaminant. This study aimed to investigate the spatial and media distribution patterns of ARGs in Jiaozhou Bay, as well as the reasons behind these patterns. The results revealed that aminoglycoside and MLSB resistant genes predominated in all samples, and the relative abundance of ARGs ranging from 10^-6 to 10^-2, 10^-6 to 10^-3 and 10^-5 to 10^-2 copies/16S rRNA in coastal water, bay water, and sediments, respectively. The significant spatial variation of ARGs was explained by the fact that the coastal water was more susceptible to human activities, whereas environmental physicochemical factors played a crucial role in the bay water. The intrinsic reason for the media distribution variation was the different assembly processes in the two media, while the external reason was that the ARGs in the water and sediments were mainly influenced by environmental physicochemical factors and heavy metals, respectively.

Evaluation of FEAST for metagenomics-based source tracking of antibiotic resistance genes

A metagenomics-based technological framework has been proposed for evaluating the potential and utility of FEAST as an ARG profile-based source apportionment tool. To this end, a large panel of metagenomic data sets was analyzed, associating with eight source types of ARGs in environments. Totally, 1089 different ARGs were found in the 604 source metagenomes, and 396 ARG indicators were identified as the source-specific fingerprints to characterize each of the source types. With the source fingerprints, predictive performance of FEAST was checked using "leave-one-out" cross-validation strategy. Furthermore, artificial sink communities were simulated to evaluate the FEAST for source apportionment of ARGs. The prediction of FEAST showed high accuracy values (0.933 ± 0.046) and specificity values (0.959 ± 0.041), confirming its suitability to discriminate samples from different source types. The apportionment results reflected well the expected output of artificial communities which were generated with different ratios of source types to simulate various contamination levels. Finally, the validated FEAST was applied to track the sources of ARGs in river sediments. Results showed STP effluents were the main contributor of ARGs, with an average contribution of 76 %, followed by sludge (10 %) and aquaculture effluent (2.7 %), which were basically consistent with the actual environment in the area.

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.

Impact of climate change on coastal water quality and its interaction with pollution prevention efforts

The impact of climate change on nearshore coastal water quality and its interaction with pollution prevention efforts (e.g., the development of green and gray water infrastructure) still lack systematic investigation. This study performed a holistic analysis of the impact of climate change on the salinity and concentrations of total nitrogen (TN), total phosphorus (TP) and chlorophyll a (Chl.a) in Shenzhen Bay between Shenzhen and Hong Kong, the two most developed megacities in South China, based on three-dimensional hydrodynamic and water quality modeling. The major study findings were as follows. First, Chl.a was the most sensitive parameter, and its bay-wide average concentration in 2100 was predicted to be approximately 13% and 46% higher than those in 2015 under mild and rapid climate change scenarios, respectively. Second, sea level rise was found to be a major driver of all four water quality parameters, while temperature and radiation mainly influenced Chl.a and precipitation mainly influenced nutrients. Third, water quality responses to climate change were highly heterogeneous over the bay. Even under a mild climate change scenario, the highest location-specific changes (2100 vs. 2015) in salinity and TN, TP and Chl.a concentrations were projected to be approximately 21%, 19%, 25%, and 65%, respectively. Fourth, changes in seasonal variation due to climate change may lead to an enhanced ecological risk of algal blooms. Finally, the effect of reducing TN and TP concentrations by proposed water infrastructure development was found to be significantly weakened (nearly 40% and 20% for TN and TP, respectively, under a mild climate change scenario), while the negative effect (i.e., increase in the Chl.a concentration) was notably accelerated. Regional cooperation is critical for protecting the water quality of the bay, particularly under climate change. The insights obtained in this study are applicable to other coastal water zones around the world with similar socioeconomic backgrounds and climatic conditions.

Geographic patterns and determinants of antibiotic resistomes in coastal sediments across complex ecological gradients

Coastal areas are highly influenced by terrestrial runoffs and anthropogenic disturbances, commonly leading to ecological gradients from bay, nearshore, to offshore areas. Although the occurrence and distribution of sediment antibiotic resistome are explored in various coastal environments, little information is available regarding geographic patterns and determinants of coastal sediment antibiotic resistomes across ecological gradients at the regional scale. Here, using high-throughput quantitative PCR, we investigated the geographic patterns of 285 antibiotic resistance genes (ARGs) in coastal sediments across a  ~  200  km scale in the East China Sea. Sediment bacterial communities and physicochemical properties were characterized to identify the determinants of sediments antibiotic resistome. Higher richness and abundance of ARGs were detected in the bay samples compared with those in nearshore and offshore samples, and significant negative correlations between the richness and/or abundance of ARGs and the distance to coastline (DTC) were identified, whereas different types of ARGs showed inconsistency in their relationships with DTC. The composition of antibiotic resistome showed significant correlations with nutrition-related variables (including NH4 +-N, NO3 --N, and total phosphorus) and metals/metalloid (including As, Cu, Ni, and Zn), suggesting that terrestrial disturbances largely shape the antibiotic resistome. The Bipartite network showed strong associations between ARGs and mobile genetic elements (MGEs), and Partial Least Squares Path Modeling further revealed that terrestrial disturbance strength (as indicated by DTC) directly affected abiotic environmental conditions and bacterial community composition, and indirectly affected antibiotic resistome via MGEs. These findings provide insights into regional variability of sediment antibiotic resistome and its shaping path across complex ecological gradients, highlighting terrestrial disturbances as determinative forces in shaping coastal sediment antibiotic resistomes.

Aquatic Environments as Hotspots of Transferable Low-Level Quinolone Resistance and Their Potential Contribution to High-Level Quinolone Resistance

The disposal of antibiotics in the aquatic environment favors the selection of bacteria exhibiting antibiotic resistance mechanisms. Quinolones are bactericidal antimicrobials extensively used in both human and animal medicine. Some of the quinolone-resistance mechanisms are encoded by different bacterial genes, whereas others are the result of mutations in the enzymes on which those antibiotics act. The worldwide occurrence of quinolone resistance genes in aquatic environments has been widely reported, particularly in areas impacted by urban discharges. The most commonly reported quinolone resistance gene, qnr, encodes for the Qnr proteins that protect DNA gyrase and topoisomerase IV from quinolone activity. It is important to note that low-level resistance usually constitutes the first step in the development of high-level resistance, because bacteria carrying these genes have an adaptive advantage compared to the highly susceptible bacterial population in environments with low concentrations of this antimicrobial group. In addition, these genes can act additively with chromosomal mutations in the sequences of the target proteins of quinolones leading to high-level quinolone resistance. The occurrence of qnr genes in aquatic environments is most probably caused by the release of bacteria carrying these genes through anthropogenic pollution and maintained by the selective activity of antimicrobial residues discharged into these environments. This increase in the levels of quinolone resistance has consequences both in clinical settings and the wider aquatic environment, where there is an increased exposure risk to the general population, representing a significant threat to the efficacy of quinolone-based human and animal therapies. In this review the potential role of aquatic environments as reservoirs of the qnr genes, their activity in reducing the susceptibility to various quinolones, and the possible ways these genes contribute to the acquisition and spread of high-level resistance to quinolones will be discussed.

Occurrence of Indicator Genes of Antimicrobial Resistance Contamination in the English Channel and North Sea Sectors and Interactions With Environmental Variables

The marine environment is a potential natural reservoir of antimicrobial resistance genes (ARGs), subject to anthropogenic effluents (wastewater, industrial, and domestic), and known as a final receiving system. The aim of this study was to investigate the abundance and geographical distribution of the three bla_TEM , sul1, and intI1 genes, proposed as indicators of contamination to assess the state of antimicrobial resistance in environmental settings, added to the tetA gene and the microbial population (tuf gene) in the English Channel and North Sea areas. Bacterial DNA was extracted from 36 seawater samples. The abundance of these genes was determined by quantitative PCR (qPCR) and was analyzed in association with environmental variables and geographical locations to determine potential correlations. The bla_TEM and tetA genes were quantified in 0% and 2.8% of samples, respectively. The sul1 and intI1 genes were detected in 42% and 31% of samples, respectively, with an apparent co-occurrence in 19% of the samples confirmed by a correlation analysis. The absolute abundance of these genes was correlated with the microbial population, with results similar to the relative abundance. We showed that the sul1 and intI1 genes were positively correlated with dissolved oxygen and turbidity, while the microbial population was correlated with pH, temperature and salinity in addition to dissolved oxygen and turbidity. The three tetA, sul1, and intI1 genes were quantified in the same sample with high abundances, and this sample was collected in the West Netherlands coast (WN) area. For the first time, we have shown the impact of anthropogenic inputs (rivers, man-made offshore structures, and maritime activities) and environmental variables on the occurrence of three indicators of environmental contamination by antimicrobial resistance in the North Sea and English Channel seawaters.

Conurbation size drives antibiotic resistance along the river

With growing concerns about antibiotic resistance, the tracking of antibiotic resistance genes (ARGs) in urban waterways will facilitate our increased understanding of the impact of urbanization on ARGs dissemination. In the current study, we assessed the ARGs profiles and antibiotic resistome in water samples along the Jiulong River basin, a distance of 250 km, to better understand the impact of anthropogenic activities. A total of 244 ARGs and 12 MGEs were detected from 21 sampling sites. Both relative and absolute abundance of the observed resistome decreased with increasing distance from urban areas. Ordinary least-squares (OLS) regression revealed that both the relative and absolute resistome abundance were positively correlated with city size. The resistome had several inputs and outputs and Fast Expectation Maximization Microbial Source Tracking (FEAST), suggested that the majority of the antibiotic resistome originated from anthropogenic activities. A total of 8 ARGs and 20 microbial OTUs were considered as biomarkers that differentiated the location of sampling sites. Bacterial communities were significantly correlated with ARGs according to Procrustes analysis and Mantel test, which was also supported by a co-occurrence network. Variation partitioning analysis revealed that ARG profiles were driven by multiple factors. Although antibiotic resistome abundance significantly increased near urban conurbations, overall resistome abundance decreased as the river flowed downstream. Our study highlights the effect of conurbation size on antibiotic resistance profiles within the river basin and the potential resilience of rivers to recover from ARGs contamination.

Occurrence and temporal variation of antibiotics and antibiotic resistance genes in hospital inpatient department wastewater: Impacts of daily schedule of inpatients and wastewater treatment process

The temporal variation of antibiotics and ARGs as well as the impact of daily schedule of inpatients on their regular occurrence in hospital wastewater (HWW) were previously obscure. In this study, the wastewater of the inpatient department pre- and posttreatment (hydraulic retention time = 8 h) was collected intraday and intraweek. The absolute concentrations of antibiotics/metabolites and ARGs in HWW were analyzed to investigate the temporal variations of their occurrence levels. Fluoroquinolones were the predominant drugs used in the inpatient department (681.30-881.66 ng/mL in the effluent) and the main contaminant in the outlet of the disinfection pond (538.29-671.47 ng/mL). Diurnal variations peaked at 19:00 for most antibiotics and ARGs, while the maximum of them occurred on weekends. Aminoglycoside resistance genes (AMRGs, 21.6-23000 copies/mL) and β-lactam resistance genes (BLGRs, 1.24-8500 copies/mL) were the dominant ARGs before and after treatment processing, respectively (p < 0.05). The significant removal rates (>50%) of most antibiotics and ARGs, as well as the integrase gene intI1 and 16S rRNA gene, were found to be subjected solely to the chloride disinfection process, suggesting the necessity of the self-contained wastewater treatment process. Meanwhile, the statistically significant correlation among antibiotics, ARGs, intI1, and 16S rRNA (p < 0.05) demonstrated that the risk of selective pressure, horizontal transfer and vertical propagation of ARGs in the effluent of the hospital was warranted. Principal component analysis (PCA) showed that the daily schedule of inpatients and wastewater treatment processes could markedly induce fluctuations in antibiotic and ARG levels in HWW, indicating that they should be considered an impact factor for environmental monitoring. This study demonstrated for the first time the temporal variations in the abundance and dissemination of antibiotics and ARGs in a semiclosed zone and provided new insight into the development of assessments of the associated ecological risk and human health.

Occurrence and distribution of antibiotics and antibiotic resistance genes in the guts of shrimp from different coastal areas of China

With the continuous increase in shrimp (Litopenaeus vannamei) aquaculture production, the widespread use of antibiotics as a means of preventing and treating diseases has adversely affected the environment, animal health and symbiotic microorganisms in gut environments. At the same time, antibiotic resistance genes (ARGs) are widespread in aquaculture and pose a great threat to aquatic organisms and humans. Therefore, in the present study, the occurrence and distribution of 17 antibiotics, ARGs and mobile genetic elements (MGEs) were detected in the guts of shrimp collected from 12 coastal regions of China. The results showed that sulfadiazine, ciprofloxacin and norfloxacin were detectable in the guts of L. vannamei at all sampling sites. Sul1, sul2, floR and intI-1 were also detected in the guts of L. vannamei at all sampling sites. The total relative abundances of ARGs and MGEs were significantly positively correlated according to Pearson correlation analysis. Sulfonamide resistance genes (sul1 and sul2) were significantly positively correlated with intI-1. These results indicated that MGEs could increase the risk of horizontal gene transfer of ARGs in a gut environment. MGEs are the most important factors promoting the spread of ARGs. Correlation analysis showed that sulfadiazine was significantly positively correlated with sul1 and sul2 and that fluoroquinolone antibiotics were significantly positively correlated with floR, indicating that antibiotics could induce the production of ARGs. Network analysis indicated that Iamia and Alkaliphilus species may harbor the most antibiotic resistance genes, and these bacteria were closely related to the proliferation and spread of ARGs in a gut environment. Antibiotic use and the spread of ARGs in mariculture systems may have negative effects on shrimp and human health. The use of antibiotics should be strictly regulated to control contaminants in mariculture systems, including pathogens and ARGs, thereby reducing potential risks to human health.

Bacterial Indicators Are Ubiquitous Members of Pelagic Microbiome in Anthropogenically Impacted Coastal Ecosystem

Coastal zones are exposed to various anthropogenic impacts, such as different types of wastewater pollution, e.g., treated wastewater discharges, leakage from sewage systems, and agricultural and urban runoff. These various inputs can introduce allochthonous organic matter and microbes, including pathogens, into the coastal marine environment. The presence of fecal bacterial indicators in the coastal environment is usually monitored using traditional culture-based methods that, however, fail to detect their uncultured representatives. We have conducted a year-around in situ survey of the pelagic microbiome of the dynamic coastal ecosystem, subjected to different anthropogenic pressures to depict the seasonal and spatial dynamics of traditional and alternative fecal bacterial indicators. To provide an insight into the environmental conditions under which bacterial indicators thrive, a suite of environmental factors and bacterial community dynamics were analyzed concurrently. Analyses of 16S rRNA amplicon sequences revealed that the coastal microbiome was primarily structured by seasonal changes regardless of the distance from the wastewater pollution sources. On the other hand, fecal bacterial indicators were not affected by seasons and accounted for up to 34% of the sequence proportion for a given sample. Even more so, traditional fecal indicator bacteria (Enterobacteriaceae) and alternative wastewater-associated bacteria (Lachnospiraceae, Ruminococcaceae, Arcobacteraceae, Pseudomonadaceae and Vibrionaceae) were part of the core coastal microbiome, i.e., present at all sampling stations. Microbial source tracking and Lagrangian particle tracking, which we employed to assess the potential pollution source, revealed the importance of riverine water as a vector for transmission of allochthonous microbes into the marine system. Further phylogenetic analysis showed that the Arcobacteraceae in our data set was affiliated with the pathogenic Arcobacter cryaerophilus, suggesting that a potential exposure risk for bacterial pathogens in anthropogenically impacted coastal zones remains. We emphasize that molecular analyses combined with statistical and oceanographic models may provide new insights for environmental health assessment and reveal the potential source and presence of microbial indicators, which are otherwise overlooked by a cultivation approach.

Microbiome and antibiotic resistance profiling in submarine effluent-receiving coastal waters in Croatia

Wastewater treatment plant (WWTP) effluents are pointed as hotspots for the introduction of both commensal and pathogenic bacteria as well as their antibiotic resistance genes (ARGs) in receiving water bodies. For the first time, the effect of partially treated submarine effluents was explored at the bottom and surface of the water column to provide a comprehensive overview of the structure of the microbiome and associated AR, and to assess environmental factors leading to their alteration. Seawater samples were collected over a 5-month period from submarine outfalls in central Adriatic Sea, Croatia. 16S rRNA amplicon sequencing was used to establish taxonomic and resistome profiles of the bacterial communities. The community differences observed between the two discharge areas, especially in the abundance of Proteobacteria and Firmicutes, could be due to the origin of wastewaters treated in WWTPs and the limiting environmental conditions such as temperature and nutrients. PICRUSt2 analysis inferred the total content of ARGs in the studied microbiomes and showed the highest abundance of resistance genes encoding multidrug efflux pumps, such as MexAB-OprM, AcrEF-TolC and MdtEF-TolC, followed by the modified peptidoglycan precursors, transporter genes encoding tetracycline, macrolide and phenicol resistance, and the bla operon conferring β-lactam resistance. A number of pathogenic genera introduced by effluents, including Acinetobacter, Arcobacter, Bacteroides, Escherichia-Shigella, Klebsiella, Pseudomonas, and Salmonella, were predicted to account for the majority of efflux pump-driven multidrug resistance, while Acinetobacter, Salmonella, Bacteroides and Pseudomonas were also shown to be the predominant carriers of non-efflux ARGs conferring resistance to most of nine antibiotic classes. Taken together, we evidenced the negative impact of submarine discharges of treated effluents via alteration of physico-chemical characteristics of the water column and enrichment of bacterial community with nonindigenous taxa carrying an arsenal of ARGs, which could contribute to the further propagation of the AR in the natural environment.

Effect of inorganic mercury exposure on reproductive system of male mice: Immunosuppression and fibrosis in testis

Mercury as a toxic heavy metal will accumulate in the body and induce various diseases through the food chain. However, it is unknown that the detailed mechanism of reproductive disorder induced by inorganic mercury in male mice to date. This study investigated the toxicological effect of mercuric chloride (HgCl₂ ) exposure on reproductive system in male mice. Male Kunming mice received normal saline daily or HgCl₂ (3 mg/kg bodyweight) by intraperitoneal injection for a week. The reproductive function was evaluated, and the HgCl₂ exposure induced the decline of sperm quality, pregnancy rate, mean litter size, and survival rate. Notably, we firstly found the HgCl₂ -induced immunosuppression and fibrosis in mice testis according to the results of RNA sequencing. Collectively, these findings demonstrate that HgCl₂ exposure disrupts the reproductive system and induces testicular immunosuppression and fibrosis via inhibition of the CD74 signaling pathway in male mice.

Occurrence of antibiotics and antibiotic resistance genes in WWTP effluent-receiving water bodies and reclaimed wastewater treatment plants

There is a growing concern on the fate and the consequent ecological or health risks of antibiotics and antibiotic resistance genes (ARGs) in natural or artificial water environment. The effluent of wastewater treatment plants (WWTPs) has been reported to be an important source of antibiotics and ARGs in the environment. WWTP effluent could be discharged into surface water bodies or recycled, either of which could lead to different exposure risks. The impact of WWTP effluents on the levels of antibiotics and ARGs in effluent-receiving water bodies and the removal efficiency of antibiotics and ARGs in reclaimed wastewater treatment plants (RWTPs) were seldom simultaneously investigated. Thus, in this study, we investigated the occurrence of antibiotics and ARGs in four WWTP effluents, and their downstream effluent-receiving water bodies and RWTPs in seasons of low-water-level. The total concentrations of ofloxacin, norfloxacin, ciprofloxacin, roxithromycin, azithromycin, erythromycin, tetracycline, oxytetracycline, chlortetracycline, and sulfamethoxazole in the secondary effluents were 1441.6-4917.6 ng L^-1. Ofloxacin had the highest concentration. The absolute and relative abundances of total ARGs (qnrD, qnrS, ermA, ermB, tetA, tetQ, sul1, and sul2) in the secondary effluents were 10³-10⁴ copies mL^-1 and 10^-4-10^-2 ARG/16S rRNA. Sul1 and sul2 were the major species with the highest detection frequencies and levels. In most cases, WWTP effluents were not the major contributors to the levels and species of antibiotics and ARGs in the surface water bodies. Four RWTPs removed 43.5-98.9% of antibiotics and - 0.19-2.91 log of ARGs. Antibiotics and ARGs increased in chlorination, ozonation and filtration units. Antibiotics had significantly positive correlations with ARGs, biological oxygen demands, total phosphorus, total nitrogen, and ammonia nitrogen in the four effluent-receiving water bodies. In RWTPs, the total concentrations of antibiotics showed a significant positive correlation with the total abundance of ARGs.

High-Throughput Single-Cell Technology Reveals the Contribution of Horizontal Gene Transfer to Typical Antibiotic Resistance Gene Dissemination in Wastewater Treatment Plants

The spread of antibiotic resistance genes (ARGs) has gained much attention worldwide, while the contribution of vertical gene transfer (VGT) and horizontal gene transfer (HGT) is still elusive. Here, we improved an emerging high-throughput single-cell-based technology, emulsion, paired isolation, and concatenation polymerase chain reaction (epicPCR), by lengthening the sequence of ARG in the fused ARG-16S rRNA fragments to cover the variance of both ARG and its hosts. The improved epicPCR was applied to track the hosts of a widely detected ARG, sul1 gene, in five urban wastewater treatment plants (UWTPs) during two seasons. The sul1 host bacteria were highly diverse and mostly classified as Proteobacteria and Bacteroidetes. Clear seasonal divergence of α-diversity and interaction networks were present in the host community. The consensus phylogenetic trees of the sul1 gene and their host demonstrated incorrespondence on the whole and regularity on abundant groups, suggesting the important role of both HGT and VGT, respectively. The relative importance of these two ways was further measured; HGT (54%) generally played an equal or even more important role as VGT (46%) in UWTPs. The application of the improved epicPCR technology provides a feasible approach to quantify the relative contributions of VGT and HGT in environmental dissemination of ARGs.

A systematic review of antibiotics and antibiotic resistance genes in estuarine and coastal environments

Antibiotics and antibiotic resistance genes (ARGs) are prevalent in estuarine and coastal environments due to substantial terrestrial input, aquaculture effluent, and sewage discharge. In this article, based on peer-reviewed papers, the sources, spatial patterns, driving factors, and environmental implications of antibiotics and ARGs in global estuarine and coastal environments are discussed. Riverine runoff, WWTPs, sewage discharge, and aquaculture, are responsible for the prevalence of antibiotics and ARGs. Geographically, pollution due to antibiotics in low- and middle-income countries is higher than that in high-income countries, and ARGs show remarkable latitudinal variations. The distribution of antibiotics is driven by antibiotic usage and environmental variables (heavy metals, nutrients, organic pollutants, etc.), while ARGs are affected by antibiotics residues, environmental variables, microbial communities, and mobile genetic elements (MGEs). Antibiotics and ARGs alter microbial communities and biogeochemical cycles, as well as pose threats to marine organisms and human health. Our results provide comprehensive insights into the transport and environmental behaviors of antibiotics and ARGs in global estuarine and coastal environments.

Acquisition of antibiotic resistance genes on human skin after swimming in the ocean

The skin is a complex organ responsible for protecting the body from physical, chemical and biological insults. The skin microbiome is known to play an important role in protecting the host from skin infections. This study examined the skin microbiome and the changes in antibiotic resistance genes (ARGs), antibiotic biosynthesis genes (ABSGs) and virulence factor genes (VFGs) on human skin before and after swimming in the ocean. Skin microbiome samples were collected from human participants before and after they swam in the ocean, and at 6 h and 24 h post-swim. The samples were analyzed using 16S rRNA gene and shotgun metagenomic sequencing. The results showed that not only is the skin microbiome composition altered after swimming, but the abundance and diversity of ARGs, ABSGs and VFGs on the skin increased post-swim. Overall, there was an increase in total ARGs by 70.6% from before to after swimming. The elevated number of ARGs persisted and continued to increase for at least 6 h post-swim with greater than a 300% increase in comparison with samples collected before ocean swimming. The outcomes of the study support the epidemiological observations of increased risk of skin infections after swimming in the ocean. Cleaning the skin immediately after recreational ocean activities is recommended to reduce the opportunity for infection.

Response of anammox granules to the simultaneous exposure to macrolide and aminoglycoside antibiotics: Linking performance to mechanism

Antibiotic pollution is becoming increasingly severe due to its extensive use. The potential application of the anaerobic ammonium oxidation (anammox) process in the treatment of wastewater containing antibiotics has attracted much attention. As common antibiotics, spiramycin (SPM) and streptomycin (STM) are widely used to treat human and animal diseases. However, their combined effects on the anammox process remain unknown. Therefore, this study systematically evaluated the response of the anammox process to both antibiotics. The half maximal inhibitory concentrations of SPM and STM were determined. The continuous-flow anammox system could adapt to SPM and STM at low concentrations, while antibiotics at high concentrations exhibited inhibitory effects. When the concentrations reached 5 mg L^-1 SPM and 50 mg L^-1 STM, the nitrogen removal efficiency dramatically decreased and then rapidly recovered within 8 days. Correspondingly, the abundances of dominant bacteria and genes also changed with antibiotic concentrations. In general, the anammox process showed a stable performance and a high resistance to SPM and STM, suggesting that acclimatization by elevating the concentrations was beneficial for the anammox process to obtain resistance to different antibiotics with high concentrations. This study provides guidance for the stable operation of anammox-based biological treatment of antibiotics containing wastewater.

Fate of antibiotics in engineered wastewater systems and receiving water environment: A case study on the coast of Hangzhou Bay, China

The occurrence of man-made antibiotics in natural environment has aroused attentions from both scientists and publics. However, few studies tracked antibiotics from their production site to the end of disposal environment. Taking the coastal region of Hangzhou Bay as the study area, the fate of 77 antibiotics from 6 categories in two-step wastewater treatment plants (WTPs, i.e. pharmaceutical WTP and integrated WTP) was focused; and the antibiotics in both dissolved and adsorbed phases were investigated simultaneously in this study. The ubiquitous occurrence of antibiotics was observed in the two-step WTPs, with antibiotic concentrations following the order of PWTP (LOQ - 1.0 × 10⁵ ng·L^-1) > IWTP_i (for industrial wastewater treatment, LOQ - 3.7 × 10³ ng·L^-1) > IWTP_d (for domestic sewage treatment, LOQ - 1.3 × 10³ ng·L^-1). And the types of antibiotics detected in excess sludge and suspended particles were in accordance with those in wastewater. Quinolones were invariably dominant in both dissolved and adsorbed fractions. High removal efficiencies (median values >50.0%) were acquired for the dissolved quinolones (except for DFX), tetracyclines, β-lactams, and lincosamides. Anaerobic/anoxic/oxic achieved the highest aqueous removal of antibiotics among the investigated treatment technologies in the three WTPs. PWTP and IWTP removed 9797 and 487 g·d^-1 of antibiotics, respectively; and a final effluent with 126.4 g·d^-1 of antibiotics was discharged into the effluent-receiving area (ERA) of Hangzhou Bay. Source apportionment analysis demonstrated that the effluents of IWTP_d and IWTP_d contributed respectively 39.3% and 8.9% to the total antibiotics in the ERA. The results illustrate quantitatively the antibiotic flows from engineered wastewater systems to natural water environment, on the basis of which the improvements of wastewater treatment technologies and discharge management would be put forward.

The fate of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) from livestock wastewater (dominated by quinolone antibiotics) treated by microbial fuel cell (MFC)

The removal characteristics of antibiotic resistance genes and mobile genetic elements from livestock wastewater (dominated by quinolone antibiotics) treated with MFC were evaluated by High-throughput quantitative (HT-qPCR). The results showed that 144 ARGs and 8 MEGs were detected in the livestock wastewater. After MFC treatment, the number of AGRs decreased as a whole, and the relative abundance of macrolide-lincosamide-streptogramin group B (MLSB) and aminoglycosider decreased by 62.7% and 92.9%, respectively. MGEs decreased by 57.3% and multidrug genes decreased by 90%. After MFC treatment, the absolute abundance of tetracycline in raw sewage decreased by two orders of magnitude from 5.8 × 105 copies L-1 to 5.1.× 103 copies L-1. However, MFC was less efficient in the removal of vancomycin and beta-lactamase genes. It was also found that chloramphenicol resistance genes slightly increased. Illumina sequencing showed that Syntrophobacterales and Synergistales were predominant in MFCs. Desulfovibrio was resistant to high concentration of moxifloxacin hydrochloride. The removal efficiency of MFC for moxifloxacin hydrochloride at a concentration of 5 mg L-1 was 86.55%. The maximum power density and coulomb efficiency were 109.3 mV·cm-3 and 41.97%, respectively. With the increase of antibiotic concentration, the sewage treatment efficiency and electrical performance were inhibited. This study shows that untreated livestock wastewater had a great risk of gene horizontal transfer. Although MFC had limited treatment capacity for high-concentration quinolone wastewater, it is an effective method to reduce ARGs and the risk of horizontal gene transfer.

Identification of the priority antibiotics based on their detection frequency, concentration, and ecological risk in urbanized coastal water

Antibiotics have raised significant concern as emerging pollutants for their increasing consumption, persistent input, and potential threat to ecological environment. Due to low concentrations and various types in coastal water, simultaneous quantification of all kinds of antibiotics is time-consuming and costly. In order to make antibiotic regular monitoring in coastal water possible, identifying the priority antibiotics in the environment is essential. Here, a method for screening the priority antibiotics in coastal water was proposed, considering individual antibiotic concentration, the positive correlation between individual and total antibiotic concentration, the detection frequency, and obvious ecological risk. Taking coastal water of the East China Sea as an example, on a list of 77 target antibiotics, 7 (SMX, TMP, SCP, SMP, CNX, ATM, and ETM) and 4 (SMX, SCP, SMP, and CNX) antibiotics were selected to be the priority antibiotics in 2017 and 2018, respectively. Furthermore, the 4 priority antibiotics in 2018 were all involved in the 7 priority antibiotics in 2017. The sum of the priority antibiotic concentrations accounted for 0.8% and 23.2% of total antibiotic concentrations, and the sum of their RQ accounted for 69.2% and 66.8% of total RQ values in 2017 and 2018, respectively. Among the above 7 priority antibiotics, ATM is mainly used in human clinical, SMX, SCP, and SMP are mainly consumed in veterinary medicine, TMP, CNX, and ETM are commonly used for humans and animals. The proposed method might provide an important reference for the monitoring and management of antibiotic pollution in coastal water.

Antibiotic Resistance Genes and Bacterial Communities of Farmed Rainbow Trout Fillets (Oncorhynchus mykiss)

The rise of antibiotic resistance is not only a challenge for human and animal health treatments, but is also posing the risk of spreading among bacterial populations in foodstuffs. Farmed fish-related foodstuffs, the food of animal origin most consumed worldwide, are suspected to be a reservoir of antibiotic resistance genes and resistant bacterial hazards. However, scant research has been devoted to the possible sources of diversity in fresh fillet bacterial ecosystems (farm environment including rivers and practices, and factory environment). In this study bacterial communities and the antibiotic resistance genes of fresh rainbow trout fillet were described using amplicon sequencing of the V3-V4 region of the 16S rRNA gene and high-throughput qPCR assay. The antibiotic residues were quantified using liquid chromatography/mass spectrometry methods. A total of 56 fillets (composed of muscle and skin tissue) from fish raised on two farms on the same river were collected and processed under either factory or laboratory sterile filleting conditions. We observed a core-bacterial community profile on the fresh rainbow trout fillets, but the processing conditions of the fillets has a great influence on their mean bacterial load (3.38 ± 1.01 log CFU/g vs 2.29 ± 0.72 log CFU/g) and on the inter-individual diversity of the bacterial community. The bacterial communities were dominated by Gamma- and Alpha-proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. The most prevalent genera were Pseudomonas, Escherichia-Shigella, Chryseobacterium, and Carnobacterium. Of the 73 antibiotic residues searched, only oxytetracycline residues were detected in 13/56 fillets, all below the European Union maximum residue limit (6.40–40.20 μg/kg). Of the 248 antibiotic resistance genes searched, 11 were found to be present in at least 20% of the fish population (tetracycline resistance genes tetM and tetV, β-lactam resistance genes bla_DHA and bla_ACC, macrolide resistance gene mphA, vancomycin resistance genes vanTG and vanWG and multidrug-resistance genes mdtE, mexF, vgaB and msrA) at relatively low abundances calculated proportionally to the 16S rRNA gene.