Contamination profiles of antibiotic resistance genes in the sediments at a catchment scale

Anthropogenic activities drive the distribution and ecological risk of antibiotics in a highly urbanized river basin

Although antibiotics are widely detected in river water, their quantitative relationships with influencing factors in rivers remain largely unexplored. Here, 15 widely used antibiotics were comprehensively analyzed in the Dongjiang River of the Pearl River system. The total antibiotic concentration in river water ranged from 13.84 to 475.04 ng/L, with fluoroquinolones increasing from 11 % in the upstream to 38 % in the downstream. The total antibiotic concentration was high downstream and significantly correlated with the spatial distribution of population density, animal production, and land-use type. The total risk quotient of antibiotics for algae was higher than that for crustaceans and fish. Based on the optimized risk quotient method, amoxicillin, ofloxacin, and norfloxacin were identified as priority antibiotics. The key predictors of antibiotic levels were screened through Mantel test, correlation analysis, and multiple regression models. Water physicochemical parameters significantly impacted antibiotics and could be used as easy-to-measure surrogates associated with elevated antibiotics. Cropland negatively affected fluoroquinolones and sulfonamides, whereas urban land exerted positive impacts on fluoroquinolones, β-lactam, and sulfonamides. In the main stream, population, animal production, urbanization status, and economic development had key effects on the distribution of florfenicol, norfloxacin, ofloxacin, and sulfadiazine.

Transmission mechanism of antibiotic resistance genes and their differences between water and sediment in the Weihe River Basin

Antibiotic resistance genes (ARGs) are emerging microbial pollutants that are regulated by many factors and pose potential threats to aquatic environments. In this study, we used network analysis, correlation analysis, and constructed models based on metagenomic sequencing results to explore the spatial patterns, impact mechanisms, transmission risks and differences in ARGs in the water and sediment of the Weihe River Basin. The findings revealed notable disparities in ARGs, mobile genetic elements (MGEs), and bacterial communities. In the sediment, the abundance of ARGs was considerably greater than that in water. Moreover, the percentage of ARGs shared by the two components reached a value of 85.8%. Through network analysis, it was determined that the presence of 16 MGEs and 20 bacterial phyla was strongly associated with ARGs (R2 > 0.7, P < 0.05). The Mantel test showed that abiotic factors including DO, pH, nutrients, and heavy metals played important roles in the distribution of ARGs (P < 0.05). A structural equation model revealed that the key factors influencing the distribution of ARGs in water were bacterial diversity and environmental parameters (standardized effects of -0.730 and -0.667), and those in sediment were bacterial diversity and MGEs (standardized effects of -0.751 and 0.851). Neutral modeling indicated that deterministic processes played an important role in the assembly of ARGs in the water of the Weihe River Basin, and stochastic processes were dominant in the sediment. There was a highly significant positive linear correlation between ARGs and pathogens, and there was more complex co-occurrence in the water than in the sediment (R2 > 0.9, P < 0.05), with stronger migration and transmission occurring. Exploring ARGs in large-scale watersheds is immensely important for elucidating their traits and transmission mechanisms and consequently paving the way for the formulation of efficient strategies to mitigate resistance threats.

Determining the Contribution of Micro/Nanoplastics to Antimicrobial Resistance: Challenges and Perspectives

Microorganisms colonizing the surfaces of microplastics form a plastisphere in the environment, which captures miscellaneous substances. The plastisphere, owning to its inherently complex nature, may serve as a "Petri dish" for the development and dissemination of antibiotic resistance genes (ARGs), adding a layer of complexity in tackling the global challenge of both microplastics and ARGs. Increasing studies have drawn insights into the extent to which the proliferation of ARGs occurred in the presence of micro/nanoplastics, thereby increasing antimicrobial resistance (AMR). However, a comprehensive review is still lacking in consideration of the current increasingly scattered research focus and results. This review focuses on the spread of ARGs mediated by microplastics, especially on the challenges and perspectives on determining the contribution of microplastics to AMR. The plastisphere accumulates biotic and abiotic materials on the persistent surfaces, which, in turn, offers a preferred environment for gene exchange within and across the boundary of the plastisphere. Microplastics breaking down to smaller sizes, such as nanoscale, can possibly promote the horizontal gene transfer of ARGs as environmental stressors by inducing the overgeneration of reactive oxygen species. Additionally, we also discussed methods, especially quantitatively comparing ARG profiles among different environmental samples in this emerging field and the challenges that multidimensional parameters are in great necessity to systematically determine the antimicrobial dissemination risk in the plastisphere. Finally, based on the biological sequencing data, we offered a framework to assess the AMR risks of micro/nanoplastics and biocolonizable microparticles that leverage multidimensional AMR-associated messages, including the ARGs' abundance, mobility, and potential acquisition by pathogens.

The occurrence and abundance of antibiotic resistance genes in rivers of tropical islands: a case of Hainan Island, China

In this study, the occurrence and distribution of 49 antibiotic resistance genes (ARGs) and two integrase genes (intl1, intl2) in three major rivers of Hainan Island, China, were investigated in July 2021, and to explore the spatial distribution of the target genes in the three rivers with the potential influencing factors such as regional characteristics and environmental factors. The results showed that a total of 46 ARGs and two integrase genes were detected in water and sediment, and the absolute abundance of ARGs ranged from 1.16 × 103 to 2.97 × 107 copies/L and 3.34 × 103-1.55 × 107 copies/g. ARGs of macrolides, aminoglycosides, and sulfonamides were this study's main types of ARGs. The aadA2, tetE, ermF, tetX, aac(6')-Ib, tetW, and qnrS genes are predominant ARGs in the water and sediment of the three rivers. The relative abundance of ARGs shows higher abundance in the midstream and downstream and lower abundance in the upstream and estuarine. After conducting a correlation analysis, it was found that there was a significant positive correlation between the ARGs detected in the water of the three main rivers. However, in sediment, tetC was negatively correlated with tetQ, macB was negatively correlated with ermF and ereA (p < 0.05), while the remaining ARGs showed positive correlations. Specifically, there was no significant positive correlation between tetQ and tetC, macB and ereA, and ermF in the sediments. Among the nine environmental factors studied, pH was found to be the main factor associated with the occurrence of ARGs in the aquatic environment, but it was also significantly associated with only nine ARGs. Among the detected heavy metals, only Cd and Zn showed significant correlations with the two ARGs in the water bodies of the three main rivers. It indicated that the pollution of ARGs in the three major rivers was in the initial stage, the detection abundance was low, the influence of environmental factors was small, and the interaction between ARGs seemed to be the main driving force. This study provides a scientific basis for further understanding the occurrence of ARGs and their influencing factors in a tropical island environment, and lays a foundation for subsequent management.

The fate of antibiotic resistance genes in the coastal lagoon with multiple functional zones

Coastal lagoons provide many important services to human society, but their year-round use for aquaculture introduces large amounts of sewage. The contamination of antibiotic resistance genes (ARGs) is therefore of great concern. In this study, 50 ARGs subtypes, two integrase genes (intl1, intl2), and 16S rRNA genes were detected by high-throughput quantitative PCR, and standard curves of all target genes were prepared for quantification. The occurrence and distribution of ARGs in a typical coastal lagoon (XinCun lagoon, China) were comprehensively explored. We detected 44 and 38 subtypes of ARGs in the water and sediment, respectively, and discuss the various factors influencing the fate of ARGs in the coastal lagoon. Macrolides-lincosamides-streptogramins B was the primary ARG type, and macB was the predominant subtype. Antibiotic efflux and antibiotic inactivation were the main ARG resistance mechanisms. The XinCun lagoon was divided into eight functional zones. The ARGs showed a distinct spatial distribution owing to the influence of microbial biomass and anthropogenic activity in different functional zones. Fishing rafts, abandoned fish ponds, the town sewage zone, and mangrove wetlands provided a large quantity of ARGs to the XinCun lagoon. Nutrients and heavy metals also significantly correlated with the fate of the ARGs, especially NO₂^--N and Cu, which cannot be ignored. It is noteworthy that lagoon-barrier systems coupled with persistent pollutant inputs result in coastal lagoons acting as a "buffer pool" for ARGs, which can then accumulate and threaten the offshore environment.

Temporal variations, distribution, and dissemination of antibiotic resistance genes and changes of bacterial communities in a biofloc-based zero-water-exchange mariculture system

Antibiotic resistance genes (ARGs) have obtained an increasing number of global concerns for the severe risks they pose to food safety and public health. Studies have investigated the concentrations and distribution of ARGs in the environment. However, the distribution and dissemination of ARGs, the bacterial communities, and the key influencing factors during the entire rearing period in the biofloc-based zero-water-exchange mariculture system (BBZWEMS) remain unclear. The current study investigated the concentrations, temporal variations, distribution, and dissemination of ARGs, the changes in the bacterial communities, as well as the key influencing factors during the rearing period in the BBZWEMS. Sul1 and sul2 were dominant ARGs. Total concentrations of ARGs followed a trend of decrease in pond water, while they followed a trend of increase in source water, biofloc, and shrimp gut. Total concentrations of targeted ARGs in the water source were higher than those in the pond water and biofloc samples for each corresponding rearing stage by 2.25-122.97-fold (p < 0.05). The bacterial communities in biofloc and pond water did not change much, while they changed considerably in the shrimp gut samples during the rearing period. Pearson correlation, redundancy analysis, and multivariable linear regression analysis showed that suspended substances and Planctomycetes were positively correlated with the concentrations of ARGs (p < 0.05). The current study indicates that the water source may be a critical source of ARGs, and that suspended substances is a key factor influencing the distribution and dissemination of ARGs in the BBZWEMS. Early intervention measures on ARGs in water sources should be implemented to aid in the prevention and control of resistance genes in aquaculture industry, and reduce the potential risks of ARGs to public health and food safety.

A Review of Antibiotics, Antibiotic Resistant Bacteria, and Resistance Genes in Aquaculture: Occurrence, Contamination, and Transmission

Antibiotics are commonly used to prevent and control diseases in aquaculture. However, long-term/overuse of antibiotics not only leaves residues but results in the development of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Antibiotics, ARB, and ARGs are widespread in aquaculture ecosystems. However, their impacts and interaction mechanisms in biotic and abiotic media remain to be clarified. In this paper, we summarized the detection methods, present status, and transfer mechanisms of antibiotics, ARB, and ARGs in water, sediment, and aquaculture organisms. Currently, the dominant methods of detecting antibiotics, ARB, and ARGs are UPLC-MS/MS, 16S rRNA sequencing, and metagenomics, respectively. Tetracyclines, macrolides, fluoroquinolones, and sulfonamides are most frequently detected in aquaculture. Generally, antibiotic concentrations and ARG abundance in sediment are much higher than those in water. Yet, no obvious patterns in the category of antibiotics or ARB are present in organisms or the environment. The key mechanisms of resistance to antibiotics in bacteria include reducing the cell membrane permeability, enhancing antibiotic efflux, and structural changes in antibiotic target proteins. Moreover, horizontal transfer is a major pathway for ARGs transfer, including conjugation, transformation, transduction, and vesiculation. Identifying, quantifying, and summarizing the interactions and transmission mechanisms of antibiotics, ARGs, and ARB would provide useful information for future disease diagnosis and scientific management in aquaculture.

The antibiotic resistance and risk heterogeneity between urban and rural rivers in a pharmaceutical industry dominated city in China: The importance of social-economic factors

Rivers are important environmental sources of human exposure to antibiotic resistance. Many factors can change antibiotic resistance in rivers, including bacterial communities, human activities, and environmental factors. However, the systematic comparison of the differences in antibiotics resistance and risks between urban rivers (URs) and rural rivers (RRs) in a pharmaceutical industry dominated city is still rare. In this study, Shijiazhuang City (China) was selected as an example to compare the differences in antibiotics resistance and risks between URs and RRs. The results showed higher concentrations of total quinolones (QNs) antibiotics in both water and sediment samples collected from URs than those from RRs. The subtypes and abundances of antibiotic resistance genes (ARGs) in URs were significantly higher than those in RRs, and most emerging ARGs (including OXA-type, GES-type, MCR-type, and tet(X)) were only detected in URs. The ARGs were mainly influenced by QNs in URs and social-economic factors (SEs) in RRs. The composition of the bacterial community was significantly different between URs and RRs. The abundance of antibiotic-resistant pathogenic bacteria (ARPBs) and virulence factors (VFs) were higher in URs than those in RRs. Therein, 371 and 326 pathogen types were detected in URs and RRs, respectively. Most emerging ARGs showed a significantly positive correlation with priority ARPBs. Variance partitioning analysis revealed that SEs were the main driving factors of ARGs (80 %) and microbial communities (92 %) both in URs and RRs. Structural equation models indicated that antibiotics (QNs) and microbial communities were the most direct influence of ARGs in URs and RRs, respectively. The cumulative resistance risk of QNs was high in URs, but relatively low in RRs. Enrofloxacin and flumequine posed the highest risk in water and sediment, respectively. This study could help us to better manage and control the risk of antibiotic resistance in different rivers.

Non-corresponding contaminants in marine surface sediments as a factor of ARGs spread in the Sea of Azov

The present study aims to analyze the level and total toxicity of the most common pollutants in surface sediments and assess their impact on the occurrence of antibiotic resistance genes (ARGs) in the Sea of Azov. Biotesting using the whole-cell bacterial lux-biosensors showed high integral toxicity of surface sediments and the presence of genotoxicants and substances that cause oxidative stress and protein damage. Using cluster analysis, it was shown that the distribution of pollutants in the Sea of Azov depends on the type of surface sediments. The relative abundance and distribution of 14 ARGs in surface sediments were shown. Principle component analyses results suggest that non-corresponding contaminants do not exert direct influence on the ARGs abundance in the surface sediments of the Sea of Azov. Thus, the need to investigate the significance of non-corresponding pollutants in the selection and distribution of ARGs in the aquatic environment remains a pressing problem.

Distribution of quinolone and macrolide resistance genes and their co-occurrence with heavy metal resistance genes in vegetable soils with long-term application of manure

The spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) has become an increasingly serious global public health issue. This study investigated the distribution characteristics and influencing factors of ARB and ARGs in greenhouse vegetable soils with long-term application of manure. Five typical ARGs, four heavy metal resistance genes (MRGs), and two mobile genetic elements (MGEs) were quantified by real-time quantitative polymerase chain reaction (qPCR). The amount of ARB in manure-improved soil greatly exceeded that in control soil, and the bacterial resistance rate decreased significantly with increases in antibiotic concentrations. In addition, the resistance rate of ARB to enrofloxacin (ENR) was lower than that of tylosin (TYL). Real-time qPCR results showed that long-term application of manure enhanced the relative abundance of ARGs in vegetable soils, and the content and proportion of quinolone resistance genes were higher than those of macrolide resistance genes. Redundancy analysis (RDA) showed that qepA and qnrS significantly correlated with total and available amounts of Cu and Zn, highlighting that certain heavy metals can influence persistence of ARGs. Integrase gene intI1 correlated significantly with the relative abundance of qepA, qnrS, and ermF, suggesting that intI1 played an important role in the horizontal transfer of ARGs. Furthermore, there was a weakly but not significantly positive correlation between specific detected MRGs and ARGs and MGEs. The results of this study enhance understanding the potential for increasing ARGs in manure-applied soil, assessing ecological risk and reducing the spread of ARGs.

The source, fate and prospect of antibiotic resistance genes in soil: A review

Antibiotic resistance genes (ARGs), environmental pollutants of emerging concern, have posed a potential threat to the public health. Soil is one of the huge reservoirs and propagation hotspot of ARGs. To alleviate the potential risk of ARGs, it is necessary to figure out the source and fate of ARGs in the soil. This paper mainly reviewed recent studies on the association of ARGs with the microbiome and the transmission mechanism of ARGs in soil. The compositions and abundance of ARGs can be changed by modulating microbiome, soil physicochemical properties, such as pH and moisture. The relationships of ARGs with antibiotics, heavy metals, polycyclic aromatic hydrocarbons and pesticides were discussed in this review. Among the various factors mentioned above, microbial community structure, mobile genetic elements, pH and heavy metals have a relatively more important impact on ARGs profiles. Moreover, human health could be impacted by soil ARGs through plants and animals. Understanding the dynamic changes of ARGs with influencing factors promotes us to develop strategies for mitigating the occurrence and dissemination of ARGs to reduce health risks.

Antibiotic resistant bacteria and genes in wastewater treatment plants: From occurrence to treatment strategies

This study aims to discuss the following: (1) occurrence and proliferation of antibiotic resistance in wastewater treatment plants (WWTPs); (2) factors influencing antibiotic resistance bacteria and genes in WWTPs; (3) tools to assess antibiotic resistance in WWTPs; (4) environmental contamination of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) from WWTPs; (5) effects of ARB and ARGs from WWTPs on human health; and (6) treatment strategies. In general, resistant and multi-resistant bacteria, including Enterobacteriaceae, Pseudomonas aeruginosa, and Escherichia coli, exist in various processes of WWTPs. The existence of ARB and ARGs results from the high concentration of antibiotics in wastewater, which promote selective pressures on the local bacteria present in WWTPs. Thus, improving wastewater treatment technology and avoiding the misuse of antibiotics is critical to overcoming the threat of proliferation of ARBs and ARGs. Numerous factors can affect the development of ARB and ARGs in WWTPs. Abiotic factors can affect the bacterial community dynamics, thereby, affecting the applicability of ARB during the wastewater treatment process. Furthermore, the organic loads and other nutrients influence bacterial survival and growth. Specifically, molecular methods for the rapid characterization and detection of ARBs or their genes comprise DNA sequencing, real-time PCR, simple and multiplex PCR, and hybridization-based technologies, including micro- and macro-arrays. The reuse of effluent from WWTPs for irrigation is an efficient method to overcome water scarcity. However, there are also some potential environmental risks associated with this practice, such as increase in the levels of antibiotic resistance in the soil microbiome. Human mortality rates may significantly increase, as ARB can lead to resistance among several types of antibiotics or longer treatment times. Some treatment technologies, such as anaerobic and aerobic treatment, coagulation, membrane bioreactors, and disinfection processes, are considered potential techniques to restrict antibiotic resistance in the environment.

Metagenomic Analysis of Urban Wastewater Treatment Plant Effluents in Tokyo

Purpose

Urban wastewater treatment plant (WWTP) effluents, even with proper treatment, may cause antimicrobial resistance (AMR) burden, with a high frequency of acquired antimicrobial resistance genes (ARGs). The dissemination of ARGs into the environment increases the risk of infectious diseases; however, there is little direct evidence regarding their epidemiological effects. This study aimed to assess effluents from urban WWTPs around the Tama River and Tokyo Bay using metagenomic analysis of (AMR) genes (ARGs) and heavy-metal resistance genes.

Methods

Metagenomic DNA-seq analysis of water samples and resistome analysis were performed.

Results

The most prevalent ARG was the sulfonamide resistance gene, sul1, followed by the quaternary ammonium compound resistance gene, qacE, suggesting that basic gene sets (sul1 and ∆qacE) in the class 1 integrons are the predominant ARGs. The aminoglycoside resistance genes, aadA and aph, and macrolide resistance genes, msr(E) and mph(E), were the predominant ARGs against each antimicrobial. bla _OXA and bla _GES were frequently detected, whereas the bla _CTX-M cluster was faintly detected. Non-metric multidimensional scaling plot analysis and canonical correspondence analysis results suggested that marked differences in ARGs could be involved in the seasonal differences; qnrS2, aac(6')-Ib, and mef(C) increased markedly in summer, whereas msr(E) was more frequently detected in winter. Heavy-metal (Hg and Cu) resistance genes (HMRGs) were significantly detected in effluents from all WWTPs.

Conclusion

We characterized a baseline level of the environmental ARG/HMRG profile in the overall community, suggesting that environmental AMR surveillance, particularly in urban WWTPs, is a valuable first step in monitoring the AMR dissemination of bacteria from predominantly healthy individuals carrying notable ARG/Bs.

Insights into highly effective catalytic persulfate activation on oxygen-functionalized mesoporous carbon for ciprofloxacin degradation

Nanocarbons have been demonstrated as promising carbon catalysts for substituting metal-based catalysts for the green treatment of wastewater. In this study, oxygen-functionalized mesoporous carbon (OCMK-3) was prepared by wet oxidation and exhibited high catalytic performance against ciprofloxacin (CIP) by activation of persulfate. The effects of environmental parameters (pH, temperature, coexisting ions) and process parameters (temperature, sodium persulfate concentration, catalyst agent dosage, initial concentration) on the removal of CIP were investigated. Compared with the pristine ordered mesoporous carbon (CMK-3), the removal efficiency of CIP by OCMK-3 was increased by 32% under optimal conditions. This rise in activity was attributed to the increase in oxygen-containing functional groups, porosity, and specific surface area of OCMK-3 with improved structural defects and electron transfer efficiency. Furthermore, based on active species scavenging experiments, a dual-pathway mechanism of the radical and nonradical pathways was discovered. The rational degradation pathway of CIP was investigated based on liquid chromatography-mass spectrometry (LC-MS). In addition, the OCMK-3/PS system exhibited high decomposition efficiency in pharmaceutical wastewater treatment. This study provides an in-depth mechanism for the degradation of organic pollutants by carbon-based PS-AOPs and provides theoretical support for further studies.

Diversity, abundances and distribution of antibiotic resistance genes and virulence factors in the South China Sea revealed by metagenomic sequencing

Antibiotic resistance genes (ARGs) and virulence factors (VFs) pose considerable health risks to humans. The occurrence and abundance of several typical ARGs in the sea have been widely investigated. However, the full profiles and abundances of the antibiotic resistome and VFs in the South China Sea remain unexplored. Therefore, in this study, we investigated the full profiles of the ARGs and VFs, as well as their abundances and distribution, in the South China Sea using metagenomic approaches. In total, 140 ARG subtypes and 155 VFs were detected. The most abundant ARG was multidrug resistance gene, followed by bacitracin resistance gene. Flagella was the most abundant VF. Pearson correlation analysis revealed a strong and positive correlation between the abundances of ARGs and VFs. Redundancy analysis and co-occurrence network analysis showed that the predominant VFs were positively correlated with the predominant ARGs in the South China Sea. Nonmetric multidimensional scaling and Procrustes analyses demonstrated that the sampling sites were clustered into three compartments according to the geographical location, i.e., offshore, open sea, and reef zones. The abundances of ARGs and VFs in the offshore zone were much higher than those in the open sea and reef zones (p < 0.05). Several physico-chemical factors most closely associated with anthropogenic activities, i.e., nitrate, lead, copper, and zinc, were positively correlated with the predominant ARGs and VFs in the South China Sea. Our results suggest that the ocean is a large reservoir of diverse and abundant ARGs and VFs, which may threaten human health and seafood safety. These findings improve the understanding of the relationship between ARG dissemination and intensive anthropogenic activities and can aid in improving ocean management and seafood product safety.

A facile solvothermal syntheses of NiFe layered double hydroxide-Bi2MoO6 heterostructure/reduced graphene oxide with efficient photodegradation for tetracycline

A heterojunction of NiFe layered double hydroxide (NiFe LDH)-Bi₂MoO₆ (BMO) loaded on reduced graphene oxide (RGO) sheets was synthesized via an eco-friendly solvothermal reaction. The structural characterization shows that NiFe LDH-BMO heterojunctions are well-distributed on the surface of silk-like transparent RGO sheets. The modification of BMO by NiFe LDH and RGO greatly enhances the photocatalytic performance of BMO for degradation of tetracycline (TC) under visible light. The photocatalyst prepared with 3 wt% RGO shows the highest activity and cycle stability. TC can be completely removed in 80 min, which is about 8.7 times that pure BMO, and showing excellent reusability even after five cycles. The excellent enhancement of photocatalytic performance of NiFe LDH-BMO/RGO composite is attributed to the unique sheet-on-sheet hierarchical heterostructure combined with RGO sheets, facilitating the visible light absorption and photogenerated charge carriers separation.

Influence of soil characteristics and metal(loid)s on antibiotic resistance genes in green stormwater infrastructure in Southern California

The synergetic effects of metal(loid)s and soil characteristics on bacterial antibiotic resistance genes (ARGs) in green stormwater infrastructure (GSI) has been relatively understudied. Surface soil samples from six GSIs in Southern California over three time periods were assessed for selected ARGs, class 1 integron-integrase genes (intI1), 16S rRNA genes, and bioavailable and total concentrations of nine metal(loid)s, to investigate the relationships among ARGs, soil characteristics, and co-occurring metal(loid)s. Significant correlations existed among relative gene abundances (sul1, sul2, tetW, and intI1), total metal(loid)s (arsenic, copper, lead, vanadium, and zinc), and bioavailable metal(loid) (arsenic) (r = 0.29-0.61, p_adj < 0.05). Additionally, soil texture, organic matter, and nutrients within GSI appeared to be significantly correlated with relative gene abundances of sul1, sul2, and tetW (r = -0.57 to 0.59, p_adj < 0.05). Multiple regression models significantly improved the estimation of ARGs in GSI when considering multiple effects of soil characteristics and metal(loid)s (r = 0.74, p_adj < 0.001) compared to correlation results. Total arsenic was a significant (positive) correlate in all the regression models of relative gene abundances. This work provides new insights into co-dependencies between GSI ARGs and co-occurring metal(loid)s, indicating the need for risk assessment of metal(loid)-influenced ARG proliferation.

Fates of intracellular and extracellular antibiotic resistance genes during the cattle farm wastewater treatment process

Cattle farm wastewater, as a significant reservoir for antibiotic resistance genes (ARGs), has received wide attention. Intracellular and extracellular ARGs (iARGs and eARGs) were detected during wastewater treatment, including solid-liquid separation, anaerobic regulation, upflow anaerobic sludge blanket (UASB) digestion, an anoxic-oxic-anoxic-oxic (A²O²) process, a membrane bioreactor (MBR), and ozone disinfection. Ten abundant ARGs were chosen as the target ARGs according to metagenomic sequencing. The concentrations of the total target iARGs and eARGs were 6.12 × 10⁷ and 3.24 × 10⁶ copy numbers/mL in raw wastewater, and then 3.79 × 10³ and 3.95 × 10⁵ copy numbers/mL in final effluent, because UASB, A²O², MBR and ozone disinfection can gradually reduce the concentrations of most ARGs. The concentrations of ARGs were positively correlated with almost all wastewater quality indicators. Positive correlation was also observed between iARGs and Bacteroidetes, Firmicutes and Spirochaetes, indicating that the bacteria in these three phyla might be the main hosts of ARGs. Wastewater quality indicators and bacterial community composition affected the distribution and removal of ARGs during cattle wastewater treatment.

Impact of chicken litter pre-application treatment on the abundance, field persistence, and transfer of antibiotic resistant bacteria and antibiotic resistance genes to vegetables

Treatment of manures prior to land application can potentially reduce the abundance of antibiotic resistance genes and thus the risk of contaminating crops or water resources. In this study, raw and composted chicken litter were applied to field plots that were cropped to carrots, lettuce and radishes. Vegetables were washed per normal culinary practice before downstream analysis. The impact of composting on manure microbial composition, persistence of antibiotic resistant bacteria in soil following application, and distribution of antibiotic resistance genes and bacteria on washed vegetables were determined. A subset of samples that were thought likely to reveal the most significant effects were chosen for shotgun sequencing. The absolute abundance of all target genes detected by qPCR decreased after composting except sul1, intI1, incW and erm(F) that remained stable. The shotgun sequencing revealed that some integron integrases were enriched by composting. Composting significantly reduced the abundance of enteric bacteria, including those carrying antibiotic resistance. Manure-amended soil showed significantly higher abundances of sul1, str(A), str(B), erm(B), aad(A), intI1 and incW compared to unmanured soil. At harvest, those genes that were detected in soil samples before the application of manure (intI1, sul1, strA and strB) were quantifiable by qPCR on vegetables, with a larger number of gene targets detected on the radishes than in the carrots or lettuce. Shotgun metagenomic sequencing suggested that the increase of antibiotic resistance genes on radishes produced in soil receiving raw manure may be due to changes to soil microbial communities following manure application, rather than transfer to the radishes of enteric bacteria. Overall, under field conditions there was limited evidence for transfer of antibiotic resistance genes from composted or raw manure to vegetables that then persisted through washing.

A review of the bioelectrochemical system as an emerging versatile technology for reduction of antibiotic resistance genes

Antibiotic contamination and the resulting resistance genes have attracted worldwide attention because of the extensive overuse and abuse of antibiotics, which seriously affects the environment as well as human health. Bioelectrochemical system (BES), a potential avenue to be explored, can alleviate antibiotic pollution and reduce antibiotic resistance genes (ARGs). This review mainly focuses on analyzing the possible reasons for the good performance of ARG reduction by BESs and potential ways to improve its performance on the basis of revealing the generation and transmission of ARGs in BES. This system reduces ARGs through two pathways: (1) the contribution of BES to the low selection pressure of ARGs caused by the efficient removal of antibiotics, and (2) inhibition of ARG transmission caused by low sludge yield. To promote the reduction of ARGs, incorporating additives, improving the removal rate of antibiotics by adjusting the environmental conditions, and controlling the microbial community in BES are proposed. Furthermore, this review also provides an overview of bioelectrochemical coupling systems including the BES coupled with the Fenton system, BES coupled with constructed wetland, and BES coupled with photocatalysis, which demonstrates that this method is applicable in different situations and conditions and provides inspiration to improve these systems to control ARGs. Finally, the challenges and outlooks are addressed, which is constructive for the development of technologies for antibiotic and ARG contamination remediation and blocking risk migration.

Wastewater treatment plants as a reservoir of integrase and antibiotic resistance genes - An epidemiological threat to workers and environment

Conventional mechanical and biological wastewater treatment is unable to completely eliminate all pollutants, which can therefore enter surface water bodies together with treated wastewater. In addition, bioaerosols produced during wastewater treatment can pose a threat to the health of the wastewater treatment plant staff. In order to control the impact of a wastewater treatment plant (WWTP) on the surrounding environment, including its employees, samples of wastewater and water from a river which received treated wastewater were analysed in terms of their content of antibiotics and heavy metals, levels of selected physiochemical parameters, concentrations of antibiotic-resistance genes (ARGs) and genes of integrases. Furthermore, a quantitative analysis of ARGs in the metagenomic DNA from nasal and throat swabs collected from the WWPT employees was made. Both untreated and treated wastewater samples were dominated by genes of resistance to sulphonamides (sul1, sul2), MLS group of drugs (ermF, ermB) and beta-lactams (bla_OXA). A significant increase in the quantities of ARGs and concentrations of antibiotics was observed in the river following the discharge of treated wastewater in comparison to their amounts in the river water upstream from the point of discharge. Moreover, a higher concentration of ARGs was detected in the DNA from swabs obtained from the wastewater treatment plant employees than from ones collected from the control group. Many statistically significant (p < 0.05) correlations between the concentration of the gene of resistance to heavy metals cnrA versus ARGs, and between the ARGs content and the concentrations of heavy metals in both wastewater and river water samples were observed. The study has demonstrated that the mechanical and biological methods of wastewater treatment are not efficient and may affect the transmission of hazardous pollutants to the aquatic environment and to the atmospheric air. It has been shown that an activated sludge bioreactor can be a potential source of the presence of multi-drug resistant microorganisms in the air, which is a health risk to persons working in WWTPs. It has also been found that an environment polluted with heavy metals is where co-selection of antibiotic resistance may occur, in the development of which integrase genes play an essential role.

Occurrence and distribution characteristics of antibiotic resistance genes in sediments between urban and rural of the Liaohe River Basin, China

Antibiotic resistance genes (ARGs) are considered to be emerging pollutants related to human activities. The rapid development of global urbanization has expanded human activities, thereby exacerbating the global human health risks caused by antibiotic resistance genes. The effects of urban and rural environments are multifarious, which makes the source and distribution of ARGs in the environment diversification. Understanding the distribution and spread of ARGs is essential for studying the environmental behavior of ARGs. In this study, the occurrence 296 genes were detected by the high-throughput qPCR technology, and FC value was used to analyze the diversity of ARGs and mobile genetic elements (MGEs) in sediments between urban and rural areas of the Liaohe River Basin, China. The co-occurrence of MGEs and ARGs was analyzed using network to decipher core genes. A total of 187 ARGs and 10 MGEs were detected in all sediment samples. The average number of genes detected in urban sites is 89 higher than that in rural sites. The high abundance and various types of ARGs and MGEs detected in urban river sediments indicate that the occurrence of urban ARGs is more complex. MGEs were detected high levels and were significantly correlated with the abundance and diversity of ARGs in river sediments providing evidence that MGEs were related to the occurrence and distribution of ARGs and tnpA (tnpA-07, tnpA-01, and tnpA-03) gene were at the key position of co-occurrence of various types of ARGs.

Metagenomics analysis reveals the distribution and communication of antibiotic resistance genes within two different red swamp crayfish Procambarus clarkii cultivation ecosystems

Antibiotic resistance genes (ARGs) are emerging contaminants that pose a potential risk to human health worldwide. In this study, a metagenomic analysis was performed to investigate the distribution of ARGs in paddy field ecosystems, crayfish monoculture pond ecosystems, and rice-crayfish cultivation field ecosystems. The results showed that MacB and BcrA are two dominant ARGs, and macrolide is the dominant antibiotic not only in the water, but also in the sediment and gut of crayfish, in both the crayfish monoculture and the rice-crayfish cultivation ecosystems. Meanwhile, some lower-abundance ARGs in the water and sediment of crayfish cultivation ecosystems were significantly different in their abundance than those in rice paddy fields, and the ARGs in crayfish culture system and rice paddy fields showed even higher dissimilarities of diversity. Comprehensive analysis with redundancy analysis（RDA）and the distribution of dominant ARGs showed that the dissimilarity was related to the higher concentrations of total nitrogen (TN), total phosphorus (TP), chlorophyll a (Chla), permanganate index (COD_Mn), and nitrate in the water of rice paddy fields, and was related to the higher contents of N, P, K, and organic matter (OM) in the sediment of rice paddy fields. The source trackers of ARGs within the crayfish cultivation ponds and the rice-crayfish cultivation fields showed that the sediment in crayfish cultivation ponds mainly played the role of the 'sink' for ARGs, and the water and gut of crayfish mutually contributed to the high rates of ARGs. The ARG contribution rates of crayfish gut and sediment decreased and increased, respectively, in rice-crayfish cultivation fields and in crayfish monoculture ponds, which might be related to the lower crayfish biomass and the lower water depth in rice-crayfish cultivation fields.

Antibiotic resistance genes and mobile genetic elements in a rural river in Southeast China: Occurrence, seasonal variation and association with the antibiotics

Human activities in rural areas, such as livestock farming, aquaculture, and rural domestic sewage discharge, may result in antibiotic resistance genes (ARGs) pollution in rural rivers. A systematic monitoring in different seasons was conducted in a typical agriculture-polluted river with Real-Time Quantitative PCR. A total of 11 ARGs and 2 related mobile genetic elements (MGEs) were detected at all sites with relative abundances of 6.9 × 10^-10-0.2 copies/16S rRNA copies. Among them, sul1, sul2 and int1 were the dominant target genes in water samples. tetW, ermB, and floR were more abundant in November (the dry season), while other ARGs, MGEs and 16s rRNA were at a higher absolute abundance in warm seasons. There was less spatial variation of ARGs in the dry season than in the other two seasons. Furthermore, the relative abundance of ARGs was higher at sampling sites adjoining pollution sources. In addition, cluster analysis implied that ARGs in upstream sediments may be released into surface water and migrate downstream in the direction of river flow. There was no significant correlation between ARGs and their corresponding antibiotics. However, the total concentration of tetracycline was significantly correlated with the non-paired ARGs, including sul3, floR, and ermB. At the same time, heavy metals (Zn, Pb, Cd, Cr⁶⁺, As) and other environmental parameters (permanganate index, pH, DO) may apply selective pressure on the spread of ARGs, according to redundancy and Pearson's correlation analysis.

Prevalence of antibiotic resistance genes in wastewater collected from ornamental fish market in northern China

Large amounts of antibiotics/disinfectants are used in the farming of ornamental fish so as to prevent and treat bacterial infection. This may exert considerable selection pressures on the prevalence and propagation of antibiotic resistance genes (ARGs). However, the levels of ARGs and their potential prevalence mechanism in the wastewater of the ornamental fish industry remains unclear. In this work, wastewater is collected from a representative ornamental fish market (OFM) that is located at the northern China to study the occurrence and abundance of 21 ARGs and 2 integrase genes. Results indicated that 15 different ARGs and 2 integrase genes are existent and prevalent in the wastewater of OFM, whereby concentrations range from 2.01 to 10.34 copies/L. Proteobacteria, Bacteroidetes, Verrucomicrobia, and Firmicutes are the predominant phyla in the wastewater samples. 17 species of human opportunistic pathogens are present with relative abundance of up to 0.01%, which suggests a considerable risk of pathogens acquiring and disseminating ARGs. Moreover, oxytetracycline, ciprofloxacin, norfloxacin, sulfadiazine, and chloramphenicol are most frequently detected in wastewater, with concentrations of up to 1150, 877, 514, 1970, and 1700 ng/L, respectively. Notably, good correlations have been determined among ARGs and antibiotics, non-antibiotic environmental factors in wastewater of OFM. This current study reveals, for the first time, that OFM is a previously unperceived reservoir for ARG prevalence in aquatic environment and water environmental factors (particularly antibiotics), and their induced shifts in the microbial communities are the key factors for distribution of ARGs in OFM.

Occurrence and antibacterial resistance of culturable antibiotic-resistant bacteria in the Fildes Peninsula, Antarctica

Quantifying the occurrence of Antarctic antibiotic-resistant bacteria (ARB) is essential for assessing the level of pollution and assessing the "baseline" or background level of ARB in human uninhabited environments. Animal feces, soil, and sediments were sampled from Fildes Peninsula. The abundance of sulfamethazine- and ciprofloxacin-resistance bacteria and antibotic resistance genes (ARGs) within ARB were investigated. The results showed Ciprofloxacin- and Sulfamethazine-resistant bacteria isolated from samples accounted for the highest abundances of 30 CFU/g and 79.8 CFU/g, respectively. The dominant genus of Sulfamethazine-and quinolone-resistance bacteria was Pseudomonas and Arthrobacter, respectively. 106 ARGs were detected from ARB. Strong positive correlations between mobile genetic elements (MGEs) and ARGs were found, what is relatively novel observation that the mechanism is confirmed to also occur in the Antarctic. This study reveals the compositional characteristics of ARGs of strains in Antarctic, providing support for the source of Antarctic antibiotic resistance and drug resistance mechanisms.

Variation in microbial populations and antibiotic resistance genes in mariculture sediments in the present of the seaweed Ulva fasciata and under selective pressure of oxytetracycline

The widely distributed seaweed Ulva fasciata has nutrient absorption abilities and can be used in the bioremediation of polluted maricultural environments. This study explored microbial community and antibiotic resistance gene (ARG) variation in mariculture sediments in response to different trace levels (10, 100, and 500 μg L^-1) of oxytetracycline (OTC) and the presence of Ulva fasciata. The increase in OTC level promoted nutrient (NO₃_-N and PO₄^3--P) removal mainly due to Ulva fasciata adsorption. The abundances of the Euryarchaeota and Planctomycetes phyla in sediments were positively related to the increase in OTC stress, while a negative correlation occurred for the Proteobacteria phylum via metagenomic analysis. Compared with the control system, the increase rates of total ARGs were 3.90%, 7.36% and 13.42% at the OTC levels of 10, 100 and 500 μg L^-1, respectively. OTC stress mainly favoured the collateral enrichment of non-corresponding polypeptide and MLS ARGs, mainly due to the enrichment of the phyla Planctomycetes and Euryarchaeota by the synergistic effect of OTC and nutrients. The results of quantitative PCR with tetracycline resistance genes (TRGs) (tetO, tetT, tetPB, tetW and otrA) and a horizontal transfer gene (intl1) demonstrated that all of genes had much higher gene numbers in sediments after 3 months of OTC stress than in those without OTC stress, which was strongly related to the variation in the phyla Bacteroidetes, Gemmatimonadetes and Acidobacteria. The significant correlation between intl1 and the target TRGs is indicative of the important role of the horizontal transfer of integron-resistant genes in the spread of TRGs.

Merging Metagenomics and Spatial Epidemiology To Understand the Distribution of Antimicrobial Resistance Genes from Enterobacteriaceae in Wild Owls

Antimicrobial resistance (AMR) is a well-documented phenomenon in bacteria from many natural ecosystems, including wild animals. However, the specific determinants and spatial distribution of resistant bacteria and antimicrobial resistance genes (ARGs) in the environment remain incompletely understood. In particular, information regarding the importance of anthropogenic sources of AMR relative to that of other biological and ecological influences is lacking. We conducted a cross-sectional study of AMR in great horned owls (Bubo virginianus) and barred owls (Strix varia) admitted to a rehabilitation center in the midwestern United States. A combination of selective culture enrichment and shotgun metagenomic sequencing was used to identify ARGs from Enterobacteriaceae Overall, the prevalence of AMR was comparable to that in past studies of resistant Enterobacteriaceae in raptors, with acquired ARGs being identified in 23% of samples. Multimodel regression analyses identified seasonality and owl age to be important predictors of the likelihood of the presence of ARGs, with birds sampled during warmer months being more likely to harbor ARGs than those sampled during cooler months and with birds in their hatch year being more likely to harbor β-lactam ARGs than adults. Beyond host-specific determinants, ARG-positive owls were also more likely to be recovered from areas of high agricultural land cover. Spatial clustering analyses identified a significant high-risk cluster of tetracycline resistance gene-positive owls in the southern sampling range, but this could not be explained by any predictor variables. Taken together, these results highlight the complex distribution of AMR in natural environments and suggest that both biological and anthropogenic factors play important roles in determining the emergence and persistence of AMR in wildlife.IMPORTANCE Antimicrobial resistance (AMR) is a multifaceted problem that poses a worldwide threat to human and animal health. Recent reports suggest that wildlife may play an important role in the emergence, dissemination, and persistence of AMR. As such, there have been calls for better integration of wildlife into current research on AMR, including the use of wild animals as biosentinels of AMR contamination in the environment. A One Health approach can be used to gain a better understanding of all AMR sources and pathways, particularly those at the human-animal-environment interface. Our study focuses on this interface in order to assess the effect of human-impacted landscapes on AMR in a wild animal. This work highlights the value of wildlife rehabilitation centers for environmental AMR surveillance and demonstrates how metagenomic sequencing within a spatial epidemiology framework can be used to address questions surrounding AMR complexity in natural ecosystems.

Hospital wastewaters: A reservoir and source of clinically relevant bacteria and antibiotic resistant genes dissemination in urban river under tropical conditions

The occurrence and dissemination of antibiotic resistant genes (ARGs) that are associated with clinical pathogens and the evaluation of associated risks are still under-investigated in developing countries under tropical conditions. In this context, cultivable and molecular approaches were performed to assess the dissemination of bacteria and the antibiotic resistance genes in aquatic environment in Kinshasa, Democratic Republic of the Congo. Cultivable approach quantified β-lactam, carbapenem resistant, and total Escherichia coli and Enterobacteriaceae in river sediments and surface waters that receive raw hospital effluents. The molecular approach utilized Quantitative Polymerase Chain Reaction (qPCR) to quantify the total bacteria and the richness of relevant bacteria (Escherichia coli, Enterococcus, and Pseudomonas), and antibiotic resistance genes (ARGs: bla_OXA-48, bla_CTX-M, bla_IMP, bla_TEM) in sediment samples. Statistical analysis were employed to highlight the significance of hospital contribution and seasonal variation of bacteria and ARGs into aquatic ecosystems in suburban municipalities of Kinshasa, Democratic Republic of the Congo. The contribution of hospitals to antibiotic resistance proliferation is higher in the dry season than during the wet season (p < 0.05). Hospital similarly contributed Escherichia coli, Enterococcus, and Pseudomonas and ARGs significantly to the sediments in both seasons (p < 0.05). The organic matter content correlated positively with E. coli (r = 0.50, p < 0.05). The total bacterial load correlated with Enterococcus, and Pseudomonas (0.49 < r < 0.69, p < 0.05). Each ARG correlated with the total bacterial load or at least one relevant bacteria (0.41 < r < 0.81, p < 0.05). Our findings confirm that hospital wastewaters contributed significantly to antibiotic resistance profile and the significance of this contribution increased in the dry season. Moreover, our analysis highlights this risk from untreated hospital wastewaters in developing countries, which presents a great threat to public health.

Occurrence and distribution of antibiotic resistance genes in various rural environmental media

Antibiotic resistance genes (ARGs) in rural environments have been poorly characterized in the literature. In this study, the diversity, abundance, and distribution of ARGs in surface waters, soils, and sediments of a typical hilly rural area in the Upper Yangtze River watershed were investigated using the high-throughput quantitative polymerase chain reaction, and their relationships with chemical properties of the samples were analyzed. No significant differences in the diversity and abundance of ARGs were observed among the three medium types while the ARG distribution pattern in the sediments was obviously different from that of the surface waters. According to the co-occurrence pattern of ARGs subtypes obtained by network analysis, blaOXA10-02, blaPSE, lnuB-02, and qacEΔ1-01 can be used to estimate the relative abundance of total ARGs for the study area. It appeared that the prevalence of ARGs in the sediments was promoted by the horizontal gene transfer (HGT) and vertical gene transfer together, while their spread in the surface waters and soils were facilitated by the supply of biogenic elements and HGT, respectively. Mobile genetic elements (MGEs) were abundant and detected in all samples, and their abundance was significantly and positively correlated with that of ARGs, implying that the potential horizontal transfer of ARGs to other bacteria and pathogens in rural environments should not be overlooked.

Sulfamethoxazole affects the microbial composition and antibiotic resistance gene abundance in soil and accumulates in lettuce

Pot experiments were set up to simulate the soil contamination by three initial concentrations of sulfamethoxazole (SMX) (S1, 100 mg/kg; S2, 200 mg/kg; S3, 300 mg/kg). The content of SMX in soil and its accumulation in lettuce were analysed. Additionally, the effects of SMX on soil microorganisms and antibiotic resistance genes were studied by Illumina high-throughput sequencing and droplet digital polymerase chain reaction (ddPCR). The results demonstrated that the SMX content in soil reduced by 97%, 86% and 75% in the S1, S2 and S3 treatment groups after 120 days, respectively. The accumulated SMX in lettuce was positively correlated with the initial concentration of SMX in soil. SMX contamination significantly reduced the bacterial diversity and altered the composition of bacterial and fungal communities in soil. The dominant bacterial and fungal genera in the SMX-contaminated soil were obviously different from those in the control soil. The relative abundance of sul1 (sulfonamide resistance gene) remarkably increased in the SMX-contaminated soil, while that of other ARGs, such as sul2 and tetracycline and quinolone resistance genes, showed no significant change.

Antibiotic resistance genes and bacterial community dynamics in the seawater environment of Dapeng Cove, South China

In recent years, the propagation of antibiotic resistance genes (ARGs) and increased antibiotic resistance in pathogens have gained serious attention. Numerous reports have investigated the influence of domestic sewage discharge, medical wastewater and aquaculture wastewater on rivers and lakes, while the dynamics of ARGs in seawater and the relationships between ARGs, bacterial community structure and environmental factors have been less thoroughly described. In this study, the abundance, distribution and source of ARGs, as well as the relationships between ARGs, bacterial community changes and environmental factors in the seawater environment and sediment of Dapeng Cove, were investigated. Real-time quantitative PCR and Illumina Miseq sequencing technology were applied to determine the effects of the production cycle of cage culture, tourism and seasonality on ARGs. Chloramphenicol resistance genes (floR, cmlA) and sulfonamide resistance genes (sul1) were the dominant resistance genes in water and sediment. Pearson's correlation analysis showed that the abundance of all ARGs and the integrase I gene intI1 was positively correlated with chemical oxygen demand and suspended solids. Class 1 integrons might facilitate the dissemination of ARGs, and intI1 was detected in all samples at high concentrations. In aqueous environments, Cyanobacteria, Proteobacteria and Bacteroidetes were the dominant phyla, among which Proteobacteria and Bacteroidetes were positively correlated with the concentration of target ARGs. In the sediment, Proteobacteria, Bacteroidetes, Chloroflexi, Acidobacteria and Planctomycetes were the dominant phyla, among which Bacteroidetes and Planctomycetes were positively correlated with most of the target ARGs and had a significant influence on changes in the abundance of ARGs. The domestic sewage was the main source of ARGs in the seawater. Our results showed that bacterial community structure and environmental factors affected the distributional dynamics of ARGs. Anthropogenic activities played significant roles in promoting ARGs abundance in the seawater environments.

Emerging High-Level Tigecycline Resistance: Novel Tetracycline Destructases Spread via the Mobile Tet(X)

Antibiotic resistance in bacteria has become a great threat to global public health. Tigecycline is a next-generation tetracycline that is the final line of defense against severe infections by pan-drug-resistant bacterial pathogens. Unfortunately, this last-resort antibiotic has been challenged by the recent emergence of the mobile Tet(X) orthologs that can confer high-level tigecycline resistance. As it is reviewed here, these novel tetracycline destructases represent a growing threat to the next-generation tetracyclines, and a basic framework for understanding the molecular epidemiology and resistance mechanisms of them is presented. However, further large-scale epidemiological and functional studies are urgently needed to better understand the prevalence and dissemination of these newly discovered Tet(X) orthologs among Gram-negative bacteria in both human and veterinary medicine.

Distribution and human health risk assessment of antibiotic residues in large-scale drinking water sources in Chongqing area of the Yangtze River

Antibiotic contamination in drinking water sources has been increasingly prominent in recent years. The water quality in the Chongqing area is not only essential for the local people but also is crucial for the downstream of Yangzi River. To understand the level of antibiotic contamination in the large-scale drinking water sources, this study measured antibiotic residues in nine large-scale drinking water sources (five urban drinking water sources and four township drinking water sources) in Chongqing area of the Yangtze River. Results demonstrated that eight antibiotics of three categories in total were detected, including sulfonamide metformin (SMX), sulfonamide metformin (SMZ), erythromycin (ERM), Roxithromycin (ROM), Tylosin (TYL), Lincomycin (LIN), Chloramphenicol (CAP), and Florfenicol (FF). The mass concentration of antibiotic residues in five urban drinking water sources ranged from 13.9 to 76.6 ng/L, with an average of 46.4 ng/L, and that in four township drinking water sources ranged from 20.6 to 188.1 ng/L, with an average of 88.45 ng/L. The mass concentrations of antibiotic residues in Chongqing area were much lower than those in other cities. Antibiotics posed the maximum risk with a value of 0.005 for 0-3 months of the infant. The risk quotients of antibiotic residues in all water sources were much lower than 1 and thus did not pose a direct threat to human health.

Contamination profile of antibiotic resistance genes in ground water in comparison with surface water

Dissemination of antibiotic resistance genes (ARGs) in the water environment has become an increasing concern. There have been many reports on ARGs in surface water, but little is known about ARGs in groundwater. In this study, we investigated the profiles and abundance of ARGs in groundwater in comparison with those in surface water of Maozhou River using high-throughput quantitative PCR (HT-qPCR). Totally 127 ARGs and 10 MGEs were detected by HT-qPCR, and among them the sulfonamides, multidrug and aminoglycosides resistance genes were the dominant ARG types. According to the results of HT-qPCR, 18 frequently detected ARGs conferring resistance to 6 classes of antibiotics and 3 MGEs were further quantified by qPCR in the wet season and dry season. The absolute abundance ranged from 1.23 × 10⁵ to 8.89 × 10⁶ copies/mL in wet season and from 8.50 × 10² to 2.65 × 10⁶ copies/mL in the dry season, with sul1 and sul2 being the most abundant ARGs. The absolute abundance of ARGs and MGEs has no significant difference between the wet season and dry season while the diversity of ARGs in the dry season was higher than that in the wet season (p < 0.05). Totally 141 and 150 ARGs were detected in the water and sediments of Maozhou River, respectively. A total of 116 ARGs were shared among the groundwater, river water, and sediment, which accounted for 67.1% of all detected genes. Redundancy analysis further demonstrated that the environmental factors contributed 70.7% of the total ARG variations. The findings of large shared ARGs, abundant Total Coliforms and large wastewater burden in the groundwater provide a clear evidence that anthropogenic activities had a significant impact on groundwater.

Continental-scale spatio-temporal distribution of antibiotic resistance genes in coastal waters along coastline of China

Antibiotic resistance genes (ARGs) have been frequently detected in various matrices all over the world to attract wide attention due to the potential risks. Rare information is available on the pollution of ARGs in the waters of critical ecologically fragile regions such as the coastal zone at a continental scale. Therefore, this study performed field sampling during winter and summer along 18000 km coastline of China to investigate the distribution of target ARGs in coastal waters at a continental scale. The absolute abundances of ARGs in coastal waters showed drastic spatio-temporal variation with a mean value of 8.79 × 10⁴/1.39 × 10⁵ copies/mL in summer/winter, much lower than those in tail water from the maricultural zone or wastewater. The average absolute abundance of class 1 integron-integrase gene (intI1) in coastal waters was 9.68 × 10³/4.15 × 10⁴ copies/mL in summer/winter, still lower than that in tail water or wastewater. Quinolone resistance genes were the dominant ARGs in coastal waters to account for over 50% of total ARGs in most of sampling sites. Bacterial communities in coastal waters showed significant difference both at phylum and genus levels. Abundances of ARGs in coastal waters of this study were comparable with those in other regions previously reported. Tail water and wastewater might be the essential sources of ARGs in coastal waters. The findings of this study provided comprehensive information on the pollution status of ARGs in coastal waters at a continental scale, indicating that ARGs pollution has become a crucial stress affecting the sustainable development of coastal regions.

Emission and fate of antibiotics in the Dongjiang River Basin, China: Implication for antibiotic resistance risk

Antibiotics used for human and veterinary purposes are released into the environment, resulting in potential adverse effects, including the development and spread of antibiotic resistant bacteria. Here we investigated the dynamic fate of 36 antibiotics in a large river basin Dongjiang in South China, and discussed their potential antibiotic resistance selection risk. Based on the usage, excretion rate, wastewater treatment rate, human population and animal numbers the emissions of 36 frequently detected antibiotics were estimated for the Dongjiang River Basin. The total usage of the 36 antibiotics in the basin was 623.4 tons, which included 37% for human use and the rest for veterinary purposes. After being metabolized and partially treated, the amount of antibiotics excreted and released into the environment decreased to 267.6 tons. By allocating the high-precision antibiotic discharge inventory to 42 sewage plants and 17 livestock farms, an improved GREAT-ER (Geography referenced Regional Exposure Assessment Tool for European Rivers) model for the Dongjiang River Basin, with a well calibration river flow network based on the SWAT (Soil and Water Assessment Tool), was established to simulate the dynamic fate of 36 antibiotics. The simulation results showed that antibiotics contaminated >50% of the river sections. The modelled concentrations in water were almost within an order of magnitude of the measured concentrations. Antibiotic contamination in the dry season was obviously higher than that in the wet season. The concentrations of the antibiotics were always higher at the discharge zones and lower reaches of the river basin than the other reaches. The antibiotic resistance risk assessment showed that 23 out of the 36 antibiotics (nearly 65%) could pose high risks in the river basin. For those river reaches with high risks, the risk levels could mostly be reduced to low risk levels with a certain distance (15 km) from the pollution source. Therefore, more attention should be paid to those impact zones in term of antibiotic resistance.

Behavior of last resort antibiotic resistance genes (mcr-1 and blaNDM-1) in a drinking water supply system and their possible acquisition by the mouse gut flora

Mcr-1 and bla_NDM-1 antibiotic resistance genes (ARGs) confer resistance to colistins and carbapenems, which are often antibiotics used as a last resort in tertiary care hospitals. Dissemination of these two ARGs in drinking water supply systems and their effect on healthy gut bacteria are poorly studied. In this study, the dissemination of mcr-1 and bla_NDM-1 in a drinking water supply system, and their effect on the antibiotic resistance of mouse gut bacteria are explored. Metagenome analysis revealed that source water (Taipu river and Jinze reservoir) was polluted with ARGs. Mcr-1 and bla_NDM-1 can be disseminated through the water distribution system. Even advanced water treatments (ozone and biological activated carbon (BAC)) could not effectively remove mcr-1 and bla_NDM-1. Low concentrations of chloramine disinfectants in the water distribution system were not effective at limiting ARG abundance. Mobile genetic elements were also found to play a major role in the dissemination of ARGs via horizontal gene transfer (HGT) throughout the water supply system. Statistical analysis revealed that there was no effect of temperature on the abundance of mcr-1 and bla_NDM-1 throughout the water supply system. A last resort ARG, mcr-1 can disseminate from drinking water to the healthy mouse gut. The presence of mcr-1 in a strain belonging to Enterococcus hirae, which is different from the strain belonging to the Bacillus cereus group isolated from drinking water, strongly supports the phenomena of HGT inside the gut. This research provides novel insights into the role of drinking water in disseminating ARGs to the gut and strongly suggests that drinking water may also play a major role apart from other factors known to be involved in the prevalence of last resort ARGs in the gut.

Occurrence and fate of antibiotic residues and antibiotic resistance genes in a reservoir with ecological purification facilities for drinking water sources

Antibiotics and antibiotic resistance genes (ARGs) are emerging contaminants in surface waters, especially drinking water sources, where they can pose a risk to human health and aquatic ecology. The ecological purification facilities constructed in the drinking water reservoirs are intended to safeguard water quality. However, their ability to remove antibiotics and ARGs from the water and the presence of ARGs in such river-reservoir systems have not been comprehensively characterized yet. The occurrence, distribution and spatiotemporal variations in antibiotics, ARGs, and mobile genetic elements (MGEs) were investigated in a representative river-reservoir system in Shanghai, China. A total of 283 ARGs and 12 MGEs were detected in the water using high- throughput quantitative PCR analysis. Antibiotic residues and the absolute abundance of total ARGs and MGEs in reservoir inflow were significantly reduced when water from the river passed through the ecological purification processes in the reservoir. Antibiotics in this river-reservoir system posed only limited risks to the aquatic ecosystem and human health. No significant correlation was observed between the distribution pattern of ARGs and spatiotemporal factors. The dominant ARGs were strongly and significantly correlated with integrons. Through redundancy analysis and variation partitioning analysis, we determined that MGEs were the major driver shifting the distribution of ARGs, and the effects of environmental factors and antibiotic residues were reflected in the joint effects with MGEs. The small ecological reservoir was verified as an effective engineering to mitigate ecological risk in the drinking water source.

Response of microbial communities of karst river water to antibiotics and microbial source tracking for antibiotics

In southwestern China, karst river water is the main source of water for humans. As emerging pollutants, antibiotics have contaminated karst river water in some areas for a long time. Microbiota is highly susceptible to environmental changes, and can be used in tracing the source of antibiotics in complex systems such as karst water. Ten karst river water samples were collected along the river flow. The diversity and structure of the microbial community were analyzed together with environmental factors through correlation analysis, the random forest algorithm and co-occurrence network analysis. At genus level, Arcobacter was significantly positively correlated with the antibiotics, indicating that Arcobacter and antibiotics probably came from the same source. Based on co-occurrence network analysis between microbes, the microbial community was divided into eight modules, and the relative abundance of three modules was significantly correlated with antibiotics. The co-occurrence networks between bacteria and antibiotic resistance genes (ARGs) showed that pathogenic bacteria potentially carried multiple ARGs. This could increase the disease risk to humans and disease transmission in the study area. When river water flowed underground, the concentration of antibiotics decreased for the two underground river outlet sites, but abundance of bacteria and ARGs increased. Microbial source tracking studies showed that contamination was derived from humans rather than livestock. The ranking importance of prediction for antibiotics in this study area from random forest follows: specific bacteria Arcobacter > ARGs > ecological clusters. This study will be helpful in identifying the effect of antibiotics discharge on the microbial community, improving evaluation of antibiotics' risks and contaminants source tracking.

Antibiotic resistome in a landfill leachate treatment plant and effluent-receiving river

Landfills leachate contained diverse antibiotic resistance genes (ARGs). Treated landfill leachate effluent could enter into the downstream environments, leading to the dissemination of ARGs, which might pose a health risk to public. Here, we used high-throughput qPCR to characterize the resistome and 16S rRNA-based Illumina sequencing to analyze the bacterial community in a leachate treatment plant and the river near the landfill. A total of 91 ARGs and 5 mobile genetic elements were detected. Leachate treatment process significantly changed the profiles of resistome and bacterial community structures. Similar bacterial community structure and ARG profiles were detected between effluent and downstream river, which were both dominated by multidrug and beta-lactams resistance genes and harbored higher ARG relative abundance than that in upstream river. In particular, seven ARGs were detected both in effluent and downstream river samples but not detected in upstream river, including genes encoding resistance to vancomycin (vanXD and vanSB) and carbapenem (cphA and blaGES), which implied the effects of the effluent on its receiving river. This study highlights the risk of discharge of processed landfill leachate in dissemination of antibiotic resistance determinants to the environments, and suggests an urgent need for surveillance of ARGs and development of techniques to mitigate the risk.

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

The distribution of 14 ARGs, intI1, and 16S rDNA were analysed in 4 wastewater treatment plants (WWTPs), 2 effluent receiving areas (ERAs), and Hangzhou Bay (HZB). The results showed that each integrated WWTP (IWWTP) received higher abundance of ARGs than pharmaceutical WWTPs (PWWTPs), and IWWTPs removed ARGs more efficiently than PWWTPs. The WWTP effluents greatly contributed to the ARGs pollution in the water environments of the ERAs and HZB, and the total abundance of the ARGs displayed a distance decay pattern. In coastal sediments, more ARGs were accumulated in remote sites. The correlation analysis showed that the occurrence of ARGs was more related to 16S rDNA and intI1 in the WWTPs. Three macrolides resistance genes (ermB, mphA, and vatB) had strong correlations with 16S rDNA and intI1 in all the sample groups. Our study clearly reveals the link between land WWTPs discharge and emerging pollution of ARGs in coastal environments.

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

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

Effects of microplastics on distribution of antibiotic resistance genes in recirculating aquaculture system

Microplastics and antibiotic resistance genes (ARGs) are two kinds of emerging contaminants with frequent detection in coastal regions. However, rare information on co-occurrence of microplastics and ARGs in coastal recirculating aquaculture system (RAS) is available. This study performed field sampling and laboratory analysis to investigate the distribution of microplastics and ARGs in a typical RAS farm. The results showed that microplastics were detected in all water samples with the abundances ranging from 58 to 72 items/m³. Absolute abundances of total 10 ARGs in water samples ranged from 3.24 × 10⁵ to 7.83 × 10⁵ copies/mL while those on microplastic samples were in the range of 1.59 × 10⁹-1.83 × 10⁹ copies/g. Microbial communities of microplastics and water showed significant difference at both phylum and genus levels. Microbial community diversity of microplastics was higher than that of water. ARGs including tetG, qnrS, sul1, sul2, and ermF possessed relatively more active relationships with bacterial community in water and on microplastics of the RAS farm. The results suggested that microplastics might be an important reservoir of ARGs in RAS farms. The findings of this study will provide useful information on pollution control and environmental management for both microplastics and ARGs in coastal aquaculture systems.

Contamination of antibiotic resistance genes (ARGs) in a typical marine aquaculture farm: source tracking of ARGs in reared aquatic organisms

Although the prevalence and concentrations of antibiotic resistance genes (ARGs) in aquaculture is receiving increasing scientific interest, there is little understanding of the direct sources and dissemination pathways of ARGs in marine aquaculture-reared organisms. This study investigated the dynamics of ARGs and the bacterial community throughout the rearing period in a typical marine aquaculture farm in South China. The results demonstrated that sul1 and qnrD were predominant in the sediment, and qnrD and qnrA were predominant in the intestinal tracts of shrimps. Network analysis showed that the chemical oxygen demand, total organic carbon, dissolved organic carbon, suspended solids, and total phosphorus were positively correlated with the predominant ARGs. The results of the network and source tracking analyses indicate that environmental factors and the bacterial community may drive the dissemination of ARGs dissemination in the environment and in shrimp reared by marine aquaculture, and sediment is the most direct and important medium in this dissemination. These results aid in improving our understanding of the sources, level, and dissemination of ARGs in marine aquaculture.

Heavy metal-induced co-selection of antibiotic resistance genes in the gut microbiota of collembolans

Heavy metal induced co-selection of antibiotic resistance genes (ARGs) has become an emerging environmental issue. The guts of soil fauna offer a unique habitat in the terrestrial ecosystem and harbor a variety of microorganisms. However, the effects of heavy metals on the gut-associated ARGs of soil fauna are poorly understood. In the present study, collembolans were cultivated with four types of heavy metals (Zn, Cu, Cd, and Cr) and one antibiotic (oxytetracycline), to investigate their impact on the gut-associated ARGs. High-throughput quantitative PCR and 16S rRNA gene amplicon sequencing were used to examine changes in the gut-associated ARGs and microbial composition caused by the metals and antibiotic. The results showed that heavy metals alone induced co-selection of ARGs in the collembolan gut, but the effects were weaker than selection by oxytetracycline. When Zn or Cu was present together with oxytetracycline, there was a strong synergistic effect between the compounds, which increased the selection of ARGs in the collembolan guts. Furthermore, redundancy analysis revealed that the gut microbiota and mobile genetic elements (MGEs) were significantly correlated with the ARG composition. These results extend our understanding on effects of heavy metals on the dispersal of ARGs in the soil food web.

Antibiotics and Resistance Genes in Awash River Basin, Ethiopia

Among contaminants of emerging concern in the environment, a growing attention has been given to antibiotics and antibiotic-resistant genes (ARGs) due to the rise in their usage and potential ecotoxicological and public health effect. However, the occurrence of these contaminants in the environment is little investigated in developing countries particularly in sub-Saharan regions. In this study, the occurrence of three groups of antimicrobials including tetracycline, sulfonamides and fluoroquinolone, and their corresponding ARGs were investigated in the sediments of Awash River Basin, Ethiopia. Out of twelve studied compounds, sulfadiazine and enrofloxacin showed the highest and lowest detection frequency, respectively. Polymerase chain reaction (PCR) analysis revealed that tetA and tetB occurred in all the samples. The relative abundance of the resistant genes was in the following order: tetA > tetB > sul2 > sul1. Redundancy analysis result indicated that some sediment characteristics were found to have influence on the distribution sul1-resistant gene.

Characterization and source-tracking of antibiotic resistomes in the sediments of a peri-urban river

The peri-urban rivers are one of the critical interfaces between urban-rural symbiotic ecosystems and appear to be a reservoir of antibiotic resistance genes (ARGs) in the environment. To prevent the transmission risks of ARGs between peri-urban river and human, it is essential to explore the prevalence and source of ARGs in the environment for designing potential mitigation strategies. In this study, we focused on the characterization and source-tracking of ARGs in the sediments of a typical peri-urban river in Beijing, Chaobai River. Twenty-seven ARGs frequently reported in the environment, and two integrons (intI1 and intI2) were detected using high-throughput quantitative PCR. The profile of bacterial community was determined by performing 16S rRNA gene sequencing. Meanwhile, crAssphage, a novel recently-discovered DNA bacteriophage, was employed for tracking the contribution of human fecal pollution to the prevalence of ARGs. Results showed that the targeted ARGs were detected widely in the sediments of Chaobai River. Relatively, the abundances of ARGs in downstream were higher than those in the upstream, likely suggesting a gradient impact of anthropogenic activities along the river. Remarkably, the int1 gene was correlated significantly with most of the ARGs and might be the key factor influencing the shaping of ARGs in the river sediments. However, no significant correlations were observed between the ARGs and selective pressure factors, including antibiotics and metals. Of the identified 1039 genera, Escherichia-Shigella, Bacteroides, Arcobacter, Dechloromonas and Pseudomonas were the top most abundant organisms. Microbial source tracking based on the crAssphage annotation suggested that human sewage might be one of the potential sources of resistance bacteria in the river sediments. The study can advance our knowledge about ARGs in the peri-urban river and provides a management reference for ARG pollution control.

Antibiotic resistance genes attenuated with salt accumulation in saline soil

Salt accumulation on the surface of the soil layer driven by the strong evaporation is a natural phenomenon that usually happens in the dry season, particularly on the coastal lands reclaimed from tidal flats. However, the influence of salt accumulation on the distribution profile of antibiotic resistance genes (ARGs) and mobile gene elements (MGEs) remains unclear. In this study, we sampled a wild saline soil where the salt accumulation was frequently observed to investigate the vertical distribution profiles of ARGs and MGEs. The results showed that an increasing gradient of ARGs and MGEs was observed from the top to deep layer with the decreasing of electrical conductivity (EC1:5 values) indicating the salt-influenced attenuation of ARGs in the saline soil. The competing test suggested that the attenuation of ARGs in response to salinity gradient was attributable to the elimination of the ARG-harboring plasmids, due to the reduction of the relative fitness of plasmid-harboring strains. Additionally, the network analyses showed that the attenuation of ARGs might be associated with decreased abundance of Actinobacteria. Overall, this study identifies that salinity as an abiotic stress could re-shape the distribution of ARGs, which may influence the dissemination of ARGs in the environment.