Determination of antibiotic resistance genes in a WWTP-impacted river in surface water, sediment, and biofilm: Influence of seasonality and water quality

Fish are poor sentinels for surveillance of riverine antimicrobial resistance

Effective surveillance of antimicrobial resistance (AMR) in the environment is crucial for assessing the human and animal health risk of AMR pollution. Wastewater treatment plants (WWTPs) are one of the main sources of AMR pollutants discharged into water bodies. One important factor for assessing the risks associated with such pollution is the colonization potential of the resistant bacteria (ARB) and resistance genes (ARGs) from the environment into human or animal microbiomes upon exposure. This study explores whether fish can act as sentinels for surveillance of AMR pollution in general and specifically the human colonization potential of ARB in rivers impacted by WWTP effluents. Two riverine fish species, Brown trout, and European bullhead, were sampled up- and downstream a German WWTP. The two fish species were chosen due to their different lifestyles: Trout are mainly actively swimming in the water phase, while bullheads are sedentary and river sediment-associated. The bacterial microbiomes and resistomes of fish gills, skin, and feces were compared with those of the respective river water and sediment up- and downstream of the WWTP. Microbiomes of both fish mirrored the changes in river water and sediment downstream of the WWTP, with significant shifts in bacterial community composition, particularly an increase in Proteobacteria and Verrucomicrobia. However, increases in ARG abundances observed in water and sediment downstream of the WWTP were not reflected in any of the fish-associated resistomes. This indicates that while the fish microbiome is sensitive to environmental changes, resistomes of poikilothermic animals such as fish are less responsive to colonization by ARB originating from WWTPs and may not serve as effective sentinels for assessing AMR pollution and colonization risks in freshwater environments. This study highlights the complexity of using wildlife as indicators for environmental AMR pollution and suggests that other species are better suited for surveillance efforts.

Holistic assessment of chemical and biological pollutants in a Mediterranean wastewater effluent-dominated stream: Interactions and ecological impacts

The discharge of treated wastewater from wastewater treatment plants (WWTPs) into river systems is a significant source of pollution, introducing a range of chemical and biological pollutants that impact the chemical and ecological quality status of rivers. This study evaluates the effect of a secondary treated wastewater effluent on the Onyar River, in the northeast of Spain. Water and biofilm samples were collected at one upstream and four downstream sampling points (up to 2.8 km from the discharge point) across four seasons. A wide array of pollutants, including metals, pharmaceuticals, microplastics (MPs), per- and polyfluoroalkyl substances (PFAS), antibiotic resistance genes (ARGs), among other emerging pollutants, were detected downstream, with significant differences between upstream and downstream concentrations. Our results show that WWTP discharge also altered biofilm microbiome composition and ARGs presence, being these changes distinguishable from seasonal variations. Nevertheless, a partial recovery further downstream (525 m) was observed for biofilm microbiome and ARGs composition. These findings highlight the value of microbiome analysis in assessing wastewater impacts on river ecosystems and emphasize the need for further research to improve pollutant attenuation and biofilm recovery strategies in river streams.

Comprehensive Study of Antibiotics and Antibiotic Resistance Genes in Wastewater and Impacted Mediterranean Water Environments

Background: The spread of antimicrobial resistance is a central public health problem. Wastewater treatment plants and impacted environments are well-known hotspots for antibiotic resistance. However, there is still limited knowledge regarding where antibiotic resistance genes (ARGs) acquire mobility. Method: In this study, we aimed to gather evidence on the seasonal patterns of ARG spread in two Mediterranean areas from NE and E of Spain (Ebro River and Ebro Delta, and Xúquer River and Albufera de València), correlating ARG presence, with special focus on the faecal bacteria Escherichia coli, with antibiotic residues and environmental conditions. The analytical methodology employed was based on a suspect screening approach, while a novel prioritisation approach for antibiotics was proposed to identify those areas more susceptible to the spread of ARG. Results: Our findings demonstrate that ARG levels in wastewater were similar across different seasons, although a greater diversity of ARGs was recorded in summer. We hypothesise that horizontal gene transfer among aquatic bacterial populations during the northeastern Mediterranean summer, when temperatures reach approximately 35~40 °C, could be a key driver of ARG dissemination. By contrast, the highest concentrations of antibiotics in winter samples, with temperatures around 5~10 °C, may promote the spread of microbial resistance. Conclusions: Our key findings highlight that water temperature and sunlight irradiation are crucial factors influencing antibiotic levels and microbial abundance, requiring further investigation in future studies.

Emerging Mobile Colistin Resistance Gene Mcr-1 and Mcr-10 in Enterobacteriaceae Isolates From Urban Sewage in China

Purpose

This study aimed to investigate the epidemiology and dissemination of mcr-positive Enterobacteriaceae in urban sewage in Yangzhou, China.

Methods

A total of 366 sewage samples were collected from the Yangzhou Wastewater Treatment Plant in Jiangsu Province. Colistin-resistant Enterobacteriaceae was identified through PCR targeting mcr-1 to mcr-10 genes. The isolates underwent antimicrobial susceptibility testing, and whole-genome sequencing was performed to analyze their genomic features. Additionally, conjugation experiments were conducted to assess the transferability of mcr-positive plasmids.

Results

Three mcr-positive Enterobacteriaceae isolates were identified, representing an isolation rate of 0.82%. These included one mcr-1-positive Escherichia coli (ST167) and two mcr-10-positive Klebsiella pneumoniae complex strains with novel sequence types ST6801 and ST6825. The mcr-1 gene was located on an IncI2 plasmid (pYZ22WS208_3) and successfully transferred to recipient strains. In contrast, the mcr-10 gene was carried on IncF plasmids (pYZ22WS067_1 and pYZ22WS223_1) but was not transferable in this study. Phylogenetic analysis revealed that the mcr-1-positive E. coli strain clustered within Clade II, alongside strains from various countries and sources. Phylogenomic analysis of mcr-10-positive isolates showed their sporadic distribution across 13 countries, with associations to diverse hosts and environments, indicating potential for widespread transmission.

Conclusion

This study demonstrates the presence of mcr-1 and mcr-10-positive Enterobacteriaceae in wastewater, emphasizing the importance of wastewater surveillance for tracking antibiotic resistance. The horizontal transfer of mcr-1 and potential spread of mcr-10 across various hosts underscore the need for ongoing monitoring and preventive measures.

Occurrence, removal, and ecological risk of antibiotics and antibiotic resistance genes in township wastewater treatment plants in the upper reaches of the Yangtze River, China

The excessive use of antibiotics contributes significantly to environmental pollution and the widespread presence of antibiotic resistance genes (ARGs), which poses a serious threat to aquatic ecosystems and human health. Despite being a critical source of antibiotics and ARGs in the environment, research exploring their occurrence and removal characteristics in township wastewater treatment plants (WWTPs) remains limited. This study investigated the abundance and removal efficiencies of 39 antibiotics and 8 ARGs in influent and effluent samples from 40 township WWTPs located in the upper reaches of the Yangtze River. Antibiotics were detected in both influents and effluents, with detection frequencies (DFs) ranging from 2.44% to 100%. In contrast, all targeted ARGs exhibied 100% DFs in both influents and effluents. The average concentrations of antibiotics in influents and effluents were 370.67 ng/L and 242.06 ng/L, respectively, and the ARGs concentrations were 9.88 × 106 and 7.10 × 105 copies/mL, respectively. Among the antibiotics analyzed, macrolides and fluoroquinolones accounted for over 70% of the total antibiotic concentrations in both influent and effluent samples. Additionally, sul1 and sul2 were identified as the predominant ARGs, constituting more than 99% of the total abundance in both influent and effluent samples. Notably, significant correlations between the ARGs and their respective antibiotics were not consistently observed. The average removal efficiencies for total antibiotics and ARGs by township WWTPs were 34.70% and 93.30%, respectively. Furthermore, all calculated ecological risk values (risk quotient, RQ) for individual antibiotics in effluent samples were below one, except for oxytetracycline, which had RQ values greater than one in three effluents. The total RQs, representing the sum of individual RQs, indicated that 11 effluents presented a high risk (27.50%), while 17 effluents exhibited a moderate risk (42.50%). These findings suggest that township WWTPs may represent a significant source of antibiotics and ARGs in the environment, necessitating further process improvements for their effective elimination.

Microplastic and antibiotics in waters: Interactions and environmental risks

Antibiotics (ATs) are ubiquitously detected in natural waters worldwide, and their tendency to co-migrate with microplastics (MPs) post-adsorption leads to heightened environmental risk. Research on the adsorption of ATs on MPs and their subsequent effects on the environmental risks is gaining significant attention globally. This adsorption process predominantly occurs through hydrophobic forces, hydrogen bonds, and electrostatic interactions and is influenced by various environmental factors. The interaction between MPs and ATs exhibited varying degrees of efficiency across different pH levels and ionic strengths. Furthermore, this paper outlines the environmental risks associated with the co-presence of MPs and ATs in aquatic environments, emphasizing the potential effect of MPs on the distribution of antibiotic resistance genes (ARGs) and related environmental risks. The potential hazards posed by MPs and ATs in aquatic systems warrant serious consideration. Future research should concentrate on the adsorption of ATs/ARGs on MPs under real environmental conditions, horizontal gene transfer on MPs, as well as biofilm formation and agglomeration behavior on MPs that needs to be emphasized.

Metagenomics-resolved genomics provide novel ecological insights into resistome community coalescence of wastewater in river environment

The discharge of wastewater into rivers can lead to resistome coalescence, thereby enhancing the spread risk of antibiotic resistance genes (ARGs) through mixing of exogenous wastewater resistome communities with indigenous riverine communities. At present, the understanding on the role of resistome community coalescence in the dissemination of ARGs is still very limited, and little is known about the process and its ecological implications. To bridge the gap, this study has conducted field-based surveys and microcosm experiments to deeply dissect the coalescence of resistome community in wastewater within river environment, utilizing genome-centric metagenomic analysis approach. The field investigation suggests resistome coalescence enhances the abundance and diversity of ARGs in the receiving river. Furthermore, the microcosm experiments reveal the effect of mixing ratio on resistome coalescence in the water-sediment system and decipher the temporal attenuation dynamics of the coalesced resistome in the environment. The results show the higher proportion of wastewater has a greater impact on ARGs in the water, whereas the effect of mixing ratio is lesser in the sediments. Temporally, the source-specific ARGs originating from wastewater exhibit decreasing trends over the experimental duration, and relatively, the attenuation in the water is more pronounced than that in the sediments. Interestingly, natural light not only facilitates the attenuation of ARGs in the water but may also induce their deposition at the water-sediment interface. Variance partitioning analyses suggest the microbiome, mobilome, and abiotic factors collectively shape the coalescence of the resistome communities in the environment. The study provides empirical evidence on resistome coalescence in river systems, which is instrumental in gaining a better understanding of the spread mechanism of ARGs in the environment.

Environmental Antimicrobial Resistance: Implications for Food Safety and Public Health

Antimicrobial resistance (AMR) is a serious global health issue, aggravated by antibiotic overuse and misuse in human medicine, animal care, and agriculture. This study looks at the different mechanisms that drive AMR, such as environmental contamination, horizontal gene transfer, and selective pressure, as well as the severe implications of AMR for human and animal health. This study demonstrates the need for concerted efforts across the scientific, healthcare, agricultural, and policy sectors to control the emergence of AMR. Some crucial strategies discussed include developing antimicrobial stewardship (AMS) programs, encouraging targeted narrow-spectrum antibiotic use, and emphasizing the significance of strict regulatory frameworks and surveillance systems, like the Global Antimicrobial Resistance and Use Surveillance System (GLASS) and the Access, Watch, and Reserve (AWaRe) classification. This study also emphasizes the need for national and international action plans in combating AMR and promotes the One Health strategy, which unifies environmental, animal, and human health. This study concludes that preventing the spread of AMR and maintaining the effectiveness of antibiotics for future generations requires a comprehensive, multidisciplinary, and internationally coordinated strategy.

The role of TiO2 and gC3N4 bimetallic catalysts in boosting antibiotic resistance gene removal through photocatalyst assisted peroxone process

Antibiotics are extensively used in human medicine, aquaculture, and animal husbandry, leading to the release of antimicrobial resistance into the environment. This contributes to the rapid spread of antibiotic-resistant genes (ARGs), posing a significant threat to human health and aquatic ecosystems. Conventional wastewater treatment methods often fail to eliminate ARGs, prompting the adoption of advanced oxidation processes (AOPs) to address this growing risk. The study investigates the efficacy of visible light-driven photocatalytic systems utilizing two catalyst types (TiO2-Pd/Cu and g-C3N4-Pd/Cu), with a particular emphasis on their effectiveness in eliminating blaTEM, ermB, qnrS, tetM. intl1, 16 S rDNA and 23 S rDNA through photocatalytic ozonation and peroxone processes. Incorporating O3 into photocatalytic processes significantly enhances target removal efficiency, with the photocatalyst-assisted peroxone process emerging as the most effective AOP. The reemergence of targeted contaminants following treatment highlights the pivotal importance of AOPs and the meticulous selection of catalysts in ensuring sustained treatment efficacy. Furthermore, Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) analysis reveals challenges in eradicating GC-rich bacteria with TiO2 and g-C3N4 processes, while slight differences in Cu/Pd loadings suggest g-C3N4-based ozonation improved antibacterial effectiveness. Terminal Restriction Fragment Length Polymorphism analysis highlights the efficacy of the photocatalyst-assisted peroxone process in treating diverse samples.

Multi-habitat distribution and coalescence of resistomes at the watershed scale based on metagenomics

The characteristics of the resistome distribution in rivers have been extensively studied. However, the distribution patterns of resistomes in multiple habitats and contributions of upstream habitats to the resistome profile in water bodies remains unclear. The current study explored the distribution and coalescence of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs) in four habitats (including water bodies, sediments, biofilms, and riparian soils) within the Shichuan River watershed. The results revealed significant variations in the abundances and diversity of resistomes across the four habitats and two seasons. Assembly processes of resistomes were predominated by stochastic processes in summer but deterministic processes in winter. The main source of the resistome in summer water bodies was the movement of genes from upstream water bodies. However, the main sources of resistome in downstream water bodies in winter were the movement of resistomes in upstream sediments and the input of external pollution. The physicochemical properties of winter water bodies significantly influenced the movement of the resistomes across habitats. The current study elucidated the multi-habitat distribution pattern and migration mechanism of the resistome in the river system, providing new insights for effectively monitoring and controlling bacterial resistance.

Recent advances in environmental antibiotic resistance genes detection and research focus: From genes to ecosystems

Antibiotic resistance genes (ARGs) persistence and potential harm have become more widely recognized in the environment due to its fast-paced research. However, the bibliometric review on the detection, research hotspot, and development trend of environmental ARGs has not been widely conducted. It is essential to provide a comprehensive overview of the last 30 years of research on environmental ARGs to clarify the changes in the research landscape and ascertain future prospects. This study presents a visualized analysis of data from the Web of Science to enhance our understanding of ARGs. The findings indicate that solid-phase extraction provides a reliable method for extracting ARG. Technological advancements in commercial kits and microfluidics have facilitated the efficacy of ARGs extraction with significantly reducing processing times. PCR and its derivatives, DNA sequencing, and multi-omics technology are the prevalent methodologies for ARGs detection, enabling the expansion of ARG research from individual strains to more intricate microbial communities in the environment. Furthermore, due to the development of combination, hybridization and mass spectrometer technologies, considerable advancements have been achieved in terms of sensitivity and accuracy as well as lowering the cost of ARGs detection. Currently, high-frequency terms such as "Antibiotic Resistance, Antibiotics, and Metagenomics" are the center of attention for study in this area. Prominent topics include the investigation of anthropogenic impacts on environmental resistance, as well as the dynamics of migration, dissemination, and adaptation of environmental ARGs, etc. The research on environmental ARGs has made significant advancements in the fields of "Microbiology" and "Biotechnology Applied Microbiology". Over the past decade, there has been a notable increase in the fields of "Environmental Sciences Ecology" and "Engineering" with a similar growth trend observed in "Water Resources". These three domains are expected to continue driving extensive study within the realm of environmental ARGs.

A metagenomic study of antibiotic resistance genes in a hypereutrophic subtropical lake contaminated by anthropogenic sources

Antibiotic resistance genes (ARGs) are a major threat to human and environmental health. This study investigated the occurrence and distribution of ARGs in Lake Cajititlán, a hypereutrophic subtropical lake in Mexico contaminated by anthropogenic sources (urban wastewater and runoff from crop and livestock production). ARGs (a total of 475 genes) were detected in 22 bacterial genera, with Pseudomonas (144 genes), Stenotrophomonas (88 genes), Mycobacterium (54 genes), and Rhodococcus (27 genes) displaying the highest frequencies of ARGs. Among these, Pseudomonas aeruginosa and Stenotrophomonas maltophilia showed the highest number of ARGs. The results revealed a diverse array of ARGs, including resistance to macrolides (11.55 %), aminoglycosides (8.22 %), glycopeptides (6.22 %), tetracyclines (4 %), sulfonamides (4 %), carbapenems (1.11 %), phenicols (0.88 %), fluoroquinolones (0.44 %), and lincosamides (0.22 %). The most frequently observed ARGs were associated with multidrug resistance (63.33 %), with MexF (42 genes), MexW (36 genes), smeD (31 genes), mtrA (25 genes), and KHM-1 (22 genes) being the most common. Lake Cajititlán is a recreational area for swimming, fishing, and boating, while also supporting irrigation for agriculture and potentially acting as a drinking water source for some communities. This raises concerns about the potential for exposure to antibiotic-resistant bacteria through these activities. The presence of ARGs in Lake Cajititlán poses a significant threat to both human and environmental health. Developing strategies to mitigate the risks of antibiotic resistance, including improving wastewater treatment, and promoting strategic antibiotic use and disposal, is crucial. This study represents a significant advancement in the understanding of antibiotic resistance dynamics in a hypereutrophic subtropical lake in a developing country, providing valuable insights for the scientific community and policymakers.

Screening for Antibiotic Resistance Genes in Bacteria and the Presence of Heavy Metals in the Upstream and Downstream Areas of the Wadi Hanifah Valley in Riyadh, Saudi Arabia

Valley surface water is considered a focal public health concern owing to the presence of multi-drug-resistant bacteria. The distribution of antimicrobial resistance (AMR) bacteria in the surface water is affected by the presence of multiple factors, including antibiotics coming from wastewater discharge or other contaminant sources such as pharmaceuticals, biocides, and heavy metals. Furthermore, there is evidence suggesting that high levels of antibiotic resistance genes (ARGs) can be transferred within bacterial communities under the influence of heavy metal stress. Hence, the primary aim of this study is to investigate the presence of heavy metals and bacterial ARGs in upstream as well as downstream locations of Wadi Hanifah Valley in Riyadh, Saudi Arabia. Sample collection was conducted at eighteen surface water sites within the valley in total. The selection of ARGs was associated with the most common antibiotics, including β-lactam, tetracycline, erythromycin, gentamicin, sulphonamide, chloramphenicol, vancomycin, trimethoprim, and colistin antibiotics, which were detected qualitatively using polymerase chain reaction (PCR) technology. The tested antibiotic resistance genes (ARGs) included (blaNDM-1 (for the antibiotic class Beta-lactamases), mecA (methicillin-resistant Staphylococcus aureus), tet(M) and tet(B) (for the antibiotic class Tetracycline), ampC (for the antibiotic class Beta-lactamases), vanA (for the antibiotic class vancomycin), mcr-1 (for the antibiotic class colistin), erm(B) (for the antibiotic class erythromycin), aac6'-Ie-aph2-Ia (for the antibiotic class Gentamicin), sulII (for the antibiotic class sulphonamide), catII (for the antibiotic class Chlorophincol), and dfrA1 (for the antibiotic class trimethoprim). Moreover, an assessment of the levels of heavy metals such as lithium (Li), beryllium (Be), chromium (Cr), cobalt (Co), arsenic (As), cadmium (Cd), tin (Sn), mercury (Hg), and lead (Pb) was conducted by using inductively coupled plasma mass spectrometry (ICPMS). According to our findings, the concentrations of sulphonamide, erythromycin, and chloramphenicol ARGs (erm(B), sulII, and catII) were observed to be the most elevated. Conversely, two ARGs, namely mecA and mcr-1, were not detected in the samples. Moreover, our data illustrated a significant rise in ARGs in the bacteria of water samples from the upstream sites as compared with the water samples from the downstream sites of Wadi Hanifah Valley. The mean concentration of Li, Be, Cr, Co, As, Cd, Sn, Hg, and Pb in the water samples was estimated to be 37.25 µg/L, 0.02 µg/L, 0.56 µg/L,0.32 µg/L, 0.93 µg/L, 0.01 µg/L, 200.4 µg/L, 0.027 µg/L, and 0.26 µg/L, respectively, for the selected 18 sites. Furthermore, it was revealed that the concentrations of the screened heavy metals in the water samples collected from various sites did not surpass the maximum limits set by the World Health Organization (WHO). In conclusion, this study offers a concise overview of the presence of heavy metals and ARGs in water samples obtained from the Wadi Hanifah Valley in Riyadh, KSA. Such findings will contribute to the ongoing monitoring and future risk assessment of ARGs spread in surface water.

Photoaged microplastics enhanced the antibiotic resistance dissemination in WWTPs by altering the adsorption behavior of antibiotic resistance plasmids

Growing concerns have raised about the microplastic eco-coronas in the ultraviolet (UV) disinfection wastewater, which accelerated the pollution of antibiotic resistance genes (ARGs) in the aquatic environment. As the hotspot of gene exchange, microplastics (MPs), especially for the UV-aged MPs, could alter the spread of ARGs in the eco-coronas and affect the resistance of the environment through adsorbing antibiotic resistant plasmids (ARPs). However, the relationship between the MP adsorption for ARPs and ARG spreading characteristics in MP eco-corona remain unclear. Herein, this study explored the distribution of ARGs in the MP eco-corona through in situ investigations of the discharged wastewater, and the adsorption behaviors of MPs for ARPs by in vitro adsorption experiments and in silico calculations. Results showed that the adsorption capacity of MPs for ARPs was enhanced by 42.7-48.0 % and the adsorption behavior changed from monolayer to multilayer adsorption after UV-aging. It was related to the increased surface roughness and oxygen-containing functional groups of MPs under UV treatment. Moreover, the abundance of ARGs in MP eco-corona of UV-treated wastewater was 1.33-1.55 folds higher than that without UV treatment, promoting the proliferation of drug resistance. DFT and DLVO theoretical calculations indicated that the MP-ARP interactions were dominated by electrostatic physical adsorption, endowing the aged MPs with low potential oxygen-containing groups to increase the electrostatic interaction with ARPs. Besides, due to the desorption of ARPs on MPs driven by the electrostatic repulsion, the bioavailability of ARGs in the MP eco-coronas was increased with pH and decreased with salinity after the wastewater discharge. Overall, this study advanced the understanding of the adsorption behavior of MPs for ARPs and provided inspirations for the evaluation of the resistance spread in the aquatic environment mediated by MP eco-coronas.

Linking antibiotic resistance gene patterns with advanced faecal pollution assessment and environmental key parameters along 2300 km of the Danube River

The global spread of antimicrobial resistance (AMR) in the environment is a growing health threat. Large rivers are of particular concern as they are highly impacted by wastewater discharge while being vital lifelines serving various human needs. A comprehensive understanding of occurrence, spread and key drivers of AMR along whole river courses is largely lacking. We provide a holistic approach by studying spatiotemporal patterns and hotspots of antibiotic resistance genes (ARGs) along 2311 km of the navigable Danube River, combining a longitudinal and temporal monitoring campaign. The integration of advanced faecal pollution diagnostics and environmental and chemical key parameters allowed linking ARG concentrations to the major pollution sources and explaining the observed patterns. Nine AMR markers, including genes conferring resistance to five different antibiotic classes of clinical and environmental relevance, and one integrase gene were determined by probe-based qPCR. All AMR targets could be quantified in Danube River water, with intI1 and sul1 being ubiquitously abundant, qnrS, tetM, blaTEM with intermediate abundance and blaOXA-48like, blaCTX-M-1 group, blaCTX-M-9 group and blaKPC genes with rare occurrence. Human faecal pollution from municipal wastewater discharges was the dominant factor shaping ARG patterns along the Danube River. Other significant correlations of specific ARGs were observed with discharge, certain metals and pesticides. In contrast, intI1 was not associated with wastewater but was already established in the water microbiome. Animal contamination was detected only sporadically and was correlated with ARGs only in the temporal sampling set. During temporal monitoring, an extraordinary hotspot was identified emphasizing the variability within natural waters. This study provides the first comprehensive baseline concentrations of ARGs in the Danube River and lays the foundation for monitoring future trends and evaluating potential reduction measures. The applided holistic approach proved to be a valuable methodological contribution towards a better understanding of the environmental occurrence of AMR.

Temporal variations of antimicrobial resistance genes in aerosols: A one-year monitoring at the puy de Dôme summit (Central France)

The recent characterization of antibiotic resistance genes (ARGs) in clouds evidenced that the atmosphere actively partakes in the global spreading of antibiotic resistance worldwide. Indeed, the outdoor atmosphere continuously receives large quantities of particles of biological origins, emitted from both anthropogenic or natural sources at the near Earth's surface. Nonetheless, our understanding of the composition of the atmospheric resistome, especially at mid-altitude (i.e. above 1000 m a.s.l.), remains largely limited. The atmosphere is vast and highly dynamic, so that the diversity and abundance of ARGs are expected to fluctuate both spatially and temporally. In this work, the abundance and diversity of ARGs were assessed in atmospheric aerosol samples collected weekly between July 2016 and August 2017 at the mountain site of puy de Dôme (1465 m a.s.l., central France). Our results evidence the presence of 33 different subtypes of ARGs in atmospheric aerosols, out of 34 assessed, whose total concentration fluctuated seasonally from 59 to 1.1 × 105 copies m-3 of air. These were heavily dominated by genes from the quinolone resistance family, notably the qepA gene encoding efflux pump mechanisms, which represented >95 % of total ARGs concentration. Its abundance positively correlated with that of bacteria affiliated with the genera Kineococcus, Neorhizobium, Devosia or Massilia, ubiquitous in soils. This, along with the high abundance of Sphingomonas species, points toward a large contribution of natural sources to the airborne ARGs. Nonetheless, the increased contribution of macrolide resistance (notably the erm35 gene) during winter suggests a sporadic diffusion of ARGs from human activities. Our observations depict the atmosphere as an important vector of ARGs from terrestrial sources. Therefore, monitoring ARGs in airborne microorganisms appears necessary to fully understand the dynamics of antimicrobial resistances in the environment and mitigate the threats they may represent.

Mobile genetic elements affect the dissemination of antibiotic resistance genes (ARGs) of clinical importance in the environment

The prevalence of antibiotic resistance genes (ARGs) in the environment is a quintessential One Health issue that threats both human and ecosystem health; however, the source and transmission of ARGs, especially clinically important ARGs (CLIARGs), in the environment have not yet been well studied. In the present study, shotgun metagenomic approaches were used to characterize the microbiome, resistome, and mobilome composition in human feces and six different environment sample types in South China. Overall, the resistome harbored 157 CLIARGs, with specific ARG hotspots (e.g., human feces, wastewater treatment plants, livestock manure and wastewater) excreting significantly higher abundance of CLIARGs compared with the natural environment. A redundancy analysis (RDA) was performed and revealed that the bacterial community compositions and mobile genetic elements (MGEs) explained 55.08% and 34.68% of the variations in ARG abundance, respectively, indicating that both bacterial community and MGEs are key contributors to the maintenance and dissemination of CLIARGs in the environment. The network analysis revealed non-random co-occurrence patterns between 200 bacterial genera and 147 CLIARGs, as well as between 135 MGEs and 123 CLIARGs. In addition to numerous co-shared CLIARGs among different sample types, the source tracking program based on the FEAST probabilistic model was used to estimate the relative contributions of the CLIARGs from potential sources to the natural environment. The source tracking analysis results delineated that mobilome, more than microbiome, contributed CLIARG transmission from those ARG hotspots into natural environment, and the MGEs in WWTPs seem to play the most significant role in the spread of CLIARGs to the natural environment (average contribution 32.9%-46.4%). Overall, this study demonstrated the distribution and dissemination of CLIARGs in the environment, and aimed to better inform strategies to control the spread of CLIARGs into the natural environment.

Monitoring indicator genes to assess antimicrobial resistance contamination in phytoplankton and zooplankton communities from the English Channel and the North Sea

Phytoplankton and zooplankton play a crucial role in marine ecosystems as the basis of the food webs but are also vulnerable to environmental pollutants. Among emerging pollutants, antimicrobial resistance (AMR) is a major public health problem encountered in all environmental compartments. However, the role of planktonic communities in its dissemination within the marine environment remains largely unexplored. In this study, we monitored four genes proposed as AMR indicators (tetA, blaTEM, sul1, and intI1) in phytoplankton and zooplankton samples collected in the English Channel and the North Sea. The indicator gene abundance was mapped to identify the potential sources of contamination. Correlation was assessed with environmental parameters to explore the potential factors influencing the abundance of AMR in the plankton samples. The prevalence in phytoplankton and zooplankton of sul1 and intI1, the most quantified indicator genes, ranged from 63 to 88%. A higher level of phytoplankton and zooplankton carrying these genes was observed near the French and English coasts in areas subjected to anthropogenic discharges from the lands but also far from the coasts. Correlation analysis demonstrated that water temperature, pH, dissolved oxygen and turbidity were correlated to the abundance of indicator genes associated with phytoplankton and zooplankton samples. In conclusion, the sul1 and intI1 genes would be suitable indicators for monitoring AMR contamination of the marine environment, either in phytoplankton and zooplankton communities or in seawater. This study fills a part of the gaps in knowledge about the AMR transport by marine phytoplankton and zooplankton, which may play a role in the transmission of resistance to humans through the marine food webs.

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 antibiotic resistome in backwater zones of large cascade reservoirs: Co-occurrence patterns, horizontal transfer directions and health risks

The widespread occurrence of antibiotic resistant genes (ARGs) throughout aquatic environments has raised global concerns for public health. However, the profiles and patterns of antibiotic resistome in backwater zone of cascade reservoirs, where water flow is slowed down, are still poorly understood. Here, we proposed a metagenomic analysis framework to comprehensively reveal the diversity, abundance, co-occurrence patterns and transfer direction of ARGs in cascade reservoirs system and evaluated their health risks through a procedure based on contigs. A total of 364 ARGs subtypes conferring resistance to different antibiotics classes were detected in our water samples, and the dominant ARGs (macB, bacA, vanRA, bcrA) were similar in different reservoirs. Meanwhile, the distribution of ARGs was influenced by the presence of biotic factors such as metal resistant genes (MRGs) and mobile genetic elements (MGEs), as well as abiotic factors such as dissolved oxygen (DO) and pH. Remarkably, ARGs (vanR, rosB, MexT) co-occurred with plasmids and virulence factor genes (VFGs), which can lead to the emergence and spread of highly virulent and antibiotic resistant bacteria in microbial communities. Overall, this study helps administrators to better understand the complex patterns of ARGs in backwater zones of large cascade reservoirs and provides a proper procedure for detecting the presence of high-risk of ARGs.

Towards the fate of antibiotics and the development of related resistance genes in stream biofilms

Antibiotics are ubiquitously found in natural surface waters and cause great harm to aquatic organisms. Stream biofilm is a complex and active community composed of algae, bacteria, fungi and other microorganisms, which mainly adheres to solid substances such as rocks and sediments. The durability and diverse structural and metabolic characteristics of biofilms make them a representative of microbial life in aquatic micrecosystems and can reflect major ecosystem processes. Microorganisms and extracellular polymeric substances in biofilms can adsorb and actively accumulate antibiotics. Therefore, biofilms are excellent biological indicators for detecting antibiotic in polluted aquatic environments, but the biotransformation potential of stream biofilms for antibiotics has not been fully explored in the aquatic environment. The characteristics of stream biofilm, such as high abundance and activity of bacterial community, wide contact area with pollutants, etc., which increases the opportunity of biotransformation of antibiotics in biofilm and contribute to bioremediation to improve ecosystem health. Recent studies have demonstrated that both exposure to high and sub-minimum inhibitory concentrations of antibiotics may drive the development of antibiotic resistance genes (ARGs) in natural stream biofilms, which are susceptible to the effects of antibiotic residues, microbial communities and mobile genetic elements, etc. On the basis of peer-reviewed papers, this review explores the distribution behavior of antibiotics in stream biofilms and the contribution of biofilms to the acquisition and spread of antibiotic resistance. Considering that antibiotics and ARGs alter the structure and ecological functions of natural microbial communities and pose a threat to river organisms and human health, our research findings provide comprehensive insights into the migration, transformation, and bioavailability of antibiotics in biofilms.

Prevalence of antibiotic resistance genes and virulence factors in the sediment of WWTP effluent-dominated rivers

In the context of increasing aridity due to climate changes, effluent from wastewater treatment plants (WWTPs) became dominant in some rivers. However, the prevalence of antibiotic resistance genes (ARGs) and virulence factors (VFs) in effluent-dominated rivers was rarely investigated. In this study, the profiles of ARGs and VFs in the sediment of two effluent-dominated rivers were revealed through the metagenomic sequencing technique. In each river, samples from the effluent discharge point (P site) and approximately 500 m downstream (D site) were collected. Results showed that the abundances of ARGs and VFs were both higher in D sites than those in P sites, indicating higher risks in the downstream areas. The compositions of ARGs were similar in the P sites of two rivers while being distinct in the D sites. The same was true for changes in the VFs compositions. Microbial community structure variations were the main driver for the changes in ARGs and VFs. Network analysis revealed that the interaction of ARGs and VF genes (VFGs) in sediment was intense. Two VFGs and eleven ARGs were identified to play important roles in the network. Metagenome-assembled genomes (MAGs) were generated to evaluate the coexistence of ARGs and VFGs at the single genome level. It was found that 38.4 % of the MAGs contained both ARGs and VFGs, and two MAGs were from pathogenic genera. These results suggested that high microbiological risks existed in effluent-dominated rivers, and necessary measures should be taken to prevent the potential threat to public health.

Dynamics of antibiotic resistance markers and Escherichia coli invasion in riverine heterotrophic biofilms facing increasing heat and flow stagnation

As motivation to address environmental dissemination of antimicrobial resistance (AMR) is mounting, there is a need to characterize mechanisms by which AMR can propagate under environmental conditions. Here we investigated the effect of temperature and stagnation on the persistence of wastewater-associated antibiotic resistance markers in riverine biofilms and the invasion success of genetically-tagged Escherichia coli. Biofilms grown on glass slides incubated in-situ downstream of a wastewater treatment plant effluent discharge point were transferred to laboratory-scale flumes fed with filtered river water under potentially stressful temperature and flow conditions: recirculation flow at 20 °C, stagnation at 20 °C, and stagnation at 30 °C. After 14 days, quantitative PCR and amplicon sequencing were used to quantify bacteria, biofilms diversity, resistance markers (sul1, sul2, ermB, tetW, tetM, tetB, blaCTX-M-1, intI1) and E. coli. Resistance markers significantly decreased over time regardless of the treatment applied. Although invading E. coli were initially able to colonize the biofilms, its abundance subsequently declined. Stagnation was associated with a shift in biofilm taxonomic composition, but there was no apparent effect of flow conditions or the simulated river-pool warming (30 °C) on AMR persistence or invasion success of E. coli. Results however indicated that antibiotic resistance markers in the riverine biofilms decreased under the experimental conditions in the absence of exposure to external inputs of antibiotics and AMR.

Antibiotic resistance indicator genes in biofilm and planktonic microbial communities after wastewater discharge

The spread of bacteria with antibiotic resistance genes (ARGs) in aquatic ecosystems is of growing concern as this can pose a risk of transmission to humans and animals. While the impact of wastewater treatment plant (WWTP) effluent on ARG abundance in surface waters has been studied extensively, less is known about the fate of ARGs in biofilms. The proximity and dense growth of microorganisms in combination with the accumulation of higher antibiotic concentrations in biofilms might render biofilms a reservoir for ARGs. Seasonal parameters such as water temperature, precipitation, and antibiotic concentrations should be considered as well, as they may further influence the fate of ARGs in aquatic ecosystems. Here we investigated the effect of WWTP effluent on the abundance of the sulfonamide resistance genes sul1 and sul2, and the integrase gene intI1 in biofilm and surface water compartments of a river in Germany with a gradient of anthropogenic impact using quantitative PCR. Furthermore, we analyzed the bacterial community structure in both compartments via 16S rRNA gene amplicon sequencing, following the river downstream. Additionally, conventional water parameters and sulfonamide concentrations were measured, and seasonal aspects were considered by comparing the fate of ARGs and bacterial community diversity in the surface water compartment between the summer and winter season. Our results show that biofilm compartments near the WWTP had a higher relative abundance of ARGs (up to 4.7%) than surface waters (<2.8%). Sulfonamide resistance genes were more persistent further downstream (>10 km) of the WWTP in the hot and dry summer season than in winter. This finding is likely a consequence of the higher proportion of wastewater and thus wastewater-derived microorganisms in the river during summer periods. We observed distinct bacterial communities and ARG abundance between the biofilm and surface water compartment, but even greater variations when considering seasonal and spatiotemporal parameters. This underscores the need to consider seasonal aspects when studying the fate of ARGs in aquatic ecosystems.

[Therapy-relevant antibiotic resistances in a One Health context]

One Health refers to a concept that links human, animal, and environmental health. In Germany, there is extensive data on antibiotic resistance (AMR) and multidrug-resistant (micro)organisms (MDRO) in human and veterinary medicine, as well as from studies in various environmental compartments (soil, water, wastewater). All these activities are conducted according to different specifications and standards, which makes it difficult to compare data. A focus on AMR and MDRO of human therapeutic importance is helpful to provide some guidance. Most data are available across sectors on methicillin-resistant Staphylococcus aureus (MRSA) and multiresistant Enterobacterales such as Escherichia coli and Klebsiella pneumoniae. Here, the trends of resistance are heterogeneous. Antibiotic use leads to MRE selection, which is well documented. Success in minimizing antibiotic use has also been demonstrated in recent years in several sectors and could be correlated with success in containing AMR and MDRO (e.g., decrease in MRSA in human medicine). Sector-specific measures to reduce the burden of MDRO and AMR are also necessary, as not all resistance problems are linked to other sectors. Carbapenem resistance is still rare, but most apparent in human pathogens. Colistin resistance occurs in different sectors but shows different mechanisms in each. Resistance to antibiotics of last resort such as linezolid is rare in Germany, but shows a specific One Health correlation. Efforts to harmonize methods, for example in the field of antimicrobial susceptibility testing and genome-based pathogen and AMR surveillance, are an important first step towards a better comparability of the different data collections.

Occurrence and influencing factors of antibiotics and antibiotic resistance genes in sediments of the largest multi-habitat lakes in Northern China

Baiyangdian Lake is a typical and largest multi-habitat lake in the North plain of China. To understand the generation and transmission of antibiotics resistance genes (ARGs) in multi-habitat lakes, the contents of nutrients (TC, TOC, TN, TP and TS), heavy metals (Zn, Cr, Ni, Cu, Pb, As, Cd and Hg), 22 antibiotics, 16S-rRNA(16S), Class I integron (intI1) and 20 ARGs were determined. Samples were taken from the Fuhe river, river estuaries, reed marshes, living area, fish ponds and open water of Baiyangdian Lake. The results showed that quinolones were the main pollutants in six habitats, and the content range was ND-104.94 ng/g. Thereinto, aac (6') -IB, blaTEM-1, ermF, qnrA, qnrD, tetG, sul1, sul2 and tetM were detected in all the analyzed samples. The absolute abundance of sul1 was the highest (5.25 × 10⁵ copies/g-6.21 × 10⁷ copies/g) in most of the samples. In these different habitats, the abundance of antibiotics and ARGs in river estuary was the highest, and that in reed marshes was the lowest. There was a significant positive correlation between the abundance of heavy metals (Cu, Pb, Zn, Ni, Cd, Hg) and the absolute abundance of 11 ARGs (P < 0.01). Redundancy analysis showed that Cu, Zn, intI1, TP and macrolides were the important factors affecting the distribution of ARGs. Our finding provides a more likely driving and influencing factor for the transmission of ARGs in lakes with complex and diverse habitats.

Antibiotic resistance gene sequencing is necessary to reveal the complex dynamics of immigration from sewers to activated sludge

Microbial community composition has increasingly emerged as a key determinant of antibiotic resistance gene (ARG) content. However, in activated sludge wastewater treatment plants (AS-WWTPs), a comprehensive understanding of the microbial community assembly process and its impact on the persistence of antimicrobial resistance (AMR) remains elusive. An important part of this process is the immigration dynamics (or community coalescence) between the influent and activated sludge. While the influent wastewater contains a plethora of ARGs, the persistence of a given ARG depends initially on the immigration success of the carrying population, and the possible horizontal transfer to indigenously resident populations of the WWTP. The current study utilized controlled manipulative experiments that decoupled the influent wastewater composition from the influent microbial populations to reveal the fundamental mechanisms involved in ARG immigration between sewers and AS-WWTP. A novel multiplexed amplicon sequencing approach was used to track different ARG sequence variants across the immigration interface, and droplet digital PCR was used to quantify the impact of immigration on the abundance of the targeted ARGs. Immigration caused an increase in the abundance of over 70 % of the quantified ARGs. However, monitoring of ARG amplicon sequence variants (ARG-ASVs) at the immigration interface revealed various immigration patterns such as (i) suppression of the indigenous mixed liquor ARG-ASV by the immigrant, or conversely (ii) complete immigration failure of the influent ARG-ASV. These immigration profiles are reported for the first time here and highlight the crucial information that can be gained using our novel multiplex amplicon sequencing techniques. Future studies aiming to reduce AMR in WWTPs should consider the impact of influent immigration in process optimisation and design.

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

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

Dissemination of antibiotic resistance genes from the Pearl River Estuary to adjacent coastal areas

The spread of antibiotic resistance genes (ARGs) is a growing concern over the world's various environments. Coastal environments may receive pollutants from land runoffs via estuaries. However, the impact of ARG contamination from estuarine regions to coastal areas is rarely reported. This study used high-throughput quantitative PCR to examine the diversity and abundance of ARGs in Pearl River Estuary (PRE) and adjacent coastal areas. We found that the distribution of ARGs in seawater exhibited the distance-decay phenomenon from the estuary to coastal areas, while the sediment samples did not exhibit an obvious distribution pattern. The estuarine water was found to be the hotspot of ARGs, with 74 ARG species detected and absolute abundance being 5.93 × 10⁵ copies per mL, on average, while less species and lower abundance of ARGs were detected in coastal waters. Ordination analysis showed that estuarine ARG communities were significantly different from coastal ARG communities for water samples. SourceTracker analysis revealed that ARGs from the estuarine environment contributed only a minor fraction of ARG contamination to downstream coastal areas (1.5%-7.4% for water samples, and 0.7-1.8% for sediment samples), indicating the strong dilution effect of seawater. Mantel tests, redundancy analysis and random forest model analysis identified salinity, nutrients, microbial community structure and mobile genetic elements (MGEs) as important factors influencing ARG distribution. Partial least squares-path model revealed that, among all environmental factors, MGEs directly affected the distribution of ARGs, while other factors indirectly contributed by affecting the MGEs assemblage. Our study provides insight into the dissemination of ARGs from the PRE to adjacent coastal areas.

Leave No Trace? Ecological and anthropogenic determinants of antibiotic resistant bacteria in a recreational alpine environment

Antibiotic resistant bacteria (ARB) have been detected in remote environments, but the degree to which their presence is due to anthropogenic contamination remains unclear. Here, anthropogenic and ecological determinants of ARB were characterized in remote and highly visited areas of Rocky Mountain National Park in the United States. Soil and water samples were collected from 29 sites once a month for three months and measured for bacteria resistant to seven antibiotics with flow cytometry. A novel index of the likelihood of human presence (HPI) was generated for estimating human impact on ARB abundance. The HPI accounted for 44% of variation in ARB abundance in water samples (p < 0.0001) and 51% of variation in soil samples (p < 0.00001). Human presence index was illustrated as a reliable predictor of ARB abundance despite a tendency to underpredict at higher levels of human impact. Ecological determinants such as temperature, elevation, slope, and aspect were also found to be significantly associated with ARB abundance. These findings suggest that human presence drives the abundance of ARB in Rocky Mountain National Park, but ecological variables play a significant role in their presence and dispersal.

Metagenomic insights into resistome coalescence in an urban sewage treatment plant-river system

The effluents of sewage treatment plants (eSTP) are one of the critical contributors of antibiotic resistiome in rivers. Recently, community coalescence has been focused as the entire microbiome interchanges with one another. While works have reported the prevalence of antibiotic resistance genes (ARGs) in eSTP and their effects on river resistome, little research has investigated the extent of resistome coalescence in the environment. In the study, we have addressed the issue and focused on the resistome coalescence of eSTP in an urban river with a typical effluent/river coalescence model, by utilizing high-throughput sequencing (HTS)-based metagenomic assembly analysis. In all, a total of 609 ARGs were found in the eSTP-river system, conferring resistance to 30 antibiotic classes and including some emerging ARGs such as mcr-type, tetX and carbapenemase genes. Statistical analyses including linear discriminant analysis effect size (LEfSe) showed the coalescence of STP effluents increased the diversity and abundance of river resistome, indicating its low resistance to disturb the invasion of resistome community in eSTP. After coalescence in the river, the imprints of STP-derived ARGs presented a temporary increase and gradually decreased trend along the flow path. Further, an innovative fast expectation-maximization microbial source tracking (FEAST) method was used to quantitatively apportion the coalescence event, and demonstrated the contribution of eSTP on river resistome and its attenuation dynamics in the downstream. Notably, correlation-based network analysis and contig-based co-occurrence analysis showed the coalesced resistome in the downstream river co-occurred with human bacterial pathogens, mobile genetic elements and virulence factor genes, indicating potential resistome dissemination risk in the environment. This study provides more profound understanding of resistome coalescence between engineered and natural contexts, which is helpful for optimizing strategies to prevent and control resistome risk in aquatic environment.

Chemical characterization of riverine sediments affected by wastewater treatment plant effluent discharge

This study was aimed at assessing the contribution of wastewater treatment effluents to the contamination profile of the sediments of receiving waterways. Three wastewater treatment plants (WWTP) were addressed, encompassing different population equivalent sizes, urbanization degrees and treatment methods translating differences in expected contamination patterns. Within each WWTP system, the assessment targeted the effluent and sediment samples collected upstream and downstream the effluent discharge point; contaminants belonging to several concerning chemical classes (metals and metalloids; pesticides; pharmaceuticals and personal care products, PPCPs; and polycyclic aromatic hydrocarbons, PAHs) were quantified both in effluent and sediment samples. Clear associations between contaminants present in the effluent and corresponding sediment samples were not always verified. In fact, a noticeable difference between the number or abundance of contaminants detected in effluents and in sediments, suggesting that effluents are not always the most likely source (e.g. PAHs). However, sediment contaminants that were likely sourced by the effluents were also identified (e.g. PPCPs). Sediment analysis offers an important historical view of contamination, especially in flowing recipient ecosystems where any characterization over the water matrix is ephemeral and linking exclusively to the moment of sampling. Hence, sediments should be considered for the establishment of WWTP operational benchmarks regulating the emission of contaminants, which is currently focused mostly on effluent composition thus potentially over/underestimating the longer-term impact of effluent discharge in the recipient waterways.

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

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

Antibiotics and antibiotic resistant bacteria/genes in urban wastewater: A comparison of their fate in conventional treatment systems and constructed wetlands

There is a growing concern that the use and misuse of antibiotics can increase the detection of antibiotic resistant genes (ARGs) in wastewater. Conventional wastewater treatment plants provide a pathway for ARGs and antibiotic resistant bacteria (ARB) to be released into natural water bodies. Research has indicated that conventional primary and secondary treatment systems can reduce ARGs/ARB to varying degrees. However, in developing/low-income countries, only 8-28% of wastewater is treated via conventional treatment processes, resulting in the environment being exposed to high levels of ARGs, ARB and pharmaceuticals in raw sewage. The use of constructed wetlands (CWs) has the potential to provide a low-cost solution for wastewater treatment, with respect to removal of nutrients, pathogens, ARB/ARGs either as a standalone treatment process or when integrated with conventional treatment systems. Recently, CWs have also been employed for the reduction of antibiotic residues, pharmaceuticals, and emerging contaminants. Given the benefits of ARG removal, low cost of construction, maintenance, energy requirement, and performance efficiencies, CWs offer a promising solution for developing/low-income countries. This review promotes a better understanding of the performance efficiency of treatment technologies (both conventional systems and CWs) for the reduction of antibiotics and ARGs/ARB from wastewater and explores workable alternatives.

Research trends and hotspots of aquatic biofilms in freshwater environment during the last three decades: a critical review and bibliometric analysis

Freshwater periphytic biofilms (FPBs), existing widely in various aquatic environments, have attracted extensive attention for many years. In the present study, a bibliometric analysis based on Web of Science Core Collection (WoSCC) was used to understand the research progress, trends, and hot topics of FPBs qualitatively and quantitatively. The results indicated that publications on FPBs have increased from 1991 to 2020 rapidly, and researchers have focused more on the areas of environmental sciences, microbiology, and marine freshwater biology. The most influential countries were mainly the USA, Spain, France, and Germany. Cooperation network analysis reflected that the USA and its affiliated institutions played crucial roles in the research of FPB cooperation, but the collaboration between core author groups still fell short. Based on the analysis of top 20 high-cited FPB documents over the last 30 years, research hotspots mainly included micro-observation and assembly mechanisms of FPBs; interactions of FPBs and pollutants including heavy metals, antibiotic resistance genes, pathogens, organic pollutants, and nanoparticles; and the role of FPBs for biogeochemical cycling, especially nitrogen cycling. Additionally, future research directions were proposed. Overall, this study provides a comprehensive and systematic overview of FPBs, which is useful for research development and researchers who are interested in this area.

Antimicrobial Resistance Development Pathways in Surface Waters and Public Health Implications

Human health is threatened by antibiotic-resistant bacteria and their related infections, which cause thousands of human deaths every year worldwide. Surface waters are vulnerable to human activities and natural processes that facilitate the emergence and spread of antibiotic-resistant bacteria in the environment. This study evaluated the pathways and drivers of antimicrobial resistance (AR) in surface waters. We analyzed antibiotic resistance healthcare-associated infection (HAI) data reported to the CDC's National Healthcare Safety Network to determine the number of antimicrobial-resistant pathogens and their isolates detected in healthcare facilities. Ten pathogens and their isolates associated with HAIs tested resistant to the selected antibiotics, indicating the role of healthcare facilities in antimicrobial resistance in the environment. The analyzed data and literature research revealed that healthcare facilities, wastewater, agricultural settings, food, and wildlife populations serve as the major vehicles for AR in surface waters. Antibiotic residues, heavy metals, natural processes, and climate change were identified as the drivers of antimicrobial resistance in the aquatic environment. Food and animal handlers have a higher risk of exposure to resistant pathogens through ingestion and direct contact compared with the general population. The AR threat to public health may grow as pathogens in aquatic systems adjust to antibiotic residues, contaminants, and climate change effects. The unnecessary use of antibiotics increases the risk of AR, and the public should be encouraged to practice antibiotic stewardship to decrease the risk.

Occurrence and distribution of Carbapenem-resistant Enterobacterales and carbapenemase genes along a highly polluted hydrographic basin

We determined the distribution and temporal variation of Carbapenem Resistant Enterobacterales (CRE), carbapenemase-encoding genes and other antibiotic resistance genes (ARGs) in a highly polluted river (Lis River; Portugal), also assessing the potential influence of water quality to this distribution. Water samples were collected in two sampling campaigns performed one year apart (2018/2019) from fifteen sites and water quality was analyzed. CRE were isolated and characterized. The abundance of four ARGs (bla_NDM, bla_KPC, tetA, bla_CTX-M), two Microbial Source Tracking (MST) indicators (HF183 and Pig-2-Bac) and the class 1 integrase gene (IntI1) was measured by qPCR. RESULTS: confirmed the poor quality of the Lis River water, particularly in sites near pig farms. A collection of 23 CRE was obtained: Klebsiella (n = 19), Enterobacter (n = 2) and Raoultella (n = 2). PFGE analysis revealed a clonal relationship between isolates obtained in different sampling years and sites. All CRE isolates exhibited multidrug resistance profiles. Klebsiella and Raoultella isolates carried bla_KPC while Enterobacter harbored bla_NDM. Conjugation experiments were successful for only four Klebsiella isolates. All ARGs were detected by qPCR on both sampling campaigns. An increase in ARGs and IntI1 abundances was detected in sites located downstream of wastewater treatment plants. Strong correlations were observed between bla_CTX-M, IntI1 and the human-pollution marker HF183, and also between tetA and the pig-pollution marker Pig-2-bac, suggesting that both human- and animal-derived pollution in the Lis River are a potential source of ARGs. Plus, water quality parameters related to eutrophication and land use were significantly correlated with ARGs abundances. Our findings demonstrated that the Lis River encloses high levels of antibiotic resistant bacteria and ARGs, including CRE and carbapenemase-encoding genes. Overall, this study provides a better understanding on the impacts of water pollution resulting from human and animal activities on the resistome of natural aquatic systems.

Management-intensive grazing impacts on total Escherichia coli, E. coli O157:H7, and antibiotic resistance genes in a riparian stream

The impacts of management-intensive grazing (MIG) of cattle on concentrations of total Escherichia coli, total suspended solids (TSS), and nitrate-nitrite nitrogen (NO₃ + NO₂-N), and occurrence of E. coli O157:H7 and selected antibiotic resistance genes (ARGs) in stream water and/or sediments were evaluated. Cattle were grazed for two-week periods in May in each of three years. Overall, grazing increased total E. coli in downstream water by 0.89 log₁₀ MPN/100 mL (p < 0.0001), and downstream total E. coli concentrations were higher than upstream over all sampling intervals. Downstream TSS levels also increased (p ≤ 0.0294) during grazing. In contrast, there was a main effect of treatment for downstream NO₃ + NO₂-N to be lower than upstream (3.59 versus 3.70 mg/L; p = 0.0323). Overwintering mallard ducks increased total E. coli and TSS concentrations in January and February (p < 0.05). For precipitation events during the 24 h before sampling, each increase of 1.00 cm of rainfall increased total E. coli by 0.49 log₁₀ MPN/100 mL (p = 0.0005). In contrast, there was no association of previous 24 h precipitation volume on TSS (p = 0.1540), and there was a negative linear effect on NO₃ + NO₂-N (p = 0.0002). E. coli O157:H7 prevalence was low, but the pathogen was detected downstream up to 2½ months after grazing. Examination of ARGs sul1, ermB, bla_ctx-m-32, and intI1 identified the need for additional research to understand the impact of grazing on the ecology of these resistance determinants in pasture-based cattle production. While E. coli remained higher in downstream water compared to upstream, MIG may reduce the magnitude of the downstream E. coli concentrations. Likewise, the MIG strategy may prevent large increases in TSS and NO₃ + NO₂-N concentrations during heavy rain events. Results indicate that MIG can limit the negative effects of cattle grazing on stream water quality.

Does light-based tertiary treatment prevent the spread of antibiotic resistance genes? Performance, regrowth and future direction

The common occurrence of antibiotic-resistance genes (ARGs) originating from pathogenic and facultative pathogenic bacteria pose a high risk to aquatic environments. Low removal of ARGs in conventional wastewater treatment processes and horizontal dissemination of resistance genes between environmental bacteria and human pathogens have made antibiotic resistance evolution a complex global health issue. The phenomenon of regrowth of bacteria after disinfection raised some concerns regarding the long-lasting safety of treated waters. Despite the inactivation of living antibiotic-resistant bacteria (ARB), the possibility of transferring intact and liberated DNA containing ARGs remains. A step in this direction would be to apply new types of disinfection methods addressing this issue in detail, such as light-based advanced oxidation, that potentially enhance the effect of direct light interaction with DNA. This study is devoted to comprehensively and critically review the current state-of-art for light-driven disinfection. The main focus of the article is to provide an insight into the different photochemical disinfection methods currently being studied worldwide with respect to ARGs removal as an alternative to conventional methods. The systematic comparison of UV/chlorination, UV/H₂O₂, sulfate radical based-AOPs, photocatalytic processes and photoFenton considering their mode of action on molecular level, operational parameters of the processes, and overall efficiency of removal of ARGs is presented. An in-depth discussion of different light-dependent inactivation pathways, influence of DBP and DOM on ARG removal and the potential bacterial regrowth after treatment is presented. Based on presented revision the risk of ARG transfer from reactivated bacteria has been evaluated, leading to a future direction for research addressing the challenges of light-based disinfection technologies.

Occurrence of Antimicrobial Resistance in the Environment in Germany, Austria, and Switzerland: A Narrative Review of Existing Evidence

(1) Background: This study summarizes the current research on antibiotic resistance (AR) in the environment conducted in Austria, Germany, and Switzerland; (2) Methods: A narrative systematic literature review of epidemiological studies based on searches in EMBASE and CAB abstracts (up to 16 June2021) was conducted. Environmental reservoirs included water sources, wastewater, animal husbandry, wildlife, soil, and sediment; (3) Results: Four hundred and four records were screened, and 52 studies were included. Thirteen studies examined aquatic environments, and eleven investigated wastewater. Eight studies investigated both wildlife and animal husbandry. Less evidence was available for sediments, soil, and air. Considerable heterogeneity in research focus, study design, sampling, and measurement of resistance was observed. Resistance to all categories of antimicrobials in the WHO CIA list was identified. Resistance to critically important and highly important substances was reported most frequently; (4) Conclusions: The current research scope presents data-gathering efforts. Usage of a unified protocol for isolate collection, selecting sampling sites, and susceptibility testing is required to provide results that can be compared between the studies and reservoirs. Epidemiological, environmental, and ecological factors should be considered in surveys of the environmental dissemination of AR. Systematic epidemiological studies investigating AR at the interface of human, animal, and environmental health are needed.

Risk assessment of pollutants in flowback and produced waters and sludge in impoundments

Due to the growing hydraulic fracturing (HF) practices in China, the environmental risks of pollutants in flowback and produced waters (FPW) and sludge in impoundments for FPW reserves have drawn increasing attention. In this context, we first characterized the comparative geochemical characteristics of the FPW and the sludge in impoundments that collected FPW from 75 shale gas wells, and then the risks associated with the pollutants were assessed. The results demonstrated that four organic compounds detected in the FPW, naphthalene, acenaphthene, dibutyl phthalate, and bis(2-ethylhexyl)phthalate, were potential threats to surface waters. The concentrations of trace metals (copper, cadmium, manganese, chromium, nickel, zinc, arsenic, and lead) in the FPW and sludge were low; however, those of iron, barium, and strontium were high. The accumulation of chromium, nickel, zinc, and lead in the sludge became more evident as the depth increased. The environmental risks from heavy metals in the one-year precipitated sludge were comparable to those reported in the environment. However, the radium equivalent activities were 10-41 times higher than the recommended value for human health safety, indicating potential radiation risks. Although hydrophobic organic compounds, such as high-molecular-weight polycyclic aromatic hydrocarbons (PAHs), phthalate esters (PAEs), benzene, ethylbenzene, toluene, and xylene (BTEX), tended to accumulate in the sludge, their environmental risks were within tolerable ranges after proper treatment. Multiple antibiotic resistance genes (ARGs), such as those for macrolide, lincosamide, streptogramin (MLS), tetracycline, and multidrug resistances, were detected in the shale gas wastewaters and sludge. Therefore, the environmental risks of these emerging pollutants upon being discharged or leaked into surface waters require further attention.

Sulfur transformation and bacterial community dynamics in both desulfurization-denitrification biofilm and suspended activated sludge

Types of microbial aggregates have essential effects on bacterial communities' characteristics, thus affecting the pollutants removal. An up-flow biofilm reactor was used to study the different performances of S^2-/NO₂^- removal and functional genes in suspended sludge and biofilms. The metabolic pathways of sulfurous and nitrogenous pollutants in the desulfurization-denitrification process were proposed. The results showed that S⁰ formation dominated the reactor with a high S^2- concentration. Autotrophic Sulfurovum responsible for S^2-/S⁰ oxidation was the only dominant bacteria in suspended sludge. Heterotrophic Desulfocapsa responsible for SO₄^2- reduction coexisted with Sulfurovum and dominated in biofilms. S^2- oxidation to S⁰ was catalyzed via fccA/B and sqr genes in suspended sludge. S₃^2-/S⁰ oxidation to SO₄^2- was catalyzed via dsrA/B gene in biofilms. SO₄^2- and NO₂^- were removed via the dissimilatory sulfate reduction and denitrification pathway, respectively. This work provides a fundamental and practical basis for optimizing suspended sludge/biofilm systems for S^2-/NO₂^- removal.

Epidemiology of mobile colistin resistance (mcr) genes in aquatic environments

Colistin is one of the last-line therapies against multidrug-resistant Gram-negative pathogens, especially carbapenemase-producing isolates, making resistance to this compound a major global public-health crisis. Until recently, colistin resistance in Gram-negative bacteria was known to arise only by chromosomal mutations. However, a plasmid-mediated colistin resistance mechanism was described in late 2015. This mechanism is encoded by different mobile colistin resistance (mcr) genes that encode phosphoethanolamine (pEtN) transferases. These enzymes catalyse the addition of a pEtN moiety to lipid A in the bacterial outer membrane leading to colistin resistance. MCR-producing Gram-negative bacteria have been largely disseminated worldwide. However, their environmental dissemination has been underestimated. Indeed, water environments act as a connecting medium between different environments, allowing them to play a crucial role in the spread of antibiotic resistance between the natural environment and humans and other animals. For a better understanding of the role of such environments as reservoirs and/or dissemination routes of mcr genes, this review discusses primarily the various water habitats contributing to the spread of antibiotic resistance. Thereafter, we provide an overview of existing knowledge regarding the global epidemiology of mcr genes in water environments. This review confirms the global distribution of mcr genes in several water environments, including wastewater from different origins, surface water and tap water, making these environments reservoirs and dissemination routes of concern for this resistance mechanism.

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

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