Sewers as potential reservoirs of antibiotic resistance

Remediation of antibiotic pollution in the global environment by iron-based materials activating advanced oxidation processes: A systematic review

Antibiotic pollution and its associated resistance genes have emerged as a global environmental and health concern, with widespread detection in various environmental media such as water, soil, atmosphere, and sediment, as well as in organisms. Hence, it is imperative to develop effective remediation technologies for the targeted treatment of antibiotic pollution to mitigate its environmental and health risks. This paper reviews the status of antibiotic pollution in major countries, territories, and regions worldwide. Addressing the risks cause by antibiotics and their resistance genes and achieving efficient remediation of antibiotic pollutants. Additionally, the study explores the issue of antibiotic use and resistance in detail from a global perspective. It provides a critical scientific foundation for controlling global antibiotic resistance through multi-dimensional integrated analysis. In 2021, 4.71 million deaths globally were attributed to antibiotic resistance, with countries such as India and China being the most affected. It also examined the predominant types and sources of antibiotic pollutants, as well as key remediation technologies for addressing antibiotic contamination. Antibiotics such as amoxicillin and ciprofloxacin are commonly found in surface waters at concentrations ranging from 1 to 120 μg L-1. Furthermore, this paper highlighted the distinctive advantages of advanced oxidation processes (AOPs) in addressing antibiotic pollution, demonstrating removal efficiencies exceeding 90 % under optimal conditions. Our review underscored the pivotal role of iron-based materials and porous biochar in AOPs, showing promising results in various environmental settings. Future research should prioritize the development of multifunctional iron-based composites with improved catalytic stability, environmental compatibility, and recyclability. Moreover, expanding the field-scale application of these materials, particularly in low-resource or high-risk regions, will be essential to translate laboratory successes into global impact. This analysis is designed to inform and guide future initiatives to control and eliminate antibiotic contamination.

Tracing antibiotics in sewers: Concentrations, measurement techniques, and mathematical approaches

Antibiotic contamination in sewer networks has significant environmental and health concerns worldwide, primarily due to its role in promoting bacterial resistance. In this literature review, antibiotic concentrations reported in urban sewers and hospital effluents, techniques for antimicrobial compound detection and quantification, and current modeling strategies are analyzed and discussed based on 91 papers published between 2014 and 2024. One-hundred and nine antibiotic compounds were reported across 80 studies, with sulfonamides, fluoroquinolones, and macrolides being the most frequently detected classes, while amphenicols and aminocyclitols were the least monitored. Advanced analytical techniques such as liquid chromatography and mass spectrometry are the most common approaches used for antibiotic quantification. Modeling efforts remain limited, with kinetic models, Risk Quotient (RQ) assessments, and Wastewater-Based Epidemiology (WBE) representing the main approaches identified. This review compiles 992 reports into a comprehensive dataset intended to support future research, especially for global monitoring, the development of predictive models, and the formulation of regulatory frameworks for managing antibiotic pollution in sewer systems.

Multidimensional tolerance landscapes reveal antibiotic-environment interactions affecting population dynamics of wastewater bacteria

City sewers harbor diverse bacterial communities that are continuously exposed to a myriad of antibiotic residues resulting from human consumption and excretion. Despite their sub-inhibitory concentrations in sewage, these pharmaceutical residues affect the growth rate and the yield of susceptible wastewater-associated bacteria. Moreover, environmental conditions in sewers are complex, including variations in temperature and, in many coastal city sewers, salinity. These variables can modulate antibiotic tolerance and therefore affect the dynamics of microbial populations. To explore such interactions between antibiotics and abiotic environmental factors, we built continuous multivariate tolerance landscapes for three bacterial species commonly detected in sewage: Escherichia coli, the emerging pathogen Streptococcus suis, and a typical sewer dweller, Arcobacter cryaerophilus. We projected their intrinsic growth rate and carrying capacity onto a complex environment including temperature, salinity, and a range of concentrations of two antibiotics frequently measured in urban wastewater (ciprofloxacin and azithromycin). We revealed that antibiotic tolerance was maximal at salinities close to seawater for both E. coli and S. suis, and that the direction of the interaction between antibiotics and temperature is species dependent. In E. coli, we additionally observed a third-order interaction among salinity, temperature and antibiotics, highlighting the limits of predicting field dynamics of bacterial populations using standard laboratory measures. We projected these tolerance curves onto time series data of temperature and conductivity measured in the sewers of Barcelona. Our model highlights that low concentrations of antibiotics could exclude the most sensitive species, while interactions between antibiotics, temperature, and salinity substantially affected the dynamics of the more tolerant ones.

Interaction of sulfate-reducing bacteria and methanogenic archaea in urban sewers, leads to increased risk of proliferation of antibiotic resistance genes

Sewers are considered a potential reservoir of antibiotic resistance. However, the generation of antibiotic resistance genes (ARGs) in microbial communities in pipeline biofilms under antibiotic stress remains unexplored. In this study, the biodegradation efficiency of tetracycline (TCY) and sulfamethoxazole (SMX) was evaluated in a pilot reactor of the sewers. The results showed that under TCY and SMX stress, the degradation efficiency of sewage water was inhibited. The most abundant ARGs detected in the biofilm samples were TCY-related genes (e.g., tetW/N/W, tetC, and tetM), accounting for 34.1%. The microbial community composition varied, and the correlation analysis showed that antibiotic stress had a certain impact on the biological metabolic activity and function of the urban sewers. The community structure and diversity of biofilms enabled the evaluation of the bioconversion of antibiotics. Notably, Anaerocella and Paludibacter directly influenced the methanogenesis and sulfate reduction processes, playing a key role in the interaction between sulfate-reducing bacteria and methanogenic archaea. These microorganisms facilitated the proliferation of ARGs (tet and sul) in the biofilms through horizontal gene transfer. This study provides insight into the front-end control of ARGs, further improving sewage treatment plant processes and reducing the environmental and health risks caused by antibiotic abuse.

Bacterial Communities and Resistance and Virulence Genes in Hospital and Community Wastewater: Metagenomic Analysis

Metagenomic studies have made it possible to deepen the analysis of the abundance of bacterial populations that carry resistance and virulence determinants in the wastewater environment. In this study, a longitudinal collection of samples of community and hospital wastewater from August 2021 to September 2022 was obtained. Shotgun metagenomic sequencing and bioinformatic analysis were performed to characterize the bacterial abundance, antimicrobial resistance genes (ARGs), plasmids, and virulence factor genes (VFGs) contained in the wastewater. The microbial composition of the community and hospital wastewater showed that the most abundant bacterial phyla detected in all samples were: Proteobacteria, Bacteroides, Firmicutes, Campylobacterota, and Actinobacteria. Seasonal differences in the relative abundances of species, ARGs, plasmids, and VFGs were observed. In this study, a total of 270 ARGs were detected, and it was found that the absolute abundance of ARGs only showed a 39% reduction in the treated wastewater. Furthermore, the ARGs detected in this study were found to encode resistance to antibiotics of the last choice. Our results showed that plasmids carrying resistance genes were more abundant in raw wastewater, and 60% more abundant in hospital wastewater compared to community wastewater. Several of the VFGs detected in this study encode for adhesion, motility, and biofilm formation, which likely allows bacteria to remain and persist in the wastewater environment and survive WWTP treatment systems, thus managing to escape into the environment via treated wastewater.

Antibiotic resistance gene levels within a highly urbanised estuary

Antibiotic resistant bacteria are increasingly being found in aquatic environments, representing a potential threat to public health. To examine the dynamics and potential sources of antibiotic-resistant genes (ARGs) in urbanised waterways, we performed a six-month temporal study at six locations within the Sydney Harbour estuary. These locations spanned a salinity gradient from seawater at the mouth of the harbour to freshwater at the more urbanised western sites. We quantified the abundances of three ARGs (sulI, tetA, and dfrA1) and an anthropogenic pollution marker (intI1). To assess potential sources of environmental ARGs, we also quantified levels of the sewage marker (Lachnospiraceae), bird-associated faecal pollution markers (GFD), and a common wastewater pipe-dwelling genus of bacteria (Arcobacter). We assessed the impact of a major rainfall event on ARG levels during this period. The strong rainfall event led to increases in intI1 and ARGs (sulI and dfrA) across sites, but the potential source for ARGs was different. Some sites experienced sewage intrusions, as defined using the human-faecal marker Lachnospiraceae, which were clearly correlated with ARG levels. However, at the two sites furthest from the ocean, links between ARG levels and sewage were less evident, with correlations to other contaminants, including heavy metals, apparent. These results highlight the potential complexities associated with identifying, and ultimately remediating, the causes and sources of antimicrobial resistance within natural aquatic ecosystems.

The Impact of Wastewater on Antimicrobial Resistance: A Scoping Review of Transmission Pathways and Contributing Factors

BACKGROUND/OBJECTIVES

Antimicrobial resistance (AMR) is a global issue driven by the overuse of antibiotics in healthcare, agriculture, and veterinary settings. Wastewater and treatment plants (WWTPs) act as reservoirs for antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). The One Health approach emphasizes the interconnectedness of human, animal, and environmental health in addressing AMR. This scoping review analyzes wastewater's role in the AMR spread, identifies influencing factors, and highlights research gaps to guide interventions.

METHODS

This scoping review followed the PRISMA-ScR guidelines. A comprehensive literature search was conducted across the PubMed and Web of Science databases for articles published up to June 2024, supplemented by manual reference checks. The review focused on wastewater as a source of AMR, including hospital effluents, industrial and urban sewage, and agricultural runoff. Screening and selection were independently performed by two reviewers, with conflicts resolved by a third.

RESULTS

Of 3367 studies identified, 70 met the inclusion criteria. The findings indicated that antibiotic residues, heavy metals, and microbial interactions in wastewater are key drivers of AMR development. Although WWTPs aim to reduce contaminants, they often create conditions conducive to horizontal gene transfer, amplifying resistance. Promising interventions, such as advanced treatment methods and regulatory measures, exist but require further research and implementation.

CONCLUSIONS

Wastewater plays a pivotal role in AMR dissemination. Targeted interventions in wastewater management are essential to mitigate AMR risks. Future studies should prioritize understanding AMR dynamics in wastewater ecosystems and evaluating scalable mitigation strategies to support global health efforts.

Preliminary insights on carbapenem resistance in Enterobacteriaceae in high-income and low-/middle-income countries

The emergence of carbapenem-resistant Enterobacteriaceae in the hospital sector as well as in the natural environment is a problem that affects both high-income countries (HICs) and low-/middle-income countries (LMICs). The observed differences in the prevalence of carbapenem-resistant strains between HICs and LMICs can be attributed mainly to antibiotic consumption in healthcare facilities and the quantity of treated wastewater. Hospital wastewater is a major hotspot for the spread of carbapenem-resistant Enterobacteriaceae (CRE) and carbapenem resistance genes (CRGs) between the hospital sector and the environment. In this review article, attempts were made to describe and compare antibiotic consumption in hospitals, antimicrobial concentrations in both hospital and municipal wastewater, and the prevalence of CRE and CRGs in patients and in hospital and municipal wastewater in HICs and LMICs. A review of the literature has shown that carbapenems are more widely used in LMICs, but Saudi Arabia, an HIC, is a country with the highest carbapenem consumption in the world. The results of research conducted in both groups of countries indicate that Klebsiella sp./K. pneumoniae is the most common CRE in samples isolated from patients. Escherichia coli was the dominant pathogen in hospital and municipal wastewater in HICs, whereas Enterobacter spp. were most prevalent in LMICs. An analysis of the prevalence of CRGs demonstrated that the same genes are present in both groups of countries (blaKPC, blaKPC-2, blaVIM, blaVIM-1,2, blaNDM, blaIMP, blaIMP-8, blaOXA-48,181, blaNDM-1,5, blaGES, blaGES-5,6, blaIMI-1). The fact that the same CRGs are most prevalent in countries with different levels of economic development could suggest that these genes have a high potential to persist in the natural environment. These findings underscore the need for enhanced monitoring, effective control techniques, and a better understanding of carbapenem resistance pathways to mitigate public health hazards, notwithstanding the constraints of data analysis.

Methanogenic Potential of Sewer Microbiomes and Its Implications for Methane Emission

The sewer system, despite being a significant source of methane emissions, has often been overlooked in current greenhouse gas inventories due to the limited availability of quantitative data. Direct monitoring in sewers can be expensive or biased due to access limitations and internal heterogeneity of sewer networks. Fortunately, since methane is almost exclusively biogenic in sewers, we demonstrate in this study that the methanogenic potential can be estimated using known sewer microbiome data. By combining data mining techniques and bioinformatics databases, we developed the first data-driven method to analyze methanogenic potentials using a data set containing 633 observations of 53 variables obtained from literature mining. The methanogenic potential in the sewer sediment was around 250-870% higher than that in the wet biofilm on the pipe and sewage water. Additionally, k-means clustering and principal component analysis linked higher methane emission rates (9.72 ± 51.3 kgCO2 eq m-3 d-1) with smaller pipe size, higher water level, and higher potentials of sulfate reduction in the wetted pipe biofilm. These findings exhibit the possibility of connecting microbiome data with biogenic greenhouse gases, further offering insights into new approaches for understanding greenhouse gas emissions from understudied sources.

Cyanobacteria mediate the dissemination of bacterial antibiotic resistance through conjugal transfer

Cyanobacterial blooms are expanding world-wide in freshwater and marine environments, and can cause serious ecological and environmental issues, which also contribute to the spread of antibiotic resistance genes (ARGs). However, the mechanistic understanding of cyanobacteria-mediated resistance dynamics is not fully elucidated yet. We selected Microcystis aeruginosa as a model cyanobacteria to illustrate how cyanobacteria mediate the evolution and transfer processes of bacterial antibiotic resistance. The results show that the presence of cyanobacteria significantly decreased the abundance of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) by 3%-99% and 2%-18%, respectively. In addition, it clearly altered bacterial community structure, with the dominant genera evolving from Acinetobacter (27%) and Enterobacter (42%) to Porphyrobacter (59%). The abundance of ARGs positively correlated with Proteobacteria and Firmicutes, rather than Cyanobacteria, and Bacteroidetes. In the presence of cyanobacteria, the transfer events of bacterial resistance genes via conjugation were found to decrease by 10%-89% (p < 0.05). Surprisingly, we found an extradentary high transfer frequency (about 0.1) for the ARGs via plasmid conjugation from the bacteria into M. aeruginosa population. It confirmed the role of cyanobacterial population as the competent hosts to facilitate ARGs spreading. Our findings provide valuable information on the risk evaluation of ARGs caused by cyanobacterial blooms in aquatic environments, key for the protection and assessment of aquatic environmental quality.

On-Site Inactivation for Disinfection of Antibiotic-Resistant Bacteria in Hospital Effluent by UV and UV-LED

The problem of antimicrobial resistance (AMR) is not limited to the medical field but is also becoming prevalent on a global scale in the environmental field. Environmental water pollution caused by the discharge of wastewater into aquatic environments has caused concern in the context of the sustainable development of modern society. However, there have been few studies focused on the treatment of hospital wastewater, and the potential consequences of this remain unknown. This study evaluated the efficacy of the inactivation of antimicrobial-resistant bacteria (AMRB) and antimicrobial resistance genes (AMRGs) in model wastewater treatment plant (WWTP) wastewater and hospital effluent based on direct ultraviolet (UV) light irradiation provided by a conventional mercury lamp with a peak wavelength of 254 nm and an ultraviolet light-emitting diode (UV-LED) with a peak emission of 280 nm under test conditions in which the irradiance of both was adjusted to the same intensity. The overall results indicated that both UV- and UV-LED-mediated disinfection effectively inactivated the AMRB in both wastewater types (>99.9% after 1-3 min of UV and 3 min of UV-LED treatment). Additionally, AMRGs were also removed (0.2-1.4 log10 for UV 254 nm and 0.1-1.3 log10 for UV 280 nm), and notably, there was no statistically significant decrease (p < 0.05) in the AMRGs between the UV and UV-LED treatments. The results of this study highlight the importance of utilizing a local inactivation treatment directly for wastewater generated by a hospital prior to its flow into a WWTP as sewage. Although additional disinfection treatment at the WWTP is likely necessary to remove the entire quantity of AMRB and AMRGs, the present study contributes to a significant reduction in the loads of WWTP and urgent prevention of the spread of infectious diseases, thus alleviating the potential threat to the environment and human health risks associated with AMR problems.

One Health Threat of Treated Wastewater Discharge in Urban Ohio Rivers: Implications for Surface Water and Fish Gut Microbiome and Resistome

Wastewater treatment plants (WWTPs) are thought to be a major disseminating source of antibiotic resistance (AR) to the environment, establishing a crucial connection between human and environmental resistome. The objectives of this study were to determine how wastewater effluents impact microbiome and resistome of freshwater and fish, and identify potential AR-carrying clinically relevant pathogens in these matrices. We analyzed wastewater influent and effluent from four WWTPs in three metropolitan areas of Ohio, USA via shotgun metagenomic sequencing. We also sequenced river water and fish guts from three reaches (upstream, at the WWTP outfall, and downstream). Notably, we observed a decline in microbiome diversity and AR gene abundance from wastewater to the receiving river. We also found significant differences by reach and trophic level (diet) in beta-diversity of the fish gut microbiomes. SourceTracker revealed that 0.443 and 0.248 more of the of the fish gut microbiome was sourced from wastewater effluent in fish from the outfall and downstream locations, respectively, compared to upstream fish. Additionally, AR bacteria of public health concern were annotated in effluent and river water samples, indicating potential concern for human exposure. In summary, our findings show the continued role of wastewater as a significant AR reservoir and underscores the considerable impact of wastewater discharge on aquatic wildlife, which highlights the One Health nature of this issue.

The CRISPR/Cas system as an antimicrobial resistance strategy in aquatic ecosystems

With the growing population, demand for food has dramatically increased, and fisheries, including aquaculture, are expected to play an essential role in sustaining demand with adequate quantities of protein and essential vitamin supplements, employment generation, and GDP growth. Unfortunately, the incidence of emerging/re-emerging AMR pathogens annually occurs because of anthropogenic activities and the frequent use of antibiotics in aquaculture. These AMR pathogens include the WHO's top 6 prioritized ESKAPE pathogens (nosocomial pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), extended-spectrum beta lactases (ESBLs) and carbapenemase-producing E. coli, which pose major challenges to the biomagnification of both nonnative and native antibiotic-resistant bacteria in capture and cultured fishes. Although implementing the rational use of antibiotics represents a promising mitigation measure, this approach is practically impossible due to the lack of awareness among farmers about the interplay between antimicrobial use and the emergence of antimicrobial resistance (AMR). Nevertheless, to eradicate these 'superbugs,' CRISPR/Cas (clustered regularly interspersed short palindromic repeats/CRISPR associate protein) has turned out to be a novel approach owing to its ability to perform precise site-directed targeting/knockdown/reversal of specific antimicrobial resistance genes in vitro and to distinguish AMR-resistant bacteria from a plethora of commensal aquatic bacteria. Along with highlighting the importance of virulent multidrug resistance genes in bacteria, this article aims to provide a holistic picture of CRISPR/Cas9-mediated genome editing for combating antimicrobial-resistant bacteria isolated from various aquaculture and marine systems, as well as insights into different types of CRISPR/Cas systems, delivery methods, and challenges associated with developing CRISPR/Cas9 antimicrobial agents.

Metagenomics insights into microbiome and antibiotic resistance genes from free living amoeba in chlorinated wastewater effluents

Free living amoeba (FLA) are among the organisms commonly found in wastewater and are well-established hosts for diverse microbial communities. Despite its clinical significance, there is little knowledge on the FLA microbiome and resistome, with previous studies relying mostly on conventional approaches. In this study we comprehensively analyzed the microbiome, antibiotic resistome and virulence factors (VFs) within FLA isolated from final treated effluents of two wastewater treatment plants (WWTPs) using shotgun metagenomics. Acanthamoeba has been identified as the most common FLA, followed by Entamoeba. The bacterial diversity showed no significant difference (p > 0.05) in FLA microbiomes obtained from the two WWTPs. At phylum level, the most dominant taxa were Proteobacteria, followed by Firmicutes and Actinobacteria. The most abundant genera identified were Enterobacter followed by Citrobacter, Paenibacillus, and Cupriavidus. The latter three genera are reported here for the first time in Acanthamoeba. In total, we identified 43 types of ARG conferring resistance to cephalosporins, phenicol, streptomycin, trimethoprim, quinolones, cephalosporins, tigecycline, rifamycin, and kanamycin. Similarly, a variety of VFs in FLA metagenomes were detected which included flagellar proteins, Type IV pili twitching motility proteins (pilH and rpoN), alginate biosynthesis genes AlgI, AlgG, AlgD and AlgW and Type VI secretion system proteins and general secretion pathway proteins (tssM, tssA, tssL, tssK, tssJ, fha, tssG, tssF, tssC and tssB, gspC, gspE, gspD, gspF, gspG, gspH, gspI, gspJ, gspK, and gspM). To the best of our knowledge, this is the first study of its kind to examine both the microbiomes and resistome in FLA, as well as their potential pathogenicity in treated effluents. Additionally, this study showed that FLA can host a variety of potentially pathogenic bacteria including Paenibacillus, and Cupriavidus that had not previously been reported, indicating that their relationship may play a role in the spread and persistence of antibiotic resistant bacteria (ARBs) and antibiotic resistance genes (ARGs) as well as the evolution of novel pathogens.

The relationship between water quality and the microbial virulome and resistome in urban streams in Brazil

Urban streams that receive untreated domestic and hospital waste can transmit infectious diseases and spread drug residues, including antimicrobials, which can then increase the selection of antimicrobial-resistant bacteria. Here, water samples were collected from three different urban streams in the state of São Paulo, Brazil, to relate their range of Water Quality Indices (WQIs) to the diversity and composition of aquatic microbial taxa, virulence genes (virulome), and antimicrobial resistance determinants (resistome), all assessed using untargeted metagenome sequencing. There was a predominance of phyla Proteobacteria, Actinobacteria, and Bacteroidetes in all samples, and Pseudomonas was the most abundant detected genus. Virulence genes associated with motility, adherence, and secretion systems were highly abundant and mainly associated with Pseudomonas aeruginosa. Furthermore, some opportunistic pathogenic genera had negative correlations with WQI. Many clinically relevant antimicrobial resistance genes (ARGs) and efflux pump-encoding genes that confer resistance to critically important antimicrobials were detected. The highest relative abundances of ARGs were β-lactams and macrolide-lincosamide-streptogramin. No statistically supported relationship was detected between the abundance of virulome/resistome and collection type/WQI. On the other hand, total solids were a weak predictor of gene abundance patterns. These results provide insights into various microbial outcomes given urban stream quality and point to its ecological complexity. In addition, this study suggests potential consequences for human health as mediated by aquatic microbial communities responding to typical urban outputs.

Development of an in vitro biofilm model for the study of the impact of fluoroquinolones on sewer biofilm microbiota

Sewer biofilms are likely to constitute hotspots for selecting and accumulating antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). This study aimed to optimize culture conditions to obtain in vitro biofilms, mimicking the biofilm collected in sewers, to study the impact of fluoroquinolones (FQs) on sewer biofilm microbiota. Biofilms were grown on coupons in CDC Biofilm Reactors®, continuously fed with nutrients and inoculum (1/100 diluted wastewater). Different culture conditions were tested: (i) initial inoculum: diluted wastewater with or without sewer biofilm, (ii) coupon material: concrete vs. polycarbonate, and (iii) time of culture: 7 versus 14 days. This study found that the biomass was highest when in vitro biofilms were formed on concrete coupons. The biofilm taxonomic diversity was not affected by adding sewer biofilm to the initial inoculum nor by the coupon material. Pseudomonadales, Burkholderiales and Enterobacterales dominated in the sewer biofilm composition, whereas in vitro biofilms were mainly composed of Enterobacterales. The relative abundance of qnrA, B, D and S genes was higher in in vitro biofilms than sewer biofilm. The resistome of sewer biofilm showed the highest Shannon diversity index compared to wastewater and in vitro biofilms. A PCoA analysis showed differentiation of samples according to the nature of the sample, and a Procrustes analysis showed that the ARG changes observed were linked to changes in the microbial community. The following growing conditions were selected for in vitro biofilms: concrete coupons, initial inoculation with sewer biofilm, and a culture duration of 14 days. Then, biofilms were established under high and low concentrations of FQs to validate our in vitro biofilm model. Fluoroquinolone exposure had no significant impact on the abundance of qnr genes, but high concentration exposure increased the proportion of mutations in gyrA (codons S83L and D87N) and parC (codon S80I). In conclusion, this study allowed the determination of the culture conditions to develop an in vitro model of sewer biofilm; and was successfully used to investigate the impact of FQs on sewer microbiota. In the future, this setup could be used to clarify the role of sewer biofilms in disseminating resistance to FQs in the environment.

Characteristics of fungi formation in urban sewer at different flow conditions: Distribution, metabolism, and pathogenicity

Fungi are the significant components of the sewer ecology system which can consume substances and exhibit pathogenicity. However, the characteristics of fungi formation and metabolism in the complex sewer environment have not been revealed in depth. In this study, gradient flow conditions were conducted in a pilot sewer and the formation characteristics of fungi were synthetically investigated. The results showed that the low flow rate at 0.1-0.4 m/s led to the loose morphology of biofilms, while the overly loose environment did not allow fungi communities to thrive in sewer. The dense biofilms were found at the middle flow condition (0.4-0.6 m/s), and the fungal communities with degradation functions were exuberant at this condition (such as Tremellales with relative abundance of 6.18% and Talaromyces with relative abundance of 6.51%). In particular, eleven kinds of fungi with known pathogenicity of the sewer biofilm were found in this study, and it is worth noting that the abundance of pathogenic fungi at medium flow rates is significantly higher than that at other flow conditions (higher than 10 %). While, excessive flow shear force (0.8-1.2 m/s) led to biofilm shedding which caused hindering the proper generation of fungi. In summary, the pollutant transformation and pathogenic exposure conducted by fungi communities could affect the sewer management process significantly, and this study could provide research foundation for wastewater quality prediction and management of pathogenic risk in sewer systems.

Insights into the circular: The cryptic plasmidome and its derived antibiotic resistome in the urban water systems

Plasmids have been a concern in the dissemination and evolution of antibiotic resistance in the environment. In this study, we investigated the total pool of plasmids (plasmidome) and its derived antibiotic resistance genes (ARGs) in different compartments of urban water systems (UWSs) in three European countries representing different antibiotic usage regimes. We applied a direct plasmidome approach using wet-lab methods to enrich circular DNA in the samples, followed by shotgun sequencing and in silico contig circularisation. We identified 9538 novel sequences in a total of 10,942 recovered circular plasmids. Of these, 66 were identified as conjugative, 1896 mobilisable and 8970 non-mobilisable plasmids. The UWSs' plasmidome was dominated by small plasmids (≤10 Kbp) representing a broad diversity of mobility (MOB) types and incompatibility (Inc) groups. A shared collection of plasmids from different countries was detected in all treatment compartments, and plasmids could be source-tracked in the UWSs. More than half of the ARGs-encoding plasmids carried mobility genes for mobilisation/conjugation. The richness and abundance of ARGs-encoding plasmids generally decreased with the flow, while we observed that non-mobilisable ARGs-harbouring plasmids maintained their abundance in the Spanish wastewater treatment plant. Overall, our work unravels that the UWS plasmidome is dominated by cryptic (i.e., non-mobilisable, non-typeable and previously unknown) plasmids. Considering that some of these plasmids carried ARGs, were prevalent across three countries and could persist throughout the UWSs compartments, these results should alarm and call for attention.

Inactivation of antibiotic-resistant bacteria in hospital wastewater by ozone-based advanced water treatment processes

The emergence and spread of antimicrobial resistance (AMR) continue on a global scale. The impacts of wastewater on the environment and human health have been identified, and understanding the environmental impacts of hospital wastewater and exploring appropriate forms of treatment are major societal challenges. In the present research, we evaluated the efficacy of ozone (O3)-based advanced wastewater treatment systems (O3, O3/H2O2, O3/UV, and O3/UV/H2O2) for the treatment of antimicrobials, antimicrobial-resistant bacteria (AMRB), and antimicrobial resistance genes (AMRGs) in wastewater from medical facilities. Our results indicated that the O3-based advanced wastewater treatment inactivated multiple antimicrobials (>99.9%) and AMRB after 10-30 min of treatment. Additionally, AMRGs were effectively removed (1.4-6.6 log10) during hospital wastewater treatment. The inactivation and/or removal performances of these pollutants through the O3/UV and O3/UV/H2O2 treatments were significantly (P < 0.05) better than those in the O3 and O3/H2O2 treatments. Altered taxonomic diversity of microorganisms based on 16S rRNA gene sequencing following the O3-based treatment showed that advanced wastewater treatments not only removed viable bacteria but also removed genes constituting microorganisms in the wastewater. Consequently, the objective of this study was to apply advanced wastewater treatments to treat wastewater, mitigate environmental pollution, and alleviate potential threats to environmental and human health associated with AMR. Our findings will contribute to enhancing the effectiveness of advanced wastewater treatment systems through on-site application, not only in wastewater treatment plants (WWTPs) but also in medical facilities. Moreover, our results will help reduce the discharge of AMRB and AMRGs into rivers and maintain the safety of aquatic environments.

Characterization of urban sources of antibiotics and antibiotic-resistance genes in a Dutch sewer catchment

A one year study was conducted in the city of Nijmegen, The Netherlands, to characterize various urban sources of antibiotics and antibiotic resistant genes (ARGs) in wastewater within a single sewer catchment. Prevalence of ermB, tet(W), sul1, sul2, intl1, and 16S rRNA gene was determined at 10 locations within the city. Sampling locations included a nursing home, a student residence, a hospital and an industrial area, among others. Wastewater concentrations of 23 antibiotics were measured using passive sampling. Additionally, excreted loads of 22 antibiotics were estimated based on ambulatory prescription and clinical usage data. Genes sul1 and intl1 were most abundant across most locations. Ciprofloxacin and amoxicillin together contributed over 92 % of the total estimated antibiotic selective pressure at all sampling points. The present study highlights the prominent role that hospitals can have in the prevalence and proliferation of ARGs in urban wastewater. Furthermore, results suggest that even short-term changes in the therapeutic regimen prescribed in hospitals may translate into shifting ARG abundance patterns in hospital wastewater. The methods applied present an opportunity to identify emission hotspots and prioritize intervention options to limit ARG spread from urban wastewater to the environment.

Comparison of concentration and extraction workflows for qPCR quantification of intI1 and vanA in untreated wastewater

Quantitative polymerase chain reaction (qPCR) measurement of antibiotic resistance genes (ARGs) in untreated municipal wastewater may prove useful in combating the antimicrobial resistance crisis. However, harmonizing and optimizing qPCR-based workflows is essential to facilitate comparisons across studies, and includes achieving highly-effective ARG capture through efficient concentration and extraction procedures. In the current study, combinations of sample volume, membrane types and DNA extraction kits within filtration and centrifugation-based workflows were used to quantify 16S ribosomal RNA (16S rRNA), class 1 integron-integrase gene (intI1) and an ARG encoding resistance to vancomycin (vanA) in untreated wastewater sampled from three wastewater treatment plants (WWTPs). Highly abundant 16S rRNA and intI1 were detected in 100 % of samples from all three WWTPs using both 2 and 20 mL sample volumes, while lower prevalence vanA was only detected when using the 20 mL volume. When filtering 2 mL of wastewater, workflows with 0.20-/0.40-μm polycarbonate (PC) membranes generally yielded greater concentrations of the three targets than workflows with 0.22-/0.45-μm mixed cellulose ester (MCE) membranes. The improved performance was diminished when the sample volume was increased to 20 mL. Consistently greater concentrations of 16S rRNA, intI1 and vanA were yielded by filtration-based workflows using PC membranes combined with a DNeasy PowerWater (DPW) Kit, regardless of the sample volume used, and centrifugation-based workflows with DNeasy Blood & Tissue Kit for 2-mL wastewater extractions. Within the filtration-based workflows, the DPW kit yielded more detection and quantifiable results for less abundant vanA than the DNeasy PowerSoil Pro Kit and FastDNA™ SPIN Kit for Soil. These findings indicate that the performance of qPCR-based workflows for surveillance of ARGs in wastewater varies across targets, sample volumes, concentration methods and extraction kits. Workflows must be carefully considered and validated considering the target ARGs to be monitored.

Synergistic removal of pharmaceuticals and antibiotic resistance from ultrafiltered WWTP effluent: Free-floating ARGs exceptionally susceptible to degradation

To protect the environment and human health, antibiotic resistance genes (ARGs) and persistent pharmaceuticals need to be removed from WWTP effluent prior to its reuse. However, an efficient process for removing free-floating extracellular DNA (exDNA) in combination with a wide range of pharmaceuticals is yet to be reported for real process conditions. As a possible solution, we treated real ultrafiltered WWTP effluent with UV/H₂O₂ and combined GAC and zeolite sorption. In terms of exDNA, sequencing and high-throughput quantitative PCR (HT-qPCR) showed that exDNA is a potent carrier of numerous ARGs in ultrafiltered WWTP effluent (123 ARGs), including multi-drug efflux pump mexF that became the dominant exARG in GAC effluent over time. Due to the exposure to degradation agents, exDNA was reduced more efficiently than intracellular DNA, and overall levels of ARGs were substantially lowered. Moreover, GAC sorption was particularly effective in the removal of almost all the 85 detected pharmaceutical residues, with fresh GAC demonstrating an efficiency of up to 100%. However, zeolite (Si/Al 0.8) addition was needed to enhance the removal of persistent pollutants such as gabapentin and diclofenac to 57% and up to 100%, respectively. Our combined approach eminently decreases the hazardous effects of pharmaceuticals and antibiotic resistance in the ultrafiltered WWTP effluent, producing effluent suitable for multiple reuse options according to the latest legislation. In addition, we provided similarly promising but less extensive data for surface water and treated greywater.

Sub-MIC antibiotics influence the microbiome, resistome and structure of riverine biofilm communities

The effects of sub-minimum inhibitory concentrations (sub-MICs) of antibiotics on aquatic environments is not yet fully understood. Here, we explore these effects by employing a replicated microcosm system fed with river water where biofilm communities were continuously exposed over an eight-week period to sub-MIC exposure (1/10, 1/50, and 1/100 MIC) to a mix of common antibiotics (ciprofloxacin, streptomycin, and oxytetracycline). Biofilms were examined using a structure-function approach entailing microscopy and metagenomic techniques, revealing details on the microbiome, resistome, virulome, and functional prediction. A comparison of three commonly used microbiome and resistome databases was also performed. Differences in biofilm architecture were observed between sub-MIC antibiotic treatments, with an overall reduction of extracellular polymeric substances and autotroph (algal and cyanobacteria) and protozoan biomass, particularly at the 1/10 sub-MIC condition. While metagenomic analyses demonstrated that microbial diversity was lowest at the sub-MIC 1/10 antibiotic treatment, resistome diversity was highest at sub-MIC 1/50. This study also notes the importance of benchmarking analysis tools and careful selection of reference databases, given the disparity in detected antimicrobial resistance genes (ARGs) identity and abundance across methods. Ultimately, the most detected ARGs in sub-MICs exposed biofilms were those that conferred resistance to aminoglycosides, tetracyclines, β-lactams, sulfonamides, and trimethoprim. Co-occurrence of microbiome and resistome features consistently showed a relationship between Proteobacteria genera and aminoglycoside ARGs. Our results support the hypothesis that constant exposure to sub-MICs antibiotics facilitate the transmission and promote prevalence of antibiotic resistance in riverine biofilms communities, and additionally shift overall microbial community metabolic function.

Wastewater treatment plants, an "escape gate" for ESCAPE pathogens

Antibiotics are an essential tool of modern medicine, contributing to significantly decreasing mortality and morbidity rates from infectious diseases. However, persistent misuse of these drugs has accelerated the evolution of antibiotic resistance, negatively impacting clinical practice. The environment contributes to both the evolution and transmission of resistance. From all anthropically polluted aquatic environments, wastewater treatment plants (WWTPs) are probably the main reservoirs of resistant pathogens. They should be regarded as critical control points for preventing or reducing the release of antibiotics, antibiotic-resistant bacteria (ARB), and antibiotic-resistance genes (ARGs) into the natural environment. This review focuses on the fate of the pathogens Enterococcus faecium, Staphylococcus aureus, Clostridium difficile, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae spp. (ESCAPE) in WWTPs. All ESCAPE pathogen species, including high-risk clones and resistance determinants to last-resort antibiotics such as carbapenems, colistin, and multi-drug resistance platforms, were detected in wastewater. The whole genome sequencing studies demonstrate the clonal relationships and dissemination of Gram-negative ESCAPE species into the wastewater via hospital effluents and the enrichment of virulence and resistance determinants of S. aureus and enterococci in WWTPs. Therefore, the efficiency of different wastewater treatment processes regarding the removal of clinically relevant ARB species and ARGs, as well as the influence of water quality factors on their performance, should be explored and monitored, along with the development of more effective treatments and appropriate indicators (ESCAPE bacteria and/or ARGs). This knowledge will allow the development of quality standards for point sources and effluents to consolidate the WWTP barrier role against the environmental and public health AR threats.

Insights on the particle-attached riverine archaeal community shifts linked to seasons and to multipollution during a Mediterranean extreme storm event

Even if Archaea deliver important ecosystem services and are major players in global biogeochemical cycles, they remain poorly understood in freshwater ecosystems. To our knowledge, no studies specifically address the direct impact of xenobiotics on the riverine archaeome. Using environmental DNA metabarcoding of the 16S ribosomal gene, we previously demonstrated bacterial communities significant shifts linked to pollutant mixtures during an extreme flood in a typical Mediterranean coastal watercourse. Here, using the same methodology, we sought to determine whether archaeal community shifts coincided with the delivery of environmental stressors during the same flood. Further, we wanted to determine how archaea taxa compared at different seasons. In contrast to the bacteriome, the archaeome showed a specific community in summer compared to winter and autumn. We also identified a significant relationship between in situ archaeome shifts and changes in physicochemical parameters along the flood, but a less marked link to those parameters correlated to river hydrodynamics than bacteria. New urban-specific archaeal taxa significantly related to multiple stressors were identified. Through statistical modeling of both domains, our results demonstrate that Archaea, seldom considered as bioindicators of water quality, have the potential to improve monitoring methods of watersheds.

Effect of erythromycin on epiphytic bacterial communities and water quality in wetlands

The occurrence of antibiotics such as erythromycin (ERY) under macrolide group, has long been acknowledged for negatively affecting ecosystems in freshwater environments. However, the effects of ERY on water quality and microbial communities in epiphytic biofilms are poorly understood. Here, Scanning Electron Microscopy (SEM), High-throughput sequencing, and physicochemical analytical methods were employed to unravel the impact of ERY on the water quality and bacterial morphology, biodiversity, composition, interaction, and ecological function in epiphytic biofilms attached to Vallisneria natans and artificial plants in mesocosmic wetlands. The study showed that ERY exposure significantly impaired the nutrient removal capacity (TN, TP, and COD) and altered the epiphytic bacterial morphology of V. natans and artificial plants. ERY did not affect the bacterial α-diversity. Notwithstanding ERY decreased the bacterial composition, but the relative abundance of Proteobacteria and Patescibacteria spiked by 62.2 % and 54 %, respectively, in V. natans, while Desulfobacteria and Chloroflexi increased by 8.9 % and 11.2 %, respectively, in artificial plants. Notably, ERY disturbed the food web structure and metabolic pathways such as carbohydrate metabolism, amino acid metabolism, energy metabolism, cofactor and vitamin metabolism, membrane transport, and signal transduction. This study revealed that ERY exposure disrupted the bacterial morphology, composition, interaction or food web structure, and metabolic functions in epiphytic biofilm. These data underlined that ERY negatively impacts epiphytic bacterial communities and nutrient removal in wetlands.

Wastewater surveillance of antibiotic-resistant bacterial pathogens: A systematic review

Infectious diseases caused by antibiotic-resistant bacterial (ARB) pathogens are a serious threat to human and animal health. The active surveillance of ARB using an integrated one-health approach can help to reduce the emergence and spread of ARB, reduce the associated economic impact, and guide antimicrobial stewardship programs. Wastewater surveillance (WWS) of ARB provides composite samples for a total population, with easy access to the mixed community microbiome. This concept is emerging rapidly, but the clinical utility, sensitivity, and uniformity of WWS of ARB remain poorly understood especially in relation to clinical evidence in sewershed communities. Here, we systematically searched the literature to identify studies that have compared findings from WWS of ARB and antibiotic resistance genes (ARG) with clinical evidence in parallel, thereby evaluating how likely WWS of ARB and ARG can relate to the clinical cases in communities. Initially, 2,235 articles were obtained using the primary search keywords, and 1,219 articles remained after de-duplication. Among these, 35 articles fulfilled the search criteria, and an additional 13 relevant articles were included by searching references in the primary literature. Among the 48 included papers, 34 studies used a culture-based method, followed by 11 metagenomics, and three PCR-based methods. A total of 28 out of 48 included studies were conducted at the single sewershed level, eight studies involved several countries, seven studies were conducted at national or regional scales, and five at hospital levels. Our review revealed that the performance of WWS of ARB pathogens has been evaluated more frequently for Escherichia coli, Enterococcus spp., and other members of the family Enterobacteriaceae, but has not been uniformly tested for all ARB pathogens. Many wastewater-based ARB studies comparing the findings with clinical evidence were conducted to evaluate the public health risk but not to relate with clinical evidence and to evaluate the performance of WWS of ARB. Indeed, relating WWS of ARB with clinical evidence in a sewershed is not straightforward, as the source of ARB in wastewater cannot be only from symptomatic human individuals but can also be from asymptomatic carriers as well as from animal sources. Further, the varying fates of each bacterial species and ARG within the sewerage make the aim of connecting WWS of ARB with clinical evidence more complicated. Therefore, future studies evaluating the performance of many AMR pathogens and their genes for WWS one by one can make the process simpler and the interpretation of results easier.

A Metagenomic Investigation of Spatial and Temporal Changes in Sewage Microbiomes across a University Campus

Wastewater microbial communities are not static and can vary significantly across time and space, but this variation and the factors driving the observed spatiotemporal variation often remain undetermined. We used a shotgun metagenomic approach to investigate changes in wastewater microbial communities across 17 locations in a sewer network, with samples collected from each location over a 3-week period. Fecal material-derived bacteria constituted a relatively small fraction of the taxa found in the collected samples, highlighting the importance of environmental sources to the sewage microbiome. The prokaryotic communities were highly variable in composition depending on the location within the sampling network, and this spatial variation was most strongly associated with location-specific differences in sewage pH. However, we also observed substantial temporal variation in the composition of the prokaryotic communities at individual locations. This temporal variation was asynchronous across sampling locations, emphasizing the importance of independently considering both spatial and temporal variation when assessing the wastewater microbiome. The spatiotemporal patterns in viral community composition closely tracked those of the prokaryotic communities, allowing us to putatively identify the bacterial hosts of some of the dominant viruses in these systems. Finally, we found that antibiotic resistance gene profiles also exhibit a high degree of spatiotemporal variability, with most of these genes unlikely to be derived from fecal bacteria. Together, these results emphasize the dynamic nature of the wastewater microbiome, the challenges associated with studying these systems, and the utility of metagenomic approaches for building a multifaceted understanding of these microbial communities and their functional attributes. IMPORTANCE Sewage systems harbor extensive microbial diversity, including microbes derived from both human and environmental sources. Studies of the sewage microbiome are useful for monitoring public health and the health of our infrastructure, but the sewage microbiome can be highly variable in ways that are often unresolved. We sequenced DNA recovered from wastewater samples collected over a 3-week period at 17 locations in a single sewer system to determine how these communities vary across time and space. Most of the wastewater bacteria, and the antibiotic resistance genes they harbor, were not derived from human feces, but human usage patterns did impact how the amounts and types of bacteria and bacterial genes we found in these systems varied over time. Likewise, the wastewater communities, including both bacteria and their viruses, varied depending on location within the sewage network, highlighting the challenges and opportunities in efforts to monitor and understand the sewage microbiome.

Occurrence and Quantitative Microbial Risk Assessment of Methicillin-Resistant Staphylococcus aureus (MRSA) in a Sub-Catchment of the Yodo River Basin, Japan

The occurrence of Staphylococcus aureus (S. aureus) and methicillin-resistant S. aureus (MRSA) in a sub-catchment of the Yodo River Basin, a representative water system of a drinking water source in Japan, was investigated. The chromogenic enzyme-substrate medium method was used for the detection of S. aureus and MRSA by the presence or absence of antimicrobials in the medium for viable bacteria in a culture-based setting. The contributions of S. aureus and MRSA from wastewater to the rivers were estimated based on mass flux-based analysis, and quantitative microbial risk assessment (QMRA) was further conducted for S. aureus and MRSA in river environments. The mean abundance of S. aureus and MRSA was 31 and 29 CFU/mL in hospital effluent, 124 and 117 CFU/mL in sewage treatment plant (STP) influent, 16 and 13 CFU/mL in STP effluent, and 8 and 9 CFU/mL in river water, respectively. Contribution of the pollution load derived from the target STP effluent to river water ranged from 2% to 25%. The QMRA showed that to achieve the established health benchmarks, the drinking water treatment process would need to yield 1.7 log10 and 2.9 log10 inactivation in terms of infection risk and disability-adjusted life year (DALY) indexes, respectively. These findings highlight the link between medical environment and the importance of environmental risk management for antimicrobial-resistant bacteria in aquatic environments.

Distribution and characteristics of carbapenem-resistant and extended-spectrum β-lactamase (ESBL) producing Escherichia coli in hospital effluents, sewage treatment plants, and river water in an urban area of Japan

Occurrence of profiles of the carbapenem-resistant Escherichia coli (CRE-E) and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-E) in an urban river in a sub-catchment of the Yodo River Basin, one of the representative water systems of Japan was investigated. We conducted seasonal and year-round surveys for the antimicrobial-resistant bacteria (AMRB) and antimicrobial-resistance genes (AMRGs) in hospital effluents, sewage treatment plant (STP) wastewater, and river water; subsequently, contributions to wastewater discharge into the rivers were estimated by analyses based on the mass flux. Furthermore, the characteristics of AMRB in the water samples were evaluated on the basis of antimicrobial susceptibility tests. CRE-E and ESBL-E were detected in all water samples with mean values 11 and 1900 CFU/mL in the hospital effluent, 58 and 4550 CFU/mL in the STP influent, not detected to 1 CFU/mL in the STP effluent, and 1 and 1 CFU/mL in the STP discharge into the river, respectively. Contributions of the pollution load derived from the STP effluent discharged into the river water were 1 to 21%. The resistome profiles for bla_IMP, bla_TEM, and bla_CTX-M genes in each water sample showed that AMRGs were not completely removed in the wastewater treatment process in the STP, and the relative abundances of bla_IMP, bla_TEM, and bla_CTX-M genes were almost similar (P<0.05). Susceptibility testing of antimicrobial-resistant E. coli isolates showed that CRE-E and ESBL-E detected in wastewaters and river water were linked to the prevalence of AMRB in clinical settings. These results suggest the importance of conducting environmental risk management of AMRB and AMRGs in the river environment. To our knowledge, this is the first detailed study that links the medical environment to CRE-E and ESBL-E for evaluating the AMRB and AMRGs in hospital effluents, STP wastewater, and river water at the basin scale on the basis of mass flux as well as the contributions of CRE-E and ESBL-E to wastewater discharge into the river.

Evaluating the Role of Wastewaters as Reservoirs of Antibiotic-Resistant ESKAPEE Bacteria Using Phenotypic and Molecular Methods

Introduction

Methodology

Results

Conclusion

Guts of the Urban Ecosystem: Microbial Ecology of Sewer Infrastructure

Microbes have inhabited the oceans and soils for millions of years and are uniquely adapted to their habitat. In contrast, sewer infrastructure in modern cities dates back only ~150 years. Sewer pipes transport human waste and provide a view into public health, but the resident organisms that likely modulate these features are relatively unexplored. Here, we show that the bacterial assemblages sequenced from untreated wastewater in 71 U.S. cities were highly coherent at a fine sequence level, suggesting that urban infrastructure separated by great spatial distances can give rise to strikingly similar communities. Within the overall microbial community structure, temperature had a discernible impact on the distribution patterns of closely related amplicon sequence variants, resulting in warm and cold ecotypes. Two bacterial genera were dominant in most cities regardless of their size or geographic location; on average, Arcobacter accounted for 11% and Acinetobacter 10% of the entire community. Metagenomic analysis of six cities revealed these highly abundant resident organisms carry clinically important antibiotic resistant genes blaCTX-M, blaOXA, and blaTEM. In contrast, human fecal bacteria account for only ~13% of the community; therefore, antibiotic resistance gene inputs from human sources to the sewer system could be comparatively small, which will impact measurement capabilities when monitoring human populations using wastewater. With growing awareness of the metabolic potential of microbes within these vast networks of pipes and the ability to examine the health of human populations, it is timely to increase our understanding of the ecology of these systems. IMPORTANCE Sewer infrastructure is a relatively new habitat comprised of thousands of kilometers of pipes beneath cities. These wastewater conveyance systems contain large reservoirs of microbial biomass with a wide range of metabolic potential and are significant reservoirs of antibiotic resistant organisms; however, we lack an adequate understanding of the ecology or activity of these communities beyond wastewater treatment plants. The striking coherence of the sewer microbiome across the United States demonstrates that the sewer environment is highly selective for a particular microbial community composition. Therefore, results from more in-depth studies or proven engineering controls in one system could be extrapolated more broadly. Understanding the complex ecology of sewer infrastructure is critical for not only improving our ability to treat human waste and increasing the sustainability of our cities but also to create scalable and effective sewage microbial observatories, which are inevitable investments of the future to monitor health in human populations.

The Sources and Potential Hosts Identification of Antibiotic Resistance Genes in the Yellow River, Revealed by Metagenomic Analysis

The fate of antibiotic resistance genes (ARGs) has been revealed in various environmental media in recent years. Namely, the emergence of genes that resist colistin and carbapenems has attracted wide attention. However, the pollution condition of ARGs and sources in the Yellow River is still little understood, despite the river being the second longest in China. The present study determined the levels of ARG pollution in the Henan section of the Yellow River and evaluated the role of the aquaculture industry in the spread of ARGs. As revealed by the results, a total of 9 types of ARGs were detected in the sediments of the Yellow River, and the total ARG content in the Yellow River ranges from 7.27 to 245.45 RPKM. Sul1 and sul2 are the dominant ARGs, and the huge usage of sulfonamides, horizontal gene transfer, and wide bacteria host contribute to the prevalence of these two genes. The results of Spearman correlation analysis indicate that the breeding industry has little influence on ARGs in the Yellow River. Network analysis reveals that the opportunistic pathogen Pseudomonas is the potential host of sul1, tetG, and ANT(3'')-IIa, which can pose a risk to human health.

Rainfall leads to elevated levels of antibiotic resistance genes within seawater at an Australian beach

Anthropogenic waste streams can be major sources of antibiotic resistant microbes within the environment, creating a potential risk to public health. We examined patterns in the occurrence of a suite of antibiotic resistance genes (ARGs) and their links to enteric bacteria at a popular swimming beach in Australia that experiences intermittent contamination by sewage, with potential points of input including stormwater drains and a coastal lagoon. Samples were collected throughout a significant rainfall event (40.8 mm over 3 days) and analysed using both qPCR and 16S rRNA amplicon sequencing. Before the rainfall event, low levels of faecal indicator bacteria and a microbial source tracking human faeces (sewage) marker (Lachno3) were observed. These levels increased over 10x following rainfall. Within lagoon, drain and seawater samples, levels of the ARGs sulI, dfrA1 and qnrS increased by between 1 and 2 orders of magnitude after 20.4 mm of rain, while levels of tetA increased by an order of magnitude after a total of 40.8 mm. After 40.8 mm of rain sulI, tetA and qnrS could be detected 300 m offshore with levels remaining high five days after the rain event. Highest levels of sewage markers and ARGs were observed adjacent to the lagoon (when opened) and in-front of the stormwater drains, pinpointing these as the points of ARG input. Significant positive correlations were observed between all ARGs, and a suite of Amplicon Sequence Variants that were identified as stormwater drain indicator taxa using 16S rRNA amplicon sequencing data. Of note, some stormwater drain indicator taxa, which exhibited correlations to ARG abundance, included the human pathogens Arcobacter butzleri and Bacteroides fragilis. Given that previous research has linked high levels of ARGs in recreationally used environments to antimicrobial resistant pathogen infections, the observed patterns indicate a potentially elevated human health risk at a popular swimming beach following significant rainfall events.

Non-point source fecal contamination from aging wastewater infrastructure is a primary driver of antibiotic resistance in surface waters

Antibiotic resistance is a global threat to human health. Many surface water resources are environmental hotspots of antibiotic resistant gene (ARG) transfer, with agricultural runoff and human waste highlighted as common sources of ARGs to aquatic systems. Here we quantified fecal marker genes and ARGs in 992 stream water samples collected seasonally during a 5-year period from 115 sites across the Upper Oconee watershed (Georgia, USA), an area characterized by gradients of agricultural and urban development. Widespread fecal contamination was found from humans (48% of samples), ruminants (55%), and poultry (19%), and 73% of samples tested positive for at least one of the six targeted ARGs (ermB, tet(B), bla_CTX-M-1, bla_KPC, bla_SHV, and qnrS). While ARGs were strongly correlated with human fecal markers, many highly contaminated samples were not associated with sewage outfalls, an expected source of fecal and ARG pollution. To determine sources of contamination, we synthesized ARG and fecal marker data with geospatial data on land use/land cover and wastewater infrastructure across the watershed. This novel analysis found strong correlations between ARGs and measures of sewer density, sewer length, and septic system age within sample watersheds, indicating non-point sources of fecal contamination from aging wastewater infrastructure can be critical disseminators of anthropogenic ARGs in the environment.

Reclaimed wastewater reuse in irrigation: Role of biofilms in the fate of antibiotics and spread of antimicrobial resistance

Reclaimed wastewater associated biofilms are made up from diverse class of microbial communities that are continuously exposed to antibiotic residues. The presence of antibiotic resistance bacteria (ARB) and their associated antibiotic resistance genes (ARGs) ensures also a continuous selection pressure on biofilms that could be seen as hotspots for antibiotic resistance dissemination but can also play a role in antibiotic degradation. In this study, the antibiotic degradation and the abundance of four ARGs (qnrS, sul1, blaTEM, ermB), and two mobile genetic elements (MGEs) including IS613 and intl1, were followed in reclaimed wastewater and biofilm samples collected at the beginning and after 2 weeks of six antibiotics exposure (10 µg L^-1). Antibiotics were partially degraded and remained above lowest minimum inhibitory concentration (MIC) for environmental samples described in the literature. The most abundant genes detected both in biofilms and reclaimed wastewater were sul1, ermB, and intl1. The relative abundance of these genes in biofilms increased during the 2 weeks of exposure but the highest values were found in control samples (without antibiotics pressure), suggesting that bacterial community composition and diversity are the driven forces for resistance selection and propagation in biofilms, rather than exposure to antibiotics. Planktonic and biofilm bacterial communities were characterized. Planktonic cells are classically defined "as free flowing bacteria in suspension" as opposed to the sessile state (the so-called biofilm): "a structured community of bacterial cells enclosed in a self-produced polymeric matrix and adherent to an inert or living. surface" as stated by Costerton et al. (1999). The abundance of some genera known to harbor ARG such as Streptococcus, Exiguobacterium, Acholeplasma, Methylophylaceae and Porphyromonadaceae increased in reclaimed wastewater containing antibiotics. The presence of biofilm lowered the level of these genera in wastewater but, at the opposite, could also serve as a reservoir of these bacteria to re-colonize low-diversity wastewater. It seems that maintaining a high diversity is important to limit the dissemination of antimicrobial resistance among planktonic bacteria. Antibiotics had no influence on the biofilm development monitored with optical coherence tomography (OCT). Further research is needed in order to clarify the role of inter-species communication in biofilm on antibiotic degradation and resistance development and spreading.

Year-long wastewater monitoring for SARS-CoV-2 signals in combined and separate sanitary sewers

COVID-19 wastewater-based epidemiology has been performed in catchments of various sizes and sewer types with many short-term studies available and multi-seasonal studies emerging. The objective of this study was to compare weekly observations of SARS-CoV-2 genes in municipal wastewater across multiple seasons for different systems as a factor of sewer type (combined, separate sanitary) and system size. Sampling occurred following the first wave of SARS-CoV-2 cases in the study region (June 2020) and continued through the third wave (May 2021), the period during which clinical testing was widely available and different variants dominated clinical cases. The strongest correlations were observed between wastewater N1 concentrations and the cumulative clinical cases reported in the 2 weeks prior to wastewater sampling, followed by the week prior, new cases, and the week after wastewater sampling. Sewer type and size did not necessarily explain the strength of the correlations, indicating that other non-sewer factors may be impacting the observations. In-system sampling results for the largest system sampled are presented for 1 month. Removing wet weather days from the data sets improved even the flow-normalized correlations for the systems, potentially indicating that interpreting results during wet weather events may be more complicated than simply accounting for dilution. PRACTITIONER POINTS: SARS-CoV-2 in wastewater correlated best with total clinical cases reported in 2 weeks before wastewater sampling at the utility level. Study performed when clinical testing was widespread during the year after the first COVID-19 wave in the region. Sewer type and size did not necessarily explain correlation strength between clinical cases and wastewater-based epidemiology results. Removing wet weather days improved correlations for 3/4 utilities studied, including both separate sanitary and combined sewers.

Molecular microbiological approaches reduce ambiguity about the sources of faecal pollution and identify microbial hazards within an urbanised coastal environment

Urbanised beaches are regularly impacted by faecal pollution, but management actions to resolve the causes of contamination are often obfuscated by the inability of standard Faecal Indicator Bacteria (FIB) analyses to discriminate sources of faecal material or detect other microbial hazards, including antibiotic resistance genes (ARGs). We aimed to determine the causes, spatial extent, and point sources of faecal contamination within Rose Bay, a highly urbanised beach within Sydney, Australia's largest city, using molecular microbiological approaches. Sampling was performed across a network of transects originating at 9 stormwater drains located on Rose Bay beach over the course of a significant (67.5 mm) rainfall event, whereby samples were taken 6 days prior to any rain, on the day of initial rainfall (3.8 mm), three days later after 43 mm of rain and then four days after any rain. Quantitative PCR (qPCR) was used to target marker genes from bacteria (i.e., Lachnospiraceae and Bacteroides) that have been demonstrated to be specific to human faeces (sewage), along with gene sequences from Heliobacter and Bacteriodes that are specific to bird and dog faeces respectively, and ARGs (sulI, tetA, qnrS, dfrA1 and vanB). 16S rRNA gene amplicon sequencing was also used to discriminate microbial signatures of faecal contamination. Prior to the rain event, low FIB levels (mean: 2.4 CFU/100 ml) were accompanied by generally low levels of the human and animal faecal markers, with the exception of one transect, potentially indicative of a dry weather sewage leak. Following 43 mm of rain, levels of both human faecal markers increased significantly in stormwater drain and seawater samples, with highest levels of these markers pinpointing several stormwater drains as sources of sewage contamination. During this time, sewage contamination was observed up to 1000 m from shore and was significantly and positively correlated with often highly elevated levels of the ARGs dfrA1, qnrS, sulI and vanB. Significantly elevated levels of the dog faecal marker in stormwater drains at this time also indicated that rainfall led to increased input of dog faecal material from the surrounding catchment. Using 16S rRNA gene amplicon sequencing, several indicator taxa for stormwater contamination such as Arcobacter spp. and Comamonadaceae spp. were identified and the Bayesian SourceTracker tool was used to model the relative impact of specific stormwater drains on the surrounding environment, revealing a heterogeneous contribution of discrete stormwater drains during different periods of the rainfall event, with the microbial signature of one particular drain contributing up to 50% of bacterial community in the seawater directly adjacent. By applying a suite of molecular microbiological approaches, we have precisely pinpointed the causes and point-sources of faecal contamination and other associated microbiological hazards (e.g., ARGs) at an urbanised beach, which has helped to identify the most suitable locations for targeted management of water quality at the beach.

Trace antibiotics increase the risk of antibiotic resistance genes transmission by regulating the biofilm extracellular polymeric substances and microbial community in the sewer

Sewer is considered a potential hotspot for antibiotic resistance, but the occurrence and proliferation of antibiotic resistance genes (ARGs) under trace antibiotics exposure have received little attention. This work evaluated the effects of tetracycline (TC) and sulfamethoxazole (SMX) individually and in combination in the sewer system and revealed the related mechanisms of ARG proliferation. The relative abundance of tetA and sul1 increased the most under TC and SMX stress, respectively, whereas sul1 increased the most under combined stress. Intl1 was abundant in both the liquid phase and the biofilm, and redundancy analysis confirmed that horizontal gene transfer was the main reason for the proliferation of ARGs. The increase in extracellular polymeric substances (EPS) secretion and the enhancement of the main hydrophobic functional groups facilitated the accumulation of biofilms, which promoted the proliferation of ARGs in biofilms. The relative abundance of most ARGs in the liquid phase was significantly correlated with EPS, protein and tryptophan-like substances. Furthermore, the microbial community structure and diversity affected the proliferation and spread of ARGs in the sewer. These findings contribute to our further understanding of the proliferation and development of ARGs in the sewer and lay the foundation for the front-end control of ARGs.

Occurrence of veterinary drugs and resistance genes during anaerobic digestion of poultry and cattle manures

In the present paper, the mesophilic (35 °C) and thermophilic (55 °C) biomethanization of poultry and cattle manures were investigated using biochemical methane potential (BMP) tests. Specific methane production (SMP), 24 pharmaceutical compounds (PhACs), and five antibiotic resistance genes (ARGs) (bla_KPC, ermB, qnrS, sul1 and tetW) together with the microbial community were analyzed. Mesophilic BMP tests resulted in the highest SMP when poultry manure was used (285.5 mL CH₄/g VSS with poultry vs 239.6 mL CH₄/g VSS with cattle manure) while thermophilic temperatures led to the highest SMP with cattle manure (231.2 mL CH₄/g VSS with poultry vs 238.0 mL CH₄/g VSS with cattle manure). Higher removals of veterinary pharmaceuticals were detected at 55 °C with both manures indicating that thermophilic digestion is better suited for the removal of these compounds. Tylosin, tilmicosin, chlortetracycline, and sulfamethoxazole presented removals higher than 50%, being the first two completely removed under mesophilic and thermophilic conditions. When comparing the relative abundance of ARGs at the end of each treatment, the most significant removal was found for qnrS which was not detected after the anaerobic treatment. The remaining ARGs did not suffer significant changes. Finally, microbial composition analysis showed that temperature affected the final microbial population more than the microorganisms present in the substrate or inoculum.

Anaerobic treatment of swine manure under mesophilic and thermophilic temperatures: Fate of veterinary drugs and resistance genes

The effect of anaerobic treatment of swine manure at 35 °C (mesophilic) and 55 °C (thermophilic) on methane production, microbial community and contaminants of emerging concern was investigated. Pasteurization pretreatment and post treatment was also investigated in combination with anaerobic treatment at 35 °C. Specific methane production (SMP), 26 pharmaceutical compounds (PhACs) and five antibiotic resistance genes (ARGs) (qnrS, tetW, ermB, sul1 and bla_TEM) were evaluated. Mesophilic treatment resulted in the highest SMP regardless of whether pasteurization was applied. Marbofloxacin was the most abundant antibiotic in swine manure. In general, all groups of PhACs showed higher removals under thermophilic temperatures as compared to mesophilic. In general, pasteurization pretreatment followed by mesophilic anaerobic digestion provided the highest removals of ARGs. Finally, the genera Streptococcus, Clostridium and Pseudomonas which contain pathogenic species, were present in the swine manure. Streptococcus, which was the most abundant, was decreased during all the treatments, while the others only decreased under certain treatments.

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.

Metabolically Active Prokaryotes and Actively Transcribed Antibiotic Resistance Genes in Sewer Systems: Implications for Public Health and Microbially Induced Corrosion

Sewer systems are reservoirs of pathogens and bacteria carrying antibiotic resistance genes (ARGs). However, most recent high-throughput studies rely on DNA-based techniques that cannot provide information on the physiological state of the cells nor expression of ARGs. In this study, wastewater and sewer sediment samples were collected from combined and separate sanitary sewer systems. The metabolically active prokaryote community was evaluated using 16S rRNA amplicon sequencing and actively transcribed ARG abundance was measured using mRNA RT-qPCR. Three (sul1, bla_TEM, tet(G)) of the eight tested ARGs were quantifiable in select samples. Sewer sediment samples had greater abundance of actively transcribed ARGs compared to wastewater. Microbiome analysis showed the presence of metabolically active family taxa that contain clinically relevant pathogens (Pseudomonadaceae, Enterobacteraceae, Streptococcaceae, Arcobacteraceae, and Clostridiaceae) and corrosion-causing prokaryotes (Desulfobulbaceae and Desulfovibrionaceae) in both matrices. Spirochaetaceae and methanogens were more common in the sediment matrix while Mycobacteraceae were more common in wastewater. The microbiome obtained from 16S rRNA sequencing had a significantly different structure from the 16S rRNA gene microbiome. Overall, this study demonstrates active transcription of ARGs in sewer systems and provides insight into the abundance and physiological state of taxa of interest in the different sewer matrices and sewer types relevant for wastewater-based epidemiology, corrosion, and understanding the hazard posed by different matrices during sewer overflows.

River Biofilms Microbiome and Resistome Responses to Wastewater Treatment Plant Effluents Containing Antibiotics

Continuous exposure to low concentrations of antibiotics (sub-minimal inhibitory concentration: sub-MIC) is thought to lead to the development of antimicrobial resistance (AMR) in the environmental microbiota. However, the relationship between antibiotic exposure and resistance selection in environmental bacterial communities is still poorly understood and unproven. Therefore, we measured the concentration of twenty antibiotics, resistome quality, and analyzed the taxonomic composition of microorganisms in river biofilms collected upstream (UPS) and downstream (DWS) (at the point of discharge) from the wastewater treatment plant (WWTP) of Poitiers (France). The results of statistical analysis showed that the antibiotic content, resistome, and microbiome composition in biofilms collected UPS were statistically different from that collected DWS. According to Procrustes analysis, microbial community composition and antibiotics content may be determinants of antibiotic resistance genes (ARGs) composition in samples collected DWS. However, network analysis showed that the occurrence and concentration of antibiotics measured in biofilms did not correlate with the occurrence and abundance of antibiotic resistance genes and mobile genetic elements. In addition, network analysis suggested patterns of co-occurrence between several ARGs and three classes of bacteria/algae: Bacteroidetes incertae sedis, Cyanobacteria/Chloroplast, and Nitrospira, in biofilm collected UPS. The absence of a direct effect of antibiotics on the selection of resistance genes in the collected samples suggests that the emergence of antibiotic resistance is probably not only due to the presence of antibiotics but is a more complex process involving the cumulative effect of the interaction between the bacterial communities (biotic) and the abiotic matrix. Nevertheless, this study confirms that WWTP is an important reservoir of various ARGs, and additional efforts and legislation with clearly defined concentration limits for antibiotics and resistance determinants in WWTP effluents are needed to prevent their spread and persistence in the environment.

Inactivation of Antibiotic-Resistant Bacteria in Wastewater by Ozone-Based Advanced Water Treatment Processes

The inactivating effect of ozone (O₃)-based advanced oxidation processes (AOPs) (O₃/H₂O₂, O₃/UV, and O₃/UV/H₂O₂ systems) on antimicrobial-resistant bacteria (AMRB) and antimicrobial-susceptible bacteria (AMSB) in sewage treatment plant (STP) wastewater was investigated. The AMRB were grouped into six classes: carbapenem-resistant Enterobacteriaceae (CRE), extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-E), multidrug-resistant Acinetobacter (MDRA), multidrug-resistant Pseudomonas aeruginosa (MDRP), methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant Enterococcus (VRE); these classes constituted the World Health Organization (WHO) global priority list of AMRB. The results indicate that O₃-based advanced wastewater treatment inactivated all AMRB and AMSB (>99.9%) after 10 min of treatment, and significant differences (p < 0.5) were not observed in the disinfection of AMRB and AMSB by each treatment. Altered taxonomic diversity of micro-organisms based on 16S rRNA gene sequencing via O₃/UV and O₃/UV/H₂O₂ treatment showed that advanced wastewater treatments not only inactivated AMRB but also removed antimicrobial resistance genes (AMRGs) in the wastewater. Consequently, this study recommends the use of advanced wastewater treatments for treating the STP effluent, reducing environmental pollution, and alleviating the potential hazard to human health caused by AMRB, AMSB, and infectious diseases. Overall, this study provides a new method for assessing environmental risks associated with the spread of AMRB and AMSB in aquatic environments, while keeping the water environment safe and maintaining human health.

Environmental Biofilms as Reservoirs for Antimicrobial Resistance

Characterizing the response of microbial communities to a range of antibiotic concentrations is one of the strategies used to understand the impact of antibiotic resistance. Many studies have described the occurrence and prevalence of antibiotic resistance in microbial communities from reservoirs such as hospitals, sewage, and farm feedlots, where bacteria are often exposed to high and/or constant concentrations of antibiotics. Outside of these sources, antibiotics generally occur at lower, sub-minimum inhibitory concentrations (sub-MICs). The constant exposure to low concentrations of antibiotics may serve as a chemical "cue" that drives development of antibiotic resistance. Low concentrations of antibiotics have not yet been broadly described in reservoirs outside of the aforementioned environments, nor is the transfer and dissemination of antibiotic resistant bacteria and genes within natural microbial communities fully understood. This review will thus focus on low antibiotic-concentration environmental reservoirs and mechanisms that are important in the dissemination of antibiotic resistance to help identify key knowledge gaps concerning the environmental resistome.

Urinary lead level and colonization by antibiotic resistant bacteria: Evidence from a population-based study

BACKGROUND

Infection by antibiotic resistant bacteria (ARB) is a global health crisis and asymptomatic colonization increases risk of infection. Nonhuman studies have linked heavy metal exposure to the selection of ARB; however, few epidemiologic studies have examined this relationship. This study analyzes the association between urinary lead level and colonization by ARB in a nonclinical human population.

METHODS

Data came from the Survey of the Health of Wisconsin 2016-2017, and its ancillary Wisconsin Microbiome Study. Urinary lead levels, adjusted for creatinine, were used to assess exposure. ARB included methicillin resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), fluoroquinolone resistant Gram-negative bacilli (RGNB), and Clostridium difficile (C. diff), from skin, nose, and mouth swabs, and saliva and stool samples. Logistic regression, adjusted for covariates, was used to evaluate associations between Pb and ARB. Secondary analysis investigated Pb resistance from ARB isolates.

RESULTS

Among 695 participants, 239 (34%) tested positive for ARB. Geometric mean urinary Pb (unadjusted) was 0.286 µg/L (95% confidence intervals [CI] = 0.263, 0.312) for ARB negative participants and 0.323 µg/L (95% CI = 0.287, 0.363) for ARB positive participants. Models adjusted for demographics, diet, and antibiotic use showed elevated odds of positive colonization for those in the 95th percentile (vs. below) of Pb exposure (odds ratio [OR] = 2.05, 95% CI = 0.95, 4.44), and associations were highest in urban residents (OR = 2.85, 95% CI = 1.07, 7.59). RGNB isolates were most resistant to Pb.

DISCUSSION

These novel results suggest that Pb exposure is associated with increased colonization by ARB, and that RGNB are particularly resistant to Pb.

Impacts of antibiotics on biofilm bacterial community and disinfection performance on simulated drinking water supply pipe wall

Overuse of antibiotics is accelerating the spread of resistance risk in the environment. In drinking water supply systems, the effect of antibiotics on the resistance of biofilm is unclear, and there have been few studies in disinfectant-containing systems. Here, we designed a series of drinking water supply reactors to investigate the effects of antibiotics on biofilm and bacteria in the water. At low concentrations, antibiotics could promote the growth of bacteria in biofilm; among the tested antibiotics (tetracycline, sulfadiazine and chloramphenicol), tetracycline had the strongest ability to promote this. And the antibiotic resistant bacteria (ARB) could inhibit the growth of bacteria in drinking water. Results have shown that antibiotics enhanced the bacterial chlorine resistance in the effluent, but reduced that in the biofilm. Furthermore, metagenomic analysis showed that antibiotics reduced the richness of biofilm communities. The dominant phyla in the biofilm were Proteobacteria, Planctomycetes, and Firmicutes. In tetracycline-treated biofilm, the dominant phylum was Planctomycetes. In sulfadiazine- and chloramphenicol-treated groups, bacteria with complex cell structures preferentially accumulated. The dominant class in biofilm in the ARB-added group was Gammaproteobacteria. The abundance of antibiotic resistant genes (ARGs) was correlated with biofilm community structure. This study shows that antibiotics make the biofilm community structure of drinking water more resistant to chlorine. ARGs may be selective for certain bacteria in the process, and there may ultimately be enhanced chlorine and antibiotic resistance of effluent bacteria in drinking water.

Ecological impact of antibiotics on bioremediation performance of constructed wetlands: Microbial and plant dynamics, and potential antibiotic resistance genes hotspots

Constructed wetlands (CWs) are nature-based solutions for treating domestic and livestock wastewater which may contain residual antibiotics concentration. Antibiotics may exert selection pressure on wetland's microbes, thereby increasing the global antibiotics resistance problems. This review critically examined the chemodynamics of antibiotics and antibiotics resistance genes (ARGs) in CWs. Antibiotics affected the biogeochemical cycling function of microbial communities in CWs and directly disrupted the removal efficiency of total nitrogen, total phosphorus, and chemical oxygen demand by 22%, 9.3%, and 24%, respectively. Since changes in microbial function and structure are linked to the emergence and propagation of antibiotic resistance, antibiotics could adversely affect microbial diversity in CWs. The cyanobacteria community seemed to be particularly vulnerable, while Proteobacteria could resist and persist in antibiotics contaminated wetlands. Antibiotics triggered excitation responses in plants and increased the root activities and exudates. Microbes, plants, and substrates play crucial roles in antibiotic removal. High removal efficiency was exhibited for triclosan (100%) > enrofloxacin (99.8%) > metronidazole (99%) > tetracycline (98.8%) > chlortetracycline (98.4%) > levofloxacin (96.69%) > sulfamethoxazole (91.9%) by the CWs. This review showed that CWs exhibited high antibiotics removal capacity, but the absolute abundance of ARGs increased, suggesting CWs are potential hotspots for ARGs. Future research should focus on specific bacterial response and impact on microbial interactions.

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.