Antibiotic-Resistance Genes in Waste Water

Highly sensitive detection of the tetracycline resistance gene tetA in water supply systems with an autocatalytic deoxyribonucleic acid-based cascade circuit

Antibiotic resistance genes (ARGs)-contamination in water systems is a global concern, accelerating antimicrobial resistance and threatening public health, which demands an effective, low-cost and stable method for their on-site detection. Herein, we developed an innovative approach by combining the hybridization chain reaction (HCR) with deoxyribozymes to design an isothermal enzyme-free cascade initiator regenerating (IR) HCR-based amplification system. Minute quantities of targets can trigger exponentially amplified fluorescence signals through the self-catalytic feedback loop of the HCR mechanism. Tetracycline resistance genes (tetA) were specifically and sensitively detected with a remarkably low detection limit as low of 4.6 pM by introducing auxiliary hairpins. Furthermore, the adaptable nature of auxiliary hairpins enabled easy customization for detecting other ARGs by simply altering the recognition site, resulting in a high degree of specificity and versatility. The IR-HCR-based amplifier was used to analyze real water samples, and it was found that the detection results showed a good correlation with the detection results of ddPCR (R2=0.997), demonstrating its practical utility. The designed sensor operated in the absence of the polymerase chain reaction and accurately quantified the targets. It was sensitive and dependable for the on-site detection of ARGs within the environment and is expected to be broadly applied in environmental monitoring and detection. SYNOPSIS: This study developed an isothermal, enzyme-free cascade DNA circuit for the specific and sensitive detection of tetracycline resistance genes in aquatic environments. It provides valuable guidance for the on-site detection of antibiotic resistance genes without PCR technology.

Investigating the impact of fecal contamination on antibiotic resistance genes in urban environments using host-associated molecular indicators

Antibiotic resistome of gut microbiota can be transmitted into the urban ecosystems via fecal pollution, potentially leading to a public health crisis. It is essential to determine the primary sources of fecal contamination and accurately evaluate the health risks for the propagation of antibiotic resistance genes (ARGs) from the intestinal microbiota. In this research, the occurrence, sources and potential hosts of ARGs in urban environmental samples collected from a wastewater treatment plant (WWTP), natural water bodies, tap water and farmland soil were comprehensively investigated. Host-associated fecal indicators for general warm-blooded animals (BacGeneral), humans (crAssphage), and other animals (bovines and swine) were employed for reliable microbial source tracking (MST). Results showed that the fecal indicator BacGeneral was detected in 84.00 % of collected environmental samples, indicating the widespread fecal contamination in local water and farmland. The WWTP was the reservoir and main source of fecal contamination in local environment, harboring the highest total abundances of ARGs (3.85 ± 2.72 ARGs/16S rRNA) and mobile genetic elements (MGEs) (0.32 ± 0.12 MGEs/16S rRNA) from multiple animals and humans. Although the swine-associated indicator was undetected, fecal contamination from both bovines and humans was prevalent in collected samples, with detection rates of pollution indicators at 52.00 % for bovine and 28.00 % for human sources. The co-occurrence of ARGs, fecal indicators and MGEs was analyzed, and significant correlation (P < 0.01) between total ARG abundance and fecal indicator (BacGeneral) in contaminated environments demonstrated that fecal pollution exhibited a great influence on overall resistome in local environment. This research offers a comprehensive understanding of the sources and dissemination of ARGs in feces-polluted urban environments, providing data for the monitoring and prevention of ARG pollution.

Manure input propagated antibiotic resistance genes and virulence factors in soils by regulating microbial carbon metabolism

Antibiotic resistance genes (ARGs) and virulence factors (VFs) in soils represent a significant threat to ecological security and human health. The carbon-rich soil formed by manure fertilization provides an energy source for soil microbes. However, we still know little about how microbial-dominated carbon metabolism affects ARGs and VFs proliferation in soils subjected to long-term fertilization and irrigation practices in wheat-maize system. Here, we investigated soil microbial carbon metabolism, ARGs and VFs distribution, and microbial composition in soils under 9-year of different fertilization and irrigation managements during wheat growing period. Results showed that manure (M) increased total abundance of soil ARGs by 5.9 %-8.0 % and 2.1 %-4.8 % and VFs by 5.4 %-7.5 % and 2.0 %-4.9 % compared to no fertilizer (CK) and NPK fertilizer (C), respectively, regardless of irrigation. M enriched more number of ARGs and VFs types, and increased abundance of host microbes involved in carbon fixation and carbon degradation, such as Streptomyces, Lysobacter and Agromyces. M increased abundance of carbohydrate-active enzymes (CAZymes) and carbon cycle functional pathways, as well as microbial carbon metabolism capacity. Partial least squares path modeling and correlation analysis showed that microbial diversity, CAZymes, carbon cycle functional pathways (particularly carbon fixation and degradation) and microbial carbon metabolism capacity of microbial community had direct positive effects on the proliferation and spread of ARGs and VFs. In conclusion, our results highlight the importance of microbial mediated carbon metabolism in driving the dissemination of ARGs and VFs in soils under long-term manure application.

Fish are poor sentinels for surveillance of riverine antimicrobial resistance

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

ROS-induced stress promotes enrichment and emergence of antibiotic resistance in conventional activated sludge processes

Since the Great Oxidation Event 2.4 billion years ago, microorganisms have evolved sophisticated responses to oxidative stress. These ancient adaptations remain relevant in modern engineered systems, particularly in conventional activated sludge (CAS) processes, which serve as significant reservoirs of antibiotic resistance genes (ARGs). While ROS-induced stress responses are known to promote ARG enrichment/emergence in pure cultures, their impact on ARG dynamics in wastewater treatment processes remains unexplored. Shotgun-metagenomics analysis of two hospital wastewater treatment plants showed that only 35-53 % of hospital effluent resistome was retained in final effluent. Despite this reduction, approximately 29-36 % of ARGs in CAS showed higher abundance than upstream stages, of which 20-22 % emerged de novo. Beta-lactamases and efflux pumps constituted nearly 47-53 % of these enriched ARGs. These ARGs exhibited significant correlations (p < 0.05) with ROS stress response genes (oxyR, soxR, sodAB, katG and ahpCF). The CAS resistome determined 58-75 % of the effluent ARG profiles, indicating treatment processes outweigh influent composition in shaping final resistome. Proof-of-concept batch reactor experiments confirmed increased ROS and ARG levels under high dissolved oxygen (8 mg/L) compared to low oxygen (2 mg/L) concentrations. Untargeted metaproteomics revealed higher expression of resistant proteins (e.g., OXA-184, OXA-576, PME-1, RpoB2, Tet(W/32/O)) under elevated ROS levels. Our findings demonstrate that CAS processes actively shape effluent resistome through ROS-mediated selection, indicating that treatment processes, rather than initial wastewater composition, determine final ARG profiles. This study indicates that the emergence of ARGs needs to be considered as an integral aspect of wastewater treatment design and operation to prevent antibiotic resistance dissemination.

Elimination of antibiotic resistance genes and adaptive response of Firmicutes during chicken manure composting

Aerobic composting is an effective method for reducing the abundance of antibiotic resistance genes (ARGs), but its effectiveness is influenced by the complex conditions during the process. However, the impact of composting conditions on the fate of ARGs and the underlying mechanisms remains unclear. This study examined the profile of ARGs, their mobility potential, hosts, and the risk of antibiotic resistome under different chicken manure composting conditions. A total of 708 ARGs were identified, and composting reduced their relative abundance by 29.4 %-82.4 %. Composting amendments and aeration rates exhibited similar elimination efficiencies for ARGs at different levels. However, low initial moisture content (50 %) caused a rebound in ARG abundance during the maturation phase. ARGs were mainly located on plasmids. After composting, the percentage of plasmid-born ARGs decreased from 46.3 %-70.8 % to 28.4 %-49.0 %. ARGs co-localized with mobile genetic elements displayed similar trends. The tolerance of Firmicutes to low moisture content played a key role in the rebound of ARGs and variations in their mobility potential. Composting reduced antibiotic resistance and ARG mobility in pathogens. Conversely, low moisture content hindered this attenuation effect in Firmicutes, which increased antibiotic resistome risk. This study provides comprehensive insights into the fate of ARGs and highlights the environmental risks of ARGs during composting.

Drug resistant Klebsiella pneumoniae from patients and hospital effluent: a correlation?

BACKGROUND

The application of wastewater-based epidemiology has gained traction as a cost effective tool in antimicrobial resistance (AMR) surveillance with studies showing a correlation between the presence of resistant bacteria from hospital sewage and patients. This study compared Klebsiella pneumoniae from patients and hospital effluent in terms of antibiotic resistance patterns, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and phylogenomic relationships.

RESULTS

Pooled effluent samples were collected from the final effluent point of a regional hospital and K. pneumoniae isolates were identified on selective media. Clinical isolates were also collected from the same hospital. Antimicrobial susceptibility testing (AST) was performed using the VITEK® 2 system. DNA was extracted prior to whole genome sequencing (WGS). The resistome, mobilome, and phylogenetic lineages of sequenced isolates were assessed using bioinformatics analysis. A total of 10 randomly selected presumptive and 10 clinical K. pneumoniae constituted the sample and were subjected to AST. Total resistance was observed in the clinical samples to cefuroxime, cefotaxime, piperacillin/tazobactam, gentamicin, tobramycin and trimethoprim/sulfamethoxazole. The effluent isolates exhibited total susceptibility to most antibiotics but showed resistance to amoxicillin/clavulanic acid and piperacillin/tazobactam (100%), and tigecycline (10%). The effluent isolates did not exhibit a diverse resistome, while the clinical isolates harboured genes conferring resistance to aminoglycoside (aph(6)-Id, aph(3'')-Ib, aac(6')-Ib-cr, aadA16), ß-lactam (blaSVH group, blaOXA group, blaTEM group), and fluoroquinolone (oqxA, oqxB) antibiotics. Only class 1 integrons were identified. Phylogenetic analysis revealed that effluent isolates from this study were not closely related to the clinical isolates.

CONCLUSION

This study showed no correlation between the resistance profiles of the clinical and effluent isolates. The relationship between AMR in hospital effluent and clinical resistance may depend on the antimicrobial agents and bacterial species studied.

Wastewater surveillance of antibiotic-resistant bacteria for public health action: potential and challenges

Antibiotic resistance is an urgent public health threat. Actions to reduce this threat include requiring prescriptions for antibiotic use, antibiotic stewardship programs, educational programs targeting patients and healthcare providers, and limiting antibiotic use in agriculture, aquaculture, and animal husbandry. Wastewater surveillance might complement clinical surveillance by tracking time/space variation essential for detecting outbreaks and evaluating efficacy of evidence-based interventions, identifying high-risk populations for targeted monitoring, providing early warning of the emergence and spread of antibiotic-resistant bacteria (ARBs), and identifying novel antibiotic-resistant threats. Wastewater surveillance was an effective early warning system for SARS-CoV-2 spread and detection of the emergence of new viral strains. In this data-driven commentary, we explore whether monitoring wastewater for antibiotic-resistant genes (ARGs) and/or bacteria resistant to antibiotics might provide useful information for public health action. Using carbapenem resistance as an example, we highlight technical challenges associated with using wastewater to quantify temporal/spatial trends in ARBs and ARGs and compare with clinical information. While ARGs and ARBs are detectable in wastewater enabling early detection of novel ARGs, quantitation of ARBs and ARGs with current methods is too variable to reliably track space/time variation.

Presence of high-risk ARGs with greater diversity and abundance in the rare resistome in wastewater across China

Antibiotic resistance genes (ARGs) are widely recognized as hazardous materials that pose risks to public health. The core resistome, with its low ARG diversity yet accounting for the majority of the total ARG abundance, dominating the profile of antibiotic resistance. In this study, nationwide wastewater surveillance in China using metagenomic sequencing also identified a core resistome of 117 ARGs that accounted for 69.6 % of the total abundance. The emphasis of the work was to examine the rare resistome that included 1503 ARGs outside the core resistome. The abundances of clinically relevant ARG types (e.g., β-lactams and quinolones) were significantly higher in the rare resistome compared to the core resistome. Human pathogen-related ARGs were much greater in subtype number (96 vs. 34) and significantly higher in abundance (67.0 % vs. 33.0 %) in the rare relative to the core resistome, indicating that the rare resistome was the major contributor to the human pathogen resistome. The majority of ARG types accounting for the highest proportions of the rare resistome were plasmid-originated (65.5 %-100 %). In addition, human pathogen-related ARGs also had a significantly higher proportion of plasmid sources than non-pathogen ARGs, further highlighting their importance in wastewater-based surveillance.

pH-gated activation of nematodes-secreted NUC-1 accelerates extracellular antibiotic resistance gene degradation in aquatic environments

The global dissemination of extracellular antibiotic resistance genes (eARGs) in environmental matrices necessitates urgent development of mitigation approaches. Although nematodes exhibit potential as biological agents for eARG degradation, significant research gaps exist in understanding their performance under diverse environmental conditions and strategies for enhancing degradation efficiency through systematic parameter optimization. Here, we systematically evaluated the degradation of plasmid-borne tetM by Caenorhabditis elegans across eight high nematodes-prevalent habitats, revealing a remarkable 38-fold variation in efficacy. Solution pH was identified as the pivotal regulatory parameter through controlled experiments. Acidification to pH 6 enhanced nematodes-mediated eARG degradation by 25-fold, effectively reducing the transformation efficiency below the detectable limit within 15 min. Through multidisciplinary analyses incorporating gene mutation analysis, mRNA quantification, capillary electrophoresis, and zymographic analysis, we demonstrate that environmental pH specifically modulates NUC-1 activity rather than expression. Structural modeling and pKa calculation reveal this pH-dependent regulation operates through protonation state change in the NUC-1 catalytic center, achieving maximal enzymatic activity at pH 6. Remarkably, this pH-gated regulatory mechanism is conserved across five nematode species spanning two distinct families, highlighting its broad biological significance and biotechnological potential. Our study establishes the first comprehensive environmental assessment framework for nematodes-mediated eARG degradation and elucidates a pH-gated regulation mechanism at the molecular level, providing a novel foundation for developing biotechnologies to control AR dissemination with spatiotemporal accuracy.

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.

Antibiotic resistance profiles and mutations that might affect drug susceptibility in metagenome-assembled genomes of Legionella pneumophila and Aeromonas species from municipal wastewater

Antibiotic resistance (AR) has emerged as a significant global health issue. Wastewater treatment plants (WWTPs) contain diverse bacterial communities, including pathogens, and have been identified as crucial reservoirs for the emergence and dissemination of AR. The present study aimed to identify antibiotic resistance genes (ARGs) and screen for the presence of mutations associated with AR in Legionella pneumophila and Aeromonas spp. from municipal wastewater. Metagenome-assembled genomes (MAGs) of L. pneumophila and Aeromonas spp. were reconstructed to investigate the molecular mechanisms of AR in these organisms. A total of 138 nonsynonymous single nucleotide variants (SNVs) in seven genes associated with AR and one deletion mutation in the lpeB gene were identified in L. pneumophila. In Aeromonas spp., two (aph(6)-Id and aph(3'')-Ib) and five (blaMOX-4, blaOXA-1143, blaOXA-724, cepH, and imiH) ARGs conferring resistance to aminoglycosides and β-lactams were identified, respectively. Moreover, this study presents β-lactam resistance genes, blaOXA-1143 and blaOXA-724, for the first time in Aeromonas spp. from a municipal WWTP. In conclusion, these findings shed light on the molecular mechanisms through which clinically relevant pathogenic bacteria such as L. pneumophila and Aeromonas spp. found in natural environments like municipal wastewater acquire AR.

The Antimicrobial Resistance-Water-Corporate Interface: Exploring the Connections Between Antimicrobials, Water, and Pollution

Antibiotic resistance is a public health emergency, with ten million deaths estimated annually by the year 2050. Water systems are an important medium for the development and dissemination of antibiotic resistance from a variety of sources, explored in this perspective review. Hospital wastewater and wastewater systems more broadly are breeding grounds for antibiotic resistance because of the nature of their waste and how it is processed. Corporations from various sectors contribute to antibiotic resistance in many direct and indirect ways. Pharmaceutical factory runoff, agricultural antibiotic use, agricultural use of nitrogen fertilizers, heavy metal pollution, air pollution (atmospheric deposition, burning of oil and/or fossil fuels), plastic/microplastic pollution, and oil/petroleum spills/pollution have all been demonstrated to contribute to antibiotic resistance. Mitigation strategies to reduce these pathways to antibiotic resistance are discussed and future directions hypothesized.

Emerging Trends in Antimicrobial Resistance in Polar Aquatic Ecosystems

The global spread of antimicrobial resistance (AMR) threatens to plummet society back to the pre-antibiotic era through a resurgence of common everyday infections' morbidity. Thus, studies investigating antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in urban, agricultural, and clinical settings, as well as in extreme environments, have become increasingly relevant in the One Health perspective. Since the Antarctic and Arctic regions are considered amongst the few remaining pristine environments on Earth, the characterization of their native resistome appears to be of the utmost importance to understand whether and how it is evolving as a result of anthropogenic activities and climate change. In the present review, we report on the phenotypic (e.g., disk diffusion test) and genotypic (e.g., PCR, metagenomics) approaches used to study AMR in the aquatic environment of polar regions, as water represents one of AMR main dissemination routes in nature. Their advantages and limits are described, and the emerging trends resulting from the analysis of ARB and ARGs diffusion in polar waters discussed. The resistome detected in these extreme environments appears to be mostly comparable to those from more anthropized areas, with the predominance of tetracycline, β-lactam, and sulfonamide resistance (and related ARGs). Indeed, AMR is, in all cases, more consistently highlighted in sites impacted by human and wildlife activities with respect to more pristine ones. Surprisingly, aminoglycoside and fluroquinolone determinants seem to have an even higher incidence in the Antarctic and Arctic aquatic environment compared to that from other areas of the world, corroborating the need for a more thorough AMR surveillance in these regions.

Geographical distribution and risk of antibiotic resistance genes in sludge anaerobic digestion process across China

Anaerobic digestion (AD) is gaining increasing attention as the central reservoir of antibiotic resistance genes (ARGs), while the geographical distribution of ARGs in AD is neglected. Accordingly, a sampling scheme on full-scale AD plants across China was implemented, and the resistome therein was excavated. The abundance of ARGs in AD sludge ranged from 0.198 to 0.574 copies/cell. Some of the frequently reported and emergent ARGs were detected in our AD system. Both the abundance and composition of ARGs presented significant differences between the south and north regions of China, hinting the physical/economic factors may function in the formation of ARG profiles. The risk scores of AD samples were in middle of domestic and hospital wastewater. Risk scores were significantly higher in the north. Besides, the proportion of Rank I and Rank II ARGs was also higher in north, which explained the regional difference of ARG composition in a micro-perspective. This study provides a fundamental survey on the of ARG level and profile in AD process across China, reveals the biogeography of ARGs and inspires the control strategies of antibiotic resistance.

Effect of subinhibitory concentrations on the spreading of the ampicillin resistance gene blaCMY-2 in an activated sludge microcosm

As the problem of multi-resistant bacteria grows a better understanding of the spread of antibiotic resistance genes is of utmost importance for society. Wastewater treatment plants contain subinhibitory concentrations of antibiotics and are thought to be hotspots for antibiotic resistance gene propagation. Here we evaluate the influence of sub-minimum inhibitory concentrations of antibiotics on the spread of resistance genes within the bacterial community in activated sludge laboratory-scale sequencing batch reactors. The mixed communities were fed two different ampicillin concentrations (500 and 5000 µg/L) and the reactors were run and monitored for 30 days. During the experiment the β-lactamase resistance gene blaCMY-2 was monitored via qPCR and DNA samples were taken to monitor the effect of ampicillin on the microbial community. The relative copy number of blaCMY-2 in the reactor fed with the sub-minimum inhibitory concentration of 500 µg/L ampicillin was spread out over a wider range of values than the control and 5000 µg/L ampicillin reactors indicating more variability of gene number in the 500 µg/L reactor. This result emphasises the problem of sub-minimum inhibitory concentrations of antibiotics in wastewater. High-throughput sequencing showed that continuous exposure to ampicillin caused a shift from a Bacteroidetes to Proteobacteria in the bacterial community. The combined use of qPCR and high-throughput sequencing showed that ampicillin stimulates the spread of resistance genes and leads to the propagation of microbial populations which are resistant to it.

Distribution patterns and ecological risks of antibiotic resistance genes in the Yap Trench

Antibiotic resistance genes (ARGs) are a global environmental concern, yet their vertical distribution in pristine marine ecosystems remains poorly understood. This study investigated the distribution of ARG distribution in both the water column and sediments of the Yap Trench, which reaches depths over 6500 m Results revealed significant variations in ARG diversity and abundance across depths and habitats. The deep-water (DW) zones exhibited the highest diversity (291-472 subtypes) and abundance (1.79 copies/cell), followed by upper-water (UW) zones (240-314 subtypes, 0.31 copies/cell), while sediments had the lowest diversity (72-236 subtypes) and abundance (0.03 copies/cell). The most prevalent resistance genes included those conferring resistance to multidrug, polymyxin, and beta-lactam in the Yap Trench. ARG distribution closely correlated with microbial hosts, including Pseudomonadota, Chloroflexota, Bacteroidota, and Planctomycetota. Risk assessment showed high-risk ARGs were most abundant in DW zones, with pathogenic groups capable of spreading multiple ARGs (e.g., macAB, mexDJKW, mdtE, muxC). This study provides a systematic understanding of the distribution patterns and potential risks of ARGs in the water column and sediments of pristine marine ecosystems, underscoring the penetration of antibiotic pollution into the deep ocean and offering new insights for marine pollution control strategies.

A Review on the Prevalence and Treatment of Antibiotic Resistance Genes in Hospital Wastewater

Antibiotic resistance is a global environmental and health threat. Approximately 4.95 million deaths were associated with antibiotic resistance in 2019, including 1.27 million deaths that were directly attributable to bacterial antimicrobial resistance. Hospital wastewater is one of the key sources for the spread of clinically relevant antibiotic resistance genes (ARGs) into the environment. Understanding the current situation of ARGs in hospital wastewater is of great significance. Here, we review the prevalence of ARGs and antibiotic-resistant bacteria (ARB) in hospital wastewater and wastewater from other places and the treatment methods used. We further discuss the intersection between ARGs and COVID-19 during the pandemic. This review highlights the issues associated with the dissemination of critical ARGs from hospital wastewater into the environment. It is imperative to implement more effective processes for hospital wastewater treatment to eliminate ARGs, particularly during the current long COVID-19 period.

Metagenomic Insights in Antimicrobial Resistance Threats in Sludge from Aerobic and Anaerobic Membrane Bioreactors

Sludge is a biohazardous solid waste that is produced during wastewater treatment. It contains antibiotic resistance genes (ARGs) that pose significant antimicrobial resistance (AMR) threats. Herein, aerobic and anaerobic membrane bioreactors (AeMBRs and AnMBRs, respectively) were compared in terms of the volume of waste sludge generated by them, the presence of ARGs in the sludge, and the potential for horizontal gene transfer (HGT) events using metagenomics to determine which treatment process can better address AMR concerns associated with the generation of waste sludge. The estimated abundance of ARGs in the suspended sludge generated by the AnMBR per treated volume is, on average, 5-55 times lower than that of sludge generated by the AeMBR. Additionally, the ratio of potential HGT in the two independent runs was lower in the anaerobic sludge (0.6 and 0.9) compared with that in the aerobic sludge (2.4 and 1.6). The AnMBR sludge exhibited reduced HGT of ARGs involving potential opportunistic pathogens (0.09) compared with the AeMBR sludge (0.27). Conversely, the AeMBR sludge displayed higher diversity and more transfer events, encompassing genes that confer resistance to quinolones, rifamycin, multidrug, aminoglycosides, and tetracycline. A significant portion of these ARGs were transferred to Burkholderia sp. By contrast, the AnMBR showed a lower abundance of mobile genetic elements associated with conjugation and exhibited less favorable conditions for natural transformation. Our findings suggest that the risk of potential HGT to opportunistic pathogens is greater in the AeMBR sludge than in AnMBR sludge.

Determination of Antibiotic Resistance Genes in the Interior Bay of Puno-Peru, Lake Titicaca

Water can serve as a source of genetic resistance and act as an amplifier and/or reservoir for genes acquired by human pathogens, which can be released into the environment as pollutants. The interior bay of Puno, part of Lake Titicaca, is a popular tourist attraction, being an active component of the dynamics of the city of Puno. Therefore, the determination of the presence of antibiotic resistance genes (ARGs) in water samples from the interior bay of Puno of six collection points was the main objective of this research work. DNA extraction was conducted, followed by the identification and quantification of 16S rRNA and Escherichia coli uidA gene, two ARGs (bla TEM and qacEΔ1), and class 1 integron-integrase gene (intI1) by means of quantitative PCR. The intI1 and qacEΔ1 genes were detected throughout the interior bay of Puno; however, the abundance of the bla TEM gene was comparatively lower. The uidA gene was reported only in some sampled points with < LOQ. These findings should raise concerns regarding the potential risk of their dissemination in Lake Titicaca and their impact on public health.

Biofilms as potential reservoirs of antimicrobial resistance in vulnerable settings

Antimicrobial resistance is a major global health threat, characterized by the ability of microorganisms to withstand the effects of antimicrobial agents. Biofilms, as unique microbial communities, significantly contribute to this threat. They provide a protective environment for pathogens, facilitate horizontal gene transfer, and create an ideal setting for the persistence and evolution of resistant bacteria. This issue can be particularly important in low-income settings and vulnerable communities, such as formal and informal refugee and migrant camps. These settings usually have limited access to healthcare resources and appropriate treatments, contributing to the selective pressure that promotes the survival and proliferation of resistant bacteria. Thus, biofilms formed in wastewater in these areas can play a critical role in spreading antimicrobial resistance or acting as hidden reservoirs for future outbreaks. While emerging efforts focus on detecting antibiotic resistance genes and planktonic bacteria in wastewater, biofilms may be a source of under-appreciated antimicrobial resistance, creating a significant gap in our understanding of resistance dynamics in wastewater systems. Incorporating biofilm surveillance into wastewater monitoring strategies in vulnerable settings can help develop a more comprehensive understanding of resistance transmission and more effective intervention measures in these settings.

Genetic diversity of dissolved free extracellular DNA compared to intracellular DNA in wastewater treatment plants

Dissolved free extracellular DNA (free-exDNA) coexists with intracellular DNA (inDNA) in aquatic environments. Free-exDNA can be taken up by bacteria through transformation, and wastewater treatment plants (WWTPs) are positioned as potential hot spots for genetic contamination. However, studies comparing the composition of free-exDNA and inDNA is limited. This study employed colloidal adsorption and foam concentration method to recover free-exDNA from different WWTP stages and compared its diversity with inDNA via metagenomic analysis. Free-exDNA concentrations were observed to increase after chlorination. Genetic analysis revealed a higher abundance of specific genes following chlorination, suggesting that free-exDNA in effluent originated from bacterial death in secondary treated water. This result indicates that free-exDNA, which increases due to chlorination, is subsequently released into the catchment. Additionally, several high-risk antibiotic-resistance genes (ARGs) were detected that colocalized with mobile genetic elements. These ARGs were expected to have a high potential for gene transfer via transformation, and the risk was highlighted. Overall, these findings deepen our understanding of horizontal gene transfer risks in WWTPs.

Distribution and risk assessment of antibiotic resistance genes in swine farm wastewater and its surrounding environments: from soil to water

Livestock farms are important reservoirs of antibiotic resistance genes (ARGs). However, how wastewater irrigation from swine farms affects the surrounding environments, especially water bodies, is not fully understood. In this study, the occurrence pattern and potential risk of ARGs and mobile gene elements (MGEs) in a biogas slurry from a large-scale swine farm and its surrounding environments were investigated. Genes conferring resistance to tetracycline, sulfonamide, and multidrugs were found to be predominant in the biogas slurry, while sulfonamide and multidrug resistance genes exhibited the highest abundance in the surrounding environments. Overall, the total relative abundance of ARGs in the biogas slurry was 1.4-7 fold higher than that in the surrounding environments. PCA revealed the cluster pattern of samples based on sample types and a better correlation between swine farm wastewater and groundwater. A higher abundance of ARGs was found in groundwater farther away from the swine farm than that in nearby groundwater and surface water. Correlation analysis indicated that ARGs had a significant positive correlation with MGEs at each sampling site. The most abundant MGE IS6100 may mediate the horizontal transfer of lnuA from the swine farm to nearby groundwater. Considering the abundance, mobility, host pathogenicity, and the co-occurrence patterns with MGEs of ARGs, nine high-risk ARGs, namely, aadA2, aadA17, aac (6')-Ib, tetX, tetG, tetM, oprJ, sul1, and ermF, were screened in the environment. Our results indicated that the swine farm wastewater had long-term effects on the surrounding surface water and groundwater and that MGEs can serve as a medium that contributes to the widespread distribution of various ARGs. This study provides a theoretical basis for the risk assessment of ARGs in farms and the reuse of farm wastewater.

Controllable Supply-Demand Effect during Superior Fe Single-Atom Catalyst Synthesis for Targeted Guanine Oxidation of Antibiotic Resistance Genes

Nonradical Fenton-like catalysis offers an opportunity to degrade extracellular antibiotic resistance genes (eARGs). However, high-loading single-atom catalysts (SACs) with controllable configurations are urgently required to selectively generate high-yield nonradicals. Herein, we constructed high-loading Fe SACs (5.4-34.2 wt %) with uniform Fe-N4 sites via an optimized coordination balance of supermolecular assembly for peroxymonosulfate activation. The selectivity of singlet oxygen (1O2) generation and its contribution to eARGs degradation were both >98%. This targeting strategy of oxidizing guanines with low ionization potentials by 1O2 allowed 7 log eARGs degradation within 10 min and eliminated their transformation within 2 min, outperforming most reported advanced oxidation processes. Relevant interactions between 1O2 and guanines were revealed at a single-molecule resolution. The high-loading Fe SACs exhibited excellent universality and stability for different eARGs and water matrices. These findings provide a promising route for constructing high-loading SACs for efficient and selective Fenton-like water treatment.

Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes

The dissemination of mobile antibiotic resistance genes (ARGs) via horizontal gene transfer is a significant threat to public health globally. The flow of ARGs into and between pathogens, however, remains poorly understood, limiting our ability to develop strategies for managing the antibiotic resistance crisis. Therefore, we aim to identify genetic and ecological factors that are fundamental for successful horizontal ARG transfer. We used a phylogenetic method to identify instances of horizontal ARG transfer in ~1 million bacterial genomes. This data was then integrated with >20,000 metagenomes representing animal, human, soil, water, and wastewater microbiomes to develop random forest models that can reliably predict horizontal ARG transfer between bacteria. Our results suggest that genetic incompatibility, measured as nucleotide composition dissimilarity, negatively influences the likelihood of transfer of ARGs between evolutionarily divergent bacteria. Conversely, environmental co-occurrence increases the likelihood, especially in humans and wastewater, in which several environment-specific dissemination patterns are observed. This study provides data-driven ways to predict the spread of ARGs and provides insights into the mechanisms governing this evolutionary process.

Novel anionic functionalized magnetic β-cyclodextrin composites with excellent adsorption capacity for moxifloxacin and wide pH adaptive adsorption capability for copper ion

Antibiotics and heavy metals pose severe risks to human health and ecological environment. Therefore, developing a multifunctional adsorbent to remove these contaminants from wastewater is an urgent need. Herein, novel anionic sulfonic acid groups functionalized magnetic β-cyclodextrin (β-CD) composites (FCD@AA) were synthesized by coating poly(2-acrylamido-2-methyl-1-propane sulfonic acid (AMPS)) on the surface of magnetic β-CD particles (FCD). Several characterization techniques were utilized to comprehensively analyze the surface physicochemical properties of FCD@AA. The adsorption properties of FCD@AA toward antibiotics (moxifloxacin (MOX) as model) and heavy metals (copper ion (Cu2+) as model) were systematically studied under different conditions on adsorption time, temperature, initial concentration, solution pH and coexisting ionic strength. In single systems, the adsorption isotherm data for MOX and Cu2+ were well fitted to Langmuir and Freundlich models, respectively. The maximum adsorption capacities of FCD@AA toward MOX and Cu2+ were 118.98 and 19.29 mg g-1, respectively. The pseudo-second-order model could better describe the kinetic processes. In binary systems, the presence of Cu2+ exhibited a pronounced antagonism on the adsorption of MOX. The influence of co-existing MOX on the capture of Cu2+ changed from inhibition to promotion as the initial Cu2+ concentration increased. And after five adsorption cycles, FCD@AA still had satisfactory reusability. The results indicate that FCD@AA is a promising adsorbent for treating water contaminated by MOX and Cu2+, which broadens the application of magnetic β-CD adsorbents in environmental protection.

Per- and polyfluoroalkyl substances exacerbate the prevalence of plasmid-borne antibiotic resistance genes by enhancing natural transformation, in vivo stability, and expression in bacteria

Per- and polyfluoroalkyl substances (PFAS) as emerging pollutants are ubiquitous and disrupt biological processes across water boundaries. Their coexistence with antibiotic resistance genes (ARGs) in water matrix is associated with the spread of ARGs via conjugative transfer, posing a threat to public health. However, their role in natural transformation-where microorganisms actively take up extracellular ARGs (eARGs)-and the subsequent persistence and expression of ARGs after transformation remains poorly understood. Here, we demonstrated that environmentally relevant concentrations (0.1-10 µg/L) of perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), two typical PFAS, increased transformation frequencies by 2.54- and 3.26-fold, respectively. This increase was driven by increased cell envelope permeability, biofilm formation, reactive oxygen species (ROS) production, and upregulation of DNA uptake genes. At higher concentrations (100 µg/L), PFAS inhibited transformation. Nevertheless, PFOA and PFOS at all tested concentrations promoted long-term plasmid in vivo stability, reducing plasmid loss rates from 68.5% to 6% and 38.7%, respectively. Furthermore, they induced ARGs expression in transformants by up to 1.33- and 1.37-fold. Our findings revealed that PFOA and PFOS impacted the spread, persistence, and expression of ARGs, from extracellular uptake to intracellular activity in bacteria. These results highlight the underestimated environmental health risks posed by PFAS and underscore the intricate chemical and biological co-contamination in aquatic ecosystems and wastewater treatment.

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.

The Invisible Threat of Antibiotic Resistance in Food

The continued and improper use of antibiotics has resulted in the emergence of antibiotic resistance (AR). The dissemination of antibiotic-resistant microorganisms occurs via a multitude of pathways, including the food supply. The failure to comply with the regulatory withdrawal period associated with the treatment of domestic animals or the illicit use of antibiotics as growth promoters has contributed to the proliferation of antibiotic-resistant bacteria in meat and dairy products. It was demonstrated that not only do animal and human pathogens act as donors of antibiotic resistance genes, but also that lactic acid bacteria can serve as reservoirs of genes encoding for antibiotic resistance. Consequently, the consumption of fermented foods also presents a potential conduit for the dissemination of AR. This review provides an overview of the potential for the transmission of antibiotic resistance in a range of traditional and novel foods. The literature data reveal that foodborne microbes can be a significant factor in the dissemination of antibiotic resistance.

Antibiotic Resistance Dissemination and Mapping in the Environment Through Surveillance of Wastewater

Antibiotic resistance is one of the major health threat for humans, animals, and the environment, according to the World Health Organization (WHO) and the Global Antibiotic-Resistance Surveillance System (GLASS). In the last several years, wastewater/sewage has been identified as potential hotspots for the dissemination of antibiotic resistance and transfer of resistance genes. However, systematic approaches for mapping the antibiotic resistance situation in sewage are limited and underdeveloped. The present review has highlighted all possible perspectives by which the dynamics of ARBs/ARGs in the environment may be tracked, quantified and assessed spatio-temporally through surveillance of wastewater. Moreover, application of advanced methods like wastewater metagenomics for determining the community distribution of resistance at large has appeared to be promising. In addition, monitoring wastewater for antibiotic pollution at various levels, may serve as an early warning system and enable policymakers to take timely measures and build infrastructure to mitigate health crises. Thus, by understanding the alarming presence of antibiotic resistance in wastewater, effective action plans may be developed to address this global health challenge and its associated environmental risks.

Detection of Antibiotic-Resistance Genes in Drinking Water: A Study at a University in the Peruvian Amazon

This study investigated the presence of antibiotic-resistance genes in drinking water consumed by the university community in the Peruvian Amazon. Water samples were collected from three primary sources: inflow from the distribution network, a storage cistern, and an underground intake. Conventional PCR was employed to detect genes associated with resistance to erythromycin (ermC), ampicillin (amp), ciprofloxacin (QEP), multidrug resistance (marA), and specific multidrug resistance in E. coli (qEmarA). Physicochemical analysis revealed compliance with most regulatory standards; however, groundwater samples showed lead concentrations exceeding legal limits (0.72 mg/L) and lacked residual chlorine. All sampling points tested positive for the evaluated resistance genes, demonstrating the widespread dissemination of resistance factors in drinking water. Contrary to initial expectations, resistance genes were also prevalent in treated sources. These findings reveal a critical public health risk for the university community, emphasising the need for effective disinfection systems and robust monitoring protocols to ensure water safety. The presence of these resistance genes in water is a critical public health concern as it can facilitate the spread of resistant bacteria, reducing the effectiveness of medical treatments and increasing the risk of infections that are difficult to control.

From soil to surface water: exploring Klebsiella 's clonal lineages and antibiotic resistance odyssey in environmental health

In the last decade, the presence of resistant bacteria and resistance genes in the environment has been a cause for increasing concern. However, understanding of its contribution to the spread of bacteria remains limited, as the scarcity of studies on how and under what circumstances the environment facilitates the development of resistance poses challenges in mitigating the emergence and spread of mobile resistance factors. Antimicrobial resistance in the environment is considered one of the biggest challenges and threats currently emerging. Thus, monitoring the presence of antibiotic-resistant species, in this particular case, Klebsiella spp., in the environment can be an added value for understanding the epidemiology of infections caused by Klebsiella spp.. Investigating soils and waters as potential reservoirs and transmission vehicles for these bacteria is imperative. Therefore, in this review, we aimed to describe the main genetic lineages present in environmental samples, as well as to describe the multidrug resistance strains associated with each environmental source. The studies analyzed in this review reported a high diversity of species and strains of Klebsiella spp. in the environment. K. pneumoniae was the most prevalent species, both in soil and water samples, and, as expected, often presented a multi-resistant profile. The presence of K. pneumoniae ST11, ST15, and ST147 suggests human and animal origin. Concerning surface waters, there was a great diversity of species and STs of Klebsiella spp. These studies are crucial for assessing the environmental contribution to the spread of pathogenic bacteria.

Metagenomic profiling of antibiotic resistance genes and their associations with the bacterial community along the Kanda River, an urban river in Japan

Antibiotic resistance genes (ARGs) present in urban rivers have the potential to disseminate antibiotic-resistant bacteria into other environments, posing significant threats to both ecological and public health. Although metagenomic analyses have been widely employed to detect ARGs in rivers, our understanding of their dynamics across different seasons in diverse watersheds remains limited. In this study, we performed a comprehensive genomic analysis of the Kanda River in Japan at 11 sites from upstream to estuary throughout the year to assess the spread of ARGs and their associations with bacterial communities. Analysis of 110 water samples using the 16S rRNA gene revealed variations in bacterial composition corresponding to seasonal changes in environmental parameters along the river. Shotgun metagenomics-based profiling of ARGs in 44 water samples indicated higher ARG abundance downstream, particularly during the summer. Weighted gene co-expression network analysis (WGCNA) linking bacterial lineages and ARGs revealed that 12 ARG subtypes co-occurred with 128 amplicon sequence variants (ASVs). WGCNA suggested potential hosts for ErmB, ErmF, ErmG, tetQ, tet (W/N/W), aadA2, and adeF, including gut-associated bacteria (e.g., Prevotella, Bacteroides, Arcobacter) and indigenous aquatic microbes (e.g., Limnohabitans and C39). In addition, Pseudarcobacter (a later synonym of Arcobater) was identified as a host for adeF, which was also confirmed by single cell genomics. This study shows that ARG distribution in urban rivers is affected by seasonal and geographical factors and demonstrates the importance of monitoring rivers using multiple types of genome sequencing, including 16S rRNA gene sequencing, metagenomics, and single cell genomics.

The photo-based treatment technology simultaneously removes resistant bacteria and resistant genes from wastewater

Because of the recent widespread usage of antibiotics, the acquisition and dissemination of antibiotic-resistance genes (ARGs) were prevalent in the majority of habitats. Generally, the biological wastewater treatment processes used in wastewater treatment plants have a limited efficiencies of antibiotics resistant bacteria (ARB) disinfection and ARGs degradation and even promote the proliferation of ARGs. Problematically, ARB and ARGs in effluent pose potential risks if they are not further treated. Photocatalytic oxidation is considered a promising disinfection technology, where the photocatalytic process generates many free radicals that enhance the interaction between light and deoxyribonucleic acid (DNA) for ARB elimination and subsequent degradation of ARGs. This review aims to illustrate the progress of photocatalytic oxidation technology for removing antibiotics resistant (AR) from wastewater in recent years. We discuss the sources and transfer of ARGs in wastewater. The overall removal efficiencies of ultraviolet radiation (UV)/chlorination, UV/ozone, UV/H2O2, and UV/sulfate-radical based system for ARB and ARGs, as well as the experimental parameters and removal mechanisms, are systematically discussed. The contribution of photocatalytic materials based on TiO2 and g-C3N4 to the inactivation of ARB and degradation of ARGs is highlighted, producing many free radicals to attack ARB and ARGs while effectively limiting the horizontal gene transfer (HGT) in wastewater. Finally, based on the reviewed studies, future research directions are proposed to realize specific photocatalytic oxidation technology applications and overcome current challenges.

Microplastics Exacerbated Conjugative Transfer of Antibiotic Resistance Genes during Ultraviolet Disinfection: Highlighting Difference between Conventional and Biodegradable Ones

Microplastics (MPs) have been confirmed as a hotspot for antibiotic resistance genes (ARGs) in wastewater. However, the impact of MPs on the transfer of ARGs in wastewater treatment remains unclear. This study investigated the roles and mechanisms of conventional (polystyrene, PS) and biodegradable (polylactic acid, PLA) MPs in the conjugative transfer of ARGs during ultraviolet disinfection. The results showed that MPs significantly facilitated the conjugative transfer of ARGs compared with individual ultraviolet disinfection, and PSMPs exhibited higher facilitation than PLAMPs. The facilitation effects were attributed to light shielding and the production of reactive oxygen species (ROS) and nanoplastics from ultraviolet irradiation of MPs. The light shielding of MPs protected the bacteria and ARGs from ultraviolet inactivation. More importantly, ROS and nanoplastics generated from irradiated MPs induced intracellular oxidative stress on bacteria and further increased the cell membrane permeability and intercellular contact, ultimately enhancing the ARG exchange. The greater fragmentation of PSMPs than PLAMPs resulted in a higher intracellular oxidative stress and a stronger enhancement. This study highlights the concerns of conventional and biodegradable MPs associated with the transfer of ARGs during wastewater treatment, which provides new insights into the combined risks of MPs and ARGs in the environment.

Plasmid and integron-associated antibiotic resistance in Escherichia coli isolated from domestic wastewater treatment plants

The rapid dissemination of antibiotic resistance genes (ARGs) represents a significant global threat, with wastewater treatment plants (WWTPs) playing an important role as reservoirs and propagation hubs. In this study, we performed whole-genome sequencing and bioinformatic analyses on eight multidrug-resistant Escherichia coli isolates previously obtained from domestic WWTPs in Costa Rica. We identified 61 ARGs (23 unique), with 40 located on plasmids, and 21 on chromosomal sequences, seven of which were within integrons. Several ARGs were associated with resistance to clinically and veterinary important antibiotics, including sulfamethoxazole/trimethoprim, beta-lactams, and tetracyclines. One hundred twenty-one virulence-associated genes (29 unique) were detected, with 16 located on plasmids. Notably, the presence of virulence factors such as ompT and hlyF genes alongside ARGs on plasmids underscores the transmissible pathogenic potential of WWTP-associated E. coli strains. These findings highlight the role of small domestic WWTPs in disseminating pathogenic and multidrug-resistant bacteria and their mobile genetic elements, emphasizing the need for further research to understand how these discharges impact aquatic environments.

Treatment of antibiotic-manufacturing wastewater enriches for Aeromonas veronii, a zoonotic antibiotic-resistant emerging pathogen

Antibiotic-manufacturing wastewater treatment plants primarily target chemical pollutants, but their processes may select for antibiotic-resistant pathogens and antibiotic resistance genes. Leveraging the combined strengths of deep metagenomic sequencing, 16S rRNA gene sequencing, quantitative polymerase chain reaction, and bacterial culturing, we investigated bacterial communities and antibiotic resistomes across eleven treatment units in a full-scale antibiotic-manufacturing wastewater treatment plant processing wastewater from a β-lactam manufacturing facility. Both bacterial communities and antibiotic resistance gene compositions varied across the treatment units, but were associated. Certain antibiotic resistance gene persisted through treatment, either carried by identical bacterial species, or linked to mobile genetic elements in different species. Despite the satisfactory performance in chemical removal, this plant continuously enriched zoonotic antibiotic-resistant Aeromonas veronii (an emerging pathogen responsible for substantial economic losses in aquaculture and human health) from influent to effluent, probably due to prolonged β-lactam selection pressure and aquatic nature of A. veronii. This enrichment resulted in a significantly higher abundance of A. veronii than other aquatic samples worldwide. Furthermore, the closest evolutionary relative to the retrieved A. veronii was an isolate obtained from the stool of a local diarrhea patient. These findings highlighted a substantial public health risk posed by antibiotic-manufacturing wastewater treatment, underlining its potential role in enriching and disseminating zoonotic antibiotic-resistant pathogens. Beyond chemical monitoring, enhanced surveillance of antibiotic-resistant pathogens and antibiotic resistance genes is needed in effluent discharge standard for antibiotic-manufacturing wastewater treatment plants.

Wastewater microbiology: occurrence and prevalence of antibiotic-resistant extended-spectrum β-lactamase-producing Enterobacteriaceae in the district wastewater system

Extended spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, including Klebsiella pneumoniae and Escherichia coli, pose a serious risk to human health because of antibiotic resistance. Wastewater serves as a reservoir for these bacteria, contributing to the evolution and transmission of antibiotic-resistant strains. The research aims to identify ESBL bacterium in wastewater samples from District Kohat. K. pneumoniae and E. coli were confirmed as ESBL-producing bacteria through a comprehensive array of diagnostic procedures, including Gram staining, biochemical analyses, and antibiotic susceptibility testing. Fecal coliform count (FCC) analyses revealed varying microorganism levels. Both E. coli and K. pneumoniae isolates showed ESBL enzyme expression, indicating antibiotic resistance. Resistance patterns included ciprofloxacin, ampicillin, cefotaxime, cefoxitin, and amoxicillin-clavulanic acid for both species. E. coli displayed higher sensitivity for chloramphenicol, trimethoprim- sulfamethoxazole, and gentamicin. Ceftazidime minimum inhibitory concentration results showed E. coli's higher resistance. The study accentuates the presence of antibiotic-resistant strains, emphasizing the value of effective wastewater treatment. The study provides crucial insights into microbial characteristics, fecal contamination, ESBL production, and antibiotic resistance in E. coli and K. pneumoniae isolates, advocating for monitoring and mitigation strategies.

Escherichia coli: An arduous voyage from commensal to Antibiotic-resistance

Escherichia coli (E. coli), a normal intestinal microbiota is one of the most common pathogen known for infecting urinary tract, wound, lungs, bone marrow, blood system and brain. Irrational and overuse of commercially available antibiotics is the most imperative reason behind the emergence of the life threatening infections caused due to antibiotic resistant pathogens. The World Health Organization (WHO) identified antimicrobial resistance (AMR) as one of the 10 biggest public health threats of our time. This harmless commensal can acquire a range of mobile genetic elements harbouring genes coding for virulence factors becoming highly versatile human pathogens causing severe intestinal and extra intestinal diseases. Although, E. coli has been the most widely studied micro-organism, it never ceases to astound us with its ability to open up new research avenues and reveal cutting-edge survival mechanisms in diverse environments that impact human and surrounding environment. This review aims to summarize and highlight persistent research gaps in the field, including: (i) the transfer of resistant genes among bacterial species in diverse environments, such as those associated with humans and animals; (ii) the development of resistance mechanisms against various classes of antibiotics, including quinolones, tetracyclines, etc., in addition to β-lactams; and (iii) the relationship between resistance and virulence factors for understanding how virulence factors and resistance interact to gain a better grasp of how resistance mechanisms impact an organism's capacity to spread illness and interact with the host's defences. Moreover, this review aims to offer a thorough overview, exploring the history and factors contributing to antimicrobial resistance (AMR), the different reported pathotypes, and their links to virulence in both humans and animals. It will also examine their prevalence in various contexts, including food, environmental, and clinical settings. The objective is to deliver a more informative and current analysis, highlighting the evolution from microbiota (historical context) to sophisticated diseases caused by highly successful pathogens. Developing more potent tactics to counteract antibiotic resistance in E. coli requires filling in these gaps. By bridging these gaps, we can strengthen our capacity to manage and prevent resistance, which will eventually enhance public health and patient outcomes.

High Concentrations of Tilmicosin Promote the Spread of Multidrug Resistance Gene tolC in the Pig Gut Microbiome Through Mobile Genetic Elements

The impact of antibiotic therapy on the spread of antibiotic resistance genes (ARGs) and its relationship to gut microbiota remains unclear. This study investigated changes in ARGs, mobile genetic elements (MGEs), and gut microbial composition following tilmicosin administration in pigs. Thirty pigs were randomly divided into control (CK), low-concentration (0.2 g/kg; L), and high-concentration (0.4 g/kg; H) groups. Tilmicosin concentration in manure peaked on day 16 of dosing and dropped below detectable levels by day 13 of the withdrawal period. While tilmicosin did not significantly affect the total abundance of macrolide resistance genes (MRGs) (p > 0.05), it significantly increased the abundance of the multidrug resistance gene tolC in the H group compared with the L and CK groups during the withdrawal period (p < 0.05). This increase was associated with a coincidental rise in the abundance of MGEs (e.g., int1 and int2) and the growth of potential tolC-hosting bacteria such as Paenalcaligenes and Proteiniclasticum. Redundancy analysis showed gut microbial composition as the primary driver of MRG abundance, with MGEs, tilmicosin concentration, and manure physicochemical properties playing secondary roles. These findings suggest that high-dose tilmicosin may alter the gut microbiota and promote ARG spread via MGE-mediated transfer.

Portable microfluidic devices for monitoring antibiotic resistance genes in wastewater

Antibiotic resistance genes (ARGs) pose serious threats to environmental and public health, and monitoring ARGs in wastewater is a growing need because wastewater is an important source. Microfluidic devices can integrate basic functional units involved in sample assays on a small chip, through the precise control and manipulation of micro/nanofluids in micro/nanoscale spaces, demonstrating the great potential of ARGs detection in wastewater. Here, we (1) summarize the state of the art in microfluidics for recognizing ARGs, (2) determine the strengths and weaknesses of portable microfluidic chips, and (3) assess the potential of portable microfluidic chips to detect ARGs in wastewater. Isothermal nucleic acid amplification and CRISPR/Cas are two commonly used identification elements for the microfluidic detection of ARGs. The former has better sensitivity due to amplification, but false positives due to inappropriate primer design and contamination; the latter has better specificity. The combination of the two can achieve complementarity to a certain extent. Compared with traditional microfluidic chips, low-cost and biocompatible paper-based microfluidics is a very attractive test for ARGs, whose fluid flow in paper does not require external force, but it is weaker in terms of repeatability and high-throughput detection. Due to that only a handful of portable microfluidics detect ARGs in wastewater, fabricating high-throughput microfluidic chips, developing and optimizing recognition techniques for the highly selective and sensitive identification and quantification of a wide range of ARGs in complex wastewater matrices are needed.

Antibiotic resistance genes are transferred from manure-contaminated water bodies to the gut microbiota of animals through the food chain

Fecal-contaminated water may enter the food chain and become an important route for the transmission of antibiotic resistance genes (ARGs) to the human microbiome. However, little is known about the spread of ARGs from fecal contamination in water bodies along the aquatic food chain. In this study, laboratory-raised Daphnia magna and Aristichthys nobilis were used to investigate the effects of the addition of manure on target ARGs in water and their intestinal contents to determine the potential transmission route of ARGs in the aquatic food chain system. The abundance of target ARGs in water as well as D. magna and A. nobilis intestinal contents significantly increased when fecal contamination was present. ARGs bioaccumulated along the food chain, with four ARGs (tetM-01, tetX, qnrS, and sul2) detected regularly. Mn and Cr were key environmental factors that promoted the transfer of ARGs along the food chain. Fecal addition significantly changed the structure of microbial communities in water, D. magna gut, and A. nobilis gut. The ARG spectrum was significantly correlated with the composition and structure of the bacterial community. Proteobacteria, Bacteroidetes, and Firmicutes were identified as the main host bacteria and were likely to act as carriers of ARGs to promote the spread of antibiotic resistance in the food chain. The composition and structure of bacterial communities, along with mobile genetic elements, were two key drivers of ARG transfer. These findings provide new insights into the distribution and spread of ARGs along the freshwater food chain.

Decoding the whole-genome sequence of multidrug-resistant Escherichia coli strain Hakim RU_BHWS isolated from wastewater in Bangladesh

This report presents the draft genome sequence of the multidrug-resistant Escherichia coli strain Hakim RU_BHWS isolated from wastewater. The genome assembly is 4.6 Mb, with 32.16× coverage and a GC content of 50.7%. It includes five CRISPR arrays, 16 prophages, 56 antibiotic resistance genes, and 35 virulence factor genes.

Prevalence and genetic characterization of linezolid resistance gene reservoirs in hospital sewage from Zhejiang Province, China

Hospital sewage represented important hotspots for the aggregation and dissemination of clinically relevant pathogens and antimicrobial resistance genes. To investigate the prevalence and molecular epidemiology of linezolid resistance genes in hospital sewage, both influent and effluent samples from 11 hospitals in Zhejiang Province, China, were collected and analyzed for linezolid resistance gene carriers. Thirty colonies of putative isolates that grew on the selective media with 10 mg/L florfenicol were randomly picked per sample. A total of 420 Gram-positive isolates, including 330 from 11 influent samples and 90 from three effluent samples, were obtained. Each isolate carried at least one of the linezolid resistance genes, including optrA, poxtA, cfr, and cfr(D), and the optrA gene was highly dominant (388/420). Enterococci displayed predominance among the linezolid resistance gene carriers in the hospital sewage, exhibiting a resistance rate to linezolid of 77.8 %. The wild-type OptrA and OptrA variants KLDP, RDK, and KLDK, all associated with high linezolid MICs, were most frequently detected. Phylogenetic analysis revealed the multispecies and polyclonal distribution of linezolid-resistant bacteria in hospital sewage, while Enterococcus faecalis sequence types (STs) 16 and 179 demonstrated the widest dissemination across different hospitals. Despite generally high genetic diversity, phylogenetic analysis showed that 87 isolates, assigned to ten STs from both sewage and other sources, were genetically related. Moreover, the genetic environment of linezolid resistance genes in isolates from sewage was similar to that from animals, humans, or the environment, with "Tn554-fexA-optrA" as the most common structure. These findings revealed the potential risk of the transmission of linezolid resistance genes through hospital sewage to other environments.

Antibiotic Resistance as a Functional Characteristic of Urban Dust Particles' Microbial Communities

Urban dust samples were collected in Moscow (Russia) in June 2021. The samples were collected in three functional zones of Moscow (traffic, residential, and recreational) and included air microparticles, leaf dust, and paved dust. Data on the taxonomic composition of bacterial communities were obtained for dust samples, and their functional characteristics were predicted using PICRUSt2 2.5.0 and FAPROTAX 1.8.0 software. The culturable part of the bacterial community was examined for the presence of antibiotic-resistant strains with respect to β-lactams, tetracyclines, amphenicols, and aminoglycosides. The presence of bacteria resistant to ceftazidime, cefepime, and tetracycline was detected in all dust samples. The presence of bacteria resistant to meropenem and amikacin was only observed in the dust collected from leaves in the residential and traffic zones. The overall abundance of cultured antibiotic-resistant bacteria from the total heterotrophs ranged from 0.03% to 1.88%, with the highest percentage observed in dust from the residential zone. Notably, strains resistant to all antibiotics tested were observed in the leaf dust bacterial community.

Antimicrobial resistance profile of Escherichia coli in drinking water from one health perspective in low and middle income countries

Introduction

Antimicrobial resistance is a major global public health concern, especially in low-resource settings. In low- and middle-income countries, the existing evidence about antimicrobial resistance in drinking water is inconsistence and not comprehensive. Therefore, this study aimed to estimate the pooled prevalence of antimicrobial resistance profiles of Escherichia coli from drinking water in low- and middle-income countries.

Methods

This study was conducted using comprehensive literature searches using various databases such as PubMed, Scientific Direct, HINARI, and Google Scholar. Data extraction was performed using Microsoft Excel and exported to STATA 14/SE software for analysis. We used the Joanna Briggs Institute's quality appraisal tool to ensure the quality of the included studies. A random effects model was employed to estimate the pooled prevalence. Publication bias was evaluated using funnel plots and Egger's regression test. Subgroup and sensitivity analysis were also conducted in this study.

Results

The study found that the pooled prevalence of Escherichia coli isolates in drinking water was 37.94% (95% CI: 26.73-49.13). The prevalence of multidrug resistance was 43.65% (95% CI: 31.15-56.15). Regarding specific antimicrobials, the pooled resistance levels of Escherichia coli were 54.65% (95% CI: 41.35-67.96) against contrimoxazole, followed by 48.64% (95% CI: -3.6-101) against amoxicillin and 48% (95% CI: -18.1-114.2) against cefuroxime.

Conclusion

The findings indicated a significant prevalence of antimicrobial resistance of Escherichia coli isolated from drinking water and its multidrug resistance. To address this issue, it recommends focusing on improving basic hygiene and sanitation practices and enhancing water and wastewater treatment systems.

Systematic review registration

Identifier CRD42024533592.

Transfer dynamics of antimicrobial resistance among gram-negative bacteria

Antimicrobial resistance (AMR) in gram-negative bacteria (GNBs) is a significant global health concern, exacerbated by mobile genetic elements (MGEs). This review examines the transfer of antibiotic resistance genes (ARGs) within and between different species of GNB facilitated by MGEs, focusing on the roles of plasmids and phages. The impact of non-antibiotic chemicals, environmental factors affecting ARG transfer frequency, and underlying molecular mechanisms of bacterial resistance evolution are also discussed. Additionally, the study critically assesses the impact of fitness costs and compensatory evolution driven by MGEs in host organisms, shedding light on the transfer frequency of ARGs and host evolution within ecosystems. Overall, this comprehensive review highlights the factors and mechanisms influencing ARG movement among diverse GNB species and underscores the importance of implementing holistic One-Health strategies to effectively address the escalating public health challenges associated with AMR.

Characterization of methicillin resistant Staphylococcus Aureus in municipal wastewater in Finland

Wastewater-based surveillance (WBS) of multidrug-resistant bacteria could complement clinical data, serving as a population-level early warning tool. This study evaluated WBS as a pandemic preparedness tool, by selectively isolating and culturing methicillin-resistant Staphylococcus aureus (MRSA) with CHROMagar MRSA. Some 24-h composite wastewater samples (n = 80) were collected from ten treatment plants across Finland between February 2021 and January 2022. MRSA prevalence in wastewater samples was 27.5% (n = 22/80), showing seasonal and temporal variations. Phenotypic antimicrobial susceptibility testing (AST) with microdilution showed that over 80% of isolates were drug-resistant to clindamycin, sulfamethoxazole/trimethoprim, tetracycline, fusidic acid, and erythromycin. Four isolates (18.2%) were vancomycin-resistant. WGS revealed that 31.8% (n = 7) of the isolates belonged to the ST8-t008 and ST6-t304 spa types, respectively. In addition, two spa types (t011 and t034) belong to the CC398 complex. The mecA gene was found in all isolates (n = 22) and three tetracycline resistance determinants (tet38, tetK, and tetM) were detected with tet38 being the most abundant (81.8%, n = 18/22). Three isolates harboured the plasmid-mediated sat4 gene that confers resistance to Streptothricin. In addition, resistance determinants to macrolide antibiotics (mph (C)/msr (A) and fosfomycin (fosB) were detected in the seven isolates that belonged to spa type t008. All isolates except one harboured the SCCmec_type_IVa(2B). Six ST8 isolates harboured the LukS/F-PV genes encoding the Panton-Valentine leukocidin (PVL) and were also positive for the Arginine Catabolic Mobile Element (ACME), suggesting they belong to the USA300 clone. The Inc18 plasmid was the most abundant as it was detected in 72.7% (n = 16/22) of the isolates. Other plasmid replicons detected were the rep_trans and repA_N which were detected in 45.4% (n = 10/22) and 40.9% (n = 9/22) of the isolates respectively. Ten isolates harboured at least three plasmid replicons and no plasmid replicons were detected in four isolates (ST6/t304). The cgMLST revealed that some isolates aggregated into two genomically indistinguishable clusters: ST6/t304 belonging to cluster type CT12405 (≤20 allelic differences) and ST8/t008 belonging to cluster type CT1925 (<8 allelic differences). Overall, we found a high genotypic concordance with the national clinical bacterial resistance data. Our study demonstrates the sensitivity of culture-based wastewater surveillance for MRSA using clinical media following pre-enrichment, reliably predicting pathogen occurrence at the population level.

Bacterial membrane vesicles from swine farm microbial communities harboring and safeguarding diverse functional genes promoting horizontal gene transfer

Antibiotic resistance (AMR) poses a significant global health challenge, with swine farms recognized as major reservoirs of antibiotic resistance genes (ARGs). Recently, bacterial membrane vesicles (BMVs) have emerged as novel carriers mediating horizontal gene transfer. However, little is known about the ARGs carried by BMVs in swine farm environments and their transfer potential. This study investigated the distribution, sources, and microbiological origins of BMVs in three key microbial habitats of swine farms (feces, soil, and fecal wastewater), along with the ARGs and mobile genetic elements (MGEs) they harbor. Characterization of BMVs revealed particle sizes ranging from 20 to 500 nm and concentrations from 108 to 1012 particles/g, containing DNA and proteins. Metagenomic sequencing identified BMVs predominantly composed of members of the Proteobacteria phyla, including Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae, carrying diverse functional genes encompassing resistance to 14 common antibiotics and 74,340 virulence genes. Notably, multidrug resistance, tetracycline, and chloramphenicol resistance genes were particularly abundant. Furthermore, BMVs harbored various MGEs, primarily plasmids, and demonstrated the ability to protect their DNA cargo from degradation and facilitate horizontal gene transfer, including the transmission of resistance genes. In conclusion, this study reveals widespread presence of BMVs carrying ARGs and potential virulence genes in swine farm feces, soil, and fecal wastewater. These findings not only provide new insights into the role of extracellular DNA in the environment but also highlight concerns regarding the gene transfer potential mediated by BMVs and associated health risks.