Contribution of bacteriophage and plasmid DNA to the mobilization of antibiotic resistance genes in a river receiving treated wastewater discharges

Occurrence of emerging contaminants in three river basins impacted by wastewater treatment plant effluents: Spatio-seasonal patterns and environmental risk assessment

The concern on the fate and distribution of contaminants of emerging concern (CECs) is a burning topic due to their widespread occurrence and potential harmful effects. Particularly, antibiotics have received great attention due to their implications in antimicrobial resistance occurrence. The impact of wastewater treatment plants (WWTP) is remarkable, being one of the main pathways for the introduction of CECs into aquatic systems. The combination of novel analytical methodologies and risk assessment strategies is a promising tool to find out environmentally relevant compounds posing major concerns in freshwater ecosystems impacted by those wastewater effluents. Within this context, a multi-target approach was applied in three Spanish river basins affected by different WWTP treated effluents for spatio-temporal monitoring of their chemical status. Solid phase extraction followed by ultra-high-performance liquid chromatography were used for the quantification of a large panel of compounds (n = 270), including pharmaceuticals and other consumer products, pesticides and industrial chemicals. To this end, water samples were collected in four sampling campaigns at three locations in each basin: (i) upstream from the WWTPs; (ii) WWTP effluent discharge points (effluent outfall); and (iii) downstream from the WWTPs (500 m downriver from the effluent outfall). Likewise, 24-h composite effluent samples from each of the WWTPs were provided in all sampling periods. First the occurrence and distribution of these compounds were assessed. Diverse seasonal trends were observed depending on the group of emerging compounds, though COVID-19 outbreak affected variations of certain pharmaceuticals. Detection frequencies and concentrations in effluents generally exceeded those in river samples and concentrations measured upstream WWTPs were generally low or non-quantifiable. Finally, risks associated with maximum contamination levels were evaluated using two different approaches to account for antibiotic resistance selection as well. From all studied compounds, 89 evidenced environmental risk on at least one occasion in this study.

The potential contribution of aquatic wildlife to antibiotic resistance dissemination in freshwater ecosystems: A review

Antibiotic resistance (AR) is one of the major health threats of our time. The presence of antibiotics in the environment and their continuous release from sewage treatment plants, chemical manufacturing plants and animal husbandry, agriculture and aquaculture, result in constant selection pressure on microbial organisms. This presence leads to the emergence, mobilization, horizontal gene transfer and a selection of antibiotic resistance genes, resistant bacteria and mobile genetic elements. Under these circumstances, aquatic wildlife is impacted in all compartments, including freshwater organisms with partially impermeable microbiota. In this narrative review, recent advancements in terms of occurrence of antibiotics and antibiotic resistance genes in sewage treatment plant effluents source compared to freshwater have been examined, occurrence of antibiotic resistance in wildlife, as well as experiments on antibiotic exposure. Based on this current state of knowledge, we propose the hypothesis that freshwater aquatic wildlife may play a crucial role in the dissemination of antibiotic resistance within the environment. Specifically, we suggest that organisms with high bacterial density tissues, which are partially isolated from the external environment, such as fishes and amphibians, could potentially be reservoirs and amplifiers of antibiotic resistance in the environment, potentially favoring the increase of the abundance of antibiotic resistance genes and resistant bacteria. Potential avenues for further research (trophic transfer, innovative exposure experiment) and action (biodiversity eco-engineering) are finally proposed.

The role of rhizosphere phages in soil health

While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.

Quantification of β-lactamase producing bacteria in German surface waters with subsequent MALDI-TOF MS-based identification and β-lactamase activity assay

Environmental oligotrophic bacteria are suspected to be highly relevant carriers of antimicrobial resistance (AMR). However, there is a lack of validated methods for monitoring in the aquatic environment. Since extended-spectrum β-lactamases (ESBLs) play a particularly important role in the clinical sector, a culturing method based on R2A-medium spiked with different combinations of β-lactams was applied to quantify β-lactamase-producing environmental bacteria from surface waters. In German surface water samples (n = 28), oligotrophic bacteria ranging from 4.0 × 103 to 1.7 × 104 CFU per 100 mL were detected on the nutrient-poor medium spiked with 3rd generation cephalosporins and carbapenems. These numbers were 3 log10 higher compared to ESBL-producing Enterobacteriales of clinical relevance from the same water samples. A MALDI-TOF MS identification of the isolates demonstrated, that the method leads to the isolation of environmentally relevant strains with Pseudomonas, Flavobacterium, and Janthinobacterium being predominant β-lactam resistant genera. Subsequent micro-dilution antibiotic susceptibility tests (Micronaut-S test) confirmed the expression of β-lactamases. The qPCR analysis of surface waters DNA extracts showed the presence of β-lactamase genes (blaTEM, blaCMY-2, blaOXA-48, blaVIM-2, blaSHV, and blaNDM-1) at concentrations of 3.7 (±1.2) to 1.0 (±1.9) log10 gene copies per 100 mL. Overall, the results demonstrate a widespread distribution of cephalosporinase and carbapenemase enzymes in oligotrophic environmental bacteria that have to be considered as a reservoir of ARGs and contribute to the spread of antibiotic resistance.

Research Progress of Ozone/Peroxymonosulfate Advanced Oxidation Technology for Degrading Antibiotics in Drinking Water and Wastewater Effluent: A Review

Nowadays, antibiotics are widely used, increasing the risk of contamination of the water body and further threatening human health. The traditional water treatment process is less efficient in degrading antibiotics, and the advanced oxidation process (AOPs) is cleaner and more efficient than the traditional biochemical degradation process. The combined ozone/peroxymonosulfate (PMS) advanced oxidation process (O3/PMS) based on sulfate radical (SO4•-) and hydroxyl radical (•OH) has developed rapidly in recent years. The O3/PMS process has become one of the most effective ways to treat antibiotic wastewater. The reaction mechanism of O3/PMS was reviewed in this paper, and the research and application progress of the O3/PMS process in the degradation of antibiotics in drinking water and wastewater effluent were evaluated. The operation characteristics and current application range of the process were summarized, which has a certain reference value for further research on O3/PMS process.

Bacteriophages: Vectors of or weapons against the transmission of antibiotic resistance genes in hospital wastewater systems?

Antimicrobial resistance poses a serious threat to human health and is responsible for the death of millions of people annually. Hospital wastewater is an important hotspot for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). However, little is known about the relationship between phages and ARGs in hospital wastewater systems (HWS). In the present study, the viral diversity of 12 HWSs using data from public metagenomic databases was investigated. Viruses were widely found in both the influent and effluent of each HWS. A total of 45 unique ARGs were carried by 85 viral contigs, which accounted for only 0.14% of the total viral populations, implying that ARGs were not commonly present in phages. Three efflux pump genes were identified as shared between phages and bacterial genomes. However, the predominant types of ARGs in HWS such as aminoglycoside- and beta-lactam-resistance genes were rarely found in phages. Based on CRISPR spacer and tRNA matches, interactions between 171 viral contigs and 60 antibiotic-resistant genomes were predicted, including interactions involving phages and vancomycin-resistant Enterococcus_B faecium or beta-lactam-resistant Klebsiella pneumoniae. More than half (56.1%) of these viral contigs indicated lytic and none of them carried ARGs. As the vOTUs in this study had few ARGs and were primarily lytic, HWS may be a valuable source for phage discovery. Future studies will be able to experimentally validate these sequence-based results to confirm the suitability of HWS phages for pathogen control measures in wastewater.

Distribution of Antibiotic Resistance in a Mixed-Use Watershed and the Impact of Wastewater Treatment Plants on Antibiotic Resistance in Surface Water

The aquatic environment has been recognized as a source of antibiotic resistance (AR) that factors into the One Health approach to combat AR. To provide much needed data on AR in the environment, a comprehensive survey of antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs), and antibiotic residues was conducted in a mixed-use watershed and wastewater treatment plants (WWTPs) within the watershed to evaluate these contaminants in surface water. A culture-based approach was used to determine prevalence and diversity of ARB in surface water. Low levels of AR Salmonella (9.6%) and Escherichia coli (6.5%) were detected, while all Enterococcus were resistant to at least one tested antibiotic. Fewer than 20% of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (17.3%) and carbapenem-resistant Enterobacteriaceae (CRE) (7.7%) were recovered. Six ARGs were detected using qPCR, primarily the erythromycin-resistance gene, ermB. Of the 26 antibiotics measured, almost all water samples (98.7%) had detectable levels of antibiotics. Analysis of wastewater samples from three WWTPs showed that WWTPs did not completely remove AR contaminants. ARGs and antibiotics were detected in all the WWTP effluent discharges, indicating that WWTPs are the source of AR contaminants in receiving water. However, no significant difference in ARGs and antibiotics between the upstream and downstream water suggests that there are other sources of AR contamination. The widespread occurrence and abundance of medically important antibiotics, bacteria resistant to antibiotics used for human and veterinary purposes, and the genes associated with resistance to these antibiotics, may potentially pose risks to the local populations exposed to these water sources.

Functional annotation of rhizospheric phageome of the wild plant species Moringa oleifera

Introduction

The study aims to describe phageome of soil rhizosphere of M.oleifera in terms of the genes encoding CAZymes and other KEGG enzymes.

Methods

Genes of the rhizospheric virome of the wild plant species Moringa oleifera were investigated for their ability to encode useful CAZymes and other KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes and to resist antibiotic resistance genes (ARGs) in the soil.

Results

Abundance of these genes was higher in the rhizospheric microbiome than in the bulk soil. Detected viral families include the plant viral family Potyviridae as well as the tailed bacteriophages of class Caudoviricetes that are mainly associated with bacterial genera Pseudomonas, Streptomyces and Mycobacterium. Viral CAZymes in this soil mainly belong to glycoside hydrolase (GH) families GH43 and GH23. Some of these CAZymes participate in a KEGG pathway with actions included debranching and degradation of hemicellulose. Other actions include biosynthesizing biopolymer of the bacterial cell wall and the layered cell wall structure of peptidoglycan. Other CAZymes promote plant physiological activities such as cell-cell recognition, embryogenesis and programmed cell death (PCD). Enzymes of other pathways help reduce the level of soil H₂O₂ and participate in the biosynthesis of glycine, malate, isoprenoids, as well as isoprene that protects plant from heat stress. Other enzymes act in promoting both the permeability of bacterial peroxisome membrane and carbon fixation in plants. Some enzymes participate in a balanced supply of dNTPs, successful DNA replication and mismatch repair during bacterial cell division. They also catalyze the release of signal peptides from bacterial membrane prolipoproteins. Phages with the most highly abundant antibiotic resistance genes (ARGs) transduce species of bacterial genera Pseudomonas, Streptomyces, and Mycobacterium. Abundant mechanisms of antibiotic resistance in the rhizosphere include "antibiotic efflux pump" for ARGs soxR, OleC, and MuxB, "antibiotic target alteration" for parY mutant, and "antibiotic inactivation" for arr-1.

Discussion

These ARGs can act synergistically to inhibit several antibiotics including tetracycline, penam, cephalosporin, rifamycins, aminocoumarin, and oleandomycin. The study highlighted the issue of horizontal transfer of ARGs to clinical isolates and human gut microbiome.

Spatio-seasonal patterns of the impact of wastewater treatment plant effluents on antibiotic resistance in river sediments

There is a growing concern about the risk of antibiotic resistance emergence and dissemination in the environment. Here, we evaluated the spatio-seasonal patterns of the impact of wastewater treatment plant (WWTP) effluents on antibiotic resistance in river sediments. To this purpose, sediment samples were collected in three river basins affected by WWTP effluents in wet (high-water period) and dry (low-water period) hydrological conditions at three locations: (i) upstream the WWTPs; (ii) WWTP effluent discharge points (effluent outfall); and (iii) downstream the WWTPs (500 m downriver from the effluent outfall). The absolute and relative abundances of 9 antibiotic resistance genes (ARGs), 3 mobile genetic element (MGE) genes, and 4 metal resistance genes (MRGs) were quantified in sediment samples, as well as a variety of physicochemical parameters, metal contents, and antibiotic concentrations in both sediment and water samples. In sediments, significantly higher relative abundances of most genes were observed in downstream vs. upstream sampling points. Seasonal changes (higher values in low-water vs. high-water period) were observed for both ARG absolute and relative abundances in sediment samples. Chemical data revealed the contribution of effluents from WWTPs as a source of antibiotic and metal contamination in river ecosystems. The observed positive correlations between ARG and MGE genes relative abundances point out to the role of horizontal gene transfer in antibiotic resistance dissemination. Monitoring plans that take into consideration spatio-temporal patterns must be implemented to properly assess the environmental fate of WWTP-related emerging contaminants in river ecosystems.

Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms

Most bacteria attach to biotic or abiotic surfaces and are embedded in a complex matrix which is known as biofilm. Biofilm formation is especially worrisome in clinical settings as it hinders the treatment of infections with antibiotics due to the facilitated acquisition of antibiotic resistance genes (ARGs). Environmental settings are now considered as pivotal for driving biofilm formation, biofilm-mediated antibiotic resistance development and dissemination. Several studies have demonstrated that environmental biofilms can be hotspots for the dissemination of ARGs. These genes can be encoded on mobile genetic elements (MGEs) such as conjugative and mobilizable plasmids or integrative and conjugative elements (ICEs). ARGs can be rapidly transferred through horizontal gene transfer (HGT) which has been shown to occur more frequently in biofilms than in planktonic cultures. Biofilm models are promising tools to mimic natural biofilms to study the dissemination of ARGs via HGT. This review summarizes the state-of-the-art of biofilm studies and the techniques that visualize the three main HGT mechanisms in biofilms: transformation, transduction, and conjugation.

Antibiotics in sewage treatment plants, receiving water bodies and groundwater of Chennai city and the suburb, South India: Occurrence, removal efficiencies, and risk assessment

The presence of antibiotics in the aqueous environment can alter the water microbiome, inducing antimicrobial resistance genes. Hence, the occurrence of 18 antibiotics belonging to sulfonamides, fluoroquinolones, tetracyclines, phenicols, and macrolides classes were investigated in surface water, groundwater, and sewage treatment plants in Chennai city and the suburbs. Fluoroquinolones had the maximum detection frequency in both influent and effluent samples of urban and suburban STPs, with ofloxacin and ciprofloxacin showing the highest influent concentrations. Erythromycin was the predominant antibiotic in surface water samples with an average concentration of 194.4 ng/L. All the detected antibiotic concentrations were higher in the Buckingham Canal compared to those in Adyar and Cooum rivers, possibly due to direct sewer outfalls in the canal. In groundwater samples, ciprofloxacin showed the highest levels with an average of 20.48 ng/L and the concentrations were comparable to those of surface water. The average sulfamethazine concentration in groundwater (5.2 ng/L) was found to be slightly higher than that of the surface water and much higher than the STP influent concentrations. High levels of ciprofloxacin and sulfamethazine in groundwater may be because of their high solubility and wide use. Moreover, erythromycin was completely removed after treatment in urban STPs; FQs showed relatively lesser removal efficiency (2.4-54%) in urban STPs and (8-44%) in suburban STP. Tetracyclines and phenicols were not detected in any of the samples. Ciprofloxacin and azithromycin in surface water pose a high risk in terms of estimated antibiotic resistance. This study revealed that the measured surface water concentration of antibiotics were 500 times higher for some compounds than the predicted calculated concentrations from STP effluents. Therefore, we suspect the direct sewage outlets or open drains might play an important role in contaminating surface water bodies in Chennai city.

Does phage-mediated horizontal gene transfer represent an environmental risk?

A growing number of recent studies suggest that the contribution of phages to antibiotic resistance should not be underestimated. Here we describe their implications for public and environmental health, with a special emphasis on the mechanisms underlying phage-mediated horizontal gene transfer.

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

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

Isolation and Characterization of Lytic Pseudomonas aeruginosa Bacteriophages Isolated from Sewage Samples from Tunisia

Bacteriophages could be a useful adjunct to antibiotics for the treatment of multidrug-resistant Pseudomonas aeruginosa infections. In this study, lytic P. aeruginosa myoviruses PsCh, PsIn, Ps25, and Ps12on-D were isolated from Tunisian sewage samples. Phage Ps12on-D displayed an adsorption time of ~10 min, a short latency period (~10 min), and a large burst size (~115 PFU per infected cell) under standard growth conditions. All phages were active at broad temperature (4 °C to 50 °C) and pH (3.0 to 11.0) ranges and were able to lyse a wide variety of P. aeruginosa strains isolated from clinical and environmental samples worldwide. Illumina sequencing revealed double-stranded DNA genomes ranging from 87,887 and 92,710 bp with high sequence identity to Pseudomonas phage PAK_P1. All four phages based on sequence analysis were assigned to the Pakpunavirus genus. The presented characterization and preclinical assessment are part of an effort to establish phage therapy treatment as an alternative strategy for the management of multidrug-resistant P. aeruginosa infections in Tunisia.

Seasonal dynamics survey and association analysis of microbiota communities, antibiotic resistance genes distribution, and biotoxicities characterization in landfill-leachate

OBJECTIVE

To reflect the potential and intrinsic association among microbiota structure, antibiotic resistance genes distribution and biological toxicity of landfill-leachate according to seasonal change, and accurately assess the potential threat of leachate to the surrounding environment.

METHODS

On the basis of the leachate water quality monitoring data from January to December 2020, principal component analysis (PCA) was used to identify the main pollutants in the leachate; Vibrio fischeri luminescence inhibition test was used to detect the comprehensive biotoxicity of the leachate; 16S rDNA amplicon sequencing was used for leachate microbiota. q-PCR was used to detect the class 1 integron (intI1), and eight antibiotic resistance genes (sul1, sul2, tetA, tetB, tetM, tetQ, mefA, and mexF); Canonical correspondence (CCA) analysis was carried out for the association analysis.

RESULT

The biotoxicity of leachate in the second quarter was the highest. The dominant phylum of leachate microbiota from 1st quarters to 4th quarters was Proteobacteria (94.97 %, 85.43 %, 88.20 %, and 84.11 %), and the dominant genera were Thiomonas (60.41 %, 26.83 %, 25.66 %, and 30.51 %), Pseudomonas (5.89 %, 1.86 %, 0.68 %, and 4.72 %), Desulfurella (8.52 %, 0.57 %, 3.81 %, and 8.25 %), and Acidithiobacillus (4.71 %, 0.69 %, 0.87 %, and 5.91 %); Nitrospirillum was negatively correlated with chemical oxygen demand (COD) (R=-0.561, P = 0.008) and five-day biochemical oxygen demand (BOD₅) (R=-0.591, P = 0.005); Limnohabitans was positively correlated with pH (R=0.444, P = 0.044). Four AR genes (sul1, sul2，tetM, and tetQ) were detected in all the samples, while the second quarter had the highest concentration of sul1(6.31 ± 0.49 lg copies/ng DNA), tetM (3.01 ± 1.38 lg copies/ng DNA) and tetQ (3.64 ± 0.90 lg copies/ng DNA).

CONCLUSION

As the mature landfill, the quality of this leachate met the pollution control standards for domestic waste landfills. Thiomycetes, Pseudomonas, Desulfurization, and Thiopterus acidophyllum constitute the dominant microbiota. However, leachate in the second quarter had more serious contamination, the higher biotoxicity, higher concentration of AR genes, together with higher microbiota richness and diversity, which deserved more attention for the potential threat to the surrounding environment.

Co-driving factors of tidal effect on the abundance and distribution of antibiotic resistance genes in the Yongjiang Estuary, China

The unreasonable use of antibiotics and the transmission of antibiotic resistance genes (ARGs) induced by antibiotics have led to a large number of ARGs entered the water environment, which seriously threatened human health and environmental safety. The estuarine aquatic environment connects with inland rivers and sea and is frequently influenced by human activities. This study aims to reveal the occurrences and abundances of ARGs and bacterial community composition by high-throughput quantitative PCR including 296 primers and high-throughput sequencing in the tide rising and ebbing of surface water in the Yongjiang Estuary, China. The results showed that there were a large number of ARGs and mobile genetic elements (MGEs) detected in the rising tide and ebb tide water bodies. The numbers of detected ARGs in each sample at rising and ebb tide ranged from 16 to 77 and 61 to 88, respectively, and the absolute abundance ranges were 1.69 × 10⁴-1.69 × 10⁹ copies/L and 3.18 × 10³-2.57 × 10⁹ copies/L, respectively. Obvious tidal distribution characteristics of ARGs were showed. Most of ARGs conferred resistance to multidrug, aminoglycosides and sulfanilamides. Proteobacteria, Actinobacteria and Bacteroidetes were the dominantly bacterial phylum in the Yongjiang Estuary. Network analysis results indicated that multi-genera were identified as possible ARGs hosts, and they carried more than two types of ARGs genes. Partial least squares path modeling further revealed that MGEs and bacterial community composition were the most important driving factors. The results of the study can provide the corresponding scientific basis for the diffusion and control of ARGs in estuaries.

Impact of mesophilic anaerobic digestion and post-treatment of digestates on the transfer of conjugative antimicrobial resistance plasmids

Manure is a major source of antimicrobial-resistant bacteria and resistance genes carried by mobile genetic elements such as plasmids. In France, the number of on-farm biogas plants has increased significantly in recent years. Our study investigated the impact of mesophilic anaerobic digestion (AD) and the post-treatment of digestates on the fate of conjugative plasmids, along with their potential transfer of antimicrobial resistance. Samples of raw manure, digestates and post-treated digestates were collected from three on-farm biogas plants. Conjugative plasmids were captured using the Escherichia coli CV601 recipient strain and media supplemented with rifampicin and kanamycin - to which the recipient strain is resistant - and tetracycline, sulfamethoxazole, gentamicin, trimethoprim, amoxicillin, cefotaxime, ciprofloxacin or colistin. Putative transconjugants were identified and characterised by disc diffusion and whole genome sequencing. The results showed that the antimicrobial resistance genes transferred from the different matrices conferred resistance to tetracyclines, sulphonamides, trimethoprim, and/or streptomycin. Transconjugants were obtained from raw manure samples but not from digestates or post-digestates, suggesting that mesophilic AD processes may produce fewer conjugative plasmids potentially able to be transferred to Enterobacterales.

Current Progress in Natural Degradation and Enhanced Removal Techniques of Antibiotics in the Environment: A Review

Antibiotics are used extensively throughout the world and their presence in the environment has caused serious pollution. This review summarizes natural methods and enhanced technologies that have been developed for antibiotic degradation. In the natural environment, antibiotics can be degraded by photolysis, hydrolysis, and biodegradation, but the rate and extent of degradation are limited. Recently, developed enhanced techniques utilize biological, chemical, or physicochemical principles for antibiotic removal. These techniques include traditional biological methods, adsorption methods, membrane treatment, advanced oxidation processes (AOPs), constructed wetlands (CWs), microalgae treatment, and microbial electrochemical systems (such as microbial fuel cells, MFCs). These techniques have both advantages and disadvantages and, to overcome disadvantages associated with individual techniques, hybrid techniques have been developed and have shown significant potential for antibiotic removal. Hybrids include combinations of the electrochemical method with AOPs, CWs with MFCs, microalgal treatment with activated sludge, and AOPs with MFCs. Considering the complexity of antibiotic pollution and the characteristics of currently used removal technologies, it is apparent that hybrid methods are better choices for dealing with antibiotic contaminants.

Genome plasticity as a paradigm of antibiotic resistance spread in ESKAPE pathogens

The major reason behind the spread of antibiotic resistance genes (ARGs) is persistent selective pressure in the environment encountered by bacteria. Genome plasticity plays a crucial role in dissemination of antibiotic resistance among bacterial pathogens. Mobile genetic elements harboring ARGs are reported to dodge bacterial immune system and mediate horizontal gene transfer (HGT) under selective pressure. Residual antibiotic pollutants develop selective pressures that force the bacteria to lose their defense mechanisms (CRISPR-cas) and acquire resistance. The present study targets the ESKAPE organisms (namely, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) causing various nosocomial infections and emerging multidrug-resistant species. The role of CRISPR-cas systems in inhibition of HGT in prokaryotes and its loss due to presence of various stressors in the environment is also focused in the study. IncF and IncH plasmids were identified in all strains of E. faecalis and K. pneumoniae, carrying Beta-lactam and fluoroquinolone resistance genes, whereas sal3, phiCTX, and SEN34 prophages harbored aminoglycoside resistance genes (aadA, aac). Various MGEs present in selected environmental niches that aid the bacterial genome plasticity and transfer of ARGs contributing to its spread are also identified.

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.

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

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

Viral Metagenomics Reveals Widely Diverse Viral Community of Freshwater Amazonian Lake

Despite the importance of understanding the ecology of freshwater viruses, there are not many studies on the subject compared to marine viruses. The microbiological interactions in these environments are still poorly known, especially between bacteriophages and their host bacteria and between cyanophages and cyanobacteria. Lake Bologna, Belém, capital of the Brazilian State of Pará, is a water source that supplies the city and its metropolitan region. However, it remains unexplored regarding the contents of its virome and viral diversity composition. Therefore, this work aims to explore the taxonomic diversity of DNA viruses in this lake, especially bacteriophages and cyanophages, since they can act as transducers of resistance genes and reporters of water quality for human consumption. We used metagenomic sequencing data generated by previous studies. We analyzed it at the taxonomic level using the tools Kraken2, Bracken, and Pavian; later, the data was assembled using Genome Detective, which performs the assembly of viruses. The results observed here suggest the existence of a widely diverse viral community and established microbial phage-regulated dynamics in Lake Bolonha. This work is the first ever to describe the virome of Lake Bolonha using a metagenomic approach based on high-throughput sequencing, as it contributes to the understanding of water-related public health concerns regarding the spreading of antibiotic resistance genes and population control of native bacteria and cyanobacteria.

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.

Hiding in plain sight - Wildlife as a neglected reservoir and pathway for the spread of antimicrobial resistance: A narrative review

Antimicrobial resistance represents a global health problem, with infections due to pathogenic antimicrobial resistant bacteria (ARB) predicted to be the most frequent cause of human mortality by 2050. The phenomenon of antimicrobial resistance has spread to and across all ecological niches, and particularly in livestock used for food production with antimicrobials consumed in high volumes. Similarly, hospitals and other healthcare facilities are recognized as significant “hotspots” of ARB and antimicrobial resistance genes (ARGs); however, over the past decade, new and previously overlooked ecological niches are emerging as hidden reservoirs of ARB/ARGs. Increasingly extensive and intensive industrial activities, degradation of natural environments, burgeoning food requirements, urbanization, and global climatic change have all dramatically affected the evolution and proliferation of ARB/ARGs, which now stand at extremely concerning ecological levels. While antimicrobial resistant bacteria and genes as they originate and emanate from livestock and human hosts have been extensively studied over the past 30 years, numerous ecological niches have received considerably less attention. In the current descriptive review, the authors have sought to highlight the importance of wildlife as sources/reservoirs, pathways and receptors of ARB/ARGs in the environment, thus paving the way for future primary research in these areas.

Gut Virome of the World's Highest-Elevation Lizard Species (Phrynocephalus erythrurus and Phrynocephalus theobaldi) Reveals Versatile Commensal Viruses

The gut virome is a reservoir of diverse symbiotic and pathogenic viruses coevolving with their hosts, and yet limited research has explored the gut viromes of highland-dwelling rare species. Using viral metagenomic analysis, the viral communities of the Phrynocephalus lizards living in the Qinghai-Tibet Plateau were investigated. Phage-encoded functional genes and antibiotic resistance genes (ARGs) were analyzed. The viral communities of different lizard species were all predominated by bacteriophages, especially the Caudovirales order. The virome of Phrynocephalus erythrurus living around the Namtso Lake possessed a unique structure, with the greatest abundance of the Parvoviridae family and the highest number of exclusive viral species. Several vertebrate-infecting viruses were discovered, including caliciviruses, astroviruses, and parvoviruses. Phylogenetic analyses demonstrated that the virus hallmark genes of bacteriophages possessed high genetic diversity. After functional annotation, the majority of phage-associated functional genes were classified in the energy metabolism category. In addition, plenty of ARGs belonging to the multidrug category were discovered, and five ARGs were exclusive to the virome from Phrynocephalus theobaldi. This study provided the first insight into the structure and function of the virome in highland lizards, contributing to the protection of threatened lizard species. Also, our research is of exemplary significance for the gut virome research of lizard species and other cold-blooded and highland-dwelling animals, prompting a better understanding of the interspecific differences and transmission of commensal viruses. IMPORTANCE The Phrynocephalus lizards inhabiting the Qinghai-Tibet Plateau (QTP) are considered to be the highest-altitude lizard species in the world, and they have been added to the IUCN list of threatened species. Living in the QTP with hypoxic, arid, natural conditions, the lizards presented a unique pattern of gut virome, which could provide both positive and negative effects, such as the enrichment of functional genes and the dissemination of antibiotic resistance genes (ARGs). This work provides the foundation for further research on the gut virome in these endangered lizard species and other cold-blooded and highland-dwelling animals, contributing to the maintenance of ecological balance on the plateau.

Investigation of the microbial community structure and diversity in the environment surrounding a veterinary antibiotic production factory

The ecological toxicity caused by antibiotic residues and resistance genes in the environment affects the community structures and activities of environmental microorganisms; the ecological toxicity effects of a long-term exposure to low doses antibiotic residues on microorganisms have not however been well-studied. In this work, sequence analysis and species annotation of the full-length 16S rRNA gene were carried out on the extracted whole genome by a 3-generation sequencing method to analyze the diversity of the microbial populations and the population differences among different sampling sites in the environment surrounding a veterinary antibiotic production factory. A total of 1720 OTUs (Operational Taxonomic Unit, OTU) were found, of which 1055 OTUs were in the river samples and 993 OTUs were in the soil samples. 643 and 438 bacterial strains were identified in the river water and soil samples respectively. The bacterial populations are classified into 29 phylum, 612 genus, and 849 species. The dominant phylum of bacteria was Proteobacteria, which was also the absolutely dominant phylum. Shannon diversity index of the bacteria showed that the bacterial abundance in downstream river was significantly higher than that in an upstream non-polluted area (P < 0.001), but the difference of bacterial abundance between soil samples was not significant. There were 61 biomarkers in the river water samples from different sampling points, and 14 biomarkers in soil samples. It was found by the difference statistics of the microbial community that there are multiple biomarkers between this veterinary drug production site and the upstream non-polluted area. Significant differences between multiple functional genes were also found in metabolic pathways of the microorganisms. A similar trend was found for the distribution of antibiotic resistance genes (ARGs). It is concluded that the population composition of microorganisms and diversity are likely related to antibiotic residues and to the distributions of ARGs in the environment surrounding the antibiotic production factory.

Legacy and Emerging Pollutants in an Urban River Stretch and Effects on the Bacterioplankton Community

River contamination is due to a chemical mixture of point and diffuse pollution, which can compromise water quality. Polycyclic Aromatic Hydrocarbons (PAHs) and emerging compounds such as pharmaceuticals and antibiotics are frequently found in rivers flowing through big cities. This work evaluated the presence of fifteen priority PAHs, eight pharmaceuticals including the antibiotics ciprofloxacin (CIP) and sulfamethoxazole (SMX), together with their main antibiotic resistant genes (ARGs) and the structure of the natural bacterioplankton community, in an urbanized stretch of the river Danube. SMX and diclofenac were the most abundant chemicals found (up to 20 ng/L). ARGs were also found to be detected as ubiquitous contaminants. A principal component analysis of the overall microbiological and chemical data revealed which contaminants were correlated with the presence of certain bacterial groups. The highest concentrations of naphthalene were associated with Deltaproteobacteria and intI1 gene. Overall, the most contaminated site was inside the city and located immediately downstream of a wastewater treatment plant. However, both the sampling points before the river reached the city and in its southern suburban area were still affected by emerging and legacy contamination. The diffuse presence of antibiotics and ARGs causes particular concern because the river water is used for drinking purposes.

Uses of Bacteriophages as Bacterial Control Tools and Environmental Safety Indicators

Bacteriophages are bacterial-specific viruses and the most abundant biological form on Earth. Each bacterial species possesses one or multiple bacteriophages and the specificity of infection makes them a promising alternative for bacterial control and environmental safety, as a biotechnological tool against pathogenic bacteria, including those resistant to antibiotics. This application can be either directly into foods and food-related environments as biocontrol agents of biofilm formation. In addition, bacteriophages are used for microbial source-tracking and as fecal indicators. The present review will focus on the uses of bacteriophages like bacterial control tools, environmental safety indicators as well as on their contribution to bacterial control in human, animal, and environmental health.

Making waves: How does the emergence of antimicrobial resistance affect policymaking?

This article considers current trends in antimicrobial resistance (AMR) research and knowledge gaps relevant to policymaking in the water sector. Specifically, biological indicators of AMR (antibiotic-resistant bacteria and their resistance genes) and detection methods that have been used so far are identified and discussed, as well as the problems with and solutions to the collection of AMR data, sewage surveillance lessons from the COVID-19 pandemic, and the financial burden caused by AMR, which could be synergically used to improve advocacy on AMR issues in the water sector. Finally, this article proposes solutions to overcoming existing hurdles and shortening the time it will take to have an impact on policymaking and regulation in the sector.

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

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

Persisting antibiotic resistance gene pollution and its association with human sewage sources in tropical marine beach waters

Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are pollutants of worldwide concern that threaten human health and ecosystems. Anthropogenic activities and wastewater could be ARB and ARG pollution sources; however, research on ARG abundance and microbial source tracking (MST) of contamination in tropical marine waters is limited. This study examined spatiotemporal variations of six ARGs (bla_NDM, bla_TEM, bla_VIM, mcr-1, sul1, and tetQ) against the widely used antibiotic groups and a class 1 integron-integrase gene (intI1) at two Thai tropical recreational beaches (n = 41). Correlations between ARGs and sewage-specific MST markers (i.e., crAssphage and human polyomaviruses [HPyVs]) and fecal indicator bacteria (i.e., total coliforms, fecal coliforms, and enterococci) were also investigated. Bla_TEM, intI1, sul1, and tetQ were ubiquitous at both beaches (85.4-100% detection rate); intI1 was the most abundant (3-6 orders in log₁₀ copies/100 mL), followed by bla_TEM (2-4 orders), sul1 (2-3 orders), and tetQ (2-4 orders). Bla_NDM was found in 7.3% (up to 4 orders), and no mcr-1 was detected. Interestingly, bla_VIM was prevalent at one beach (2-5 orders; n = 17), but found in only one sample at the other (4 orders). Temporal, but not spatial, differences were noticed; bla_TEM was at higher levels in the wet season. IntI1 correlated with sul1 and tetQ (Spearman's rho = 0.47-0.97), suggesting potential horizontal gene transfer. CrAssphage, but not HPyVs, correlated with intI1, sul1, and tetQ (Spearman's rho = 0.50-0.74). Higher numbers of ARGs tended to co-occur in samples with higher crAssphage concentrations, implying sewage contribution to the marine water, with a persisting ARG background. This study provides insight into the ARG pollution status of tropical coastal waters and suggests crAssphage as a proxy for ARG pollution, which could facilitate effective management policies to minimize ARG dissemination in marine environments.

Effects of the Newly Isolated T4-like Phage on Transmission of Plasmid-Borne Antibiotic Resistance Genes via Generalized Transduction

Bacteriophages are the most abundant biological entities on earth and may play an important role in the transmission of antibiotic resistance genes (ARG) from host bacteria. Although the specialized transduction mediated by the temperate phage targeting a specific insertion site is widely explored, the carrying characteristics of “transducing particles” for different ARG subtypes in the process of generalized transduction remains largely unclear. Here, we isolated a new T4-like lytic phage targeting transconjugant Escherichia coli C600 that contained plasmid pHNAH67 (KX246266) and encoded 11 different ARG subtypes. We found that phage AH67C600_Q9 can misload plasmid-borne ARGs and package host DNA randomly. Moreover, for any specific ARG subtype, the carrying frequency was negatively correlated with the multiplicity of infection (MOI). Further, whole genome sequencing (WGS) identified that only 0.338% (4/1183) of the contigs of an entire purified phage population contained ARG sequences; these were floR, sul2, aph(4)-Ia, and fosA. The low coverage indicated that long-read sequencing methods are needed to explore the mechanism of ARG transmission during generalized transduction.

Profiles of antibiotic resistance genes in an inland salt-lake Ebinur Lake, Xinjiang, China: The relationship with antibiotics, environmental factors, and microbial communities

Lakes in arid northwestern China, as the main pollutant-holding water bodies in the typical ecologically fragile areas, are facing the unknown risk of exposure to antibiotics and antibiotic resistance genes (ARGs). In this study, five ARGs and one mobile genetic element (intI1) and their relation with antibiotics, microbial communities and water quality were investigated in Ebinur Lake Basin, a typical salt-lake of China. Quantitative PCR analysis indicated that ARGs decreasing order in both surface water and sediment was sul1 >sul2 >tetW>ermB>qnrS, which means sulfonamide resistance genes were the main pollution ARGs. Macrolide antibiotics were the predominant antibiotics in the surface water and sediment in winter, while sulfonamides and quinolones accounted for a high proportion in summer. There was a non-corresponding relationship between ARGs and antibiotics. Moreover, the relationship between ARGs and microbial communities were defined. Sulfonamide resistance genes were carried by a greater diversity of potential host bacteria (76 genera) than other ARGs (9 genera). And their positive correlation with intI1 (p < 0.05) which promotes their migration and provides possibility of their co-occurrence in bacterial populations (e.g., Nitrospira). Bacterial genera were the main driver of ARGs distribution pattern in highly saline lake sediment. Environmental factors like salinity, total nitrogen and organic matter could have a certain influence on the occurrence of ARGs by affecting microorganisms. The results systematically show the distribution and propagation characteristics of ARGs in typical inland salt-lakes in China, and preliminarily explored the relationship between ARGs and antibiotics, resistance genes and microorganisms in lakes in ecologically fragile areas.

β-Lactam Resistance Gene NDM-1 in the Aquatic Environment: A Review

New Delhi Metallo-β-lactamase-1 (NDM-1) offers carbapenem antibiotics resistance that creates an evolving challenge in treating bacterial infections. NDM-1-bearing strains were observed in surface waters around New Delhi in 2010 and after then identified globally. The usage of antibiotics may hasten the growth of the NDM-1-producing bacteria, which pose severe hazards to human and animal health. The emergence of the NDM-1 in the aquatic environment is turning out to be a growing concern worldwide. NDM-1 gene conferring resistance to a widespread class of antibiotics has been observed in bacteria disseminated in animal production wastewaters, hospital sewage, domestic sewage, industrial effluents, wastewater treatment plants, drinking water, surface water, and even in groundwater. This review recapitulates the currently published research studies on the prevalence and geographical distribution of the NDM-1 gene in the aquatic environment, its habitats, and healthcare risk associated with NDM-1-producing bacteria, in addition to molecular techniques employed to reveal the occurrence of the NDM-1 in the aquatic environment, including conventional polymerase chain reaction, real-time qPCR, DNA hybridization, and microarray-based methods.

The variation of antibiotic resistance genes and their links with microbial communities during full-scale food waste leachate biotreatment processes

The prevalence of antibiotic resistance genes (ARGs) has been widely reported in various environments. However, little is known of them in food waste (FW) leachate with high organic content and how their distribution is influenced by biotreatment processes. Here, twelve ARGs, two integrase genes and bacterial communities were investigated during two full-scale FW biotreatment processes. High ARGs abundances (absolute: 1.03 × 10⁷-2.82 × 10⁹copies/mL; relative: 0.076-2.778copies/16S rRNA) were observed across all samples. Although biotreatment effectively reduced absolute abundance of ARGs, additional bacteria acquiring ARGs caused an increase in their relative abundance, which further increased the transmission risk of ARGs. mexF, blaCTX-M, sul1 played crucial roles and sul1 might be considered as an indicator for the prediction of total ARGs. It is worrying that the discharge (effluent and sludge) included highly abundant ARGs (5.09 × 10¹⁴-4.83 × 10¹⁵copies/d), integrons (1.11 × 10¹⁴-6.04 × 10¹⁴copies/d) and potential pathogens (such as Pseudomonas and Streptococcus), which should be given more attentions. blaCTX-M and tetQ possessed most potential hosts, Proteobacteria-L and Firmicutes-W were predominant contributors of ARGs-hosts at genus level. This study suggested FW leachate biotreatment systems could be reservoirs of ARGs and facilitated the proliferation of them. The exploration of effective removal methods and formulation of emission standard are necessary for future ARGs mitigation.

Bacterial and Bacteriophage Antibiotic Resistance in Marine Bathing Waters in Relation to Rivers and Urban Streams

Fecal pollution of surface water may introduce bacteria and bacteriophages harboring antibiotic resistance genes (ARGs) into the aquatic environment. Watercourses discharging into the marine environment, especially close to designated bathing waters, may expose recreational users to fecal pollution and therefore may increase the likelihood that they will be exposed to ARGs. This study compares the bacterial and bacteriophage ARG profiles of two rivers (River Tolka and Liffey) and two small urban streams (Elm Park and Trimleston Streams) that discharge close to two marine bathing waters in Dublin Bay. Despite the potential differences in pollution pressures experienced by these waterways, microbial source tracking analysis showed that the main source of pollution in both rivers and streams in the urban environment is human contamination. All ARGs included in this study, bla_TEM, bla_SHV, qnrS, and sul1, were present in all four waterways in both the bacterial and bacteriophage fractions, displaying a similar ARG profile. We show that nearshore marine bathing waters are strongly influenced by urban rivers and streams discharging into these, since they shared a similar ARG profile. In comparison to rivers and streams, the levels of bacterial ARGs were significantly reduced in the marine environment. In contrast, the bacteriophage ARG levels in freshwater and the marine were not significantly different. Nearshore marine bathing waters could therefore be a potential reservoir of bacteriophages carrying ARGs. In addition to being considered potential additional fecal indicators organism, bacteriophages may also be viewed as indicators of the spread of antimicrobial resistance.

A Point Prevalence Survey of Antibiotic Resistance in the Irish Environment, 2018-2019

Water bodies worldwide have proven to be vast reservoirs of clinically significant antibiotic resistant organisms. Contamination of waters by anthropogenic discharges is a significant contributor to the widespread dissemination of antibiotic resistance. The aim of this research was to investigate multiple different anthropogenic sources on a national scale for the role they play in the environmental propagation of antibiotic resistance. A total of 39 water and 25 sewage samples were collected across four local authority areas in the West, East and South of Ireland. In total, 211 Enterobacterales were isolated (139 water, 72 sewage) and characterised. A subset of isolates (n=60) were chosen for whole genome sequencing. Direct comparisons of the water versus sewage isolate collections revealed a higher percentage of sewage isolates displayed resistance to cefoxitin (46%) and ertapenem (32%), while a higher percentage of water isolates displayed resistance to tetracycline (55%) and ciprofloxacin (71%). Half of all isolates displayed extended spectrum beta-lactamase (ESBL) production phenotypically (n = 105/211; 50%), with bla_CTX-M detected in 99/105 isolates by PCR. Carbapenemase genes were identified in 11 isolates (6 sewage, 5 water). The most common variant was bla_OXA-48 (n=6), followed by bla_NDM-5 (n=2) and bla_KPC-2 (n=2). Whole genome sequencing analysis revealed numerous different sequence types in circulation in both waters and sewage including E. coli ST131 (n=15), ST38 (n=8), ST10 (n=4) along with Klebsiella ST405 (n=3) and ST11 (n=2). Core genome MLST (cgMLST) comparisons uncovered three highly similar Klebsiella isolates originating from hospital sewage and two nearby waters. The Klebsiella isolates from an estuary and seawater displayed 99.1% and 98.8% cgMLST identity to the hospital sewage isolate respectively. In addition, three pairs of E. coli isolates from different waters also revealed cgMLST similarities, indicating widespread dissemination and persistence of certain strains in the aquatic environment. These findings highlight the need for routine monitoring of water bodies used for recreational and drinking purposes for the presence of multi-drug resistant organisms.

Recent trends in advanced oxidation process-based degradation of erythromycin: Pollution status, eco-toxicity and degradation mechanism in aquatic ecosystems

Wide spread documentation of antibiotic pollution is becoming a threat to aquatic environment. Erythromycin (ERY), a macrolide belonging antibiotic is at the top of this list with its concentrations ranging between ng/L to a few μg/L in various global waterbodies giving rise to ERY-resistance genes (ERY-RGs) and ERY- resistance bacteria (ERY-RBs) posing serious threat to the aquatic organisms. ERY seems resistant to various conventional water treatments, remained intact and even increased in terms of mass loads after treatment. Enhanced oxidation potential, wide pH range, elevated selectivity, adaptability and greater efficiency makes advance oxidation processes (AOPs) top priority for degrading pollutants with aromatic rings and unsaturated bonds like ERY. In this manuscript, recent developments in AOPs for ERY degradation are reported along with the factors that affect the degradation mechanism. ERY, marked as a risk prioritized macrolide antibiotic by 2015 released European Union watch list, most probably due to its protein inhibition capability considered third most widely used antibiotic. The current review provides a complete ERY overview including the environmental entry sources, concentration in global waters, ERY status in STPs, as well as factors affecting their functionality. Along with that this study presents complete outlook regarding ERY-RGs and provides an in depth detail regarding ERY's potential threats to aquatic biota. This study helps in figuring out the best possible strategy to tackle antibiotic pollution keeping ERY as a model antibiotic because of extreme toxicity records.

Solar photon-Fenton process eliminates free plasmid DNA harboring antimicrobial resistance genes from wastewater

This work aimed to assess the elimination and inactivation of resistance-conferring plasmids (RCPs) present in suspension in secondary wastewater by solar photo-Fenton as these are important vectors for the dissemination of antimicrobial resistance. Experiments were performed in synthetic secondary wastewater (SWW) and municipal wastewater treatment plant effluent (MWWTPE). Solar photo-Fenton (50 mg L^-1 of H₂O₂ and 30 mg L^-1 of Fe²⁺) was carried out for 60 min at neutral pH by applying the intermittent iron addition strategy. The removal of RCPs was assessed by Real-Time Polymerase Chain Reaction (qPCR). The transformation of competent non-resistant E. coli was used to evaluate the inactivation of target RCPs harboring antibiotic resistance genes (ARGs) to ampicillin (pSB1A2) or kanamycin (pSB1K3) after treatment and controls. Solar photo-Fenton completely removed RCPs initially present in both matrixes (SWW and MWWTPE), showing enhanced performance compared to the dark Fenton process. Both RCPs were inactivated after 30 min of solar photo-Fenton treatment, while 60 min were necessary to achieve the same effect for the dark Fenton reaction under similar conditions. These results indicate the potential of solar photo-Fenton to improve wastewater quality and reduce the spread of antimicrobial resistance in the environment by hampering the discharge of cell-free RCPs present in suspension in MWWTP onto environmental waters.

Dispersion of Antibiotic Resistance Genes (ARGs) from stored swine manure biogas digestate to the atmosphere

Biogas digestate is a reservoir of antibiotic resistance genes (ARGs) and could pose a high health risk to both human and animals if the host microorganisms of ARGs become aerosolized. The purpose of this study was to investigate the diversity and relative abundance characteristics of aerosol-loaded ARGs from biogas digestate during storage, and to explore whether the change of ARGs in biogas digestate directly affect the dispersion of aerosol-loaded ARGs. This study reported for the first time that 28 of 42 ARG subtypes detected in the biogas digestate could be dispersed to the atmosphere via aerosol dispersion in a lab-scale dynamic emission vessels experiment. The relative abundance or diversity of ARGs in aerosols were different from that in biogas digestate, and no significant correlation were observed between the relative abundance of ARGs in biogas digestate and aerosols. The dominant ARGs were tetracycline resistance genes in biogas digestate and β-lactam resistance genes in aerosols. The process of biogas digestate storage reduced the total relative abundance of targeted ARGs in biogas digestate, decreased by 0.35 copies/16S rRNA after 30 days of storage, but increased the abundance of some ARG subtypes, including tetM, tetX, tetQ, tetS, ermF and sul2. High-concerned ARGs, including NDM-1, mcr-1 and vancomycin resistance genes (including vanA, vanB, vanRA and vanSA), were found in biogas digestate, and NDM-1 and vanB were also detected in aerosols. These results indicated a potential risk of ARGs dispersion during biogas digestate storage. Further research on the dispersion of ARGs from biogas digestate is required to elucidate the emission mechanism and develop mitigation measures.

Contamination, distribution, and risk assessment of antibiotics in the urban surface water of the Pearl River in Guangzhou, South China

To assess the impact of antibiotic pollution to the ecosystem in urban water, the occurrence, seasonal, and spatial distributions, potential sources, and ecological risks of 18 targeted antibiotics in urban river, Pearl River located in Guangzhou city, were investigated. Surface water samples were sampled from 24 sites in Guangzhou center of Pearl River during dry and wet seasons. The results indicated that the concentrations of antibiotic residues were at the nanogram per liter level, except sulfamethazine (SMD) (μg/L). Sulfonamides (SAs) were the dominant antibiotics, contributing 60.4-65.0% to the total antibiotics. The concentrations of SAs, fluoroquinolones (QUs), macrolides (MLs), tetracyclines (TCs), and lincosamides (LCs) were higher in dry season than those in wet season at most sampling sites, which possibly resulted from the dilution effect of heavy rainfall. The concentrations of the antibiotic residues in Guangzhou were comparable or higher than other urban rivers. The calculation on risk quotients indicated that erythromycin-H₂O (ETM-H₂O) and tetracycline (TC) were of high risks. The source identification by the Pearson correlation analysis and principal component analysis-multiple linear regression (PCA-MLR) method suggested that municipal wastewater treatment plants were primary sources of antibiotics. These results would provide important information for the environmental protect.

The Prevalence of Virulent and Multidrug-Resistant Enterococci in River Water and in Treated and Untreated Municipal and Hospital Wastewater

The aim of this study is to describe the drug resistance and virulence of enterococci in river water sampled downstream (DRW) and upstream (URW) from the wastewater discharge point, to determine the pool of virulent and drug-resistant enterococci in untreated wastewater (UWW) and the extent to which these bacteria are eliminated from hospital wastewater (HWW) and municipal wastewater treated (TWW) by biological and mechanical methods in a wastewater treatment plant (WWTP). A total of 283 strains were identified with the use of culture-dependent methods and PCR, including seven different species including E. faecalis and E. faecium which were predominant in all analyzed samples. Majority of the strains were classified as multidrug resistant (MDR), mostly on streptomycin and trimethoprim. Strains isolated from wastewater and DRW harbored van genes conditioning phenotypic resistance to vancomycin, the highest percentage of vancomycin-resistant strains (57.0%), mostly strains harboring vanC1 genes (27.6%), was noted in TWW. More than 65.0% of the isolated strains had different virulence genes, the highest number of isolates were positive for cell wall adhesin efaA and sex pheromones cob, cpd, and ccf which participate in the induction of virulence. Many of the strains isolated from TWW were resistant to a higher number of drugs and were more virulent than those isolated from UWW and HWW. The enterococci isolated from DRW and wastewater were characterized by similar multidrug resistance and virulence profiles, and significant correlations were observed between these groups of isolates. These findings suggest that pathogenic enterococci are released with TWW and can spread in the river, pose a serious epidemiological threat and a risk to public health.

Intracellular versus extracellular antibiotic resistance genes in the environment: Prevalence, horizontal transfer, and mitigation strategies

Antibiotic resistance genes (ARGs) are present as both intracellular and extracellular fractions of DNA in the environment. Due to the poor yield of extracellular DNA in conventional extraction methods, previous studies have mainly focused on intracellular ARGs (iARGs). In this review, we evaluate the prevalence/persistence and horizontal transfer of iARGs and extracellular ARGs (eARGs) in different environments, and then explore advanced mitigation strategies in wastewater treatment plants (WWTPs) for preventing the spread of antibiotic resistance in the environment. Although iARGs are the main fraction of ARGs in nutrient-rich environments, eARGs are predominant in receiving aquatic environments. In such environments, natural transformation of eARGs occurs with a comparable frequency to conjugation of iARGs. Further, eARGs can be adsorbed by soil and sediments particles, protected from DNase degradation, and consequently persist longer than iARGs. Collectively, these characteristics emphasize the crucial role of eARGs in the spread of antibiotic resistance in the environment. Fate of iARGs and eARGs through advanced treatment technologies (disinfection and membrane filtration) indicates that different mitigation strategies may be required for each ARG fraction to be significantly removed. Finally, comprehensive risk assessment is needed to evaluate/compare the effect of iARGs versus eARGs in the environment.

Bacteriophages in water pollution control: Advantages and limitations

Wastewater is a breeding ground for many pathogens, which may pose a threat to human health through various water transmission pathways. Therefore, a simple and effective method is urgently required to monitor and treat wastewater. As bacterial viruses, bacteriophages (phages) are the most widely distributed and abundant organisms in the biosphere. Owing to their capacity to specifically infect bacterial hosts, they have recently been used as novel tools in water pollution control. The purpose of this review is to summarize and evaluate the roles of phages in monitoring pathogens, tracking pollution sources, treating pathogenic bacteria, infecting bloom-forming cyanobacteria, and controlling bulking sludge and biofilm pollution in wastewater treatment systems. We also discuss the limitations of phage usage in water pollution control, including phage-mediated horizontal gene transfer, the evolution of bacterial resistance, and phage concentration decrease. This review provides an integrated outlook on the use of phages in water pollution control.

Biofilms: hot spots of horizontal gene transfer (HGT) in aquatic environments, with a focus on a new HGT mechanism

Biofilms in water environments are thought to be hot spots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). ARGs can be spread via HGT, though mechanisms are known and have been shown to depend on the environment, bacterial communities and mobile genetic elements. Classically, HGT mechanisms include conjugation, transformation and transduction; more recently, membrane vesicles (MVs) have been reported as DNA reservoirs implicated in interspecies HGT. Here, we review the current knowledge on the HGT mechanisms with a focus on the role of MVs and the methodological innovations in the HGT research.

Water safety screening via multiplex LAMP-Au-nanoprobe integrated approach

Contaminated water resources remain a major global concern regarding public health. The majority of water safety protocols include indicators of microbial contamination to evaluate the potential risk to public health and are key elements of quality guidelines. Among these, markers for total coliforms and fecal coliforms are strong indicators of co-contamination with other pathogens. Traditional methods, recurring to slow and cumbersome culture-based approaches, have been gradually replaced by molecular methods, capable of faster and more specific screening. These are usually PCR-based methods that may allow for multiple pathogen detection but require dedicated laboratory equipment, hindering the rapid on-site assessment. Here, we used a multiplex Loop-Mediated Isothermal Amplification (mLAMP) strategy for the amplification of two markers associated with the contamination by total and fecal coliforms (e.g. Escherichia coli) - lacZ and uidA genes, respectively - thus allowing for single tube multiplex detection. The mLAMP products were then subject to an Au-nanoprobe colorimetric detection assay for precise discrimination of targets. This approach was validated in 22 water samples that were also screened for the presence of lacZ and uidA using standard and quantitative PCR, with the capability for discriminating the contamination level, e.g. a semi-quantitative evaluation of water quality.

Dissemination of antibiotic resistance genes (ARGs) via integrons in Escherichia coli: A risk to human health

With the induction of various emerging environmental contaminants such as antibiotic resistance genes (ARGs), environment is considered as a key indicator for the spread of antimicrobial resistance (AMR). As such, the ARGs mediated environmental pollution raises a significant public health concern worldwide. Among various genetic mechanisms that are involved in the dissemination of ARGs, integrons play a vital role in the dissemination of ARGs. Integrons are mobile genetic elements that can capture and spread ARGs among environmental settings via transmissible plasmids and transposons. Most of the ARGs are found in Gram-negative bacteria and are primarily studied for their potential role in antibiotic resistance in clinical settings. As one of the most common microorganisms, Escherichia coli (E. coli) is widely studied as an indicator carrying drug-resistant genes, so this article aims to provide an in-depth study on the spread of ARGs via integrons associated with E. coli outside clinical settings and highlight their potential role as environmental contaminants. It also focuses on multiple but related aspects that do facilitate environmental pollution, i.e. ARGs from animal sources, water treatment plants situated at or near animal farms, agriculture fields, wild birds and animals. We believe that this updated study with summarized text, will facilitate the readers to understand the primary mechanisms as well as a variety of factors involved in the transmission and spread of ARGs among animals, humans, and the environment.

Antibiotic resistance in wastewater treatment plants: understanding the problem and future perspectives

Antibiotics residues (AR), antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG) are a new class of water contaminants, due to their adverse effects on aquatic ecosystems and human health. Contamination of water bodies occurs mainly by the excretion of antibiotics incompletely metabolized by humans and animals and is considered the main source of contamination of antibiotics in the environment. Given the imminent threat, the World Health Organization (WHO) has categorized the spread of antibiotics as one of the top three threats to public health in the twenty-first century. The Urban Wastewater Treatment Plants (UWWTP) bring together AR, ARB, ARG, making the understanding of this peculiar environment fundamental for the investigation of technologies aimed at combating the spread of bacterial resistance. Several methodologies have been employed focusing on reducing the ARB and ARG loads of the effluents, however the reactivation of these microorganisms after the treatment is widely reported. This work aims to elucidate the role of UWWTPs in the spread of bacterial resistance, as well as to report the efforts that have been made so far and future perspectives to combat this important global problem.

Prevalence of antibiotic resistance in the tropical rivers of Sri Lanka and India

We evaluate the imprints of urbanization, landuse and lifestyle on the prevalence and provenance of antibiotic resistance in the tropical rivers of Sri Lanka (Kelani and Gin) and India (Sabarmati, and Brahmaputra River). The prevalence of E. coli in the Kelani, Sabarmati, and Brahmaputra Rivers was in the range of 10-27, 267-76,600, and <50 CFU ml^-1 respectively. Isolated E. coli colonies were subjected to six antibiotics to assess their resistance. We found higher resistance to old generation antibiotics like tetracycline (TC), and sulfamethoxazole (ST) transcends the resistance for fluoroquinolones like norfloxacin (NFX), ciprofloxacin (CIP), and levofloxacin (LVX). Interestingly, both Indian rivers had exhibited relatively higher resistance to TC and ST than the Kelani river or Gin River, implying that the Sri Lankan situation is relatively less critical. At genetic level the resistance for β-lactams, fluoroquinolones and sulphonamides, were detected in many samples, as reported globally. While the resistance genes for aac-(6')-1b-cr, qnrS and sul1 were detected in both Sri Lankan and Indian Rivers, bla_TEM and ampC were specific to the Indian Rivers only. Decoupling of the prevalence of metal contamination and antibiotic resistance has been noticed in India and Sri Lanka. Study implies that urbanization, landuse, and lifestyle (ULL) are the three most critical factors governing multidrug resistance (MDR) and fecal contamination.

Antibiotic resistance patterns of Pseudomonas spp. isolated from faecal wastes in the environment and contaminated surface water

The Pseudomonas genus, which includes environmental and pathogenic species, is known to present antibiotic resistances, and can receive resistance genes from multi-resistant enteric bacteria released into the environment via faecal rejects. This study was aimed to investigate the resistome of Pseudomonas populations that have been in contact with these faecal bacteria. Thus, faecal discharges originating from human or cattle were sampled (from 12 points and two sampling campaigns) and 41 Pseudomonas species identified (316 isolates studied). The resistance phenotype to 25 antibiotics was determined in all isolates, and we propose a specific antibiotic resistance pattern for 14 species (from 2 to 9 resistances). None showed resistance to aminoglycosides, tetracycline, or polymyxins. Four species carried a very low number of resistances, with none to β-lactams. Interestingly, we observed the absence of the transcriptional activator soxR gene in these four species. No plasmid transfer was highlighted by conjugation assays, and a few class 1 but no class 2 integrons were detected in strains that may have received resistance genes from Enterobacteria. These results imply that the contribution of the Pseudomonas genus to the resistome of an ecosystem first depends on the structure of the Pseudomonas populations, as they may have very different resistance profiles.