Effect of Urban Wastewater Discharge on the Abundance of Antibiotic Resistance Genes and Antibiotic-Resistant Escherichia coli in Two Italian Rivers

Human health risk assessment associated with the reuse of treated wastewater in arid areas

Qatar produces more than 850,000 m3/day of highly treated wastewater. The present study aims at characterizing the effluents coming out of three central wastewater treatment plants (WWTPs) of chemical pollutants including metals, metalloids and antibiotics commonly used in the country. Additionally, the study is assessing human health risks associated with the exposure to the treated wastewater (TWW) via dermal and ingestion routes. Although the origin of domestic wastewater is desalinated water (the only source of fresh water), the results show that the targeted parameters in TWW were within the international standards. Concentrations of Cl, F, Br, NO3, NO2, SO4 and PO4, were 389, <0.1, 1.2, 25, <0.1, 346, and 2.8 mg/L, respectively. On the other hand, among all cations, metals and metalloids, only boron (B) was 2.1 mg/L which is higher than the Qatari guidelines for TWW reuse in irrigation of 1.5 mg/L. Additionally, strontium (Sr) and thallium (Tl) were detected with relatively high concentrations of 30 mg/L and 12.5 μg/L, respectively, due to their natural and anthropogenic sources. The study found that the low concentrations of all tested metals and metalloids do not pose any risk to human health. However, Tl presents exposure levels above the 10 % of oral reference dose (HQ = 0.4) for accidental oral ingestion of TWW. The results for antibiotics show that exposure for adults and children to TWW are far below the admissible daily intakes set using minimum therapeutic dose and considering uncertainty factors. Treated wastewater of Qatar can be used safely for irrigation. However, further investigations are still needed to assess microbiological quality.

Comparison of the Antibiotic Resistance of Escherichia coli Populations from Water and Biofilm in River Environments

Antibiotic-resistant, facultative pathogenic bacteria are commonly found in surface water; however, the factors influencing the spread and stabilization of antibiotic resistance in this habitat, particularly the role of biofilms, are not fully understood. The extent to which bacterial populations in biofilms or sediments exacerbate the problem for specific antibiotic classes or more broadly remains unanswered. In this study, we investigated the differences between the bacterial populations found in the surface water and sediment/biofilm of the Mur River and the Drava River in Austria. Samples of Escherichia coli were collected from both the water and sediment at two locations per river: upstream and downstream of urban areas that included a sewage treatment plant. The isolates were subjected to antimicrobial susceptibility testing against 21 antibiotics belonging to seven distinct classes. Additionally, isolates exhibiting either extended-spectrum beta-lactamase (ESBL) or carbapenemase phenotypes were further analyzed for specific antimicrobial resistance genes. E. coli isolates collected from all locations exhibited resistance to at least one of the tested antibiotics; on average, isolates from the Mur and Drava rivers showed 25.85% and 23.66% resistance, respectively. The most prevalent resistance observed was to ampicillin, amoxicillin-clavulanic acid, tetracycline, and nalidixic acid. Surprisingly, there was a similar proportion of resistant bacteria observed in both open water and sediment samples. The difference in resistance levels between the samples collected upstream and downstream of the cities was minimal. Out of all 831 isolates examined, 13 were identified as carrying ESBL genes, with 1 of these isolates also containing the gene for the KPC-2 carbapenemase. There were no significant differences between the biofilm (sediment) and open water samples in the occurrence of antibiotic resistance. For the E. coli populations in the examined rivers, the different factors in water and the sediment do not appear to influence the stability of resistance. No significant differences in antimicrobial resistance were observed between the bacterial populations collected from the biofilm (sediment) and open-water samples in either river. The different factors in water and the sediment do not appear to influence the stability of resistance. The minimal differences observed upstream and downstream of the cities could indicate that the river population already exhibits generalized resistance.

Synthetic Nuclease-Producing Microbiome Achieves Efficient Removal of Extracellular Antibiotic Resistance Genes from Wastewater Effluent

Antibiotic resistance gene (ARG) transmission poses significant threats to human health. The effluent of wastewater treatment plants is demonstrated as a hotspot source of ARGs released into the environment. In this study, a synthetic microbiome containing nuclease-producing Deinococcus radiodurans was constructed to remove extracellular ARGs. Results of quantitative polymerase chain reaction (qPCR) showed significant reduction in plasmid RP4-associated ARGs (by more than 3 orders of magnitude) and reduction of indigenous ARG sul1 and mobile genetic element (MGE) intl1 (by more than 1 order of magnitude) in the synthetic microbiome compared to the control without D. radiodurans. Metagenomic analysis revealed a decrease in ARG and MGE diversity in extracellular DNA (eDNA) of the treated group. Notably, whereas eight antibiotic-resistant plasmids with mobility risk were detected in the control, only one was detected in the synthetic microbiome. The abundance of the nuclease encoding gene exeM, quantified by qPCR, indicated its enrichment in the synthetic microbiome, which ensures stable eDNA degradation even when D. radiodurans decreased. Moreover, intracellular ARGs and MGEs and pathogenic ARG hosts in the river receiving treated effluent were lower than those in the river receiving untreated effluent. Overall, this study presents a new approach for removing extracellular ARGs and further reducing the risk of ARG transmission in receiving rivers.

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

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

Geospatial Patterns of Antimicrobial Resistance Genes in the US EPA National Rivers and Streams Assessment Survey

Antimicrobial resistance (AR) is a serious global problem due to the overuse of antimicrobials in human, animal, and agriculture sectors. There is intense research to control the dissemination of AR, but little is known regarding the environmental drivers influencing its spread. Although AR genes (ARGs) are detected in many different environments, the risk associated with the spread of these genes to microbial pathogens is unknown. Recreational microbial exposure risks are likely to be greater in water bodies receiving discharge from human and animal waste in comparison to less disturbed aquatic environments. Given this scenario, research practitioners are encouraged to consider an ecological context to assess the effect of environmental ARGs on public health. Here, we use a stratified, probabilistic survey of nearly 2000 sites to determine national patterns of the anthropogenic indicator class I integron Integrase gene (intI1) and several ARGs in 1.2 million kilometers of United States (US) rivers and streams. Gene concentrations were greater in eastern than in western regions and in rivers and streams in poor condition. These first of their kind findings on the national distribution of intI1 and ARGs provide new information to aid risk assessment and implement mitigation strategies to protect public health.

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.

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

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

Effect of wastewater treatment plant discharge on the bacterial community in a receiving river

The effluent of wastewater treatment plants (WWTPs) is an important water resource for some rivers in regions with relatively low precipitation, which may pose ecological risks. Various pollutants and microorganisms are discharged into rivers, along with the WWTP effluent, but this process has not been thoroughly studied. The objective of this study was to evaluate the effect of WWTP effluent on the bacterial community in the sediment and water column of an urban river and to identify the relationship between the total and active bacterial communities. Five sites were sampled in the river, including the most upstream site of the river (Up-most), 200 m upstream of the WWTP (Up-200), at the point of effluent discharge of the WWTP (Eff-pl) and 50 m (Down-50) and 1000 m (Down-1000) downstream of the WWTP. Compared with the two upstream sites (Up-most and Up-200), the bacterial species composition of Eff-pl was significantly different (p < 0.05) in both the sediment and water columns, while the bacterial species composition at Down-1000 was significantly different (p < 0.05) in the sediment but not in the water. The relative abundance of Proteobacteria, Actinobacteriota and Verrucomicrobiota was significantly different (p < 0.05) at Eff-pl in both the sediment and water columns compared with that at the upstream sites. The shared bacterial species between the DNA and RNA 16 S rRNA analyses were only 45.5-62.2% and 43.2-52.3% for the sediment and water, respectively. Accordingly, WWTP effluent drainage significantly alters (p < 0.05) the bacterial composition in the receiving river but can be recovered in water within a short distance. However, in sediment, a longer recovery space is probably needed. Analyses of the combination of total and active bacterial compositions are recommended to evaluate the ecological consequences of WWTP effluent drainage on the bacterial composition.

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.

Antibiotic resistance gene load and irrigation intensity determine the impact of wastewater irrigation on antimicrobial resistance in the soil microbiome

Treated wastewater (TWW) irrigation is a useful counter-measure against the depletion of freshwater (FW) resources. However, TWW contains several contaminants of emerging concern, such as antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs). Thus, TWW irrigation might promote the spread of antimicrobial resistance in soil environments. In the present work, we hypothesized that the ARG load and irrigation intensity define the effect of TWW irrigation on ARG spread dynamics in soil. This hypothesis was tested using a multiphase approach: a) comparing soil from a full-scale, commercially operated, TWW irrigated field with non-irrigated soil, b) long-term sampling of the TWW irrigated field over one year with different irrigation intensities and intercepted by irrigation breaks and c) laboratory-scale soil microcosms irrigated with TWW compared to FW. Six ARGs, the integrase gene intI1 and the 16S rRNA were quantified using qPCR. In addition, effects of TWW irrigation on bacterial community composition of microcosm-samples were analysed with 16S rRNA amplicon sequencing. The genes sul1, qnrS, bla_OXA-58, tet(M) and intI1 were significantly more abundant in the TWW irrigated field soil, whereas bla_CTX--M-32 and bla_TEM, the least abundant genes in the TWW irrigation, showed higher abundance in the non-irrigated soil. The relative abundance of sul1, qnrS, bla_OXA-58, tet(M) and intI1 correlated with TWW irrigation intensity and decreased during irrigation breaks. Despite the decrease, the levels of these genes remained consistently higher than the non-irrigated soil indicating persistence upon their introduction into the soil. Microcosm experiments verified observations from the field study: TWW irrigation promoted the spread of ARGs and intI1 into soil at far elevated levels compared to FW irrigation. However, the impact of TWW irrigation on 16S rRNA absolute abundance and the soil microbial community composition was negligible. In conclusion, the impact of TWW irrigation depends mainly on the introduced ARG load and the irrigation intensity.