Antimicrobial resistant Escherichia coli prevalence in freshwaters in Belgium and human exposure risk assessment

Tracking antibiotics and antibiotic-resistant E. coli in the aquatic environment linked to agriculture

The application of manure to fertilize agricultural land is associated with the introduction of antibiotic residues and bacteria, including antibiotic-resistant bacteria, which can reach surface water through runoff and drainage and groundwater through leaching from the soil. This was investigated by sampling 50 surface water locations (before and after fertilization) and 50 groundwater wells for the presence of antibiotic residues and the presence of antibiotic-resistant bacteria. For the latter, Escherichia coli and extended-spectrum β-lactamase (ESBL) producing E. coli were used as indicators and profiled for antibiotic resistance. The presence of a wide range of antibiotic residues, though at low concentrations (0.01-10 μg/L), in freshwater ecosystems highlights the extensive spread of these substances. Only 16 % of the samples were consistently free of antibiotic residues throughout both sampling periods. Notably, the frequent occurrence of sulfonamides and lincomycin in surface waters raises concerns as their concentrations occasionally exceed the predicted no-effect levels for antimicrobial resistance selection. Maximum concentrations were reported at 8.83 μg/L and 1.60 μg/L for sulfamethoxazole and lincomycin, respectively. Additionally, resistance patterns in E. coli indicate increased resistance to sulfamethoxazole following the fertilization period, suggesting that the application of manure on fields contributes to a rise in antibiotic resistance from 20 % to 48 %. Although antibiotic contamination in groundwater is less prevalent, antibiotic resistance remains widespread. In particular, ESBL-producing E. coli exhibit heightened resistance levels, not limited to β-lactam antibiotics. The detection of resistance to critical last-resort antibiotics such as carbapenems and colistin further emphasizes the urgency of addressing antibiotic resistance in environmental contexts. This study highlights the need for continued monitoring and the implementation of legislation to reduce antibiotic pollution and tackle resistance in aquatic ecosystems.

Protective masks reduced gastrointestinal risks of antibiotic-resistant E. coli for hospital wastewater treatment plant workers: A quantitative microbial risk assessment

Antibiotic-resistant bacteria (ARB) in hospital wastewater present significant but under-researched risks for wastewater treatment plant (WWTP) workers. This study evaluated annual infection risks (Py) from exposure to ESBL-producing Escherichia coli (ESBL E. coli) and the effectiveness of protective masks. Wastewater samples from 25 hospitals in Thailand revealed 88 % of untreated samples were positive for ESBL E. coli (6.25 × 102 to 1.83 × 107 CFU/100 mL, mean 2.22 × 106), while 40 % of treated samples tested positive (1.00 × 102 to 1.97 × 105 CFU/100 mL, mean 2.45 × 104). Using quantitative microbial risk assessment and data from 917 workers, risks were calculated under three scenarios: non-resistant, antibiotic-resistant, and highly virulent E. coli. Ingestion of aerosols and droplets posed a higher infection risk than hand-to-mouth contact, with Py often exceeding the U.S. EPA benchmark of 10-4 per person per year. Mask use, particularly surgical and FFP2 masks, significantly reduced risks, bringing treated wastewater exposure below the benchmark. However, highly virulent E. coli risks remained high across all mask types. These findings highlight the need for effective protective measures and disinfection strategies to safeguard WWTP workers and mitigate ARB dissemination, protecting public health and environmental safety.

Multivariate statistical analysis of surface water quality in the capibaribe river (Pernambuco state, Northeast Brazil): Contributions to water management

Assessing the quality of surface waters is essential for identifying changes in freshwater ecosystems and supporting the planning/proposing of measures to mitigate polluting sources. However, many studies involving the identification of pathogenic bacteria and/or their resistance profile to antimicrobial agents need a more holistic approach to conditioning or modulating factors. Thus, we apply different multivariate statistical techniques to the data set from the Capibaribe River's surface water, one of the most important in the Northeast of Brazil. Our data, taken together, suggest that the waters of the Capibaribe River have been suffering impacts associated with different human activities. Due to its flow crossing a large urban area, different sources are contributing to the contamination/pollution of its aquatic ecosystem, whose multivariate analysis allowed us to identify site-dependent characteristics that reflect the degree and type of human influence. The study of physical-chemical and chemical parameters reveals the influence of the high load of effluents (industrial and domestic) on the chemical and microbiological quality of the waters sampled at the SS4 site. On the other hand, the antimicrobial resistance profile of the isolates evaluated, especially at SS1, SS2, and SS3 sites, provides a comprehensive sample of the "resistome" present in the fecal content of thousands of people living in the region surrounding the Capibaribe River. The presence of enterobacteria in water indicates contamination of fecal origin. It represents a public health problem since the waters of the Capibaribe River can be a source of dissemination and persistence of bacteria resistant to humans and the environment. In conclusion, our study provides a more comprehensive understanding of the relationships between surface water, basic sanitation, antibiotic exposure, bacterial gene transfer, and human colonization, whether in the context of the region studied or other locations.

Occurrence of Antibiotic-Resistant Bacteria in Urban Surface Water Sources in Bangladesh

Infections caused by antibiotic-resistant bacteria (ARB) result in an estimated 1.27 million human deaths annually worldwide. Surface waters are impacted by anthropogenic factors, which contribute to the emergence and spread of ARB in the aquatic environment. While research on antibiotic resistance in surface waters has increased recently in developing nations, including Bangladesh, especially in aquaculture, such studies are still limited in Bangladesh compared to developed nations. In this study, bacteria strains isolated from three rivers and two lakes in Khulna city, Bangladesh were characterized for their antibiotic resistance using disk diffusion method. Of the 106 bacterial isolates from 180 surface water samples, the majority exhibited resistance to Ciprofloxacin (75.0-87.5%) and Ceftriaxone (65.6-78.1%), while resistance to Ampicillin was comparatively lower (9.4-18.8%). Notably, the prevalence of ARB was observed to be higher during the wet seasons compared to the dry seasons. The 16S rRNA gene analysis showed that Shigella flexneri was the most dominant (17.9%) bacterium among the ARB cultured from surface waters, followed by Escherichia fergusonii (12.5%), Proteus mirabilis (10.7%), and Enterobacter quasiroggenkampii (8.9%). At the genus level, Enterobacter (23.5%), Shigella (20.6%), and Escherichia spp. (14.7%) were the most abundant among the ARB in both river and lake samples. The findings of this study highlight the prevalence of antimicrobial resistance in surface water sources and suggest the need for enhanced monitoring and improved disposal practices to mitigate potential public health risks.

Assessing microbial risks of Escherichia coli: A spatial and temporal study of virulence and resistance genes in surface water in resource-limited regions

Environmental microbial pollution can potentially cause illnesses and deaths among human populations. Environmental factors such as geomorphology, land use, human activities, and seasonality could influence pathogen dissemination. This study performed a space-temporal analysis of Escherichia coli concentrations, virulence (eaeA, bfpA, stx2, aatA, and st), and resistance (tetA, blaTEM, blaOXA, Intl-1, Intl-2, sul-1, and sul-2) genes in surface water within the Virilla sub-watershed, Costa Rica. The research employs microbiological, geostatistical, and quantitative microbial risk assessment (QMRA) techniques to evaluate the health risks associated with diarrheagenic E. coli. Samples collected monthly over a year were analyzed for fecal coliforms, E. coli, Enterococcus faecalis, physicochemical parameters, and the presence of virulence and resistance genes. The geographically weighted regression model identified significant associations between the virulence and resistance genes presence and environmental factors influence such as land use, slope, altitude, and seasonal changes. The results show that urban and grazing land use significantly influence the presence of resistance genes, while human fecal pollution is associated with higher concentrations of virulence genes. Seasonal variations showed that wet seasons contributed to increased gene presence (number of positive samples) and diversity (variety of virulence and resistance genes) compared with dry season. The QMRA results indicated that the total health disease burden was higher than the benchmark for drinking water recommended by WHO (1.00 × 10-6 DALY - Disability-Adjusted Life Years - per person per year) by between one and four magnitudes orders, particularly in regions with urban and grazing land use, human fecal pollution class, and lower altitudes. This study highlights the relevance of integrating environmental and microbial data to enhance water quality management and public health strategies in resource-limited regions. It underscores the need for targeted interventions, such as improved wastewater treatment and establishing buffer zones, to mitigate the risks associated with microbial pollution in surface waters.

Quantitative distribution of antibiotic resistance genes and crAssphage in a tropical urbanized watershed

As antimicrobial resistance continues to pose a significant threat to global health, this study provided a focused examination of the prevalence and behavior of key antibiotic resistance genes in aquatic environments. We investigated the quantitative distribution of intI1, sul1, blaTEM, blaNDM, blaVIM, mcr-1, tetQ, and crAssphage within wastewater influents (n = 12), effluents (n = 12) and river water samples (n = 12), from three municipal wastewater treatment plants and three river locations in an urbanized watershed in Central Thailand over dry and wet seasons. The qPCR method demonstrated that intI1, sul1, blaTEM, and tetQ were the most abundant in all samples (2.71-7.89 mean log10 copies/100 mL), with all genes exhibiting consistently uniform levels across diverse locations, suggesting the potential for any site to act as a monitoring sentinel. Although there is a significant reduction of ARG concentrations by WWTPs (0.62 - >4.05 LRV), the persistence of these genes in effluents points to the limited effectiveness of existing treatment methodologies. Temporal data indicated stable ARG concentrations over time, but tetQ levels rose during the wet season, in alignment with the monsoonal climate in Thailand. Additionally, we identified crAssphage, a marker of human sewage contamination, exhibited strong correlations with the more abundant ARGs (rho 0.65 - 0.81), implying that human waste contributes significantly to the environmental burden of ARGs. The results of this research highlight the widespread nature of ARGs in water systems and the need for improved treatment and sanitation strategies to mitigate the public health threat posed by antimicrobial resistance.

A One Health exploration of antimicrobial resistance in Escherichia coli originated from urban and rural lakes ecosystem

Antimicrobial resistance (AMR) has become one of the most serious threats to One Health. Aquatic environments are an ideal non-clinical AMR reservoir and can act as a key battlefront for tackling the AMR. However, AMR data using the One Health approach remain scarce in aquatic environments worldwide. Here, we extensively assessed AMR in Escherichia coli isolated from urban and rural lake ecosystems using the One Health perspective. A total of 162 E. coli isolates obtained from lakes were tested against 25 antimicrobials using an in-vitro antimicrobial susceptibility testing method. A low (2%) to moderate (45%) drug resistance rate was found for all antimicrobials used in human/veterinary medicine or animal/plant agriculture. However, <80% E. coli isolates exhibited multidrug resistance (MDR) phenotype to highly important (amikacin, gentamicin, trimethoprim) or critically important (amoxicillin, ampicillin, colistin) drugs of both human and veterinary medicine. Of concern, >50% of E. coli isolates exhibited MDR to drugs used as last-resorts (chloramphenicol, colistin) or as frontline (nitrofurantoin, sulfamethoxazole, ampicillin, gentamicin) against E. coli infections. In conclusion, the presence of MDR E. coli strains in urban or rural lake ecosystems highlights their possible role as AMR reservoirs with potential One Health risks.

Exploring the presence, genomic traits, and pathogenic potential of extended-spectrum β-lactamase Escherichia coli in freshwater, wastewater, and hospital effluents

AIMS

The purpose of this work was to study extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) in freshwaters, hospital effluents, and wastewaters during two sampling campaigns in 2021.

METHODS AND RESULTS

Water sampling was performed at 24 stations in the Ourthe watershed in Belgium. A total of 644 ESBL (n = 642) and AmpC (n = 2) E. coli strains were isolated. Disk-diffusion assays were performed following the EUCAST's recommendations. All strains were tested for the presence of blaCTX-M-1, blaCTX-M-2, and blaCTX-M-9 gene groups by PCR. Genes belonging to blaCTX-M-1 and blaCTX-M-9 groups were detected, respectively, in 73.6% and 14.9% of the strains. No blaCTX-M-2 group's gene was found. A subset of strains (n = 40) was selected for whole genome sequencing. Escherichia coli serotype O18: H7 ST 1463 was predominant (n = 14) in the sequenced strains and showed pathogenicity in the Galleria mellonella larvae model. β-lactamase genes identified were blaCTX-M (n = 21), with blaCTX-M-15 mostly represented (n = 15), as well as blaTEM (n = 11), blaOXA (n = 7), blaSHV (n = 9), and carbapenemase (CP) genes were observed in several strains-blaKPC-3 (n = 19), blaNDM-1 (n = 1), blaVIM-1 (n = 2), and blaOXA-244 (n = 2)-even from freshwaters.

CONCLUSIONS

ESBL-EC are widely distributed in the aquatic environment in Belgium and contain a variety of ESBL and CP genes.

Quantitative microbial risk assessment for ingestion of antibiotic resistance genes from private wells contaminated by human and livestock fecal sources

We used quantitative microbial risk assessment to estimate ingestion risk for intI1, erm(B), sul1, tet(A), tet(W), and tet(X) in private wells contaminated by human and/or livestock feces. Genes were quantified with five human-specific and six bovine-specific microbial source-tracking (MST) markers in 138 well-water samples from a rural Wisconsin county. Daily ingestion risk (probability of swallowing ≥1 gene) was based on daily water consumption and a Poisson exposure model. Calculations were stratified by MST source and soil depth over the aquifer where wells were drilled. Relative ingestion risk was estimated using wells with no MST detections and >6.1 m soil depth as a referent category. Daily ingestion risk varied from 0 to 8.8 × 10-1 by gene and fecal source (i.e., human or bovine). The estimated number of residents ingesting target genes from private wells varied from 910 (tet(A)) to 1,500 (intI1 and tet(X)) per day out of 12,000 total. Relative risk of tet(A) ingestion was significantly higher in wells with MST markers detected, including wells with ≤6.1 m soil depth contaminated by bovine markers (2.2 [90% CI: 1.1-4.7]), wells with >6.1 m soil depth contaminated by bovine markers (1.8 [1.002-3.9]), and wells with ≤6.1 m soil depth contaminated by bovine and human markers simultaneously (3.1 [1.7-6.5]). Antibiotic resistance genes (ARGs) were not necessarily present in viable microorganisms, and ingestion is not directly associated with infection. However, results illustrate relative contributions of human and livestock fecal sources to ARG exposure and highlight rural groundwater as a significant point of exposure.IMPORTANCEAntibiotic resistance is a global public health challenge with well-known environmental dimensions, but quantitative analyses of the roles played by various natural environments in transmission of antibiotic resistance are lacking, particularly for drinking water. This study assesses risk of ingestion for several antibiotic resistance genes (ARGs) and the class 1 integron gene (intI1) in drinking water from private wells in a rural area of northeast Wisconsin, United States. Results allow comparison of drinking water as an exposure route for antibiotic resistance relative to other routes like food and recreational water. They also enable a comparison of the importance of human versus livestock fecal sources in the study area. Our study demonstrates the previously unrecognized importance of untreated rural drinking water as an exposure route for antibiotic resistance and identifies bovine fecal material as an important exposure factor in the study setting.

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.

High throughput qPCR unveils shared antibiotic resistance genes in tropical wastewater and river water

The global challenge posed by rising antimicrobial resistance, and the adoption of a One Health approach, has led to the prioritisation of surveillance for antibiotic resistance genes (ARGs) in various environments. Herein lies an information gap, particularly in the context of Thailand, where there is scarce data on ARG prevalence across diverse environmental matrices and throughout different seasons. This study aimed to fill this void, analysing ARG prevalence by high-throughput qPCR in influent (n = 12) and effluent wastewater (n = 12) and river water (n = 12). The study reveals a substantial and largely uniform presence of ARGs across all water sample types (87 % similarity). Intriguingly, no ARGs were exclusive to specific water types, indicating an extensive circulation of resistance determinants across the aquatic environment. The genes intI1, tnpA, and intI3, part of the integrons and mobile genetic elements group, were detected in high relative abundance in both wastewater and river water samples, suggesting widespread pollution of rivers with wastewater. Additional high-prevalence ARGs across all water types included qepA, aadA2, merA, sul1, qacF/H, sul2, aadB, and ereA. More alarmingly, several ARGs (e.g., blaVIM, intI3, mcr-1, mexB, qepA, vanA, and vanB) showed higher relative abundance in effluent and river water than in influents, which suggests malfunctioning or inadequate wastewater treatment works and implicates this as a possible mechanism for environmental contamination. Nine genes (i.e., blaCTX-M, blaVIM, emrD, ermX, intI1, mphA, qepA, vanA, and vanB) were recovered in greater relative abundance during the dry season in river water samples as compared to the wet season, suggesting there are seasonal impacts on the efficacy of wastewater treatment practices and pollution patterns into receiving waters. This study highlights the urgency for more effective measures to reduce antibiotic resistance dissemination in water systems.