Gene flow between environmental and enteric bacteria with environmental coselection for metal and antibiotic resistance genes: A case study

Vieira, A.; Prasad Nair R U, V.; Giakoumis, T.; Latha, R.; Muthu, M. S.; Kiran, G. S.; Voulvoulis, N.; Selvin, J.; Sriskandan, S.

doi:10.1101/2025.09.15.676296

bioRxiv · 10.1101/2025.09.15.676296

Gene flow between environmental and enteric bacteria with environmental coselection for metal and antibiotic resistance genes: A case study

Vieira, A.·Prasad Nair R U, V.·Giakoumis, T.·Latha, R.·Muthu, M. S.·Kiran, G. S.·Voulvoulis, N.·Selvin, J.·Sriskandan, S.

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Abstract

BackgroundThe global threat of antimicrobial resistance (AMR) is driven by multiple factors, including inadequate sanitation and the suboptimal use of antibiotics in healthcare. The environment is recognised as an important and underappreciated reservoir for AMR. Pollutants can exert selective pressure that co-selects for resistant phenotypes, while faecal contamination introduces enteric bacteria capable of acquiring resistance elements that provide a survival advantage. AimsThis study aimed to characterize multidrug-resistant (MDR) bacteria in sediment and water samples collected from an industrial site and an adjacent canal in 2023 and 2024. Selective agar plating was used to isolate MDR bacteria, which were subsequently subjected to whole-genome sequencing and analysed for the presence of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and plasmid content. ResultsForty-two MDR isolates were retrieved and sequenced over two seasons. Most were Gram negative and most originated from the industrial location; no MDR bacteria were found in a control location. Species included both environmental and Enterobacteriaceae, indicative of faecal contamination by wastewater, Of the 40 bacteria that possessed at least one ARG, 87.5% (35/40) also carried at least one or more MRG. ARG identified on mobile genetic elements included CTXM-15, bla-NDM1, bla-VIM1, other carbapenemases, and 16sRMTases. MRG encoded resistance to copper, silver, tellurium, arsenic, and mercury, while plasmid assemblies showed evidence of genetic exchange within the environmental ecosystem. Levels of mercury, vanadium, zinc and copper in sediments exceeded international guideline values. ConclusionIndustrial locations harbour a spectrum of pollutants that contribute to the development and spread of AMR. In this case study, heavy metals appear to act as a potentially major selective pressure driving the evolution of multidrug resistance through co-selection. The observed diversity of mobilizable ARGs and MRGs in the environment highlights the potential for such toxic environments to serve as incubators for the emergence of novel, high-risk bacterial clones.

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Vieira, A., Prasad Nair R U, V., Giakoumis, T., Latha, R., Muthu, M. S., Kiran, G. S., Voulvoulis, N., Selvin, J., Sriskandan, S.. 2025-09-15. Gene flow between environmental and enteric bacteria with environmental coselection for metal and antibiotic resistance genes: A case study. https://doi.org/10.1101/2025.09.15.676296

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