Projects

Antimicrobial resistance (AMR) is an important issue today as it has reached dangerously high levels in all parts of the world due to the misuse and overuse of antibiotics. Antibiotic resistance genes (ARGs) have been detected in all environments, including natural, artificial and clinical habitats, over the past decade. Anthropogenic activities, including the clinical use of antibiotics, are widely recognized as the main cause of the spread of ARGs, as numerous genetic mechanisms such as conjugation, transformation and transduction enable microorganisms to evolve, adapt and survive in an environment contaminated with antibiotics and ARGs. The aquatic environment plays a crucial role in the spread of antibiotic resistance genes (ARGs), as it is both the final receiving system for most anthropogenic effluents containing ARGs (municipal wastewater, runoff from fields and livestock facilities, etc.) and the main source of recreational, irrigation and drinking water. The popularity of recreational activities that involve contact with water continues to grow worldwide. However, participation in these activities poses some potential microbiological health risks, as human exposure through skin, eye or ear contact, inhalation and ingestion of ARB and ARG in bathing waters can lead to infections that are difficult to treat.

Most clinically relevant ARGs are not randomly distributed in the genomes of antibiotic-resistant bacteria (ARB), but are bundled in mobile genetic elements (MGEs) such as plasmids or transposons, which allow horizontal transfer of ARGs between bacteria. ARGs/MGEs can be transferred as part of ARB genomes (conjugation), in the capsids of bacteriophages (or simple phages) (transduction) or as free DNA (transfection). It has been shown that the capsids of environmental phages frequently transport ARGs. Since phage genomes rarely encode ARGs, this ARG/MGE content in the capsids consists mainly of more or less randomly encapsulated bacterial DNA. It is therefore of great importance to gain new insights into the role of phages in the environment in the dissemination of ARG/MGE and the compartmentalization of the environment.

Bathing waters are assessed on the basis of compliance with certain standards (total coliform bacteria, E. coli, ... ). In the EU, the quality of bathing water is regulated by the Bathing Water Directive (BWD). Currently, only the number of microorganisms in water is measured in recreational waters to determine quality, but not in sediments, although sediments are heavily contaminated with viruses of fecal origin and indicator phages and the ARG they carry. The current Water Framework Directive

(2006/7/EC) monitors water quality at designated bathing waters and focuses on the enumeration of fecal indicator organisms (FIO); E. coli and intestinal enterococci. Phages are completely neglected at this stage in bathing waters, although the Drinking Water Directive (2020/2184) provides for methods to detect somatic and F-specific coliphages during regular monitoring. The Drinking Water Directive does not contain such a paragraph, as the presence and biological risk of phages in bathing waters appears to be non-existent or negligible.

To gain new insights and fill the existing gaps regarding the potential role of phages in the emergence and spread of antibiotic resistance in bathing waters, we will apply different sampling methods for water and sediment, conventional cultivation and cultivation-independent metagenomic analyses. The cultivation-based approach is further required to investigate the actual horizontal transmission, transmission frequency, host and environmental factors influencing the transmission frequency of ARGs via plasmids and/or phages, including their host range, as these data cannot be obtained by bioinformatic analyses alone, and finally, the obtained data will be evaluated with statistical analyses and machine learning-based model predictions.

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