Identification and isolation of antibiotic resistance gene containing freshwater bacteria in an eco-evolutionary frame
Financed: MIUR PRIN2020
Duration: 3 Years (2022-2025)
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Summary: The WHO estimates that >700’000 annual deaths are caused by diseases related to antimicrobial resistance (AMR). To tackle this problem that leads to substantial health care costs on a global level the WHO strongly suggests to use a one-health approach, meaning that the environment should also be considered in solutions to clinical problems. This is of particular interest for AMR, since antibiotic resistance genes (ARGs) both evolve from the environment and accumulate there due to e.g. waste water treatment plant (WWTP) outflows or agricultural run-offs and aquatic systems are important collectors. Despite extensive research on presence and frequency of AMR in freshwater systems there are still many essential questions that are open regarding their ecology and evolution that are, however, fundamental for a realistic risk evaluation. IdeARG will tackle these questions using Lake Maggiore as a model system, namely: Which DNA fraction (chromosomal, plasmid, free DNA or bacteriophages) contains which ARGs at what frequency? Which freshwater bacteria contain ARGs? Which is the most likely route ARGs take when entering the system? Which factors promote the maintenance of ARGs in lake sediments? What is the relatedness between environmental ARGs: Are they precursors or descendants of clinically relevant ARGs? The project uses the expertise of its three units in a collaborative effort for a holistic approach to the questions: Antimicrobial resistance in the environment (CNR-IRSA), horizontal gene transfer (University of Milano) and metagenomics analysis (University of Napoli Federico II). First, large genome contigs will be assemble from sediments and WWTP outflows to identify DNA fractions with most ARGs and the bacteria caring them. Then an isolation campaign will be conducted to have pure cultures of ARG containing freshwater bacteria. Using both natural communities and strains experiments on horizontal gene transfer and bacterial fitness related to the maintenance of ARGs will be conducted. ARG sequences from databases, the environment and strains will be used to build a phylogeny of the most important ARGs to estimate the evolutionary relatedness of clinical and environmental ARGs. All in all, the data will help to evaluate the risk that freshwater environments pose in the spread of AMR. Through an open-data policy and deposition of strains, training of (Italian) PhD students in metagenomics analysis of ARGs and international collaborations, IdeARG will ensure that the data produced in the project will be integrated in a larger scientific context. Collaboration with different associations will help to increase awareness of the public. With its scientific and other measures IdeARG will significantly contribute to integrating AMR in freshwaters in a one-health approach.
Schematic view of the general organisation of the project
IdeARG Research team, Principal Investigators:
First sampling campaign (Lake Maggiore, 2022):