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Full-length sequencing for an enhanced EFFORT to map and understand drivers and reservoirs of antimicrobial resistance (EJP FULLFORCE)

01/2020-06/2022

Funding programme / funding institution: Europäische Union Horizon2020

Grant number: 773830

Project homepage: https://onehealthejp.eu/jrp-full-force/

Project description:

The FULL_FORCE consortium will broadly introduce long-read sequencing and hybrid assemblies in national surveillance programmes of antimicrobial resistance (AMR) across Europe, including E. coli strains isolated in the context of the EFFORT and ARDIG projects. This will be followed up by detailed investigation of identified Mobile Genetic Elements (MGEs) and modelling of AMR dynamics by integration of microbiological, genomic, microbial population composition and antimicrobial usage data.  We will address the following priorities set in the AMR 2.2 call text by aiming to:

Study the clonal spread of resistant bacteria vs. horizontal gene transfer. By using hybrid assemblies of existing short-read sequences with newly generated long-read data, we will be able to dissect chromosomal from plasmid-encoded resistance determinants. A specific focus will be placed on harmonizing wet lab and dry lab procedures. Moreover, we will compare and validate software tools which allows this distinction.

Study the overlap and transmission dynamics of resistant bacteria. Transmission of AMR will be studied on both a molecular level with in-depth characterization of mobilizing capacity and fitness of MGEs, as well as by epidemiological modelling existing datasets of antimicrobial use (AMU), AMR phenotype and sequence data. Of special interest are metagenomics dataset from EFFORT and longitudinal sample sets from the ARDIG project (animal) and RIVM (NL, human).

Investigate the geographical differences and trends in AMR in the natural environment, including the influence of animal husbandry on the occurrence and spread of AMR in the environment and in people living in proximity to farms. The latter will be addressed using samples and metadata from the EFFORT and ARDIG studies, comprising E. coli strains isolates at farms in nine countries. To investigate the geographical differences, this data will be complemented with a cross-sectional and multi-sectorial set of characterized AMR Enterobacteriaceae from EU surveillance programmes.

Focus on emerging resistances and Critically Important antibiotics. In the selection of strains, we will solely focus on those resistant to antibiotics classified as Highest Priority Critically Important Antimicrobials according to the latest classification of WHO and OIE, i.e. carbapenems, 3rd and 4th generation cephalosporins and colistin.

Project partners:

• AUSTAUSCH VON SEQUENZDATEN, GEMEINSAME BIOINFORMATISCHE ANALYSE
  Sciensano
  
• AUSTAUSCH VON SEQUENZDATEN, GEMEINSAME BIOINFORMATISCHE AUSWERTUNG
  Animal and Plant Health Agency
• AUSTAUSCH VON SEQUENZDATEN, GEMEINSAME BIOINFORMATISCHE AUSWERTUNGEN
  Universidad Complutense de Madrid

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