Category Research project
  • Mikrobiologie

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

Project status
Completed
Project start
Jan 2020
Project end
Dec 2022
Acronym
EJP FULLFORCE
Department
Biologische Sicherheit
Website
https://onehealthejp.eu/jrp-full-force/

Description and Objective

The FULL_FORCE consortium will broadly introduce long-read sequencing and hybrid assemblies in national surveillance programmes of antimicrobial resistance (AMRshort forAntimicrobial resistance) across Europe, including E. colishort forEscherichia 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 AMRshort forAntimicrobial resistance dynamics by integration of microbiological, genomic, microbial population composition and antimicrobial usage data.

Result

As part of the Full_Force project, strategies for analysing complete bacterial genomes were investigated. The focus was on comparing different methods of genome sequencing (ONT and PacBio), but also on the reliability and credibility of assembly algorithms for the composition of the sequences obtained. Various bacterial genome sequences for multidrug-resistant Escherichia coli were generated at the BfRshort forGerman Federal Institute for Risk Assessment and made available to the project partners for comparative analyses. In addition, isolates were provided that were used for comparative sequencing analyses in various institutes. The DTU was responsible for comparing the data from the individual laboratories on the variability and dependence of the genome sequences on the techniques used. Extensive investigations were carried out at the BfRshort forGerman Federal Institute for Risk Assessment, including on the occurrence and diversity of quinolone and fluoroquinolone resistance plasmids. Escherichia coli isolates from zoonosis monitoring were analysed for possible resistance genes using PCR and used for sequencing studies. Selected isolates were sequenced using PacBio and then used for comparative analyses. In addition, various co-operation projects were carried out with other partners on the occurrence of specific plasmid types (e.g. IncK). Both isolates and genome sequences were provided for this purpose, which were then used for comparative analyses (One-Health approach). The project formed the basis for the establishment of long read whole genome sequencing at the BfRshort forGerman Federal Institute for Risk Assessment and provided an insight into the strengths and weaknesses of sequencing technologies and the associated bioinformatic analyses.
Type of project

Third-party funded project

Research focus

Gesundheit von Mensch, Tier und Umwelt (One Health)

Organisational units and partners

Lead specialist group: Diagnostik, Erregercharakterisierung, Parasiten in Lebensmitteln (45)
Contact persons: Dr. Jens André Hammerl, Prof. Dr. Annemarie Käsbohrer
External partner: Sciensano, Animal & Plant Health Agency, Complutense University of Madrid

Funding body and grant number

Europäische Union
Grant agreement 773830

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