FULL-FORCE

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

Start: 1 January 2020
Duration: 2.5 Years
Domain: Antimicrobial Resistance
Key Words: Mobile Genetic Elements, Long-read sequencing, Metagenome data mining, Evaluation of in silico tools
Contact: Pieter-Jan Ceyssens (Sciensano)

The Project #FULLFORCE

Current European monitoring systems for antimicrobial resistance (AMR) fall short in dissecting clonal from horizontal transmission of AMR genes. Although an increasing emphasis is put on genomic-based surveillance, mobile genetic elements (MGEs) remain challenging to reconstitute due to their chimeric, modular and repetitive nature. These MGEs often encode resistance to critical antibiotics and can spread within or across species and genera, making them a central part of any AMR transmission study.

The FULL-FORCE consortium will broadly introduce single molecule real-time (SMRT) sequencing in EU veterinary and public health institutes. This technology allows real-time sequencing with long sequence reads, providing additional information of where a read should be placed in the genome. Building on JPIAMR’s SOLIDNESS results, we will harmonise, build and test each institute’s SMRT sequencing capacity. We will apply this knowledge on six study cases which will greatly profit from MGE sequencing, incl. samples isolated in the context of national surveillance programmes, EFFORT and ARDIG projects. This will be followed up by detailed investigation of prominent MGEs, and by applying this knowledge to modelling efforts of AMR dynamics in closed production systems. At the same time, high-quality MGEs sequencing will provide an excellent dataset to test the performance of public and in-house developed tools for MGE typing, and to study associations between AMR genes and MGEs in metagenomic datasets from the EFFORT project.

In conclusion, FULL-FORCE will supply 17 EU partners with a technological toolbox and hands-on training in SMRT sequencing. This will allow a paramount step for the effective integration of MGE typing in One Health AMR surveillance, whilst delivering an unprecedented insight in dominant MGEs which are driving resistance among commensal and pathogenic Enterobacteriaceae in Europe. Full Force ahead.

Publications

Savin, M., Bierbaum, G., Kreyenschmidt, J., Sib, E., Schmoger, S., Käsbohrer, A., Hammerl, J-A. (2021). Clinically Relevant Escherichia coli Isolates from Process Waters and Wastewater of Poultry and Pig Slaughterhouses in Germany. Microorganisms. 9, 698. DOI: https://doi.org/10.3390/microorganisms9040698

Juraschek, K., Borowiak, M., Tausch, SH., Malorny, B., Käsbohrer, A., Otani, S., Schwarz, S., Meemken, D., Deneke, C., Hammerl, JA. (2021). Outcome of Different Sequencing and Assembly Approaches on the Detection of Plasmids and Localization of Antimicrobial Resistance Genes in Commensal Escherichia coli. Microorganisms. 9, 598. DOI: https://doi.org/10.3390/microorganisms903059

Diaconu, EL., Carfora, V., Alba, P., Di Matteo, P., Stravino, F., Buccella, C., Dell’Aira, E., Onorati, R., Sorbara, L., Battisti, A., Franco, A. (2020). Novel IncFII plasmid harbouring blaNDM-4 in a carbapenem-resistant Escherichia coli of pig origin, Italy. Journal of Antimicrobial Chemotherapy. 75(12), 3475–3479. DOI: https://doi.org/10.1093/jac/dkaa374

OpenAIRE Publications

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