2020 - 2021
OHEJP- Full-length sequencing for an enhanced EFFORT to map and understand drivers and reservoirs of antimicrobial resistance (FULL_FORCE)
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 harmonize, 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.