ECDC is looking to establish a scientific collaboration with an organisation which can perform whole genome sequencing (WGS), carry out related data analyses, and visualise the results. The scope of work is anticipated to encompass approximately 6 000 isolates of carbapenem-resistant and/or colistin-resistant Enterobacteriaceae that will be collected within a pan-European structured survey scheduled for 2018. For further details, please see the ECDC study protocol for genomic-based surveillance of carbapenem-resistant and/or colistin-resistant Enterobacteriaceae at the EU level.
The collaborator will benefit from access to a large and representative collection of isolates and the resulting data, in agreement with ECDC and the participating EU/EEA countries. The collaborators will also be included as co-authors on the resulting scientific publications from the EU study that will use these WGS data and/or the results generated through this collaboration, in accordance with international recommendations on authorship.
The following minimum eligibility criteria will apply to this scientific collaboration:
- Organisation and data server should be located in the European Union (EU)/European Economic Area (EEA) and meet EU data protection requirements
- Services should be offered without cost to ECDC
- The collaborator should be a public or non-commercial organisation
- The collaborator should be able to offer several different analytical approaches to support the WGS analysis, including phylogenetic analysis and resistome/virulence profiling, analysis of the correlation between phenotypic resistance to carbapenems and colistin and known carbapenem and colistin genetic resistance markers, and the characterisation of the baseline genomic population structure
- The collaborator should be able to offer visualisation solutions for the phylogenetic analysis and resistome/virulence profiling
- Generated data can only be disclosed, used and published in agreement with ECDC and the participating EU/EEA countries which participate in the survey.
Rights and obligations of ECDC and the collaborator will be specified in a memorandum of understanding to be signed by both parties prior to the start of the project. No financial contribution can be made by ECDC in the framework of this collaboration.
Please declare your interest by emailing to ECDC.Microbiology@ecdc.europa.eu
. Include a short technical proposal which describes the analytical methodology and proposed platform for WGS analysis for identification of resistance determinants and clonal type of carbapenem-resistant and/or colistin-resistant Enterobacteriaceae
ECDC will select the collaborator who best matches the criteria above.
Deadline: Friday 7 April 2017, COB