Genomic based surveillance of carbapenem resistant and/or colistin-resistant Enterobacteriaceae at the EU level (EURGenCCRE)
EURGenCCRE is an ECDC funded project aiming at establishing a European network for surveillance of antibiotic resistance by whole genome sequencing (EURGen-Net).
The network is coordinated by a consortium including the partners Karolinska University Laboratory and the EUCAST development laboratory in Växjö and is led by the Public Health Agency of Sweden (PHAS).
The project builds on the previously performed study, EuSCAPE, and includes a repeated, structured multi-centre molecular epidemiological survey of carbapenem- and/or colistin-resistant K. pneumoniae and E. coli among patients seeking hospital care. The overarching public health objective is to determine the occurrence, geographic distribution and the population dynamics of high-risk Enterobacteriaceae clones, and transmissible resistance/genetic-elements of critical public health importance in Europe.
In preparation for the structured survey (CCRE survey), capacity building efforts such as a laboratory training workshop and an external quality assessment program (EQA) was performed within the network. These activities ensure that harmonized methods are used for the genetic- and phenotypic confirmation of colistin and carbapenem resistance. The national reference laboratories in the participating countries coordinates the isolates collection and verifies the antibiotic resistance profiles. The CCRE survey collection period of six months will be finished in Q4 2019. All isolates collected in the structured survey will be subjected to whole genome sequencing at a central facility. The analysis of the whole genome sequences combined with the epidemiological data collected will enable in depth molecular epidemiology studies identifying high-risk clones and transmissible resistance elements.