Europe advances genomic surveillance of CCRE with landmark multi-country study

The results of the largest European genomic survey of CCRE to date were published in the Lancet Microbe with separate articles covering Klebsiella pneumoniae and Escherichia coli, and a detailed report from the European Centre for Disease Prevention and Control (ECDC). 

Coordinated by ECDC and conducted in collaboration with the Public Health Agency of Sweden and The Centre for Genomic Pathogen Surveillance, Pandemic Sciences Institute, University of Oxford, the survey included epidemiological, microbiological, and whole-genome sequencing data collected in 2019 from over 300 hospitals across 36 countries. As the second large-scale structured genomic survey following the European Survey of Carbapenemase-producing Enterobacteriaceae (EuSCAPE) in 2013–2014, it represents a shift from earlier epidemiological assessments toward integrated Europe-wide genomic surveillance.

The initiative went beyond data collection. Participating countries underwent capacity assessments, trainings, and external quality assurance exercises, supporting the implementation of genomic methods in national reference laboratories.

This coordinated effort enabled many European countries to advance towards routine genomic AMR surveillance, strengthening their ability to detect, monitor, and respond to antimicrobial-resistant bacteria. The capacity -building of national reference laboratories participating in the European Antimicrobial Resistance Genes Surveillance Network (EURGen-Net) has also been supported by broader European Commission initiatives, including the HERA Incubator, the EURGen-RefLabCap project, support under the EU4Health programme, and the ECDC training programme GenEpi-BioTrain, all of which have contributed to enhanced national capabilities in advancing genomic AMR surveillance.

A worsening epidemiological situation

For K. pneumoniae, the CCRE survey showed that carbapenem-resistant high-risk lineages already identified during EuSCAPE continued to circulate across European hospitals. In addition, there were concerning changes in K. pneumoniae, including the increased acquisition of carbapenemase genes by high-risk lineages, the expansion of newly emerging high-risk lineages, and the increased spread of isolates harbouring virulence genes.  

For E. coli, several warning signals indicated a worsening epidemiological situation in Europe, including the increased acquisition of carbapenemase genes by high-risk sequence types and greater clonal spread of successful multidrug-resistant lineages. One important finding was the increased detection of E. coli isolates carrying the NDM-5 carbapenemase gene. These results suggest a high risk that carbapenem-resistant E. coli could become endemic in Europe, if no further public health actions will be are implemented. 

Together, the results reveal heterogeneous yet increasingly concerning epidemiological patterns, varying across countries from sporadic cases to endemic circulation, and provide critical information to guide public health action.

The CCRE survey results highlight the critical role of genomic data in tracking the spread of AMR in Europe. In addition, it delivers reference data that enable further studies of carbapenem-resistant K. pneumoniae and E. coli. 

Data collection for the third European Survey of carbapenem-resistant Enterobacterales (CRE25) is currently underway. CRE25 applies a simplified sampling protocol with rapid reporting enabled by increased whole-genome sequencing capacity of national reference laboratories.