The largest European genomic survey of carbapenem- and/or colistin-resistant Enterobacterales (CCRE) to date paints a worrying picture of carbapenem resistance in hospitals across the continent, with expanding high-risk lineages of Klebsiella pneumoniae and Escherichia coli and a real possibility that carbapenem-resistant E. coli could become endemic if no further action is taken. The results were published in The Lancet Microbe, with separate articles covering each pathogen.
Coordinated by the European Centre for Disease Prevention and Control (ECDC), the survey gathered epidemiological, microbiological, and whole-genome sequencing data in 2019 from more than 300 hospitals across 36 countries. It is the second large-scale structured genomic survey of its kind, following the EuSCAPE survey in 2013–2014, and marks 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. The coordinated effort has helped many countries advance toward routine genomic antimicrobial resistance (AMR) surveillance, strengthening their ability to detect, monitor, and respond to resistant bacteria.
For K. pneumoniae, the survey showed that carbapenem-resistant high-risk lineages already identified during EuSCAPE continued to circulate across European hospitals. Concerning changes included the increased acquisition of carbapenemase genes by high-risk lineages, the expansion of newly emerging high-risk lineages, and the increased spread of isolates harboring virulence genes.
The findings for E. coli were similarly troubling. Several warning signals pointed to a worsening epidemiological situation, including the increased acquisition of carbapenemase genes by high-risk sequence types and greater clonal spread of successful multidrug-resistant lineages. One particularly notable 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 are implemented.
Together, the results reveal heterogeneous yet increasingly concerning epidemiological patterns that vary by country, from sporadic cases to endemic circulation, and provide critical information to guide public health action. Data collection for a third survey, CRE25, is already underway, applying a simplified sampling protocol with rapid reporting enabled by increased whole-genome sequencing capacity at national reference laboratories.
Coordinated by the European Centre for Disease Prevention and Control (ECDC), the survey gathered epidemiological, microbiological, and whole-genome sequencing data in 2019 from more than 300 hospitals across 36 countries. It is the second large-scale structured genomic survey of its kind, following the EuSCAPE survey in 2013–2014, and marks 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. The coordinated effort has helped many countries advance toward routine genomic antimicrobial resistance (AMR) surveillance, strengthening their ability to detect, monitor, and respond to resistant bacteria.
For K. pneumoniae, the survey showed that carbapenem-resistant high-risk lineages already identified during EuSCAPE continued to circulate across European hospitals. Concerning changes included the increased acquisition of carbapenemase genes by high-risk lineages, the expansion of newly emerging high-risk lineages, and the increased spread of isolates harboring virulence genes.
The findings for E. coli were similarly troubling. Several warning signals pointed to a worsening epidemiological situation, including the increased acquisition of carbapenemase genes by high-risk sequence types and greater clonal spread of successful multidrug-resistant lineages. One particularly notable 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 are implemented.
Together, the results reveal heterogeneous yet increasingly concerning epidemiological patterns that vary by country, from sporadic cases to endemic circulation, and provide critical information to guide public health action. Data collection for a third survey, CRE25, is already underway, applying a simplified sampling protocol with rapid reporting enabled by increased whole-genome sequencing capacity at national reference laboratories.