Results of the survey of carbapenem- and/or colistinresistant Enterobacterales, 2019

In response to the increasing threat of antimicrobial resistance, standardised genomic surveys such as the survey of carbapenem- and/or colistin-resistant Enterobacterales (CCRE survey) play an important role to detect emerging resistance patterns and high-risk clones, including in countries and/or regions that may not be covered by routine molecular surveillance. In the CCRE survey, we obtained a total of 2 973 Klebsiella pneumoniae species complex and 548 Escherichia coli isolates with clinical and epidemiological data together with high-quality whole-genome sequencing (WGS) data from 323 hospitals in 36 European countries in 2019. Analysis of these isolates provided a wealth of results, which give further insight into the continued spread and new emergence of carbapenemaseproducing K. pneumoniae and E. coli high-risk clones in the European Union/European Economic Area (EU/EEA) and have direct implications for control. Comparison over time with the results from the European Survey of Carbapenemase-producing Enterobacteriaceae (EuSCAPE) conducted in 2013–2014 was especially valuable.

Although the analysis was delayed because of the COVID-19 pandemic, this CCRE survey was the first study to detect the increase of blaNDM-5-carrying E. coli in the EU/EEA and the emergence of the new clade of K. pneumoniae sequence type (ST)39 carrying blaKPC-2 in Greece. In both cases, follow-up investigations have already confirmed the signal from the CCRE survey and provided relevant further insights. The CCRE survey also detected an increase of K. pneumoniae ST307 and insights into the geo-temporal spread of K. pneumoniae ST11. In addition, the CCRE survey showed that there was not one single epidemic of carbapenem-R/I K. pneumoniae SC in the 36 participating countries, but heterogenous epidemiological situations ranging from sporadic cases to endemicity, involving a varying mix of K. pneumoniae STs and carbapenemases at the national level. Further analysis and comparison with national data may yield additional relevant results. In this respect, the data set can serve as a reference for further genomic studies.

The model of repeated structured genomic surveys is now an established element of European genomic surveillance and may be used for future national and EU-level surveys for carbapenem-resistant Enterobacterales and other multidrug-resistant pathogens. At the same time, efforts to establish faster and more comprehensive genomic surveillance should continue, including those related to capacity building at the national level.