Sophia David, Anke Kohlenberg, Corin Yeats, Khalil Abu-Dahab, Barbara Albiger, Nabil-Fareed Alikhan, Erik Alm, Sara Byfors, Natacha Couto, Julio Diaz Caballero, Christian G. Giske, Corinna Glasner, Marius Linkevičius, Erika Matuschek, Daniel Palm, Olov Svartström, Hajo Grundmann, Marc J Struelens, Karin Tegmark Wisell, Dominique L. Monnet, Inga Fröding, David M Aanensen, Alma Brolund, Andi Koraqi, Artan Bego, Petra Apfalter, Rainer Hartl, Te-Din Huang, Katrien Latour, Maja Travar, Stefana Sabtcheva, Arjana Tambić-Andrašević, Jaroslav Hrabák, Helena Žemličková, Panayiota Maikanti Charalambous, Anette M Hammerum, Anastasia Bilozor, Marika Jürna‐Ellam, Jari Jalava, Kati Räisänen, Laurent Dortet, Ines Noll, Niels Pfennigwerth, Kyriaki Tryfinopoulou, Alkiviadis Vatopoulos, Ákos Tóth, Kristjan Orri Helgason, Martin Cormican, Maria Del Grosso, Maria Giufrè, Arsim Kurti, Lul Raka, Baiba Niedre-Otomere, Jelena Razmuk, Jekaterina Sinotova, Marie Meo, Monique Perrin, Denise Micallef, Nina Nestorova, Milena Lopičić, Vineta Vuksanović, Antoni P A Hendrickx, Karuna E W Vendrik, Ana Kaftandzieva, Dugagjin Osmani, Ørjan Samuelsen, Elżbieta Literacka, Manuela Caniça, Vera Manageiro, Irina Codiţă, Brandusa Lixandru, Ivana Ćirković, Deana Medić, M Nikś, Mateja Pirš, Belén Aracil, Jesús Oteo Iglesias, Petra Edquist, Karin Westmo, Hüsniye Şimşek, Serap Süzük Yildiz, Katie L Hopkins, Danièle Meunier
Background The emergence of carbapenem resistance in Escherichia coli is of major concern due to the high propensity of spread of this species and scarce treatment options. Herein, we examined the occurrence and spread of carbapenem-resistant E coli based on the carbapenem-resistant and/or colistin-resistant Enterobacterales (CCRE) survey performed across European countries in 2019. Methods We analysed epidemiological, microbiological, and whole-genome sequencing data of 548 E coli isolates from individual patients from 156 hospitals in 32 European countries over 6 months in 2019. These hospitals collected the first ten successive isolates of carbapenem-resistant or carbapenem-susceptible increased exposure (carbapenem-R/I) Klebsiella pneumoniae species complex or E coli, and carbapenem-susceptible (carbapenem-S) comparator isolates of the same species. Antimicrobial susceptibility testing was performed for 19 antimicrobial agents. Whole-genome sequencing was performed centrally using Illumina technology. Isolates from the CCRE survey were compared with those from the European Survey of Carbapenemase-Producing Enterobacteriaceae (EuSCAPE) study. Findings Of the 548 E coli isolates, 211 (38·5%) were carbapenem-resistant or susceptible, increased exposure (carbapenem-R/I), and 337 (61·5%) were carbapenem-susceptible (carbapenem-S). Five sequence types (STs) accounted for 96 (45·5%) of 211 carbapenem-R/I isolates: ST131 (27), ST410 (20), ST38 (19), ST167 (16), and ST648 (14). Carbapenemase genes were identified in 182 (86·3%) carbapenem-R/I isolates, a pronounced increase from the 2013–14 EuSCAPE study (36 of 99, 36·4%). The most common genes were bla NDM−5 (62 of 182, 34·1%) and bla OXA−48 (40 of 182, 22·0%). bla NDM−5 carriage increased substantially compared with that in EuSCAPE (two of 99, 2·02%). Phylogenetic analysis showed substantial clonal spread of globally disseminated bla NDM−5 -harbouring lineages, with numerous introductions into Europe but minimal onward transmission. Interpretation High-risk STs of E coli carrying carbapenemase genes are rapidly spreading globally, although our results indicate that, in 2019, most cases in Europe were sporadic. We urge vigilant monitoring, including genomic surveillance, and strengthening of control efforts, to reduce mortality and morbidity associated with the impending rise in carbapenem-R/I E coli cases. Funding European Centre for Disease Prevention and Control and the Centre for Genomic Pathogen Surveillance.