Phenotypic and Molecular Epidemiology of ESBL-, AmpC-, and Carbapenemase-Producing Escherichia coli in Northern and Eastern Europe

Abstract

Extended-spectrum beta-lactamases (ESBL) and AmpC producing-<i>Escherichia coli</i> have spread worldwide, but data about ESBL-producing-<i>E. coli</i> in the Northern and Eastern regions of Europe is scant. The aim of this study has been to describe the phenotypical and molecular epidemiology of different ESBL/AmpC/Carbapenemases genes in <i>E. coli</i> strains isolated from the Baltic States (Estonia, Latvia, and Lithuania), Norway and St. Petersburg (Russia), and to determine the predominant multilocus sequence type and single nucleotide polymorphisms diversity of <i>E. coli</i> isolates deduced by whole genome sequencing (WGS). A total of 10,780 clinical <i>E. coli</i> strains were screened for reduced sensitivity to third-generation cephalosporins. They were collected from 21 hospitals located in Estonia, Latvia, Lithuania, Norway and St. Petersburg during a 5 month period in 2012. The overall prevalence of ESBL/AmpC strains was 4.7% by phenotypical test and 3.9% by sequencing. We found more strains with the ESBL/AmpC phenotype and genotype in St. Petersburg and Latvia than other countries. Of phenotypic <i>E. coli</i> strains, 85% contained confirmed ESBL genes (including <i>bla</i> _CTX-M, <i>bla</i> _TEM- ₂₉, <i>bla</i> _TEM- ₇₁), AmpC genes (<i>bla</i> _CMY- ₅₉, <i>bla</i> _ACT- ₁₂ _/ _- ₁₅ _/ _- ₂₀, <i>bla</i> _ESC- ₆, <i>bla</i> _FEC- ₁, <i>bla</i> _DHA- ₁), or carbapenemase genes (<i>bla</i> _NDM- ₁). <i>bla</i> _CTX-M- ₁, <i>bla</i> _CTX-M _- ₁₄ and <i>bla</i> _CTX-M- ₁₅ were found in all countries, but <i>bla</i> _CTX-M- ₁₅ prevalence was higher in Latvia than in St. Petersburg (Russia), Estonia, Norway and Lithuania. The dominating AmpC genes were <i>bla</i> _CMY- ₅₉ in the Baltic States and Norway, and <i>bla</i> _DHA- ₁ in St. Petersburg. <i>E. coli</i> strains belonged to 83 different sequence types, of which the most prevalent was ST131 (40%). In conclusion, we generally found low ESBL/AmpC/Carbapenemase prevalence in <i>E. coli</i> strains isolated in Northern/Eastern Europe. However, several inter-country differences in distribution of particular genes and multilocus sequence types were found.