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Front. Microbiol. | doi: 10.3389/fmicb.2019.02465

Phenotypic and molecular epidemiology of ESBL-, AmpC-, and carbapenemase-producing Escherichia coli in Northern and Eastern Europe

 Epp Sepp1, Reidar Andreson2, Arta Balode3,  Anastasia .Bilozor4,  Svetlana Egorova5, Kristi Huik6, Marina Ivanova4, Lidia Kaftyreva5, Siiri Kõljalg1, Triinu Kõressaar2,  Maria Makarova5,  Jolanta Miciuleviciene7, Kristiine Pai1,  Maido Remm2,  Tiiu Rööp1 and  Paul Naaber1, 8*
  • 1Department of Microbiology, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Estonia
  • 2Department of Bioinformatics, Institute of Molecular and Cell Biology, Faculty of Science and Technology, University of Tartu, Estonia
  • 3Riga Stradiņš University, Latvia
  • 4Department of Microbiology, East Tallinn Central Hospital, Estonia
  • 5Department of Enteric Infections, Saint Petersburg Pasteur Institute, Russia
  • 6National Cancer Institute, National Institutes of Health (NIH), United States
  • 7Department of Microbiology, Vilnius City Clinical Hospital, Lithuania
  • 8Synlab (Estonia), Estonia

Extended spectrum beta-lactamases (ESBL) and AmpC producing-Escherichia coli have spread worldwide, but data about ESBL-producing-E. coli 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 E. coli strains isolated from the Baltic States (Estonia, Latvia, Lithuania), Norway and St. Petersburg (Russia), and to determine the predominant multilocus sequence type and single nucleotide polymorphisms diversity of E. coli isolates deduced by whole-genome sequencing (WGS).
A total of 10,780 clinical E. coli 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. Peterburg and Latvia than other countries. Of phenotypic E. coli strains, 85% contained confirmed ESBL genes (including blaCTX-M, blaTEM-29, blaTEM-71), AmpC genes (blaCMY-59, blaACT-12/-15/-20, blaESC-6, blaFEC-1, blaDHA-1) or carbapenemase genes (blaNDM-1). blaCTX-M-1, blaCTX-M-14 and blaCTX-M-15 were found in all countries, but blaCTX-M-15 prevalence was higher in Latvia than in St. Petersburg (Russia), Estonia, Norway and Lithuania. The dominating AmpC genes were blaCMY-59 in the Baltic States and Norway, and blaDHA-1 in St. Petersburg. E. coli 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 E. coli strains isolated in Northern/Eastern Europe. However, several inter-country differences in distribution of particular genes and multi-locus sequence types were found.

Keywords: Escherichia coli, whole genome sequencing, Multi-locus sequence typing, Northern and Eastern Europe, ESBL/AmpC/carbapenemases

Received: 15 Mar 2019; Accepted: 15 Oct 2019.

Copyright: © 2019 Sepp, Andreson, Balode, .Bilozor, Egorova, Huik, Ivanova, Kaftyreva, Kõljalg, Kõressaar, Makarova, Miciuleviciene, Pai, Remm, Rööp and Naaber. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Mr. Paul Naaber, Synlab (Estonia), Tallinn, Estonia, paul.naaber@gmail.com