Abstract
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, and 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. Petersburg 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 multilocus sequence types were found.
Highlights
Significant inter-country differences were found regarding the prevalence of E. coli showing extended-spectrum beta-lactamases (ESBLs)/AmpC phenotype (Table 1)
This study describes the phenotypic and molecular epidemiology of E. coli strains with reduced susceptibility to third-generation cephalosporins in Northern and Eastern Europe by screening of more than 10,000 E. coli strains
We found more strains with the ESBL/AmpC phenotype and genotype in St
Summary
Antimicrobial resistance is an emerging problem worldwide. Each year, 33,000 people die from an infection due to bacterial resistance to antibiotics in Europe. Data from WHO CAESAR 2016 report includes a limited number of strains from Western part of Russia and shows high proportion of invasive E. coli isolates resistant to thirdgeneration cephalosporins (66%; World Health Organisation, 2016). The aim of this study has been to describe the prevalence and molecular mechanisms of resistance to third-generation cephalosporins in E. coli strains isolated from 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). All non-duplicate E. coli isolates interpreted as a probable cause of infection were included to the study (excluding clinically irrelevant cases, such as probable colonization or contamination from indigenous microbiota), and tested for third-generation cephalosporins (at least for ceftazidime and ceftriaxone and/or cefotaxime). The prevalence of strains, genes, ST and clones were compared by Chisquared test or Fisher’s exact test; p < 0.05 was considered statistically significant
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