Data_Sheet_3_Phenotypic and Molecular Epidemiology of ESBL-, AmpC-, and Carbapenemase-Producing Escherichia coli in Northern and Eastern Europe.PDF

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.

广谱β-内酰胺酶（ESBL）和AmpC型产生的大肠杆菌已在全球范围内传播，然而关于欧洲北部和东部地区ESBL型大肠杆菌的数据却极为匮乏。本研究旨在描述从波罗的海国家（爱沙尼亚、拉脱维亚和立陶宛）、挪威以及俄罗斯圣彼得堡分离出的大肠杆菌菌株中不同ESBL/AmpC/碳青霉烯酶基因的表型及分子流行病学特征，并确定由全基因组测序（WGS）推断出的E. coli菌株优势的多重基因座序列型和单核苷酸多态性多样性。总计10,780个临床E. coli菌株被筛选出对第三代头孢菌素的敏感性降低。这些菌株收集自2012年5个月期间位于爱沙尼亚、拉脱维亚、立陶宛、挪威和圣彼得堡的21家医院。通过表型测试，ESBL/AmpC菌株的总患病率为4.7%，而通过测序为3.9%。我们发现圣彼得堡和拉脱维亚比其他国家拥有更多具有ESBL/AmpC表型和基因型的菌株。在表型E. coli菌株中，85%含有已确认的ESBL基因（包括blaCTX–M、blaTEM–29、blaTEM–71），AmpC基因（blaCMY–59、blaACT–12/–15/–20、blaESC–6、blaFEC–1、blaDHA–1）或碳青霉烯酶基因（blaNDM–1）。blaCTX–M–1、blaCTX–M–14和blaCTX–M–15在所有国家均有发现，但blaCTX–M–15在拉脱维亚的患病率高于圣彼得堡（俄罗斯）、爱沙尼亚、挪威和立陶宛。在波罗的海国家和挪威中，优势AmpC基因是blaCMY–59，而在圣彼得堡是blaDHA–1。E. coli菌株属于83种不同的序列型，其中最普遍的是ST131（占40%）。综上所述，我们在北/东欧分离的E. coli菌株中普遍发现ESBL/AmpC/碳青霉烯酶的患病率较低。然而，发现不同国家之间在特定基因和多重基因座序列型分布上存在显著差异。