Data_Sheet_1_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）及AmpC产生的大肠杆菌在全球范围内已广泛传播，然而关于北欧及东欧地区ESBL产生的大肠杆菌的数据却极为稀缺。本研究旨在描述来自波罗的海国家（爱沙尼亚、拉脱维亚和立陶宛）、挪威及圣彼得堡（俄罗斯）分离得到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，并确定通过全基因组测序（WGS）得出的主要多位点序列型和单核苷酸多态性多样性。共筛选了10,780株临床大肠杆菌菌株，以检测其对第三代头孢菌素的敏感性降低情况。这些菌株于2012年5个月期间，从位于爱沙尼亚、拉脱维亚、立陶宛、挪威和圣彼得堡的21家医院收集。根据表型测试，ESBL/AmpC菌株的总流行率为4.7%，而通过测序则为3.9%。我们发现，在圣彼得堡和拉脱维亚，具有ESBL/AmpC表型和基因型的菌株数量多于其他国家。在表型大肠杆菌菌株中，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在所有国家均被发现，但在拉脱维亚的流行率高于俄罗斯圣彼得堡、爱沙尼亚、挪威和立陶宛。在波罗的海国家和挪威，占主导地位的AmpC基因是blaCMY–59，而在圣彼得堡则是blaDHA–1。大肠杆菌菌株属于83种不同的序列型，其中最普遍的是ST131（占40%）。总之，我们发现在北欧/东欧地区分离得到的大肠杆菌菌株中，ESBL/AmpC/碳青霉烯酶的流行率普遍较低。然而，在特定基因和多位点序列型的分布上，各国之间存在显著的差异。