The prevalence and characterization of ESBL-producing strains of Salmonella enterica circulating in the territory of the Russian Federation (2016–2020)

A. S. Pavlova, A. Egorova, N.E. Krutova, S. Saenko, Y. Mikhaylova, A. N. Guseva, I. Chebotar, A. Podkolzin, K. Kuleshov, V. Akimkin
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Abstract

Objective. To analyze frequency and identify genetic determinants of resistance of non-typhoid Salmonella (NTS) producing extended-spectrum β-lactamase (ESBL) isolated in the Russian Federation over the period 2016 to 2020. Materials and Methods. Salmonella isolates, suspected to ESBL production, were collected by the All-Russia Reference Center of Salmonellosis during the national Salmonellosis surveillance program. Phenotypic resistance was determined by the broth microdilution method using G-I and G-II Mikrolatest®SensiLaTest MIC plates and by the double-disk synergy test. Whole genome sequencing was performed on the NextSeq platform (Illumina, USA), with subsequent de novo genome assembly (SPAdes 3.15.4), identification of plasmid types (MOB-suite v3.0.0), and identification of resistance genes (AMRFinderPlus v3.10.40). Results. Out of 1792 NTS isolates, 22 strains contained bla-genes of molecular classes A and D (blaTEM, blaCTX-M, blaSHV, blaOXA), one strain – AmpC (blaCMY-2) and three strains – combination ESBL of class A and AmpC (blaTEM, blaCMY-2, blaDHA). The frequency of occurrence of ESBL-producing Salmonella is 1.3%, AmpC – 0.2%. Additionally, strains were resistant to other non-β-lactam antibiotics. Six different types of plasmids were identified (IncI, IncFIB, IncC, IncHI2A, IncL/M and IncX1) in studied isolates. It was possible for 17 strains to identify location of resistance genes in plasmids of a certain type. Conclusions. The frequency of occurrence of Salmonella strains producing ESBL and AmpC was 1.45%, which were found in sporadic cases of human diseases, as well as food and environmental objects were sources of isolation. The fact of detection of such strains among various NTC serotypes and a wide range of sources of isolation confirms the relevance of monitoring antimicrobial resistance of Salmonella strains in the future.
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2016-2020年俄罗斯联邦境内流行的产esbl肠炎沙门氏菌的流行及特征分析
目标。分析2016年至2020年俄罗斯分离的产生广谱β-内酰胺酶(ESBL)的非伤寒沙门氏菌(NTS)耐药性的频率并确定其遗传决定因素。材料与方法。怀疑生产ESBL的分离沙门氏菌是在国家沙门氏菌病监测规划期间由全俄沙门氏菌病参考中心收集的。采用G-I和G-II Mikrolatest®SensiLaTest MIC板的肉汤微量稀释法和双盘协同试验测定表型抗性。在NextSeq平台(Illumina, USA)上进行全基因组测序,随后进行基因组组装(SPAdes 3.15.4),质粒类型鉴定(mobo -suite v3.0.0)和抗性基因鉴定(AMRFinderPlus v3.10.40)。在1792株NTS分离株中,22株含有A、D类bla基因(blaTEM、blaCTX-M、blaSHV、blaOXA), 1株含有AmpC基因(blaCMY-2), 3株含有A类与AmpC结合的ESBL基因(blaTEM、blaCMY-2、blaDHA)。产esbl沙门氏菌的发生频率为1.3%,AmpC - 0.2%。此外,菌株对其他非β-内酰胺类抗生素耐药。在分离株中鉴定出6种不同类型的质粒(IncI、IncFIB、IncC、incchi2a、IncL/M和IncX1)。结论产ESBL和AmpC的沙门菌的发生频率为1.45%,它们存在于散发的人类疾病病例中,食物和环境物体是分离源。在各种NTC血清型和广泛的分离来源中检测到这类菌株的事实证实了今后监测沙门氏菌菌株抗微生物药物耐药性的相关性。
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