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

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.