Comparative Whole-Genome Analysis of Russian Foodborne Multidrug-Resistant Salmonella Infantis Isolates

Abstract

Non-typhoidal Salmonella infections remain a significant public health problem worldwide. In this study, we present the first detailed genomic analysis report based on short-read (Illumina) whole-genome sequencing (WGS) of 45 multidrug-resistant (MDR) Salmonella enterica subsp. enterica serotype Infantis isolates from poultry and meat product samples obtained in Russia during 2018–2020, and long-read (MinION) WGS of five more representative isolates. We sought to determine whether foodborne S. Infantis have acquired new characteristics, traits, and dynamics in MDR growth in recent years. All sequenced isolates belonged to the sequence type ST32 and more than the half of isolates was characterized by six similar antimicrobial susceptibility profiles, most of which corresponded well with the antimicrobial resistance determinants to aminoglycosides, sulphonamides, tetracycline, and chloramphenicol revealed in silico. Some of the isolates were characterized by the presence of several types of plasmids simultaneously. Plasmid typing using WGS revealed Col440I, ColpVC, ColRNAI, IncFIB, IncFII, IncX1, IncHI2, IncHI2A, and IncN replicons. The identified virulence genes for 45 whole genomes of S. Infantis were similar and included 129 genes encoding structural components of the cell, factors responsible for successful invasion of the host, and secreted products. These data will be a valuable contribution to further comparative genomics of S. Infantis circulating in Russia, as well as to epidemiological surveillance of foodborne Salmonella isolates and investigations of Salmonella outbreaks.

Genome-Based Assessment of Antimicrobial Resistance and Virulence Potential of Isolates of Non-Pullorum/Gallinarum Salmonella Serovars Recovered from Dead Poultry in China

“…Indiana, which was considered the most resistant serovar in this study, carries plasmid types IncX1_1, IncHI2_1, IncHI2A_1, and Col156_1; these plasmids have been associated with the acquisition of resistance to different classes of antimicrobials, including aminoglycosides, sulfonamides, tetracyclines, quinolones, polymyxins, and β-lactams ( 52 , 53 ). Furthermore, our findings demonstrated that the plasmid type IncX1, in addition to IncFII(S) and IncFIB(S), is the key carrier of antimicrobial resistance determinants in Salmonella , which is in agreement with previous findings from China and elsewhere ( 54 – 57 ). Hence, the presence of these plasmids in the studied isolates is of major concern and may mediate the horizontal transmission of antimicrobial resistance along the food chain.…”

Plasmid Composition, Antimicrobial Resistance and Virulence Genes Profiles of Ciprofloxacin- and Third-Generation Cephalosporin-Resistant Foodborne Salmonella enterica Isolates from Russia

“…The isolates belonging to ST11, ST142, and ST469 carried the gene entA associated with ROX degradation, while only ST548 samples included the determinants encoding toxins ( cdtB, pltAB ). According to the hybrid assembly, the genes encoding yersiniabactin operon ( fyuA , irp12 , ybtAEPQSTUX ) were of plasmid localization; the same picture was previously observed in S. Infantis isolates [ 19 ].…”

“…ST32 was the primary ST since it is prevalent in Russia [ 19 ], together with Europe and Japan [ 7 , 17 , 41 , 42 ]. Two isolates studied belonged to ST548, and other sequence types (ST11, ST469, and ST142) had single samples, while in China the predominant ST was ST11 (12.4%) and ST469 had 3.2% [ 21 ].…”

“…A number of reports described the detection of megaplasmids harboring ESBL-encoding genes in S. enterica from Italy, Switzerland, and the USA [ 7 , 16 , 17 ]. Furthermore, recently pESI-like megaplasmids were revealed in Russia [ 18 , 19 ]. These plasmids are conjugative with up to 300 kb length and harbor AMR genes including ESBL genes, as well as genes conferring resistance to tetracyclines, sulphonamides, and aminoglycosides [ 20 ].…”

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

“…Полногеномное секвенирование и анализ 45 российских изолятов S. Infantis с множествен ной лекарственной устойчивостью (МЛУ) из образцов куриной и мясной продукции в течение 2018-2020 гг. показало наличие bla CTXM14 у 8,9% штаммов, bla TEM1B -у 24,4% и bla TEM141 -у 2,2% штаммов [27].…”