Whole-Genome Analysis of Staphylococcus aureus Isolates from Ready-to-Eat Food in Russia

Abstract

This study provides a thorough investigation of a diverse set of antimicrobial resistant (AMR) Staphylococcus aureus isolates collected from a broad range of ready-to-eat (RTE) food in various geographic regions of Russia ranging from Pskov to Kamchatka. Thirty-five isolates were characterized using the whole genome sequencing (WGS) analysis in terms of clonal structure, the presence of resistance and virulence determinants, as well as plasmid replicon sequences and CRISPR/Cas systems. To the best of our knowledge, this is the first WGS-based surveillance of Russian RTE food-associated S. aureus isolates. The isolates belonged to fifteen different multilocus sequence typing (MLST)-based types with a predominant being the ones of clonal complex (CC) 22. The isolates studied can pose a threat to public health since about 40% of the isolates carried at least one enterotoxin gene, and 70% of methicillin-resistant (MRSA) isolates carried a tsst1 gene encoding a toxin that may cause severe acute disease. In addition, plasmid analysis revealed some important characteristics, e.g., Rep5 and Rep20 plasmid replicons were a "signature" of MRSA CC22. By analyzing the isolates belonging to the same/single strain based on cgMLST analysis, we were able to identify the differences in their accessory genomes marking their dynamics and plasticity. This data is very important since S. aureus isolates studied and RTE food, in general, represent an important route of transmission and dissemination of multiple pathogenic determinants. We believe that the results obtained will facilitate performing epidemiological surveillance and developing protection measures against this important pathogen in community settings.

Keywords: CRISPR/Cas system; antibiotic resistance; foodborne pathogen; genomic epidemiology; multidrug resistance; pathogenic potential; virulence determinants.

Figure 1

Typing, geography, and phylogenetic analysis of S. aureus isolates from ready-to-eat (RTE) food studied.

Figure 2

Phenotypic and genomic antimicrobial resistance profiles of S. aureus isolates from ready-to-eat food. ‘Trime-sulf’ represents trimethoprim-sulfamethoxazole. ‘Additional’ antibiotics, to which all isolates were susceptible, include fosfomycin, fusidic acid, and tigecycline. Antibiotics belonging to the same group are colored with the same color. ‘+’ means that the gene is present in the isolate, ‘-‘ – that the gene was not found. ‘R’ means that a given isolate was resistant to particular antibiotic, ‘S’ – that an isolate was susceptible to this drug. The isolates found to belong to the same strain are highlighted with color.

Figure 3

Plasmid replicon sequences profiles of RTE food S. aureus isolates studied. ‘+’ means that the given replicon is present in the isolate, ‘-‘ – that the replicon was not found. The isolates found to belong to the same strain are highlighted with color.