Results of S. Enteritidis Strain Subtyping Using Whole-Genome Sequencing and MALDI-TOF Mass Spectrometry Data

Salmonella bacteria are a major cause of sporadic and clustered acute intestinal infections, with S. Enteritidis being the predominant serovar both in Russia and worldwide. This underscores the need to study and improve surveillance of S. Enteritidis using modern methods. The aim of this study was to investigate the antibiotic resistance phenotype and molecular genetic characteristics of S. Enteritidis circulating in the Nizhny Novgorod region, to perform molecular subtyping of strains using WGS data, and to conduct a comparative analysis with MALDI-TOF MS results. Antimicrobial susceptibility was assessed using the disk diffusion method. MALDI-TOF MS was applied for analysis of mass spectral similarities and differences, while WGS and whole-genome MLST approaches were used for strain characterization and subtyping. It was found that 11.6% of isolates exhibited reduced susceptibility to fluoroquinolones, and 4.65% were resistant, which was associated with the presence of plasmid-mediated genes (qnrB5, qnrB10, qnrB19) and point mutations in the gyrA gene (Ser83Tyr and Asp87Asn). The strains were shown to differ in the number of pathogenicity islands, and the presence of eight types of plasmid replicons was identified, indicating the presence of plasmids potentially capable of transferring antibiotic resistance genes. The studied strains were found to belong to the Global and Atlantic phylogenetic lineages. The cgMLST method was identified as the most effective approach for epidemiological investigation of local outbreaks. A comparison of the two methodological approaches demonstrated that MALDI-TOF MS results are comparable to cgMLST-based subtyping. The use of MALDI-TOF MS in epidemiological surveillance of clustered and outbreak-associated salmonellosis cases is therefore justified, cost-effective, and enables rapid epidemiological investigation.