First characterization of the resistome, virulome and genomic diversity of Salmonella enterica serovar Inganda: a rare, clinically-related and drug susceptible serovar.

Abstract

Non-typhoid Salmonella are among the main causes of foodborne diseases worldwide. However, information on rare serovars is scarce, limiting the understanding of their prevalence, distribution and pathogenesis. Salmonella enterica serovar Inganda (S. Inganda) is a rare non-typhoid serovar. Considering the few existing reports, and the current use of genomics, this study characterized for the first time the antimicrobial resistance, pathogenic potential and diversity of S. Inganda genomes worldwide. A S. Inganda strain from human feces in 2018 in Brazil (SI264) had its resistance determined against 18 antimicrobials by disk-diffusion and had its genome sequenced. S. Inganda publicly available genomes (n = 12) were analyzed for genotypic resistance, stress and virulence genes, plasmids, pathogenicity islands, prophages, Multi-Locus Sequence Typing (MLST), core-genome MLST (cgMLST), and single-nucleotide polymorphisms (SNPs). SI264 showed no phenotypic resistance. All 12 S. Inganda genomes harbored genes or mutations for aminoglycoside (aac(6')-Iaa), quinolone (parC Thr57→Ser), and acid (asr) resistance, multi-drug efflux systems (mdsAB), and gold tolerance (golST). One genome from US harbored pKPC-CAV1321 plasmid. Nine pathogenicity islands, 174 Salmonella virulence genes, and 17 prophages were found in different frequencies. Although a great genomic diversity was noticed, S. Inganda genomes from US and UK were closely related. In conclusion, genomic analyses were able to characterize the current available genomes of S. Inganda strains mostly as genetically diverse, susceptible to antimicrobials, and potentially acid and heavy metal resistant. The presence of numerous virulence features also suggested their pathogenic potential, especially among clinical strains, and reinforced the importance to better characterize rare non-typhoid serovars.