Genomic analysis of human invasive Salmonella enterica serovar Typhimurium ST313 isolate B3589 from India

Salmonella Typhimurium ST313 is known to cause invasive disease in sub Saharan African (sSA) countries while the same sequence type is often associated with gastro-intestinal infections in the UK and Brazil. Although S. Typhimurium has been frequently isolated from human samples in India, the prevalence and invasive nature of infection of ST313 is currently unknown. The present study elucidates the phenotypic and genotypic characteristics of S. Typhimurium strain B3589 that belongs to ST313. The isolate was subjected to serotyping and antimicrobial susceptibility test to understand its phenotypical characteristics. Whole genome sequencing and comparative genomic analysis was carried out to provide an insight into S. Typhimurium ST313 lineage in India. The results suggests antibiotic resistance against aminoglycoside was associated with the presence of aminoglycoside modifying enzymes aac(6′)-Ia in the genome. Phylogenetic analysis revealed the India-ST313 isolates are genotypically distinct from the known African, UK and Brazilian ST313 lineages. The isolate possess the characteristic prophage gene repertoire except BTP-5. The presence of BTP-1 and more importantly bstA virulence gene has been the distinguishable feature of strain B3589 among other non-African isolates. In addition the genome degradation of African ST313 lineage-2 was not conserved in the Indian ST313 isolates. Fewer genome degradation events as well as the absence of plasmid mediated MDR locus suggest the Indian ST313 isolates are of low risk. The identification of ST313 isolates in India reveals the previously unknown characteristics of ST313 S. Typhimurium isolated from India. •S. Typhimurium strains belong to ST313 have been identified as a major cause of invasive diseases in many sub-Saharan African countries•The ability of ST313 isolates to emerge in different locations independently suggests the potential of iNTS disease to spread outside of Africa•This study deals with the phenotypic and genotypic characterisation of S. Typhimurium ST313 strain B3589 isolated from India•Comparative genomic analysis of strain B3589 with ST313 isolates from Africa, UK and Brazil suggest the Indian isolate are genetically distinct•This study has revealed the previously unknown characteristics of ST313 S. Typhimurium isolate from India.