Genomic analysis of Indian strains of Salmonella enterica subsp. enterica serovar Typhi indicates novel genetic repertoire for pathogenicity and adaptations

In the era of emerging antibiotic resistance, Salmonella enterica subsp. enterica serovar Typhi the causative agent of typhoid, is a threat for healthcare systems in developing countries especially India, where the disease is highly endemic. Genetic diversity among different strains may be the cause of variable severity of disease in different regions of the world. To explore this genetic diversity, genome annotation by rapid annotation using subsystem technology (RAST) was carried out for genomes of four Salmonella Typhi strains from two distinct areas available in the public domain. Two clinical strains were from India (P-stx-12 and E02-1180) and the other two strains considered as reference strains were from the endemic regions of Papua New Guinea (UJ308A and UJ816A). We report that Indian clinical strains possess several similar genes responsible for virulence and pathogenicity as those present in the reference strains. Interestingly, Indian clinical strains also possess 34 additional potential virulence genes that are absent in the reference strains, suggesting the more dreadful nature of Indian clinical strains as compared to those causing endemic typhoid. Indian strains contained genes coding for; Colicin V and bacteriocin production; multidrug resistance efflux pumps; ABC transporters; Type III and Type VI secretion systems, siderophore aerobactin, pathogenicity islands and Vi polysaccharide biosynthesis and transport. These unique genes are also reported in the genomes of other six clinical strains of India analyzed through RAST and IslandViewer 4 for validation purpose. This study highlights the presence of potential genes as molecular targets to overcome the future endemic outbreaks in India.