Salmonella enterica serovar Typhi, the aetiologic agent of typhoid fever is still posing a major health problem for the developing world, as about 16 million new cases are reported each year. S. Typhi causes systemic infections (typhoid fever) as well as chronic infections (asymptomatic carriers) in humans, the latter serve as the source of infection. The transmission of S. Typhi is primarily through faecal-oral route and a significant number of infected individuals become chronic asymptomatic carriers and keep shedding S. Typhi in faeces for decades. This results in endemicity of S. Typhi in regions of the world with underdeveloped sanitation and community hygiene.
Carrier identification becomes extremely important as some of the ancestral haplotypes were observed in recent isolates suggesting their persistence in these asymptomatic carriers. Traditional methods such as culturing of bacteria from faecal samples are not fool proof as the carriers shed bacteria intermittently. Serological tests to detect specific antibodies such as anti-H and anti-O are unable to differentiate between carriers and individuals who have recovered from the infection. Especially, in areas endemic for S. Typhi, due to high background levels of these antibodies, serological tests cannot be adopted for the identification of a carrier. Thus, there is an urgent need for inexpensive and efficient detection methods for the establishment of carrier state, perhaps based on genomic markers.
The genetic typing tools such as PFGE, AFLP, ribotyping etc. can resolve limited genetic variation occurring within specific sites, and therefore are incapable of differentiating highly clonal strains such as outbreak related strains from the ones not associated with the outbreak (carrier isolates)[8–10]. High-throughput sequencing technologies have already been employed as a high resolution molecular epidemiologic tool to discern microevolution of highly related strains.
In this study, we attempted to determine if whole genome sequencing of S. Typhi isolated from a carrier individual can provide insights related to persistence and or adaptation mechanisms. We describe the genome sequence of a Salmonella enterica serovar Typhi strain (ST CR0063) isolated from a carrier individual during a prolonged outbreak of typhoid fever in Kelantan, Malaysia.