High-Throughput Genotyping of Salmonella Typhi Allows Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia

The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Department of Infectious Diseases, Leiden University Medical Centre, Leiden, Netherlands; Centre National de la Recherche Scientifique, Saint Paul Lez Durance, France ; Centre National de Référence des Salmonella, Institut Pasteur, Paris, France ; Microbiological Diagnostic Unit-Public Health Laboratory, University of Melbourne, Australia; Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada; Environmental Research Institute, University College Cork, Cork, Ireland

^* To whom correspondence should be addressed. Email: sbaker{at}oucru.org.

	Abstract

High throughput epidemiological typing systems that provide phylogenetic and genotypic information are beneficial for tracking bacterial pathogens in the field. The incidence of Salmonella enterica serovar Typhi (S. Typhi) infection in Indonesia is high and is associated with atypical phenotypic traits such as expression of the j and the z66 flagella antigens. Utilising a high throughput genotyping platform to investigate known nucleotide polymorphisms dispersed around the genome we determined the haplotypes of 140 S. Typhi isolates associated with Indonesia. We identified nine distinct S. Typhi haplotypes circulating in Indonesia over thirty years, with eight of these present in a single Jakarta suburb within a two year period. One dominant haplotype, H59, is associated with j and z66 flagella expression, representing a potential pathotype unique to Indonesia. Phylogenetic analysis suggests that H59 z66+, j+ isolates emerged relatively recently in terms of the origin of S. Typhi and are geographically restricted. These data demonstrate the potential of high throughput genotyping platforms for analysing S. Typhi populations in the field. The study also provides insight into the evolution of S. Typhi and demonstrates the value of a molecular epidemiological technique that is exchangeable, internet friendly and that has global utility.