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High-Throughput Genotyping of Salmonella enterica Serovar Typhi Allowing Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia ^,

The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom,¹ Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam,² Department of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands,³ Centre National de la Recherche Scientifique, Saint Paul Lez Durance, France,⁴ Centre National de Référence des Salmonella, Institut Pasteur, Paris, France,⁵ Microbiological Diagnostic Unit-Public Health Laboratory, University of Melbourne, Melbourne, Victoria, Australia,⁶ Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada,⁷ Environmental Research Institute, University College Cork, Cork, Ireland⁸

Received 20 November 2007/ Returned for modification 8 February 2008/ Accepted 17 February 2008

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 infection in Indonesia is high and is associated with atypical phenotypic traits such as expression of the j and the z66 flagellum antigens. Utilizing a high-throughput genotyping platform to investigate known nucleotide polymorphisms dispersed around the genome, we determined the haplotypes of 140 serovar Typhi isolates associated with Indonesia. We identified nine distinct serovar Typhi haplotypes circulating in Indonesia for more than 30 years, with eight of these present in a single Jakarta suburb within a 2-year period. One dominant haplotype, H59, is associated with j and z66 flagellum 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 serovar Typhi and are geographically restricted. These data demonstrate the potential of high-throughput genotyping platforms for analyzing serovar Typhi populations in the field. The study also provides insight into the evolution of serovar Typhi and demonstrates the value of a molecular epidemiological technique that is exchangeable, that is internet friendly, and that has global utility.

Published ahead of print on 5 March 2008.

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