title: Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immunization Program.
abstract: Vaccines against Salmonella Typhi, the causative agent of typhoid fever, are commonly used by travellers, however, there are few examples of national immunization programs in endemic areas. There is therefore a paucity of data on the impact of typhoid immunization programs on localised populations of S. Typhi. Here we have used whole genome sequencing (WGS) to characterise 44 historical bacterial isolates collected before and after a national typhoid immunization program that was implemented in Thailand in 1977 in response to a large outbreak; the program was highly effective in reducing typhoid case numbers. Thai isolates were highly diverse, including 10 distinct phylogenetic lineages or genotypes. Novel prophage and plasmids were also detected, including examples that were previously only reported in Shigella sonnei and Escherichia coli. The majority of S. Typhi genotypes observed prior to the immunization program were not observed following it. Post-vaccine era isolates were more closely related to S. Typhi isolated from neighbouring countries than to earlier Thai isolates, providing no evidence for the local persistence of endemic S. Typhi following the national immunization program. Rather, later cases of typhoid appeared to be caused by the occasional importation of common genotypes from neighbouring Vietnam, Laos, and Cambodia. These data show the value of WGS in understanding the impacts of vaccination on pathogen populations and provide support for the proposal that large-scale typhoid immunization programs in endemic areas could result in lasting local disease elimination, although larger prospective studies are needed to test this directly.
authors.affiliation: Centre for Systems Genomics, University of Melbourne, Parkville, Victoria, Australia.|Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia.
authors.forename: Zoe A
authors.identifier: 0000-0002-8887-3492
authors.initials: ZA
authors.lastname: Dyson
authors.affiliation: The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
authors.forename: Duy Pham
authors.initials: DP
authors.lastname: Thanh
authors.affiliation: Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
authors.forename: Ladaporn
authors.initials: L
authors.lastname: Bodhidatta
authors.affiliation: Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
authors.forename: Carl Jeffries
authors.initials: CJ
authors.lastname: Mason
authors.affiliation: Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
authors.forename: Apichai
authors.initials: A
authors.lastname: Srijan
authors.affiliation: The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.|Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom.
authors.forename: Maia A
authors.initials: MA
authors.lastname: Rabaa
authors.affiliation: The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
authors.forename: Phat Voong
authors.initials: PV
authors.lastname: Vinh
authors.affiliation: The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
authors.forename: Tuyen Ha
authors.initials: TH
authors.lastname: Thanh
authors.affiliation: The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.|Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom.
authors.forename: Guy E
authors.initials: GE
authors.lastname: Thwaites
authors.affiliation: The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.|Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom.|The London School of Hygiene and Tropical Medicine, London, United Kingdom.
authors.forename: Stephen
authors.initials: S
authors.lastname: Baker
authors.affiliation: Centre for Systems Genomics, University of Melbourne, Parkville, Victoria, Australia.|Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia.
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Holt
mesh_terms: D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D017589:Immunization Programs; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics / Q000378:metabolism; D012485:Salmonella typhi / Q000145:classification / Q000235:genetics* / Q000276:immunology; D013785:Thailand; D014435:Typhoid Fever / Q000382:microbiology / Q000517:prevention & control*; D014436:Typhoid-Paratyphoid Vaccines / Q000008:administration & dosage / Q000235:genetics / Q000276:immunology
chemical_list: D014436:Typhoid-Paratyphoid Vaccines