Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016

Mark R Davies; Sebastian Duchene; Mary Valcanis; Aaron P Jenkins; Adam Jenney; Varanisese Rosa; Andrew J Hayes; Aneley Getahun Strobel; Liam McIntyre; Jake A Lacey; Elizabeth J Klemm; Vanessa K Wong; Aalisha Sahukhan; Helen Thomson; Andrew Page; Dianna Hocking; Nancy Wang; Litia Tudravu; Eric Rafai; Gordon Dougan; Benjamin P Howden; John A Crump; Kim Mulholland; Richard A Strugnell

doi:10.1016/j.lanwpc.2022.100488

Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016

Lancet Reg Health West Pac. 2022 Jun 16:24:100488. doi: 10.1016/j.lanwpc.2022.100488. eCollection 2022 Jul.

Authors

Mark R Davies¹, Sebastian Duchene¹, Mary Valcanis², Aaron P Jenkins^{3

4}, Adam Jenney^{5

6}, Varanisese Rosa⁷, Andrew J Hayes¹, Aneley Getahun Strobel¹, Liam McIntyre¹, Jake A Lacey⁸, Elizabeth J Klemm⁹, Vanessa K Wong¹⁰, Aalisha Sahukhan⁷, Helen Thomson⁵, Andrew Page^{9

11}, Dianna Hocking¹, Nancy Wang¹, Litia Tudravu¹², Eric Rafai¹³, Gordon Dougan¹⁰, Benjamin P Howden^{1

2}, John A Crump¹⁴, Kim Mulholland^{5

15}, Richard A Strugnell¹

Affiliations

¹ Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia.
² Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
³ Centre for Ecosystem Management, Edith Cowan University, Western Australia.
⁴ School of Public Health, University of Sydney, Sydney, NSW, Australia.
⁵ New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia.
⁶ College of Medicine, Nursing and Health Sciences, Fiji National University, Suva, Fiji.
⁷ Fiji Centre for Disease Control, Fiji Ministry of Health, Suva, Fiji.
⁸ Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute of Infection and Immunity, Victoria, Australia.
⁹ Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom.
¹⁰ Department of Medicine, University of Cambridge, Cambridge, United Kingdom.
¹¹ Quadram Institute Bioscience, Norwich Research Park, Norfolk, United Kingdom.
¹² Colonial War Memorial Hospital, Suva, Fiji.
¹³ Fiji Ministry of Health and Medical Services, Suva, Fiji.
¹⁴ Centre for International Health, Otago Medical School, University of Otago, Dunedin, New Zealand.
¹⁵ Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom.

Abstract

Background: Typhoid fever is endemic in some Pacific Island Countries including Fiji and Samoa yet genomic surveillance is not routine in such settings. Previous studies suggested imports of the global H58 clade of Salmonella enterica var Typhi (Salmonella Typhi) contribute to disease in these countries which, given the MDR potential of H58, does not auger well for treatment. The objective of the study was to define the genomic epidemiology of Salmonella Typhi in Fiji.

Methods: Genomic sequencing approaches were implemented to study the distribution of 255 Salmonella Typhi isolates from the Central Division of Fiji. We augmented epidemiological surveillance and Bayesian phylogenomic approaches with a multi-year typhoid case-control study to define geospatial patterns among typhoid cases.

Findings: Genomic analyses showed Salmonella Typhi from Fiji resolved into 2 non-H58 genotypes with isolates from the two dominant ethnic groups, the Indigenous (iTaukei) and non-iTaukei genetically indistinguishable. Low rates of international importation of clones was observed and overall, there were very low levels an antibiotic resistance within the endemic Fijian typhoid genotypes. Genomic epidemiological investigations were able to identify previously unlinked case clusters. Bayesian phylodynamic analyses suggested that genomic variation within the larger endemic Salmonella Typhi genotype expanded at discreet times, then contracted.

Interpretation: Cyclones and flooding drove 'waves' of typhoid outbreaks in Fiji which, through population aggregation, poor sanitation and water safety, and then mobility of the population, spread clones more widely. Minimal international importations of new typhoid clones suggest that targeted local intervention strategies may be useful in controlling endemic typhoid infection. These findings add to our understanding of typhoid transmission networks in an endemic island country with broad implications, particularly across Pacific Island Countries.

Funding: This work was supported by the Coalition Against Typhoid through the Bill and Melinda Gates Foundation [grant number OPP1017518], the Victorian Government, the National Health and Medical Research Council Australia, the Australian Research Council, and the Fiji Ministry of Health and Medical Services.

Keywords: Bayesian; Fiji; Outbreak; Phylodynamics; Phylogeny; Population genomics; Public health; Salmonella Typhi; Typhoid fever.