Dataset Information

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

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.

SUBMITTER: Davies MR

PROVIDER: S-EPMC9234096 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genomic epidemiology of <i>Salmonella</i> Typhi in Central Division, Fiji, 2012 to 2016.

Davies Mark R MR Duchene Sebastian S Valcanis Mary M Jenkins Aaron P AP Jenney Adam A Rosa Varanisese V Hayes Andrew J AJ Strobel Aneley Getahun AG McIntyre Liam L Lacey Jake A JA Klemm Elizabeth J EJ Wong Vanessa K VK Sahukhan Aalisha A Thomson Helen H Page Andrew A Hocking Dianna D Wang Nancy N Tudravu Litia L Rafai Eric E Dougan Gordon G Howden Benjamin P BP Crump John A JA Mulholland Kim K Strugnell Richard A RA

The Lancet regional health. Western Pacific 20220616

<h4>Background</h4>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 <i>Salmonella enterica</i> var Typhi (<i>Salmonella</i> 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 <i>Salmonella</i> Typhi in Fiji ...[more]

PMID: 35769175

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