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

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

doi:10.1016/j.lanwpc.2022.100488

Cited by 7 publications

(15 citation statements)

References 39 publications

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“…Only isolate S5 demonstrated non-susceptibility to ciprofloxacin, consistent with the detection of S83F substitution in the gyrA gene. Similar phenomena of the locally restricted spread of antibiotic-sensitive clones of Salmonella Typhi have been observed in other regions [ 57 ]. Using data from the WGS of nearly 2000 isolates from more than 60 countries, Wong et al concluded that with the exception of the rapidly disseminating H58 lineage, the global Salmonella Typhi population is highly structured and includes many genotypes that display geographical restriction [ 17 ].…”

Section: Discussionsupporting

confidence: 75%

Genomic Investigation of Salmonella Typhi in Hong Kong Revealing the Predominance of Genotype 3.2.2 and the First Case of an Extensively Drug-Resistant H58 Genotype

Cao

Chen

et al. 2023

Microorganisms

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Typhoid fever is a notable disease in Hong Kong. We noticed two local cases of typhoid fever caused by Salmonella Typhi within a two-week period in late 2022, which had no apparent epidemiological linkage except for residing in the same region of Hong Kong. A phylogenetic study of Salmonella Typhi isolates from Hong Kong Island from 2020 to 2022 was performed, including a whole-genome analysis, the typing of plasmids, and the analysis of antibiotic-resistance genes (ARGs), to identify the dominant circulating strain and the spread of ARGs. A total of seven isolates, from six local cases and an imported case, were identified from positive blood cultures in two hospitals in Hong Kong. Five antibiotic-sensitive strains of genotype 3.2.2 were found, which clustered with another 30 strains originating from Southeast Asia. Whole-genome sequencing revealed clonal transmission between the two index cases. The remaining two local cases belong to genotype 2.3.4 and genotype 4.3.1.1.P1 (also known as the H58 lineage). The genotype 4.3.1.1.P1 strain has an extensively drug-resistant (XDR) phenotype (co-resistance to ampicillin, chloramphenicol, ceftriaxone, ciprofloxacin, and co-trimoxazole). Although the majority of local strains belong to the non-H58 genotype 3.2.2 with a low degree of antibiotic resistance, the introduction of XDR strains with the global dissemination of the H58 lineage remains a concern.

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Section: Discussionsupporting

confidence: 75%

Genomic Investigation of Salmonella Typhi in Hong Kong Revealing the Predominance of Genotype 3.2.2 and the First Case of an Extensively Drug-Resistant H58 Genotype

Cao

Chen

et al. 2023

Microorganisms

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“…Incorporating the 414 genotype 4.2 Central and Northern Divisions from 2017-2019 with our previous evolutionary framework of 367 Fijian S . Typhi genomes from (1981-2016) 12,22 identified that the genotype 4.2 isolates rapidly expanded from 2008 onwards in Fiji despite the importation of regional genotypes (such as genotype 3.5 strains commonly associated with Samoa 11 ) and the H58-like genotype 4.3.1 (Supplementary figure 2). These data indicate that sporadic importation of ‘global’ S .…”

Section: Resultsmentioning

confidence: 99%

“…Between 1980 and mid 2000s, a wide range of genotypes were sequenced. However, from 2008 onwards typhoid fever in Fiji has primarily been caused by a single genotype (4.2) with two lineages, 4.2.1 and 4.2.2, circulating concurrently in the country 12,22 . A review of publicly available genomic data (>12,000 isolates) showed the 4.2.1 and 4.2.2 lineages largely have only been detected outside of Fiji in travel-associated cases with only a single isolate being identified in New Zealand in 2019 with no travel history 41 .…”

Section: Discussionmentioning

confidence: 99%

“…Maximum–clade credibility (MCC) phylogenetic trees were constructed for each lineage to visualise the evolutionary history of isolates. Additional metadata from this study and case control study 12 was used to assess the relationship between isolates and transmission patterns. Markov chain Monte Carlo (MCMC) was used to sample the posterior distribution, as implemented in BEAST, with sufficient sampling determined according to an effective sample size of 200 for key model parameters, as visualised in Beastiary 34 ).…”

Section: Methodsmentioning

confidence: 99%

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Genetic heterogeneity in theSalmonellaTyphi Vi capsule locus: A population genomic study from Fiji

Getahun Strobel,

Hayes,

Wirth

et al. 2023

Preprint

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Typhoid fever is endemic in many parts of the world and remains a major public health concern in tropical and sub-tropical developing nations, including Fiji. To address high rates of typhoid fever, the Northern Division of Fiji is implementing a mass vaccination with typhoid conjugate vaccine (Vi-polysaccharide conjugated to tetanus toxoid) as a public health control measure in 2023. In this study we define the genomic epidemiology ofS. Typhi in the Northern Division prior to island-wide vaccination, sequencing 85% (n=419) of the total cases from the Northern Division and Central Divisions of Fiji that occurred in the period 2017-2019. We found elevated rates of nucleotide polymorphisms intviD and tviEgenes (responsible for Vi-polysaccharide synthesis) relative to core genome levels within the Fiji endemicS. Typhi genotype 4.2. Expansion of these findings within a globally representative database of 12,382S. Typhi (86 genotyphi clusters) showed evidence of convergent evolution of the sametviEmutations across theS. Typhi population, indicating thattviselection has occurred both independently and globally. The functional impact oftvimutations on the Vi-capsular structure and other phenotypic characteristics are presently unknown, yet commonly occurringtviEpolymorphisms localise adjacent to predicted active site residues when overlayed against the predicted TviE protein structure. Given the central role of the Vi-polysaccharide inS. Typhi biology and vaccination, further integrated epidemiological, genomic, and phenotypic surveillance is required to determine the spread and functional implications of these mutations.

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“…One such region is Oceania, which consists of multiple small island nations (except for Australia and New Zealand). To date, only two studies have been reported from this region (from Papua New Guinea and Fiji) with genomic data analyses of Salmonella Typhi isolates ( 5 , 6 ). Therefore, a lack of proper understanding exists regarding the emergence, population diversity, and antimicrobial resistance (AMR) of Salmonella Typhi there.…”

Section: Commentarymentioning

confidence: 99%

Salmonella enterica Serovar Typhi on an Island: No H58, No Multidrug Resistance, but for How Long?

Tanmoy

2022

mBio

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Little genomic data is available for typhoid fever from island nations, though the disease has a moderately high burden there. Sikorski et al. (M. J. Sikorski, T. H. Hazen, S. N. Desai, S. Nimarota-Brown, et al., mBio 13:e01920-22, 2022, https://doi.org/10.1128/mbio.01920-22 ) studied 306 Salmonella enterica serovar Typhi genomes from the Samoan Islands collected during 1983 to 2020 and reported dominance of a rare genotype, 2.5.4, and no H58 (genotype 4.3.1).

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

Cited by 7 publications

References 39 publications

Genomic Investigation of Salmonella Typhi in Hong Kong Revealing the Predominance of Genotype 3.2.2 and the First Case of an Extensively Drug-Resistant H58 Genotype

Genomic Investigation of Salmonella Typhi in Hong Kong Revealing the Predominance of Genotype 3.2.2 and the First Case of an Extensively Drug-Resistant H58 Genotype

Genetic heterogeneity in theSalmonellaTyphi Vi capsule locus: A population genomic study from Fiji

Salmonella enterica Serovar Typhi on an Island: No H58, No Multidrug Resistance, but for How Long?

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