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.

Salmonella enterica Serovar Typhi in Bangladesh: Exploration of Genomic Diversity and Antimicrobial Resistance

“…As the filtering criteria remain the same, the number of SNPs for all Bangladesh isolates is relatively low compared to the global or multicountry context ( 25 – 27 ) but is similar to country-specific data. For example, 1,850 SNPs were detected in isolates from Thailand ( n = 44) and 2,187 SNPs in isolates from Nepal ( n = 198) ( 29 , 39 ). The wgSNP-MLT data showed distinct differentiation of all genotypes, much like the data from the cgMLST-UPGMA tree, except the latter lacked clear inferences for different H58 lineages ( Fig.…”

A misleading description of the predominant clonal evolution model in Trypanosoma cruzi

“…However, intra-near-clade/DTU population genetics in T. cruzi calls for additional studies. Although present data support the Russian doll hypothesis in T. cruzi for all cases conveniently explored, data on T. cruzi intra-near-clade genomic diversity still are scarce by comparison with Leishmania (Imamura et al, 2016) and bacteria (Alnajar and Gupta, 2017;Dyson et al, 2017). Future genomic studies on T. cruzi intra-near-clade population genetics should take as models such approaches based on fine typing using thousands of SNP markers.…”

Typhoidal Salmonella Trends in Thailand

“…Paratyphi A, B, and C. A recent study that conducted whole-genome sequencing analysis of typhoidal Salmonella isolates noted that most indigenous strains of S. Typhi were depleted following the mass vaccination campaigns of the 1970s. 16 This analysis also indicated that recent strains of S. Typhi are closely related to the strains isolated from neighboring countries such as Laos and Cambodia, which implies that the transmission of indigenous strains is not responsible for causing typhoid in Thailand. 16 Typhoid incidence can potentially be further curbed by using the robust surveillance system in place to improve traveler and migrant screening and, therefore, reduce imported cases of typhoid fever from neighboring endemic countries.…”