A genomic snapshot of Salmonella enterica serovar Typhi in Colombia

Abstract

Little is known about the genetic diversity of Salmonella enterica serovar Typhi (S. Typhi) circulating in Latin America. It has been observed that typhoid fever is still endemic in this part of the world; however, a lack of standardized blood culture surveillance across Latin American makes estimating the true disease burden problematic. The Colombian National Health Service established a surveillance system for tracking bacterial pathogens, including S. Typhi, in 2006. Here, we characterized 77 representative Colombian S. Typhi isolates collected between 1997 and 2018 using pulse field gel electrophoresis (PFGE; the accepted genotyping method in Latin America) and whole genome sequencing (WGS). We found that the main S. Typhi clades circulating in Colombia were clades 2.5 and 3.5. Notably, the sequenced S. Typhi isolates from Colombia were closely related in a global phylogeny. Consequently, these data suggest that these are endemic clades circulating in Colombia. We found that AMR in S. Typhi in Colombia was uncommon, with a small subset of organisms exhibiting mutations associated with reduced susceptibility to fluoroquinolones. This is the first time that S. Typhi isolated from Colombia have been characterized by WGS, and after comparing these data with those generated using PFGE, we conclude that PFGE is unsuitable for tracking S. Typhi clones and mapping transmission. The genetic diversity of pathogens such as S. Typhi is limited in Latin America and should be targeted for future surveillance studies incorporating WGS.

Persistence of Rare Salmonella Typhi Genotypes Susceptible to First-Line Antibiotics in the Remote Islands of Samoa

“…Duplicate Samoan isolates were removed. Illumina reads for all clade 3.5 genomes from Colombia ( n = 20) and Chile ( n = 68) were downloaded from ENA BioProjects PRJEB42858 ( 80 ) and PRJEB20778 ( 81 ), respectively. These S. Typhi sequences from other studies and their accession numbers are listed in Table S2 .…”

Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes

“…Genotypes with ≥5% prevalence in the region were 3.5 (27%; n=28/105), 1.1 (18%; n=19/105), 2 (18%; n=19/105), 1.2.1 (5.7%; n=6/105), and 2.0.2 (5.7%; n=6/105). WGS data recently reported by Colombia’s Instituto Nacional de Salud ( Guevara et al, 2021 ) were not included in the regional prevalence estimates as they covered only a subset (5%) of surveillance isolates that were selected to maximise diversity, rather than to be representative. However, only four genotypes were detected in the Colombia study (1.1, 2, 2.5, 3.5), and two-thirds of isolates sequenced were genotype 2.5 (67%; n=51/77); 3.5 was also common, at 25% (n=20/77) ( Guevara et al, 2021 ).…”

“…WGS data recently reported by Colombia’s Instituto Nacional de Salud ( Guevara et al, 2021 ) were not included in the regional prevalence estimates as they covered only a subset (5%) of surveillance isolates that were selected to maximise diversity, rather than to be representative. However, only four genotypes were detected in the Colombia study (1.1, 2, 2.5, 3.5), and two-thirds of isolates sequenced were genotype 2.5 (67%; n=51/77); 3.5 was also common, at 25% (n=20/77) ( Guevara et al, 2021 ). Similarly, all five isolates from French Guiana (sequenced via the French reference laboratory) were genotype 2.5, consistent with limited diversity and a preponderance of genotype 2.5 organisms in the north of the continent.…”

Whole genome sequence analysis of Salmonella Typhi provides evidence of phylogenetic linkage between cases of typhoid fever in Santiago, Chile in the 1980s and 2010–2016

“…S . Typhi WGS data from a recent study in Colombia found genotypes 2, 2.5 and 3.5 to be the local endemic genotypes [ 42 ]. Genotype 2.5 was not detected among the Santiago isolates; however, genotype 3.5 and 2 were detected in Santiago, and were the nearest genomic neighbours of the Colombian isolates on the global tree.…”