Molecular analysis of clonally related Salmonella Typhi recovered from epidemiologically unrelated cases of typhoid fever, Brazil

Abstract

Background: The primary method of molecular subtyping for the identification and investigation of outbreaks has been pulsed-field gel electrophoresis (PFGE). In some cases, this technique has not been able to show discrimination between the unrelated strains that can be achieved by whole genome sequencing (WGS). Methods: The aim of this study was to determine the strengths and drawbacks of WGS using different analytic approaches compared to traditional typing method, PFGE, for retrospectively typing clusters cases of 28 S. Typhi. Results: We evaluated three analytical approaches on the WGS data set (Nucleotide Difference (ND), (SNPs) and Whole genome multi locus sequence typing (wgMLST) that identically classified the clustersrelated strains into two clusters, cluster A (with strains from 2017), and Cluster B (with strains from 2007). Conclusions: In this study WGS based typing, was able to compete with PFGE for differentiation of the clusters of S. Typhi strains.

Molecular Epidemiology of Sporadic and Outbreak-Related Salmonella Typhi Isolates in the Brazilian North Region: A Retrospective Analysis from 1995 to 2013

“…The PFGE typing revealed a higher genetic diversity of S. Typhi strains, with the presence of 20 distinct pulsotypes, and clonally related isolates causing infection in different locations and periods, also supporting the hypothesis of a localized and restricted clonal expansion [ 10 , 11 ]. Such results are different from those reported by Tiba-Casas et al [ 16 ] evaluating isolates from São Paulo, Brazil, which described a genetic background mostly composed of two main clonal clusters. Interestingly, strains ST1 and ST2, belonging to clusters A and B from Acre/1995, were related to an outbreak that occurred in the city of Tarauacá/Acre State and was detected after 17 years causing infection in the city of Belém/Pará State (subclusters A1 and B2).…”

Serotyping, MLST, and Core Genome MLST Analysis of Salmonella enterica From Different Sources in China During 2004–2019

“…In recent years, gene sequencing-based typing assays have been rapidly developed for bacterial tracing with vigorous vitality, including pulsed-field gel electrophoresis, MLST, core genome MLST (cgMLST), whole genome multilocus sequence typing (wgMLST), and whole gene single nucleotide polymorphism (wgSNP) ( Liu et al, 2016 , 2019 ; Radomski et al, 2019 ; Tiba-Casas et al, 2019 ). Among these molecular typing methods, MLST was developed to establish analytical microorganism typing ( Maiden et al, 1998 ), recognize evolutionary relationships of Salmonella ( Achtman et al, 2012 ; Ashton et al, 2016 ; Mairi et al, 2020 ; Zhang et al, 2020 ), and determine clonal isolate distributions across various environments and hosts ( Wang M. et al, 2020 ; Zhao et al, 2020 ).…”

A genomic snapshot of Salmonella enterica serovar Typhi in Colombia

“…Here, in this primary study of WGS data from S. Typhi circulating in Colombia, we show that the majority of organisms in the selected 20-year time span displayed limited genetic diversity, belonging mainly to two major clades: 3.5 and 2.5. The limited number of sequenced isolates from Latin America to date mainly belonged to primary cluster 2 and primary cluster 4, with genotype 2.0 in Argentina, Mexico, El Salvador, and Peru, genotype 2.3.2 in Argentina, El Salvador, and Mexico, genotype 4.1.0 in Brazil [19], and Argentina [3]. In the restricted number of isolates screened here, no genotype 4.3.1 (H58) isolates were found.…”

“…Since then, there have been only three additional publications describing S . Typhi isolated in Latin America and characterized using WGS, generating a further 36 genome sequences [ 4 , 19 , 20 ]…”

“…In 2015, a landmark global S. Typhi genotyping scheme was published, but comprised only 20 genome sequences originating from Latin America (Argentina, El Salvador, French Guiana, and Peru) [3]. Since then, there have been only three additional publications describing S. Typhi isolated in Latin America and characterized using WGS, generating a further 36 genome sequences [4,19,20] In response to local concern regarding the increase of typhoid fever and the international threat of AMR, the National Surveillance System Public Health (SIVIGILA) of Colombia made typhoid fever a notifiable disease in 2006, requiring laboratory follow-up [21]. Here, we aimed to generate the first insights into the molecular epidemiology of typhoid in Colombia by performing AMR profiling and comparative genotyping using both PFGE and WGS on a crosssectional collection of S. Typhi isolated in Colombia between 1997 and 2018.…”