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 clusters-related 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.
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 clusters-related 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.
Authors: Sueli Aparecida Fernandes; Ana Terezinha Tavechio; Ângela Cristina Rodrigues Ghilardi; Elisabete Aparecida de Almeida; Josefa Maria Lopes da Silva; Carlos Henrique Camargo; Monique Ribeiro Tiba-Casas Journal: Rev Inst Med Trop Sao Paulo Date: 2022-09-30 Impact factor: 2.169
Authors: Ana Judith Pires Garcia Quaresma; Yan Corrêa Rodrigues; Joseline Barbosa Aboim; Mayza Miranda Bezerra; Maria Isabel Montoril Gouveia; Ana Roberta Fusco Da Costa; Cintya de Oliveira Souza; Flávia Corrêa Bastos; Luana Nepomuceno Gondim Costa Lima; Francisco Lúzio de Paula Ramos; Karla Valéria Batista Lima Journal: Infect Dis Rep Date: 2022-08-03