Instituto Adolfo Lutz, São Paulo, Brazil.
Instituto Adolfo Lutz, São Paulo, Brazil.
Int J Infect Dis. 2019 Apr;81:191-195. doi: 10.1016/j.ijid.2019.02.009. Epub 2019 Mar 5.
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).
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.
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).
In this study WGS based typing, was able to compete with PFGE for differentiation of the clusters of S. Typhi strains.
脉冲场凝胶电泳（PFGE）是鉴定和研究暴发的分子亚型的主要方法。在某些情况下，该技术无法区分无法通过全基因组测序（WGS）实现的不相关菌株。
本研究的目的是通过不同的分析方法（与传统的 PFGE 分型方法相比）确定 WGS 的优缺点，以回顾性分析 28 株伤寒沙门氏菌的聚类病例。
我们对 WGS 数据集评估了三种分析方法（核苷酸差异（ND）、单核苷酸多态性（SNP）和全基因组多位点序列分型（wgMLST）），它们将聚类相关菌株分类为两个聚类，聚类 A（来自 2017 年的菌株）和聚类 B（来自 2007 年的菌株）。
在这项研究中，基于 WGS 的分型能够与 PFGE 竞争，以区分伤寒沙门氏菌菌株的聚类。
