ShigaPass: an in silico tool predicting Shigella serotypes from whole-genome sequencing assemblies.

ABSTRACT: Shigella is one of the commonest causes of diarrhoea worldwide and a major public health problem. Shigella serotyping is based on a standardized scheme that splits Shigella strains into four serogroups and 60 serotypes on the basis of biochemical tests and O-antigen structures. This conventional serotyping method is laborious, time-consuming, impossible to automate, and requires a high level of expertise. Whole-genome sequencing (WGS) is becoming more affordable and is now used for routine surveillance, opening up possibilities for the development of much-needed accurate rapid typing methods. Here, we describe ShigaPass, a new in silico tool for predicting Shigella serotypes from WGS assemblies on the basis of rfb gene cluster DNA sequences, phage

SUBMITTER: Yassine I 

PROVIDER: S-EPMC10132075 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature