Cookies on this website
We use cookies to ensure that we give you the best experience on our website. If you click 'Continue' we'll assume that you are happy to receive all cookies and you won't see this message again. Click 'Find out more' for information on how to change your cookie settings.

<jats:p><jats:named-content content-type="genus-species">Shigella flexneri</jats:named-content>can be phenotypically serotyped using antisera raised to type-specific somatic antigens and group factor antigens and genotypically serotyped using PCR targeting O-antigen synthesis or modification genes. The aim of this study was to evaluate a real-time PCR for serotyping<jats:named-content content-type="genus-species">S. flexneri</jats:named-content>and to use whole-genome sequencing (WGS) to investigate the phenotypic and genotypic serotype identifications. Of the 244 cultures tested retrospectively, 226 (92.6%) had concordant results between phenotypic serotyping and PCR. Seventy of the 244 isolates (including 15 of the 18 isolates where a serotype-PCR mismatch was identified) were whole-genome sequenced, and the serotype was derived from the genome. Discrepant results between the phenotypic and genotypic tests were attributed to insertions/deletions or point mutations identified in O-antigen synthesis or modification genes, rendering them dysfunctional; inconclusive serotyping results due to nonspecific cross-reactions; or novel genotypes. Phylogenetic analysis of the WGS data indicated that the serotype, regardless of whether it was phenotypically or genotypically determined, was a weak predictor of phylogenetic relationships between strains of<jats:named-content content-type="genus-species">S. flexneri</jats:named-content>. WGS data provided both genome-derived serotyping, thus supporting backward compatibility with historical data and facilitating data exchange in the community, and more robust and discriminatory typing at the single-nucleotide-polymorphism level.</jats:p>

Original publication

DOI

10.1128/jcm.03386-15

Type

Journal

Journal of Clinical Microbiology

Publisher

American Society for Microbiology

Publication Date

06/2016

Volume

54

Pages

1456 - 1461