Evaluation of Molecular Methods for Serotyping Shigella flexneri

Area of Science:

• Microbiology
• Genomics
• Molecular Biology

Background:

• Shigella flexneri serotyping traditionally relies on phenotypic methods using antisera.
• Genotypic methods, such as PCR targeting O-antigen genes, offer an alternative for serotyping.
• Whole-genome sequencing (WGS) provides comprehensive genomic data for strain characterization.

Purpose of the Study:

• To evaluate a real-time PCR assay for S. flexneri serotyping.
• To utilize WGS to investigate discrepancies between phenotypic and genotypic serotyping results.
• To assess the phylogenetic utility of serotype information.

Main Methods:

• Phenotypic serotyping using specific antisera.
• Real-time PCR targeting O-antigen synthesis or modification genes.
• Whole-genome sequencing (WGS) for serotype determination and phylogenetic analysis.

Main Results:

• High concordance (92.6%) was observed between phenotypic serotyping and PCR.
• WGS identified genetic variations (mutations, indels) in O-antigen genes as causes for discrepant results.
• Serotype was a weak predictor of phylogenetic relationships, while WGS provided robust, discriminatory typing.

Conclusions:

• Real-time PCR is a reliable method for S. flexneri serotyping, with WGS resolving discrepancies.
• WGS facilitates backward compatibility with historical serotyping data and enables advanced phylogenetic analysis.
• WGS offers superior discriminatory power compared to serotyping for S. flexneri strain typing.