title: Evaluation of Molecular Methods for Serotyping Shigella flexneri.
abstract: Shigella flexneri 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 S. flexneri 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 S. flexneri 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.
authors.affiliation: Gastrointestinal Bacteria Reference Unit, Public Health England, London, United Kingdom.
authors.forename: Amy
authors.initials: A
authors.lastname: Gentle
authors.affiliation: Gastrointestinal Bacteria Reference Unit, Public Health England, London, United Kingdom.
authors.forename: Philip M
authors.initials: PM
authors.lastname: Ashton
authors.affiliation: Gastrointestinal Bacteria Reference Unit, Public Health England, London, United Kingdom.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Dallman
authors.affiliation: Gastrointestinal Bacteria Reference Unit, Public Health England, London, United Kingdom claire.jenkins@phe.gov.uk.
authors.forename: Claire
authors.initials: C
authors.lastname: Jenkins
mesh_terms: D016680:Genome, Bacterial; D060005:Genotyping Techniques / Q000379:methods*; D010802:Phylogeny; D011446:Prospective Studies; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA; D012703:Serotyping / Q000379:methods*; D012763:Shigella flexneri / Q000145:classification* / Q000235:genetics*