Comparison of molecular serotyping approaches of Streptococcus agalactiae from genomic sequences

Georgia Kapatai,Victoria J. Chalker,Darshana Patel,Androulla Efstratiou

doi:10.1186/s12864-017-3820-5

Abstract

BackgroundGroup B streptococcus (GBS) capsular polysaccharide is one of the major virulence factors underlying invasive GBS disease and a component of forthcoming vaccines. Serotype classification of GBS is based on the capsule polysaccharide of which ten variants are known to exist (Ia, Ib, II-IX). Current methods for GBS serotype assignment rely on latex agglutination or PCR while more recently a whole genome sequencing method was reported. In this study, three distinct algorithms for serotype assignment from genomic data were assessed using a panel of 790 clinical isolates.MethodsThe first approach utilised the entire capsular locus coupled with a mapping methodology. The second approach continues from the first and utilised a SNP-based methodology across the conserved cpsD-G region to differentiate serotypes Ia-VII and IX. Finally the third approach used the variable cpsG –K region coupled with a mapping methodology. All three approaches were assessed for typeability (percentage of isolates assigned a serotype) and concordance to the latex agglutination methodology.ResultsFollowing comparisons, the third approach using the variable cpsG-K region demonstrated the best performance with 99.9% typeability and 86.7% concordance. Overall, of the 105 discordant isolates, 71 were resolved following retesting of latex agglutination and whole genome sequencing, 20 failed to assign a serotype using latex agglutination and only 14 were found to be truly discordant on re-testing. Comparison of this final approach with the previously described assembly-based approach returned identical results.ConclusionsThese results demonstrated that molecular capsular typing using whole genome sequencing and a mapping-based approach is a viable alternative to the traditional, latex agglutination-based serotyping method and can be implemented in a public health microbiology setting.

Highlights

Group B streptococcus (GBS) capsular polysaccharide is one of the major virulence factors underlying invasive GBS disease and a component of forthcoming vaccines
Selecting single nucleotide polymorphisms (SNP) for serotype identification Serotype identification using Polymerase chain reaction (PCR) amplification followed by Sanger sequencing was previously described by Kong et al for serotypes Ia to VII and later by Slotvet et al to include serotype IX [26, 27]
We examined the previously described SNPs using the capsular locus sequences from 10 reference strains

Summary

Introduction

Group B streptococcus (GBS) capsular polysaccharide is one of the major virulence factors underlying invasive GBS disease and a component of forthcoming vaccines. Current methods for GBS serotype assignment rely on latex agglutination or PCR while more recently a whole genome sequencing method was reported. Three distinct algorithms for serotype assignment from genomic data were assessed using a panel of 790 clinical isolates. A rise in the incidence of disease has been noted across multiple countries [3]. This is of particular concern because GBS is associated with a high morbidity and mortality [4]. Kapatai et al BMC Genomics (2017) 18:429 important for assessing serotype distributions in vaccine coverage and post-vaccine surveillance studies. In the central region from cpsG to –K in serotypes Ia-VII and IX and from cpsR to -K for serotype VIII the presence of genes and/or the sequence similarity varies between the serotypes (Fig. 1)

Methods

Results

Discussion

Conclusion