Evaluation of Whole-Genome Sequencing combined with a bioinformatics tool for the complete characterization of Streptococcus agalactiae infection

Background: Our aim was to evaluate the Whole-Genome Sequencing (WGS), as a new tool, in order to implement the method within the activities of the Belgian National Reference Centre Streptococcus agalactiae (NRC). The analysis of the bacterial genome by WGS could replace some current standard methods used at the NRC, unifying laboratory workflow, diminishing workload, enhancing molecular surveillance.
Methods: To determine the reliability of the WGS, the results were compared with those obtained by the standard methods used by the NRC (multiplex PCRs and MLST). The raw sequence data from WGS were analyzed with the bioinformatics tool "WGS-typer" (Hedera22, Liège, Belgium), specially designed for the NRC needs. 37 strains isolated from vaginal colonization, or invasive infections in adults and infants were selected for their varied characteristics from the NRC collection. Capsular serotype, pili proteins genes, macrolides/lincosamides/streptogramins (MLS) resistance genes and sequence types were determined by both approaches.
Results: Regarding capsular serotype and pili protein genes, the results reported by conventional PCR methods were perfectly confirmed by the WGS (100% concordance). However, for MLS resistance genes and sequence types, the comparison highlights one and three discrepancies respectively. A new sequence type 1655 was listed in the PUBMLST database thanks to this research.
Conclusion: WGS is a promising approach that can compete with the conventional methods currently used in laboratories. Indeed, this technology allows, at lower costs and workload, a complete characterization of the GBS and a huge concordance between WGS and conventional methods has been observed.