Application of a target enrichment-based next-generation sequencing protocol for identification and sequence-based prediction of pneumococcal serotypes

BACKGROUND: The use of whole-genome sequencing in microbiology at a diagnostic level, although feasible, is still limited by the expenses associated and by the complex bioinformatics pipelines in data analyses. We describe the use of target enrichment-based next-generation sequencing for pneumococcal identification and serotyping as applied to the polysaccharide 23 valent vaccine serotypes as an affordable alternative to whole genome sequencing. RESULTS: Correct identification of Streptococcus pneumoniae and prediction of common vaccine serotypes: 12 to serotype level and the rest to serogroup levels were achieved for all serotypes with >500 reads mapped against serotypes sequences. A proportion-based criterion also enabled the identification of two serotypes present in the same sample, thus indicating the possibility of using this method in detecting co-colonizing serotypes. The results obtained were comparable to or an improvement on the currently existing molecular serotyping methods for S. pneumoniae in relation to the polysaccharide vaccine serotypes. CONCLUSION: We propose that this method has the potential to become an affordable and adaptable alternative to whole-genome sequencing for pneumococcal identification and serotyping.