Open Access Research article

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

Veranja Liyanapathirana1, Irene Ang1, Dominic Tsang2, Kitty Fung3, Tak Keung Ng4, Haokui Zhou1 and Margaret Ip1*

Author Affiliations

1 Department of Microbiology, The Chinese University of Hong Kong, The Prince of Wales Hospital, Hong Kong, China

2 Queen Elizabeth Hospital, Hong Kong, China

3 United Christian Hospital, Hong Kong, China

4 Princess Margaret Hospital, Hong Kong, China

For all author emails, please log on.

BMC Microbiology 2014, 14:60  doi:10.1186/1471-2180-14-60

Published: 10 March 2014



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.


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.


We propose that this method has the potential to become an affordable and adaptable alternative to whole-genome sequencing for pneumococcal identification and serotyping.

Next generation sequencing (NGS); Streptococcus pneumoniae; Serotyping