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

BMC Microbiology

Margaret Ip¹  Haokui Zhou¹  Tak Keung Ng³  Kitty Fung⁴  Dominic Tsang²  Irene Ang¹  Veranja Liyanapathirana¹ 

[1] Department of Microbiology, The Chinese University of Hong Kong, The Prince of Wales Hospital, Hong Kong, China;Queen Elizabeth Hospital, Hong Kong, China;Princess Margaret Hospital, Hong Kong, China;United Christian Hospital, Hong Kong, China

关键词: Serotyping;    Streptococcus pneumoniae;    Next generation sequencing (NGS);   

Others  :  1141736
DOI  :  10.1186/1471-2180-14-60

 received in 2013-11-20, accepted in 2014-02-28,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Liyanapathirana et al.; licensee BioMed Central Ltd.

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