title: Application of a target enrichment-based next-generation sequencing protocol for identification and sequence-based prediction of pneumococcal serotypes.
abstract: 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.
  
  
  CONCLUSIONS
  We propose that this method has the potential to become an affordable and adaptable alternative to whole-genome sequencing for pneumococcal identification and serotyping.
authors.forename: Veranja
authors.initials: V
authors.lastname: Liyanapathirana
authors.forename: Irene
authors.initials: I
authors.lastname: Ang
authors.forename: Dominic
authors.initials: D
authors.lastname: Tsang
authors.forename: Kitty
authors.initials: K
authors.lastname: Fung
authors.forename: Tak Keung
authors.initials: TK
authors.lastname: Ng
authors.forename: Haokui
authors.initials: H
authors.lastname: Zhou
authors.affiliation: Department of Microbiology, The Chinese University of Hong Kong, The Prince of Wales Hospital, Hong Kong, China. margaretip@cuhk.edu.hk.
authors.forename: Margaret
authors.initials: M
authors.lastname: Ip
mesh_terms: D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics / Q000379:methods*; D006801:Humans; D012703:Serotyping; D013296:Streptococcus pneumoniae / Q000145:classification* / Q000235:genetics*