title: Direct detection and prediction of all pneumococcal serogroups by target enrichment-based next-generation sequencing.
abstract: Despite the availability of standard methods for pneumococcal serotyping, there is room for improvement in the available methods, in terms of throughput, multiplexing capacity, and the number of serotypes identified. We describe a target enrichment-based next-generation sequencing method applied to nasopharyngeal samples for direct detection and serogroup prediction of all known serotypes of Streptococcus pneumoniae, 32 to the serotype level and the rest to the closely related serogroup level. The method was applied to detect and to predict the serogroups of pneumococci directly in clinical samples and from sweeps of primary culture DNA, with increased detection rates versus culture-based identification and agreement with the serotypes/serogroups determined by conventional serotyping methods. We propose this method, in conjunction with traditional serotyping methods, as an alternative to rapid detection and serotyping of pneumococci.
authors.affiliation: Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR margaretip@cuhk.edu.hk.
authors.forename: Margaret
authors.initials: M
authors.lastname: Ip
authors.affiliation: Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR.
authors.forename: Veranja
authors.initials: V
authors.lastname: Liyanapathirana
authors.affiliation: Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR.
authors.forename: Irene
authors.initials: I
authors.lastname: Ang
authors.affiliation: Department of Pathology, United Christian Hospital, Hong Kong SAR.
authors.forename: Kitty S C
authors.initials: KS
authors.lastname: Fung
authors.affiliation: Department of Pathology, Princess Margaret Hospital, Hong Kong SAR.
authors.forename: T K
authors.initials: TK
authors.lastname: Ng
authors.affiliation: Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR.
authors.forename: Haokui
authors.initials: H
authors.lastname: Zhou
authors.affiliation: Department of Pathology, Queen Elizabeth Hospital, Hong Kong SAR.
authors.forename: Dominic N C
authors.initials: DN
authors.lastname: Tsang
mesh_terms: D001431:Bacteriological Techniques / Q000379:methods*; D002648:Child; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009305:Nasopharynx / Q000382:microbiology; D011008:Pneumococcal Infections / Q000175:diagnosis / Q000382:microbiology*; D012680:Sensitivity and Specificity; D065288:Serogroup; D013296:Streptococcus pneumoniae / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D013997:Time Factors