title: A molecular-capsular-type prediction system for 90 Streptococcus pneumoniae serotypes using partial cpsA-cpsB sequencing and wzy- or wzx-specific PCR.
abstract: In a previous study, a molecular capsular type (MCT) prediction system for 51 Streptococcus pneumoniae serotypes was developed based on a combination of partial cpsA-cpsB sequencing and serotype(s)/group(s)-specific PCR. In this study, another 169 S. pneumoniae isolates were added to the existing database of 427 isolates, including representatives of all 39 serotypes not previously studied. In addition to the authors' own limited sequence data for all 90 serotypes, cpsA-cpsB sequence data published by the S. pneumoniae capsular loci-sequencing group (http://www.sanger.ac.uk/Projects/S_pneumoniae/CPS/) at the Sanger Institute or available from GenBank were incorporated into the database. All serotypes, except 25A, were represented by at least two isolates. The number of sequence types identified was 138, of which 110 corresponded to single conventional serotypes (CSs); of these, 57 were represented by two or more isolates. Twenty-six sequence types were shared by between two and four CSs. To resolve these shared cpsA-cpsB sequence types and increase the discriminatory power of our system, the genes encoding the capsular polysaccharide flippase (wzx) and polymerase (wzy) were annotated and 24 new serotype(s)/group(s)-specific PCRs targeting wzy and two targeting wzx were designed. Using both cpsA-cpsB sequencing and wzx/wzy PCR, MCT correctly predicted the CSs of 516 (73 %) and the serogroup of an additional 155 (22 %) of the 708 isolates evaluated. For 5 % of isolates, MCT could not distinguish between members of five serotype pairs (37 isolates) containing members of different serogroups. Although further study of the relationship between MCT and CS is needed, this system now allows serotype or serogroup identification of 95 % of S. pneumoniae isolates.
authors.affiliation: Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, NSW 2145, Australia 2Wuhan First Hospital, Hubei Province, Wuhan 430022, PR China 3TEDA School of Biological Sciences and Biotechnology and Tianjin State Laboratory of Microbial Functional Genomics, Nankai University, TEDA College, Tianjin 300457, PR China 4School of Biotechnology and Biomolecular Sciences, The University of New South Wales, NSW 2052, Australia 5Tianjin Biochip Technology Corporation, TEDA, Tianjin 300457, PR China 6Department of Medicine, The University of Sydney, NSW 2066, Australia 7National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases, Children's Hospital at Westmead, NSW 2145, Australia.
authors.forename: Fanrong
authors.initials: F
authors.lastname: Kong
authors.affiliation: Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, NSW 2145, Australia 2Wuhan First Hospital, Hubei Province, Wuhan 430022, PR China 3TEDA School of Biological Sciences and Biotechnology and Tianjin State Laboratory of Microbial Functional Genomics, Nankai University, TEDA College, Tianjin 300457, PR China 4School of Biotechnology and Biomolecular Sciences, The University of New South Wales, NSW 2052, Australia 5Tianjin Biochip Technology Corporation, TEDA, Tianjin 300457, PR China 6Department of Medicine, The University of Sydney, NSW 2066, Australia 7National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases, Children's Hospital at Westmead, NSW 2145, Australia.
authors.forename: Weizhen
authors.initials: W
authors.lastname: Wang
authors.affiliation: Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, NSW 2145, Australia 2Wuhan First Hospital, Hubei Province, Wuhan 430022, PR China 3TEDA School of Biological Sciences and Biotechnology and Tianjin State Laboratory of Microbial Functional Genomics, Nankai University, TEDA College, Tianjin 300457, PR China 4School of Biotechnology and Biomolecular Sciences, The University of New South Wales, NSW 2052, Australia 5Tianjin Biochip Technology Corporation, TEDA, Tianjin 300457, PR China 6Department of Medicine, The University of Sydney, NSW 2066, Australia 7National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases, Children's Hospital at Westmead, NSW 2145, Australia.
authors.forename: Jiang
authors.initials: J
authors.lastname: Tao
authors.affiliation: Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, NSW 2145, Australia 2Wuhan First Hospital, Hubei Province, Wuhan 430022, PR China 3TEDA School of Biological Sciences and Biotechnology and Tianjin State Laboratory of Microbial Functional Genomics, Nankai University, TEDA College, Tianjin 300457, PR China 4School of Biotechnology and Biomolecular Sciences, The University of New South Wales, NSW 2052, Australia 5Tianjin Biochip Technology Corporation, TEDA, Tianjin 300457, PR China 6Department of Medicine, The University of Sydney, NSW 2066, Australia 7National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases, Children's Hospital at Westmead, NSW 2145, Australia.
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.affiliation: Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, NSW 2145, Australia 2Wuhan First Hospital, Hubei Province, Wuhan 430022, PR China 3TEDA School of Biological Sciences and Biotechnology and Tianjin State Laboratory of Microbial Functional Genomics, Nankai University, TEDA College, Tianjin 300457, PR China 4School of Biotechnology and Biomolecular Sciences, The University of New South Wales, NSW 2052, Australia 5Tianjin Biochip Technology Corporation, TEDA, Tianjin 300457, PR China 6Department of Medicine, The University of Sydney, NSW 2066, Australia 7National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases, Children's Hospital at Westmead, NSW 2145, Australia.
authors.forename: Quan
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, NSW 2145, Australia 2Wuhan First Hospital, Hubei Province, Wuhan 430022, PR China 3TEDA School of Biological Sciences and Biotechnology and Tianjin State Laboratory of Microbial Functional Genomics, Nankai University, TEDA College, Tianjin 300457, PR China 4School of Biotechnology and Biomolecular Sciences, The University of New South Wales, NSW 2052, Australia 5Tianjin Biochip Technology Corporation, TEDA, Tianjin 300457, PR China 6Department of Medicine, The University of Sydney, NSW 2066, Australia 7National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases, Children's Hospital at Westmead, NSW 2145, Australia.
authors.forename: Archcna
authors.initials: A
authors.lastname: Sabananthan
authors.affiliation: Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, NSW 2145, Australia 2Wuhan First Hospital, Hubei Province, Wuhan 430022, PR China 3TEDA School of Biological Sciences and Biotechnology and Tianjin State Laboratory of Microbial Functional Genomics, Nankai University, TEDA College, Tianjin 300457, PR China 4School of Biotechnology and Biomolecular Sciences, The University of New South Wales, NSW 2052, Australia 5Tianjin Biochip Technology Corporation, TEDA, Tianjin 300457, PR China 6Department of Medicine, The University of Sydney, NSW 2066, Australia 7National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases, Children's Hospital at Westmead, NSW 2145, Australia.
authors.forename: Gwendolyn L
authors.initials: GL
authors.lastname: Gilbert
mesh_terms: D016667:Bacterial Capsules / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics*; D015373:Bacterial Typing Techniques; D002352:Carrier Proteins / Q000235:genetics*; D016695:Glycosyltransferases / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction / Q000379:methods; D017027:Protein Tyrosine Phosphatases / Q000235:genetics*; D012680:Sensitivity and Specificity; D012703:Serotyping / Q000379:methods; D013296:Streptococcus pneumoniae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification
chemical_list: D001426:Bacterial Proteins; D002352:Carrier Proteins; C500439:CpsA protein, Streptococcus pneumoniae; C500441:wzy protein, Streptococcus pneumoniae; D016695:Glycosyltransferases; C500442:wzx protein, Streptococcus pneumoniae; C500440:CpsB protein, Streptococcus pneumoniae; D017027:Protein Tyrosine Phosphatases