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A molecular-capsular-type prediction system for 90 Streptococcus pneumoniae serotypes using partial cpsA–cpsB sequencing and wzy- or wzx-specific PCR

¹Centre 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

Correspondence Gwendolyn L. Gilbert lyng{at}icpmr.wsahs.nsw.gov.au

Received October 13, 2004
Accepted December 1, 2004

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.

The GenBank/EMBL/DDBJ accession numbers for the new partial cpsA (wzg)–cpsB (wzh) genes are AY508586–AY508641, AY621659, AY621660 and AY661448–AY661457.

Three phylogenetic trees, a schematic representation of related wzx genes and five tables of data are available as supplementary material in JMM Online.

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