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Using cpsA–cpsB sequence polymorphisms and serotype-/group-specific PCR to predict 51 Streptococcus pneumoniae capsular serotypes

Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, Darcy Rd, Westmead, New South Wales, 2145 Australia

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

Received April 5, 2003
Accepted August 28, 2003

Streptococcus pneumoniae polysaccharide and protein-conjugate vaccines are available against the most commonly isolated pneumococcal serotypes. Ongoing surveillance of invasive pneumococcal disease is needed in order to monitor changes in distribution of serotypes. Based on previously published sequences of capsular polysaccharide synthesis (cps) gene clusters of 16 pneumococcal serotypes, a molecular capsular typing (MCT) system has been developed, based on a combination of partial cpsA–cpsB sequencing and serotype- or serogroup-specific PCR, targeting the genes wzy and wzx (except for serotype 3). In this study, 151 S. pneumoniae isolates of known serotype (representing 51 serotypes) and 276 recent clinical isolates were used to develop MCT and compare it with conventional serotyping (CS) (total 427 isolates). On the basis of 376 heterogeneity sites in the cpsA–cpsB region, 89 sequence types (ST) were identified, of which 76 corresponded to a single serotype and 11 contained two serotypes. The correct serotypes in two of the latter (10A-23F-g and 23F-23A) were identified using serotype 23F-specific PCR. Limited CS was required for 92 (22 %) isolates to distinguish between the two serotypes in the nine other mixed ST (6A–6B-g, 6A–6B-q, 15B–22F, 33F–33A, 17F–35B, 18B–18C, 13–20, 25F–38, 31–42). MCT is a specific, objective and practical method that can predict the serotype of most S. pneumoniae isolates; it will facilitate epidemiological studies. Further study of the relationship between MCT and CS is needed in order to improve our understanding of serotype differentiation and to improve MCT methods further.

The GenBank/EMBL/DDBJ accession numbers for the new partial sequence data for cpsA–cpsB, wzy and wzx genes are respectively AF532632–AF532715, AY330713–AY330718 and AY163171–AY163232. The accession numbers for sequence data used in this study that had been previously reported by others, in addition to those listed in Tables 2 and 3, are U15171, U66846 and U66845 (partial cps gene cluster for serotype 3), AF246897 and AF298581 (cps gene cluster for serotype 6B), AF105113 (partial cps gene cluster for serotype 19A), AF105114 and AF106137 (partial cps gene clusters for serotype 19B) and AF105115 (partial cps gene cluster for serotype 19C).

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