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Pathogenicity and Medical Microbiology |
Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK1
Public Health Laboratory, Royal Sussex County Hospital, Brighton BN2 5BE, UK2
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK3
Author for correspondence: Christopher G. Dowson. Tel: +44 1203 523534. Fax: +44 1203 523568. e-mail: c.g.dowson{at}warwick.ac.uk
The population structure of Streptococcus pneumoniae in a sample of 134 carried antibiotic-susceptible isolates, and 53 resistant and susceptible invasive isolates, was examined using a DNA-based version of multilocus enzyme electrophoresis: multilocus restriction typing (MLRT). This involved RFLP analysis of PCR products generated from nine loci of housekeeping genes located around the pneumococcal chromosome. The combination of alleles at each of the nine loci gave an allelic profile or restriction type (RT). All carried (throat or nasopharyngeal) isolates from children or adults in Oxford and Manchester, UK, and from an HIV-seropositive cohort in Nairobi, Kenya, showed an epidemic population structure. Twelve carried clonal groups, each with different serotypes, were identified at both locations within the UK. Almost all of the carried clones examined (16/17) were found to possess identical RTs or sequence types (STs) to invasive isolates, indicating that frequently carried clones are also associated with cases of invasive disease. As expected from previous studies, the population of 53 invasive, mainly penicillin-resistant, isolates was also found to be at linkage equilibrium. Serotype switching was identified among 14% of RTs that possessed two or more members, or 5·7% of individual isolates within these RTs. In support of a population structure in which there is frequent recombination, there is also clear evidence that the trpA/B locus within pneumococci has evolved by horizontal gene transfer. A non-serotypable isolate from an HIV-seropositive patient in Kenya was clearly genetically distinct from other strains studied, with unique alleles at eight out of nine loci examined. However, it was initially identified as a pneumococcus by a 16S RNA gene probe (Gen-Probe), optochin susceptibility and the presence of pneumolysin and autolysin.
Keywords: molecular typing, carried clones, virulent clones, serotype stability, HIV
Abbreviations: ET, electrophoretic type; IA, index of association; MLEE, multilocus enzyme electrophoresis; MLRT, multilocus restriction typing; MLST, multilocus sequence typing; REP-PCR, repetitive element PCR; RT, restriction type; ST, sequence type; UPGMA, unweighted pair group method with arithmetic means
The GenBank accession numbers for the sequences of the trpA/B alleles determined in this study are AF157817 to AF157826.
a Present address: Laboratoire d’Ecologie, UMR 7625 CNRS Université Pierre et Marie Curie, 7 quai St Bernard, F-75252 Paris Cedex 05, France.
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