Population biology of Streptococcus pneumoniae isolated from oropharyngealcarriage and invasive disease

The population structure of Streptococcus pneumoniae in a sample of 134 car ried antibiotic-susceptible isolates, and 53 resistant and susceptible inva sive isolates, was examined using a DNA-based version of multilocus enzyme electrophoresis: multilocus restriction typing (MLRT), This involved RFLP a nalysis of PCR products generated from nine loci of housekeeping genes loca ted around the pneumococcal chromosome. The combination of alleles at each of the nine loci gave an allelic profile or restriction type (RT). All carr ied (throat or nasopharyngeal) isolates from children or adults in Oxford a nd Manchester, UK, and from an HIV-seropositive cohort in Nairobi, Kenya, s howed 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 ide ntical RTs or sequence types (STs) to invasive isolates, indicating that fr equently carried clones are also associated with cases of invasive disease. As expected from previous studies, the population of 53 invasive, mainly p enicillin-resistant, isolates was also found to be at linkage equilibrium. Serotype switching was identified among 14% of RTs that possessed two or mo re 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-seropositi ve patient in Kenya was clearly genetically distinct from other strains stu died, with unique alleles at eight out of nine loci examined. However, it w as initially identified as a pneumococcus by a 16S RNA gene probe (Cen-Prob e), optochin susceptibility and the presence of pneumolysin and autolysin.