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Separation of large restriction fragments by pulsed-field gel electrophoresis is a commonly used method for epidemiological typing ofStreptococcus pneumoniae and many other bacterial species. Information on the genetic changes underlying the restriction fragment polymorphisms that allow discrimination between isolates is scarce. In this study fragments adjacent toApa I sites in a clinical isolate ofS. pneumoniae were cloned and used to probeHin dIII andHin dIII-plus-Apa I genomic DNA digests from other isolates with very differentApa I fragment patterns. If for a given isolate theHin dIII fragment detected by the probe was reduced in size on digestion withApa I, it was deduced that theApa I site was conserved in that isolate. The results demonstrate that of sixApa I sites in PN93/908 examined, five were retained in 11 genetically different isolates and one was retained in 2 isolates but lost in 9 others. It was concluded that point mutations at restriction sites are unlikely to account for the restriction fragment length polymorphism observed and that much of the polymorphism may be due to DNA rearrangements, possibly resulting from the insertion or deletion of mobile DNA elements.

Conservation of Restriction Sites in Isolates of Streptococcus pneumoniae with Diverse Restriction Fragment Patterns