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Usefulness of Inter-IS1 Spacer Polymorphisms for Subtyping of Shigella sonnei Isolates

ABSTRACT Shigella sonnei contains numerous IS1 elements. The existence of polymorphisms in the length of the inter-IS1 spacer is a basis for the development of a PCR-based method for the subtyping of S. sonnei strains. The usefulness of inter-IS1 spacer typing (IST) was evaluated and compared with that of pulsed-field gel electrophoresis (PFGE) by characterization of S. sonnei isolates from epidemiologically nonrelated cases and outbreaks and of isolates that were indistinguishable by PFGE and that were collected from independent infection events. IST was less discriminatory than PFGE, with discriminatory indices of 0.96 and 0.63, respectively, but was able to compensate for the drawbacks of PFGE. PFGE exhibited a high level of discriminatory power for S. sonnei isolates; however, PFGE was also, at times, too discriminatory, which was a disadvantage in constructing the clonal relationships among strains circulating over a period of months or years. Furthermore, IST provided greater subtyping information for isolates indistinguishable by PFGE. The present study indicates that IST is more useful than PFGE for investigating the genetic relationships among S. sonnei strains circulating over a longer time span and also for discriminating certain strains which are indistinguishable by PFGE.