Polymorphisms in IS1311, an insertion sequence common toMycobacterium aviumandM. aviumsubsp.paratuberculosis, can be used to distinguish between and within these species

IS1311is an insertion sequence fromMycobacterium aviumandM. aviumsubsp.paratuberculosis.Using a 180 bp fragment of IS1311as a probe, 7–10 copies of IS1311were revealed in strains ofM. aviumsubsp.paratuberculosis.With a given restriction enzyme, the restriction fragment length polymorphism patterns obtained from isolates ofM. aviumsubsp.paratuberculosisfrom cattle were all identical, but they differed from those of isolates from sheep, which could be separated into two types. A 1259 bp fragment of IS1311produced by polymerase chain reaction (PCR) from two isolates ofM. aviumsubsp.paratuberculosisfrom cattle and two isolates from sheep was sequenced and compared to the sequence known fromM. avium.Apart from five point differences the sequences were identical. Restriction endonuclease analysis (REA) of the PCR product was used to distinguish isolates ofM. aviumsubsp.paratuberculosisfromM. avium, in addition to the conventional test for IS900.In isolates ofM. aviumsubsp.paratuberculosisfrom cattle the IS1311gene was polymorphic at position 223, which enabled isolates from sheep and cattle to be distinguished by PCR-REA. These simple tests will be used to enhance disease control programmes for Johne's disease in ruminants. The findings of this study raise interesting questions about the evolution ofM. aviumsubsp.paratuberculosis.