The complete genomes of two members of the Mycobacterium avium complex (MAC), Mycobacterium avium subsp. paratuberculosis(Map) and Mycobacterium avium subsp. hominissuis, have been recently published. Comparison between these two genomes of closely related bacteria has revealed a number of polymorphic genomic sequences between them, called Large Sequence Polymorphisms (LSP).

Some of those LSPs are characteristic of bacterial subspecies, and can be used as diagnostic targets to correctly identify an isolate. Besides, some other LSPs can be used to distinguish between different types within one particular subspecies. In particular, three of those LSPs have been shown to distinguish Map isolates belonging to Types I and II. However, the LSP-profile of the Type III isolates of Map has not been determined yet.

In the present study a selection of Spanish Map isolates recovered from goats and cattle from different geographic areas were selected. These strains were characterized as Type III or I/III by Pulsed-Field Gel Electrophoresis and PCR analysis aimed to the IS1311 element. Strains previously characterized as Type II recovered from cattle and goats were also included in the panel as controls. All these strains were analyzed using three-primer PCRs in order to demonstrate the presence/absence of LSPa4-II, LSPa20 and LSPa18. All isolates were further characterized by sequencing of the 65-kDa heat-shock protein gene (hsp65).

All Type III and I/III isolates showed the same LSP-profile and hsp65 sequevar than those described for Type I strains, thus confirming the relatedness between these two types. On the other hand, the analyzed Type II Map strains yielded the expected results in all PCRs, what corroborates the homogeneity within this cluster.