Molecular epidemiology of Mycobacterium avium subsp paratuberculosis: IS900 restriction fragment length polymorphism and IS1311 polymorphism analysesof isolates from animals and a human in Australia

The distribution and prevalence of strains of Mycobacterium avium subsp, pa ratuberculosis were determined among sheep, cattle, and other species with Johne's disease in Australia. A total of 328 isolates were evaluated from n umerous farms in New South Wales, Victoria, Tasmania, and South Australia, Australia. Restriction fragment length polymorphism (RFLP) analysis of geno mic DNA using BstEII and an IS900 probe and IS1311 polymorphism analysis us ing PCR and restriction endonuclease analysis (PCR-REA) was used to classif y isolates as cattle (C) or sheep (S) strains. IS1311 PCR-REA provided simi lar information to IS900 RFLP analysis but was more useful than RFLP analys is where DNA was degraded or scarce, Twelve IS900 RFLP types were found, Jo hne's disease in sheep was always due to S strains, while cattle were infec ted only with C strains. RFLP type S1 was the dominant strain in sheep in N ew South Wales (97% of isolates) and was the only strain found in sheep fro m Victoria. Seven RFLP types were present in cattle, RFLP types C3 and C1 w ere most common (collectively, 85% of isolates), but C1 was not found in Ne w South Wales and C3 was present in dairy cattle but not in beef cattle in Victoria. These differences may be explained by restricted livestock tradin g patterns between different segments of the cattle industry, Up to five RF LP types were present in some geographic regions in Victoria, while up to t hree RFLP types were found among cattle on some farms. Individual cattle us ually were infected with only one RFLP type, but one animal was infected wi th both C5 and CU4. Two isolates from goats were C type as were three from alpacas, one from a rhinoceros, and two from a human with Crohn's disease. The prevalences of specific RFLP types in Australia differ from those repor ted in Europe and elsewhere. Given the existence of geographical and farm e nterprise differences in IS900 RFLP type, this technique may be applied sel ectively to trace the spread of Johne's disease, at least in the cattle ind ustries. As these observations reflect past exposure of livestock to M. avi um subsp, paratuberculosis, the monitoring of strains present in animals in Australia is continuing.