| Summary: | <p>Abstract</p> <p>Background</p> <p>Bovine tuberculosis is a zoonotic problem in pastoral cattle and communities in Uganda. Tuberculin tests in pastoral cattle had shown a high herd but low animal prevalence, with a high proportion of avian reactors. No work had been done to identify the mycobacterial species involved. The objective of the study was to isolate and characterise Mycobacterial species causing tuberculous lesions in slaughtered animals. Lesioned organs compatible with bovine tuberculosis in slaughtered cattle from pastoral areas in Uganda were collected and cultured to isolate <it>mycobacteria</it>. AccuProbe culture identification kits for the <it>Mycobacterium tuberculosis </it>complex, <it>M. avium </it>complex and <it>M. avium </it>were used to identify the isolates. Spoligotyping and Insertion Sequence (IS) <it>1311 </it>and IS<it>1245 </it>Restriction Fragment Length Polymorphism analysis (RFLP) were used to further characterise the isolates.</p> <p>Results</p> <p>Of the 61 lesioned organs and tissues cultured, 19 isolates were identified as <it>M. bovis</it>, 3 as <it>M. avium </it>subsp.<it>hominissuis</it>, 1 as <it>M. intracellulare</it>, 1 as a mixed culture of <it>M. bovis </it>and <it>M. avium sp</it>. and 1 as <it>M. avium sp</it>. and unidentified <it>mycobacteria</it>. Eleven other <it>mycobacteria </it>outside the tuberculosis and avium complex groups were also isolated. Ten new spoligopatterns grouped into three clusters were identified from <it>M. bovis </it>isolates. Two of the three <it>M. avium </it>subsp.<it>hominissuis </it>isolates showed similar patterns on the IS<it>1311 </it>RFLP but all were different on the IS<it>1245 </it>RFLP.</p> <p>Conclusion</p> <p>The isolation of <it>M. bovis </it>confirms the ongoing infection with spoligotypes unique to Uganda. Isolation of environmental <it>mycobacteria </it>could explain the high avian or non specific tuberculin reactor patterns commonly observed in pastoral cattle and suggests their pathogenic or opportunistic role in the infection of cattle with disseminated bovine tuberculous lesions.</p>
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