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Non-tuberculous mycobacteria (NTM) are not only emerging and opportunistic pathogens of both humans and animals, but from a veterinary point of view some species induce cross-reactive immune responses that hamper the diagnosis of bovine tuberculosis (bTB) in both livestock and wildlife. Little information is available about NTM species circulating in wildlife species of South Africa. In this study, we determined the diversity of NTM isolated from wildlife species from South Africa as well as Botswana. Thirty known NTM species and subspecies, as well as unidentified NTM, and NTM closely related to  Mycobacterium goodii/Mycobacterium smegmatis  were identified from 102 isolates cultured between the years 1998 and 2010, using a combination of molecular assays viz PCR and sequencing of different Mycobacterial house-keeping genes as well as single nucleotide polymorphism (SNP) analysis. The NTM identified in this study include the following species which were isolated from tissue with tuberculosis- like lesions in the absence of  Mycobacterium tuberculosis  complex (MTBC) implying their potential role as pathogens of animals:  Mycobacterium abscessus  subsp.  bolletii, Mycobacterium gastri, Mycobacterium  species closely related to  Mycobacterium goodii/Mycobacterium smegmatis, Mycobacterium brasiliensis, Mycobacterium sinense  JMD 601,  Mycobacterium avium  subsp.  avium, Mycobacterium  sp. GR-2007,  Mycobacterium bouchedurhonense , and  Mycobacterium septicum / M. peregrinum. Mycobaterium brasiliensis, Mycobacterium gastri, Mycobacterium  sp. GR-2007, and a potential novel  Mycobacterium  species closely related to  Mycobacterium goodii  were found for the first time in this study to be potential pathogens of animals.  Mycobacterium simiae  was isolated from a sample originating from a tuberculin skin test positive reactor, demonstrating its potential to elicit inappropriate immune responses in animals that may interfere with diagnosis of tuberculosis by immunology.  Mycobacterium abscessus  subsp.  bolletti  was the most frequently detected NTM identified in 37 of the 102 isolates. Other NTM species were also isolated from animals not showing any pathological changes. Knowledge gained in this study contribute to the understanding of NTM species circulating in wild animals in South Africa and the pathogenic potential of certain species, whose role in disease causation need to be examined, as well as to a certain extent the potential of  M. simiae  to hamper the diagnosis of bTB.

Non-tuberculous Mycobacteria in South African Wildlife: Neglected Pathogens and Potential Impediments for Bovine Tuberculosis Diagnosis