In the present study, a wide range of environmental mycobacteria from the human- animal- environment interface across the Ugandan rural pastoral farming ecosystem were detected. Furthermore, 15.5% of the 310 environmental samples collected contained mycobacteria. The yield of mycobacteria in the different samples could have been affected by several factors. They were collected in Uganda and transported to Norway for examination, something that delayed analysis. This could have greatly contributed to increased bacterial overgrowth by fungi and other bacteria. Ideally the samples size for water samples could have been bigger, but 30 ml was a convenient sample size for transportation. The decontamination method may affect the yield of mycobacteria, but is necessary to avoid growth of contaminants. The water samples contained a lot of organic material, containing other bacteria and fungi, and therefore the decontamination had to be the same as for soil and faecal samples, something that could have affected the number of isolates detected.
The results indicated that soils around the water sources were heavily contaminated, as mycobacteria were detected in 29.8% of the samples. This concurs with previous studies that detected MAC in 43% of soil and water samples in the environments around HIV patients in Uganda . The high recovery of NTM in water and in soils around water sources might be linked to the runoff from carrying plant organic waste and animal waste, rich in humic and fulvic acids which in turn support the growth of NTM . Thus animals and humans stand at risk of being infected or colonized by the opportunistic mycobacteria from the environment through collection and drinking of untreated water from these sources. Unfortunately this is a common practise in these areas [2, 3, 8, 38].
Most of the isolates were detected in November, December and January (ten, ten and 19 isolates respectively). These months are in the last part of the rainy season, thus more isolates were recovered during the period that followed this season. This finding contradicts findings from Malawi , where higher recovery rates were found in the dry season samples compared to the wet seasons. The high contamination of limited water sources with faecal matter in the drier months could be playing a key role. Secondly surface evaporation from stagnant open water sources could also concentrate the level of organic matter contained in water source.
Humans can be infected/colonised with NTM without developing disease  and exposure to NTM in the environment is common. One of the major limitations of this study is the lack of accurate case diagnoses with disease in the communities sampled. As resources are limited, patients and animals presenting with granulomatous lesions in Uganda usually do not receive culture confirmation of the species involved. Therefore, the species of NTM isolated in the environment cannot be reliably linked to those causing disease in the patients exposed to them. However, the species isolated from the Ugandan ecosystems have been found to cause disease in patients in other parts of the world. For example bacteria in the M. avium complex are known to cause opportunistic infections in animals and humans , and have been isolated from cattle and humans with tuberculous lesions in Uganda [20, 21], Zambia and other parts of the world [39, 40]. M. simiae has been isolated from two Ugandan HIV infected patients . The other NTM detected in this study have been isolated from patients in different parts of the world, and may cause clinical syndromes: chronic bronchopulmonary disease, lymphadenitis, skin and soft tissue disease, skeletal disease, and disseminated and catheter-related infections [39, 40, 42–46]. In humans, immunocompromised individuals such as the malnourished, HIV/AIDS infected, children or the elderly are often affected . Given the high incidence of HIV/AIDS in Uganda, and especially in the districts of Mubende and Nakasongola, many patients might be at high risk of getting infected by NTM.
Bacteria in the M. terrae complex and M. hiberniae have been documented to be resistant to multiple anti-tuberculosis drugs . M. nonchromogenicum and M. terrae, found to be non pathogenic for guinea pigs, pigs and rabbits are known to provoke a non specific hypersensitivity reaction to bovine tuberculin in guinea pigs, pigs and cattle .
Our findings describe the potential risk for humans and animals being infected with potentially pathogenic mycobacteria in the Ugandan rural farming communities. The questionnaire revealed factors of importance for human exposure to these NTM, as NTM were more often detected in water sources shared with domestic and wild animals (especially primates), and in valley dams. Close contact with cattle and other domestic animals, and drinking of untreated water were found to be important risk behaviour for possible exposure to NTM. This behaviour is common in the pastoral communities of Uganda, and in other rural communities in developing countries. Therefore, knowing that potentially pathogenic mycobacteria are present in the environment is important for identifying control measures for the human and animal population.
In a recent study from the same areas, pastoralists' knowledge was addressed. It appeared that people had generally little knowledge about the occurrence of mycobacterial infections, that these infections could be associated with the environment and wildlife and possible transmission from animals to humans . Similarly, recent findings showed that wildlife and domestic animals had tuberculosis like lesions due to mixed infections of Corynebacterium pseudotuberculosis and NTM in Mubende, Uganda and South Africa [48, 49]. These findings confirm that domestic and wild animals represent a permanent reservoir of mycobacterial infections and therefore pose a serious threat to control and elimination programs .
The present study suggests drinking untreated water, living in close contact with cattle or other domestic animals and drinking water from the valley dams as the most important factors for human exposure to NTM species. The importance of NTM should not be under rated in these pastoral communities where people live close to domestic and wild animals, and where they depend on contaminated water sources for household use. District reports indicate an increasing number of outbreaks of water-related diseases in humans due to increased contamination levels resulting from animals sharing water sources with humans . Whether boiling of drinking water for human consumption could reduce the problems with NTM in drinking water is a subject of further research.