In the study region, mycobacteriosis most affected adult males with low schooling. Most patients presented comorbidities in particular co-infection with the HIV virus. M. avium is the most prevalent species in the region with the M. abscessus/M. massiliense/M. bolletii species being the main cause of nosocomial infections.

Summary Objective  To evaluate retrospectively the microbiological profile of Mycobacterium species isolated from HIV‐infected patients attending the HIV/TB reference health care units in São José do Rio Preto, Brazil. Method  Retrospective evaluation of all HIV‐1 positive patients whose IAL‐SJRP laboratorial analysis was positive for Mycobacterium sp. after diagnosis of HIV Infection, from January 2000 to December 2006. Results  Of 198 patients, acid‐fast staining detected mycobacteria early in 41%. Culture revealed 52.5% to be infected with Mycobacterium tuberculosis (MT). 42.4% had non‐tuberculous mycobacteria (NTM) and 5.1% had MT/NTM positive cultures. Eleven per cent of MT strains were resistant to at least one of the antimycobacterial drugs and 3.1% were multidrug resistant. 39.4% of isolated mycobacteria were NTM species. Conclusion  Our data may serve as a starting point for further comparisons with other Brazilian regions and other developing countries. The data may provide important clues to the future understanding, prevention and control of such co‐infections around the world.