Distribution of Non-Tuberculous Mycobacterium Species in Pulmonary and Extrapulmonary Infections in South India–A Retrospective Analysis

Differential diagnosis of tuberculosis (TB) and non-tuberculous mycobacteria (NTM) is extremely challenging, especially in a high TB burden setting like India. A definitive diagnosis of NTM, along with additional speciation, is warranted to improve NTM management. Beyond the diagnosis of NTM and its speciation, clinical correlation is vital for differentiating NTM colonisation or contamination from disease. In this cross-sectional, retrospective analysis, both pulmonary and extrapulmonary samples from 1121 presumptive NTM patients from Tuberculosis Units across the country and from other private hospitals were included. Composite diagnosis were performed using X-rays, nucleic acid amplification tests, smear microscopy, and mycobacterial growth indicator tube cultures, with speciation of NTM isolates confirmed by line probe assay. Of the 1121 presumptive NTM patients, 66.0% were smear-negative, 44.7% had X-ray changes, and 98.0% were M. tuberculosis-negative according to the nucleic acid amplification test. Cultures identified 310 patients as NTM-positive, including 22 extrapulmonary cases. Speciation was performed for 135 NTM-positive isolates, where M. abscessus was identified as the predominant species in 30.4%, followed by M. kansasii in 25.1%. Our study demonstrated that although the composite diagnosis of NTM holds promise for identifying pulmonary and extrapulmonary NTM, culture (mean confirmation rate of 30–40% over 5 years) remains the gold standard, with NTM speciation by line probe assay completing the diagnosis.