Environmental Mycobacteria in Clinical Specimens and Their Impact on Tuberculosis Laboratory Diagnosis in Enugu State, South East Nigeria

Non-tuberculous mycobacteria in clinical specimens can interfere with smear microscopy, culture positivity, and Xpert MTB/RIF results, creating diagnostic confusion that leads to misclassification of tuberculosis cases in endemic settings. This study investigated the prevalence of environmental mycobacteria in clinical specimens and their diagnostic impact on tuberculosis laboratory services in Enugu State, South East Nigeria. A prospective cross-sectional study was conducted at two TB reference laboratories over twelve months. Sputum and bronchoalveolar lavage specimens from 420 patients investigated for pulmonary TB were processed for AFB smear, Xpert MTB/RIF Ultra, and liquid culture on MGIT 960. All culture-positive specimens were subjected to species identification by line probe assay and 16S rRNA gene sequencing. AFB smear was positive in 22.4% of specimens. Xpert MTB/RIF detected M. tuberculosis complex in 19.8%. Culture yielded mycobacterial growth in 24.5%, of which 21.4% were M. tuberculosis and 3.1% were non-tuberculous mycobacteria, primarily M. abscessus and M. avium. Smear-positive, Xpert-negative results occurred in 2.6% of specimens, attributable to NTM in most cases. Patients with NTM were significantly more likely to have HIV co-infection and did not respond to standard TB treatment. The study highlights the diagnostic burden of NTM in South East Nigeria and recommends systematic culture-based species identification for all smear-positive Xpert-negative specimens, with NTM-specific treatment capacity at TB reference laboratories. Keywords: non-tuberculous mycobacteria, tuberculosis diagnosis, MGIT culture, Xpert MTB/RIF, Enugu State