Four-year evaluation of tuberculosis diagnostics and drug resistance patterns: A retrospective analysis of smear microscopy, MTB/RIF PCR, and culture-confirmed Mycobacterium tuberculosis isolates

Abstract

Aim: Accurate and timely diagnosis of tuberculosis remains a major clinical challenge. This study aimed to evaluate the diagnostic performance of direct smear microscopy and MTB/RIF PCR compared with culture, and to assess first-line drug resistance patterns among Mycobacterium tuberculosis complex (MTBC) isolates.

Materials and Methods: This retrospective study analyzed non-duplicate mycobacterial culture records obtained between 2020 and 2023 at a tertiary care center. Culture-confirmed MTBC cases served as the reference standard. The diagnostic performance of direct smear microscopy and MTB/RIF PCR was evaluated in patients who underwent both the index test and the culture. Drug susceptibility testing was performed for first-line antituberculosis agents, including isoniazid, rifampicin, ethambutol, and streptomycin. The study was reported in accordance with the STROBE and STARD guidelines.

Results: A total of 8,863 mycobacterial cultures were evaluated, yielding 165 MTBC-positive isolates. MTB positivity rates decreased from 2.18% in 2020 to 1.31% in 2023. When data from all years were combined, direct smear microscopy demonstrated a sensitivity of 34.5% and a specificity of 99.8%, whereas MTB/RIF PCR showed a sensitivity of 91.5% and a specificity of 98.5%, all for culture-confirmed tuberculosis. Drug susceptibility testing was available for 160 isolates. Resistance to isoniazid, rifampicin, ethambutol, and streptomycin was detected in 14.4%, 1.9%, 6.3%, and 8.8% of isolates, respectively. Multidrug-resistant tuberculosis was identified in 1.25% of cases.

Conclusion: Direct smear microscopy exhibited limited sensitivity despite high specificity, whereas MTB/RIF PCR demonstrated excellent diagnostic performance and a high negative predictive value. Although overall drug resistance rates were relatively low, the presence of isoniazid resistance underscores the importance of routine susceptibility testing in the management of tuberculosis.