Simultaneous detection and differentiation of Mycobacterium tuberculosis and nontuberculous mycobacteria in smear-negative sputum by a multiplex PCR assay: a clinical feasibility study

ABSTRACT Accurate and rapid differentiation of Mycobacterium tuberculosis ( M. tuberculosis ) and nontuberculous mycobacteria (NTM) remains challenging, especially in smear-negative samples. Routine diagnostic methods often lack specificity and rapidity, highlighting the urgency of developing applicative molecular diagnostics to guide clinical management and improve patient outcomes. We developed and validated a multiplex PCR assay employing TaqMan probes targeting the IS6110 and rpoB genes to simultaneously detect M. tuberculosis and 23 NTM species in a single reaction, while avoiding cross-reactivity. Analytical performance was assessed using reference strains, and clinical feasibility was evaluated in a prospective, single-center pilot study involving 96 smear-negative presumptive tuberculosis patients. The assay’s diagnostic performance was compared to mycobacterial culture, DNA sequencing, and the Xpert MTB/RIF assay. The multiplex PCR assay demonstrated a wide linear dynamic range (10 8 –10 3 copies/mL), low limit of detection (10 3 copies/mL), high precision (intra-assay CV 0.05–1.18%, inter-assay CV 0.08–2.57%), and complete specificity for both M. tuberculosis and NTM. In the clinical feasibility study, using a combination of clinical diagnosis and mycobacterial culture as reference standards, it achieved sensitivities of 73.33% ( M. tuberculosis ) and 100% (NTM), and specificities of 100% ( M. tuberculosis ) and 94.33% (NTM). Notably, it reliably identified M. tuberculosis /NTM co-infections. The Multiplex PCR assay fills a critical gap in the rapid, accurate diagnosis of M. tuberculosis and NTM in challenging clinical specimens. With a cost of $5 per test and a turnaround time of 3 h, our assay has the potential to improve patient care and optimize mycobacterial infection treatment strategies in resource-limited settings. IMPORTANCE Rapid and accurate differentiation between Mycobacterium tuberculosis ( M. tuberculosis ) and nontuberculous mycobacteria (NTM) is essential for ensuring timely and appropriate treatment, especially in high tuberculosis (TB) burden regions. Conventional diagnostic methods, such as smear microscopy and culture, often lack the sensitivity or speed needed for reliable results in smear-negative cases, risking misdiagnosis and delayed care. In this study, we developed a novel multiplex real-time PCR assay capable of simultaneously detecting M. tuberculosis and up to 23 clinically relevant NTM species with high specificity and sensitivity. By targeting distinct genetic markers for M. tuberculosis and NTM, our assay provides a cost-effective, 3-h diagnostic solution that enhances diagnostic accuracy in challenging samples. This innovation addresses a critical gap in mycobacterial diagnostics, supporting improved patient outcomes and aligning with global health priorities for the control and elimination of TB.