Diagnostic Performance of Multiplex PCR for Detection of Mycobacterium tuberculosis Complex in Presumptive Pulmonary Tuberculosis Patients and Its Utility in Smear Negative Specimens

Abstract

Objective The primary objective of this study was to assess the diagnostic performance of multiplex polymerase chain reaction (mPCR) for the detection of Mycobacterium tuberculosis complex (MTBC) in presumptive pulmonary TB patients, in the setting of a tertiary level teaching hospital in central India, in comparison to liquid culture using BACTEC mycobacteria growth indicator tubes (MGIT) 960 TB system as the gold standard. The secondary objective was to assess the performance of mPCR for Ziehl Neelsen smear negative samples and ascertain the utility of this assay in smear negative samples. Materials and Methods Sputum or bronchoalveolar lavage samples were collected from patients who were adults, aged 18 years or older, presenting with presumptive pulmonary TB, and subjected to three microbiological investigations, that is, Ziehl Neelsen staining, mycobacterial culture using mycobacterial growth indicator tubes in the BD BACTEC MGIT 960 instrument, and the mPCR. Statistical Analysis For statistical analysis, 2 × 2 contingency tables were prepared and analyzed separately for all samples and for smear-negative samples using GraphPad and MedCalc tools. Sensitivity, specificity, positive predictive value, and negative predictive value (NPV) of mPCR were calculated by taking MGIT culture as the reference standard. Results For all samples (n = 114), sensitivity of mPCR for the detection of (MTBC) was 93.48% (95% confidence interval [CI]: 82.10–98.63%), specificity was 95.59% (95% CI: 87.64–99.08%), positive predictive value (PPV) was 93.48% (95% CI: 82.54–97.75%), and NPV was 95.59% (95% CI: 87.87–98.48%). For smear negative samples (n = 80), sensitivity was 80.00% (95% CI: 51.91–95.67%), specificity was 98.46% (95% CI: 91.72–99.96%), PPV was 92.31% (95% CI: 62.80–98.84%), and NPV was 95.52% (95% CI: 88.57–98.33%). Conclusion In this study, we were able to demonstrate the good performance characteristics of the mPCR for the detection of MTBC from clinical samples of patients with presumptive pulmonary tuberculosis, with MGIT liquid culture as the reference standard. It may be concluded that mPCR can be considered equivalent to MGIT culture in terms of clinical decision making and yield of positivity, owing to the good sensitivity and specificity for the detection of MTBC.

Evaluation of a real-time PCR assay performance to detect Mycobacterium tuberculosis, rifampicin, and isoniazid resistance in sputum specimens: a multicenter study in two major cities of Indonesia

“…Contrarily, the same study also reported that the sensitivity ranged between 32 and 92% depending on the type of sample and the type of study design. Another study demonstrated that the performance of an IS6110 sequence-based PCR on AFB smear-negative sputum was 64.5% (Lodha et al, 2022). In addition, another previous study revealed that IS6110-TaqMan assay performed better sensitivity than GeneXpert MTB/RIF on AFB smear-negative sputum (69 vs. 48%, 19), while another study demonstrated GeneXpert MTB/RIF had a sensitivity level of 73.1% compared to culture (Lombardi et al, 2017).…”

Evaluation of Nanopore Sequencing for Diagnosing Pulmonary Tuberculosis Using Negative Smear Clinical Specimens

“…However, the sensitivity of these molecular techniques in smear-negative PTB remains relatively low. 34 Previous studies have reported sensitivities of 57.1% for Xpert MTB/RIF and 53.4% for CapitalBio Mycobacterium RT-PCR for detecting smear-negative PTB, 2 indicating the need for further improvement. Although the sensitivity of Xpert MTB/RIF ultra for smear-negative PTB has improved, 31 it is still unsatisfactory.…”