Diagnostic performance of nucleic acid MALDI-TOF MS in mycobacterial detection, species identification, and drug...

Conventional methods for detecting mycobacteria were insufficient for comprehensive species identification and full-spectrum drug resistance profiling. This study aimed to evaluate the diagnostic value of nucleic acid matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for mycobacterial detection, species identification, and Mycobacterium tuberculosis drug resistance testing.

A retrospective study was performed on clinical specimens (including sputum, bronchoalveolar lavage fluid, pleural fluid, pus, and other lesion samples) obtained from patients with tuberculosis, nontuberculous mycobacterial infection, or other infectious diseases at the Eighth Medical Center of Chinese PLA General Hospital between December 2020 and July 2023. Specimens were examined using nucleic acid MALDI-TOF MS, Gene Xpert MTB/RIF (Xpert), and Mycobacterium tuberculosis culture. Diagnostic performance and agreement were assessed using Mycobacterium tuberculosis culture and composite clinical diagnosis (integrating clinical manifestations, imaging findings, and multiple laboratory tests according to WS288-2017 Diagnostic Criteria for Tuberculosis of China) as reference standards.

A total of 138 specimens were included in the final analysis. Compared with Mycobacterium tuberculosis culture, nucleic acid MALDI-TOF MS exhibited relatively high analytical nucleic acid sensitivity (97.7%) for MTB detection (97.7%). However, the assay showed poor specificity of only 24.2%, with slight agreement between Mycobacterium tuberculosis culture and nucleic acid MALDI-TOF MS (Kappa = 0.151). When composite clinical diagnosis was used as the reference standard, nucleic acid MALDI-TOF MS yielded seemingly favorable diagnostic indicators (sensitivity: 98.1%, specificity: 73.3%, accuracy: 92.8%, Kappa = 0.770). Its sensitivity (98.1%) was numerically superior to that of culture (39.8%) and Xpert (73.1%), with all P < 0.001. The AUC of nucleic acid MALDI-TOF MS was 0.857, which was comparable to that of Xpert (0.870) with P = 0.721, but relatively higher than that of Mycobacterium tuberculosis culture with P < 0.001. In drug resistance prediction (n = 34), nucleic acid MALDI-TOF MS exhibited moderate accuracy for rifampicin, isoniazid, streptomycin, and fluoroquinolones (AUC range: 0.760-0.840), with rifampicin resistance sensitivity reaching 95.0%. Meanwhile, a total of 29 strains, including NTM and MTB co-infections, were identified by nucleic acid MALDI-TOF MS, which were descriptive only.

Nucleic acid MALDI-TOF MS is an auxiliary tool for the rapid diagnosis of MTB and NTM and for the preliminary screening of drug resistance. The assay exhibits moderately improved sensitivity compared with culture methods and reasonably good concordance with composite clinical diagnosis. It platform may serve as an auxiliary screening method when combined with mycobacterial culture, Xpert, and comprehensive clinical evaluation to avoid overdiagnosis. Its independent clinical application requires rigorous further validation in large-scale, multi-center cohorts before widespread routine use.