Molecular Diagnostics of Mycobacterial Infections

Molecular diagnostics have transformed the detection and management of infections caused by Mycobacterium species, most notably Mycobacterium tuberculosis. By targeting pathogen nucleic acids directly, these methods overcome the limitations of traditional culture and smear microscopy, offering rapid, sensitive and specific identification even in paucibacillary or extrapulmonary disease. Advances in nucleic acid amplification tests (NAATs), next-generation sequencing and CRISPR-based assays have enabled simultaneous detection of mycobacterial DNA or RNA and resistance-associated mutations. The adoption of non-invasive sampling—such as plasma cell-free DNA, oral or upper respiratory tract swabs—and integration into point-of-care platforms have broadened access to diagnostics in resource-limited settings. Together, these innovations support earlier diagnosis, tailored therapy and better surveillance of drug-resistant strains, thereby contributing to global tuberculosis control and informing approaches to other mycobacterial infections.

Research from Nature Portfolio

Recent studies have introduced WATSON, a whole-genome approach coupling tiled amplification of pathogen cell-free DNA with pooled CRISPR/Cas13 detection, achieving enhanced sensitivity for circulating mycobacterial fragments and compatibility with lateral-flow readouts. Work on a widely used cartridge-based PCR assay has dissected the factors governing its performance, demonstrating that variation in bacterial load across body compartments is the principal determinant of assay sensitivity and cycle threshold values. Another investigation has confirmed that Mycobacterium tuberculosis DNA can be non-invasively recovered from the oral mucosa of patients with active pulmonary disease, suggesting an alternative sample matrix that is simple to collect and process for molecular testing.

Molecular Diagnostics of Mycobacterial Infections publication trend

The graph below shows the total number of articles in molecular diagnostics of mycobacterial infections across all publications each year (not limited to Nature Index journals).

Technical terms

Nucleic acid amplification test (NAAT): A molecular assay that amplifies pathogen-specific DNA or RNA sequences to detect infection rapidly and with high sensitivity.

Cell-free DNA (cfDNA): Fragments of pathogen genomic material circulating in plasma or other body fluids, serving as accessible biomarkers for molecular detection.

CRISPR/Cas13: An RNA-guided enzyme system engineered for specific recognition of target RNA sequences, triggering collateral cleavage of reporter molecules to generate detectable signals.

Xpert MTB/RIF assay: A cartridge-based real-time PCR platform that simultaneously identifies Mycobacterium tuberculosis complex and rifampicin resistance within two hours.

References

1. Accuracy of cell-free Mycobacterium tuberculosis DNA testing in pleural effusion for diagnosing tuberculous pleurisy: a multicenter cross-sectional study. Military Medical Research (2024).
2. Oral swabs with a rapid molecular diagnostic test for pulmonary tuberculosis in adults and children: a systematic review. The Lancet Global Health (2023).
3. Genome-wide tiled detection of circulating Mycobacterium tuberculosis cell-free DNA using Cas13. Nature Communications (2023).
4. Accuracy of upper respiratory tract samples to diagnose Mycobacterium tuberculosis: a systematic review and meta-analysis. The Lancet Microbe (2023).
5. Determinants of PCR performance (Xpert MTB/RIF), including bacterial load and inhibition, for TB diagnosis using specimens from different body compartments. Scientific Reports (2014).
6. Detection of Mycobacterium tuberculosis DNA on the oral mucosa of tuberculosis patients. Scientific Reports (2015).