SHINE-TB: Point of Care Tuberculosis Diagnostics including in Resource-Limited Settings
- Ray Sullivan
- 2 days ago
- 3 min read
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), continues to be a formidable global health threat, particularly in under-resourced areas where accurate and accessible diagnosis remains a critical unmet need. Traditional diagnostic methods often present trade-offs: culture-based methods are sensitive but slow (weeks), while sputum smear microscopy is rapid but lacks sensitivity and specificity and relies on user expertise. PCR-based tests, like Cepheid’s Xpert® MTB/RIF, are sensitive but demand specialized equipment and proprietary cartridges, limiting their deployment in low-resource settings.
Enter SHINE-TB, a multi-institutional effort led by Padmapriya Banada and Yingda L. Xie at Rutgers PHRI, and Cameron Myhrvold at Princeton. SHINE-TB is a CRISPR-based diagnostic (CRISPR-Dx) platform poised to bridge this accessibility and accuracy gap. Developed from the broader SHINE (Streamlined Highlighting of Infections to Navigate Epidemics) platform, SHINE-TB offers a streamlined, one-pot, sample-to-answer solution for TB detection.
SHINE-TB leverages the high specificity and collateral cleavage activities of CRISPR-associated proteins (Cas12a and Cas13a), pairing them with isothermal amplification techniques, specifically recombinase polymerase amplification (RPA). This combination allows for robust, highly specific detection without the need for thermocycling, making it ideal for point-of-care use.
A key innovation in SHINE-TB is its parallelized, one-pot assay format. While previous CRISPR-Dx methods often required user manipulations and specialized instrumentation between pre-amplification and detection, SHINE-TB integrates isothermal amplification and detection into a single reaction.
The researchers explored both Cas12a and Cas13a for Mtb detection. While a Cas12a workflow requires fewer reaction components by directly detecting the RPA product, Cas13a proved to be more sensitive in a one-pot format. This is because Cas12a's cis cleavage of the DNA target can interfere with amplification, whereas Cas13a targets RNA (requiring an in vitro transcription step) and cleaves RNA in trans, thus not disrupting the DNA amplification process. For enhanced sensitivity across various Mtb strains with differing insertion sequence copy numbers, SHINE-TB’s Cas13a assay targets two conserved transposable insertion sequences in the Mtb genome: IS6110 and IS1081.
To prevent false-negative results due to sample inhibitors or poor nucleic acid extraction, SHINE-TB incorporates a Cas12a-based internal control. This control targets the long terminal repeat of the human endogenous retrovirus-K (ERVK), a highly abundant genetic element in human DNA. The internal control’s performance can indicate issues with sample inhibition, ensuring the validity of the Mtb assay results. Due to shared RPA machinery, the Mtb detection assay and the internal control are run in two separate, parallel chambers from the same processed sample, minimizing labor while maximizing sensitivity.
SHINE-TB is specifically designed for deployment in low- and middle-income countries, addressing the need for accessible and field-deployable assays.
The assay is compatible with sputum, the standard sample type for pulmonary TB diagnosis, utilizing a simple and efficient sample processing method that circumvents the need for specialized equipment.
Single-use tubes of SHINE-TB can be lyophilized, allowing for stable storage and transport with minimal effect on assay performance.
For ease of interpretation without a fluorometer, the assay can be adapted to a lateral flow readout. Cleaved reporters migrate to an upper band, providing a clear visual positive result, making it potentially an entirely equipment-free test if 37°C can be maintained.
The performance of SHINE-TB is highly encouraging:
The final assay showed a Limit of Detection ( LoD) of 69.0 CFU per milliliter for Mtb H37Rv and 80.5 CFU per milliliter for Mycobacterium bovis BCG in spiked sputum. This is comparable to or better than the published LoD of GeneXpert Ultra for BCG (143.4 CFU/ml).
SHINE-TB demonstrated no cross-reactivity to diverse bacterial or fungal isolates and nontuberculous mycobacteria (NTMs).
In clinical tests on 13 blinded sputum samples, SHINE-TB achieved 100% sensitivity (six of six) and 100% specificity (seven of seven) compared to culture. This favorably compares to GeneXpert Ultra, which showed 100% sensitivity but 86% specificity in the same cohort. These results meet the WHO's target product profile (TPP) benchmarks for TB diagnostics.
While the preliminary clinical evaluation is very promising, the authors acknowledge areas for future development. These include exploring alternatives to benchtop centrifuges for settings without reliable power, increasing multiplexing capacity to include drug susceptibility testing, and expanding compatibility to other sample types like saliva or oral swabs, which are easier for some patients to produce.
SHINE-TB represents a significant step towards more accessible and reliable TB diagnostics globally. Its streamlined workflow, robust performance, and adaptability to low-resource environments make it a beacon of hope in the fight against tuberculosis.
Bell AG, Dunkley ORS, Modi NH, Huang Y, Tseng S, Reiss R, Daivaa N, Davis JL, Vargas DA, Banada P, Xie YL, Myhrvold C. A streamlined CRISPR-based test for tuberculosis detection directly from sputum. Sci Adv. 2025 Aug 8;11(32):eadx2067. doi: 10.1126/sciadv.adx2067. Epub 2025 Aug 6. PMID: 40768573; PMCID: PMC12327463.
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