Journal
JOURNAL OF CLINICAL MICROBIOLOGY
Volume 59, Issue 8, Pages -Publisher
AMER SOC MICROBIOLOGY
DOI: 10.1128/JCM.00074-21
Keywords
DNA hybridization; DNA purification; PCR; cell-free DNA; diagnostics; sample preparation; transrenal DNA; tuberculosis; urine
Categories
Funding
- Bill and Melinda Gates Foundation [OPP1152864]
- National Institute of Allergy and Infectious Diseases of the National Institutes of Health [R21AI125975]
- CFAR developmental grant from the University of Washington/Fred Hutch Center for AIDS Research
- NIH [AI027757]
- NIAID
- NCI
- NIMH
- NIDA
- NICHD
- NHLBI
- NIA
- NIGMS
- NIDDK
- National Science Foundation Graduate Research Fellowship Program
- Bill and Melinda Gates Foundation [OPP1152864] Funding Source: Bill and Melinda Gates Foundation
Ask authors/readers for more resources
This study aimed to improve the diagnostic sensitivity of TB urine cfDNA by increasing recovery of short fragments during sample preparation. A highly sensitive sequence-specific purification method was developed, which showed high efficiency in capturing short TB cfDNA. In a clinical cohort study in South Africa, the urine cfDNA assay had high sensitivity and specificity for diagnosing active pulmonary TB.
Transrenal urine cell-free DNA (cfDNA) is a promising tuberculosis (TB) biomarker, but is challenging to detect because of the short length (,100 bp) and low concentration of TB-specific fragments. We aimed to improve the diagnostic sensitivity of TB urine cfDNA by increasing recovery of short fragments during sample preparation. We developed a highly sensitive sequence-specific purification method that uses hybridization probes immobilized on magnetic beads to capture short TB cfDNA (50 bp) with 91.8% average efficiency. Combined with short-target PCR, the assay limit of detection was #5 copies of cfDNA in 10ml urine. In a clinical cohort study in South Africa, our urine cfDNA assay had 83.7% sensitivity (95% CI: 71.0 to 91.5%) and 100% specificity (95% CI: 86.2 to 100%) for diagnosis of active pulmonary TB when using sputum Xpert MTB/RIF as the reference standard. The detected cfDNA concentration was 0.14 to 2,804 copies/ml (median 14.6 copies/ml) and was inversely correlated with CD4 count and days to culture positivity. Sensitivity was nonsignificantly higher in HIV-positive (88.2%) compared to HIV-negative patients (73.3%), and was not dependent on CD4 count. Sensitivity remained high in sputum smear-negative (76.0%) and urine lipoarabinomannan (LAM)-negative (76.5%) patients. With improved sample preparation, urine cfDNA is a viable biomarker for TB diagnosis. Our assay has the highest reported accuracy of any TB urine cfDNA test to date and has the potential to enable rapid non-sputum-based TB diagnosis across key underserved patient populations.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available