Plasma MTB cfDNA Before Bronchoscopy

Prospective Evaluation of Plasma Mycobacterium Tuberculosis Cell-free DNA Sequencing as a Non-Invasive Alternative to Bronchoscopy for Diagnosing Pulmonary Tuberculosis

Tuberculosis (TB) remains a major global health challenge, affecting over 10 million people annually. Hong Kong carries an intermediate TB burden, with ~3,200 new cases reported yearly. Pulmonary TB (PTB), the most common form, presents diagnostic difficulties. Traditional methods like sputum smear and culture often fail in patients unable to produce adequate samples, necessitating bronchoscopy to collect bronchoalveolar lavage (BAL) for mycobacterial testing.

These limitations pose risks for patients and strain healthcare systems. Bronchoscopy is invasive, resource-intensive, and may delay treatment-especially for elderly patients with comorbidities. Blood-based inflammatory markers lack diagnostic specificity. A rapid, non-invasive alternative is urgently needed.

The investigators developed a plasma-based assay that detects Mycobacterium tuberculosis cell-free DNA (MTB cfDNA) in blood. This liquid biopsy leverages metagenomic sequencing and computational analysis to identify TB-specific genetic material while minimizing contamination. Preliminary data show excellent diagnostic performance, with area under the receiver operating characteristic curve values >0.94 for TB pleurisy.

The investigators propose a prospective clinical validation study comparing plasma MTB cfDNA testing to bronchoscopy with BAL culture and molecular testing. The primary aim is to demonstrate non-inferiority of plasma cfDNA within a 10% sensitivity margin. Secondary aims include assessing how clinical and radiological features affect test performance and evaluating the assay's ability to detect drug resistance mutations for personalized therapy.

Validation could transform TB diagnosis by offering a rapid, safe, and accurate blood test. Patients could avoid invasive procedures, receive faster diagnoses, and begin treatment sooner. Detecting resistance mutations directly from plasma would enable timely, targeted therapy-critical for addressing multidrug-resistant TB. This represents a paradigm shift toward precision medicine in TB care.

Tailored to Hong Kong's epidemiological context, this study addresses a key diagnostic gap. The approach has global relevance, with potential to improve clinical outcomes, reduce costs, and accelerate progress toward WHO's TB elimination goals.

Study Overview

• Status: Not yet recruiting
• Conditions: Tuberculosis Diagnosis
• Intervention / Treatment: Diagnostic test: Diagnostic Test: Plasma MTB cfDNA assay

Detailed Description

Tuberculosis (TB) remains a global health challenge, particularly in East Asia. According to the Global TB Report by the World Health Organisation (WHO) in 2024, over 10 million people contracted TB in 2023, with 1.25 million deaths attributed to the disease. India, Indonesia and China bear the highest burden, while Hong Kong maintains an intermediate incidence, averaging 3,200 new cases annually.

Pulmonary tuberculosis (PTB) is the most common form of active TB disease. Diagnosis typically relies on detecting Mycobacterium tuberculosis (MTB) in the sputum via smear microscopy, culture, or polymerase chain reaction (PCR). However, sputum smear has limited sensitivity, culture requires 6-8 weeks, and sputum production is often difficult in certain patients. PTB may present with heterogeneous radiological features, sometimes mimicking malignancy, prompting bronchoscopy with bronchoalveolar lavage (BAL) in smear-negative patients. BAL fluid (BALF) is then tested via MTB culture, PCR, and cytology. Bronchoscopy, while informative, is invasive and poses risks for elderly patients or with cardiopulmonary comorbidities. Temporary interruption of oral anticoagulants, now widely prescribed, can lead to cardioembolic complications, contributing to up to 2.6% of stroke events. Delays in scheduling bronchoscopy and awaiting BALF MTB culture results further hinder timely diagnosis. Blood inflammatory markers are non-specific. These limitations underscore the need for a non-invasive, rapid, and accurate diagnostic tool for PTB.

Advances in sequencing technology offer new diagnostic possibilities. When bacteria die, their DNA fragments enter the bloodstream as cell-free (cfDNA). Detecting microbial cfDNA in plasma, combined with bioinformatics, provides a minimally invasive method to identify pathogens directly, outperforming blood culture or surrogate markers. Plasma MTB cfDNA is an emerging diagnostic tool. The IntelliGenome CRISPR-TB Blood Test can detect MTB cfDNA and its landmark study focused on paediatric and HIV-positive populations. However, its clinical application remains limited, with no validation in intermediate-burden regions like Hong Kong, where HIV prevalence is low.

The investigator has developed a novel targeted MTB cfDNA sequencing assay. The assay uses whole-genome-based sequencing to enrich the MTB cfDNA, followed by bioinformatic filtering to remove human DNA, distinguishing MTB from non-tuberculous Mycobacterium (NTM), and exclude microbial contaminants. A prospective study would be required to confirm diagnostic accuracy and clinical utility of this new sequencing assay. The investigators hypothesise that plasma targeted MTB cfDNA sequencing is non-inferior to BALF MTB culture and PCR in diagnostic smear-negative patients undergoing bronchoscopy.

• Study Type: Observational
• Enrollment (Estimated): 600

Contacts and Locations

• Study Contact: Name: Ka Pang Chan, MBChB; Phone Number: 35052211; Email: chankapang@cuhk.edu.hk

Study Locations

• Hong Kong
  • Hong Kong, Hong Kong
    • Prince of Wales Hospital
    • Contact: Ka Pang Chan, MBChB; Phone Number: 35052211; Email: chankapang@cuhk.edu.hk
    • Contact: Karen Yiu; Phone Number: 35053532; Email: ysyiu@cuhk.edu.hk

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Adult; Older Adult
• Accepts Healthy Volunteers: No

• Sampling Method: Non-Probability Sample

Study Population

Patients with clinical indications for undergoing bronchoscopy and BAL who meet the inclusion and exclusion criteria will be prospectively enrolled in consecutive sequences

Description

Inclusion Criteria:

• Aged 18 years or above
• Presence of respiratory indication requiring bronchoscopy
• Sputum AFB smear negative or unable to expectorate sputum for investigations

Exclusion Criteria:

• BALF collected but not sent for MTB PCR
• History of PTB or EPTB
• Concomitant use of at least two anti-TB medications for more than 14 consecutive days in the past 3 months
• Repeated bronchoscopy in the same subject within the study period
• Expected survival of less than 12 months from a different pathology
• Use of unregistered therapeutic agents in the 30 days before the study
• Consent not obtained from the subjects

Study Plan

How is the study designed?

Number of groups / cohorts

2

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
PTB; Patients with pulmonary tuberculosis	Diagnostic test: Diagnostic Test: Plasma MTB cfDNA assay; Quantitative measurement of MTB cfDNA level in the plasma
Non-PTB; Patients without pulmonary tuberculosis	Diagnostic test: Diagnostic Test: Plasma MTB cfDNA assay; Quantitative measurement of MTB cfDNA level in the plasma

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Area under ROC curve of MTB cfDNA assay	The area under ROC curve of MTB cfDNA assay in discriminating PTB and non-PTB in a prospective non-selective cohort of bronchoscopy procedures	27 months

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
The effect of radiological features on the diagnostic performance (sensitivity and specificity) of the MTB cfDNA assay	To compare the diagnostic performance (sensitivity and specificity) of the MTB cfDNA assay in patients with different radiological features (cavitary vs non-cavitary)	27 months

Collaborators and Investigators

• Sponsor: Chinese University of Hong Kong

Study record dates

Study Major Dates

• Study Start (Estimated): October 1, 2026
• Primary Completion (Estimated): December 31, 2028
• Study Completion (Estimated): June 30, 2029

Study Registration Dates

• First Submitted: September 30, 2025
• First Submitted That Met QC Criteria: November 13, 2025
• First Posted (Actual): November 17, 2025

Study Record Updates

• Last Update Posted (Actual): November 17, 2025
• Last Update Submitted That Met QC Criteria: November 13, 2025
• Last Verified: November 1, 2025

More Information

Terms related to this study

• Keywords: Cell-free DNA; Pulmonary tuberculosis
• Additional Relevant MeSH Terms: Respiratory Tract Infections; Infections; Respiratory Tract Diseases; Lung Diseases; Gram-Positive Bacterial Infections; Bacterial Infections; Bacterial Infections and Mycoses; Actinomycetales Infections; Mycobacterium Infections; Tuberculosis; Tuberculosis, Pulmonary
• Other Study ID Numbers: Plasma_MTB_cfDNA_FOB

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: NO

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No