Clinical Evaluation of tNGS for Diagnosis of DR-TB

NCT04239326 | Completed

• 1 other identifier: TB038
• Study Type: observational
• Target: 800
• Locations: 3 countries
• Sites: 3

Brief Summary

Current rapid molecular assays for detection of drug-resistant TB from direct clinical samples have important limitations. They are not suited for high-throughput settings; can only be used to detect a limited number of target gene regions and are not ideal for detection of phenotypic resistance conferred by mutations across large gene regions (e.g. pyrazinamide). Culture-free, end-to-end targeted NGS (tNGS) Solutions for Diagnosis of Drug Resistant TB can offer higher throughput and greater accuracy across more TB drugs than current WHO endorsed molecular assays, and a significantly faster time to result than phenotypic drug susceptibility testing (DST). Evidence regarding the clinical diagnostic accuracy and operational characteristics of tNGS solutions is needed to comprehensively evaluate tNGS for diagnosis of drug-resistant TB among patients who have been diagnosed with TB, and will be critical to inform global and national policy.

Conditions

Tuberculosis, Multidrug-Resistant

Outcome Measures

Primary Outcomes (5)

• Point estimates, with 95% confidence intervals, of sensitivity and specificity for RIF resistance detection for each of up to 3 tNGS solutions

  Outcomes 1.1 to 1.5 will be evaluated on the PP population. Point estimates (with 95% CI) of sensitivity and specificity will be derived based on pooled data for all sites. In order to assess whether there is an association between the results and the clinical site from where the samples were collected, the estimates of sensitivity and specificity for each site will be compared with each other by use of a Pearson's chi-squared test, at a significance level of 5%, adjusted by Bonferroni correction for the total number of tests performed. A random effect model will be used if it is believed that a high site-effect is present: this will be assessed by the evaluation of heterogeneity using Cochran's Q (with a significance level set at 0.1) and the I2 statistics (with a value \>0.5).

  January 2021 - March 2021

• Point estimates, with 95% confidence intervals, of sensitivity and specificity for INH resistance detection for each of up to 3 tNGS solutions

  Outcomes 1.1 to 1.5 will be evaluated on the PP population. Point estimates (with 95% CI) of sensitivity and specificity will be derived based on pooled data for all sites. In order to assess whether there is an association between the results and the clinical site from where the samples were collected, the estimates of sensitivity and specificity for each site will be compared with each other by use of a Pearson's chi-squared test, at a significance level of 5%, adjusted by Bonferroni correction for the total number of tests performed. A random effect model will be used if it is believed that a high site-effect is present: this will be assessed by the evaluation of heterogeneity using Cochran's Q (with a significance level set at 0.1) and the I2 statistics (with a value \>0.5).

  January 2021 - March 2021

• Point estimates, with 95% confidence intervals, of sensitivity and specificity for fluoroquinolone (moxifloxacin, levofloxacin) resistance detection for each of up to 3 tNGS solutions

  Outcomes 1.1 to 1.5 will be evaluated on the PP population. Point estimates (with 95% CI) of sensitivity and specificity will be derived based on pooled data for all sites. In order to assess whether there is an association between the results and the clinical site from where the samples were collected, the estimates of sensitivity and specificity for each site will be compared with each other by use of a Pearson's chi-squared test, at a significance level of 5%, adjusted by Bonferroni correction for the total number of tests performed. A random effect model will be used if it is believed that a high site-effect is present: this will be assessed by the evaluation of heterogeneity using Cochran's Q (with a significance level set at 0.1) and the I2 statistics (with a value \>0.5).

  January 2021 - March 2021

• Point estimates, with 95% confidence intervals, of sensitivity and specificity for second-line injectable (amikacin, capreomycin, kanamycin) resistance detection for each of up to 3 tNGS solutions

  Outcomes 1.1 to 1.5 will be evaluated on the PP population. Point estimates (with 95% CI) of sensitivity and specificity will be derived based on pooled data for all sites. In order to assess whether there is an association between the results and the clinical site from where the samples were collected, the estimates of sensitivity and specificity for each site will be compared with each other by use of a Pearson's chi-squared test, at a significance level of 5%, adjusted by Bonferroni correction for the total number of tests performed. A random effect model will be used if it is believed that a high site-effect is present: this will be assessed by the evaluation of heterogeneity using Cochran's Q (with a significance level set at 0.1) and the I2 statistics (with a value \>0.5).

  January 2021 - March 2021

• Point estimates, with 95% confidence intervals, of sensitivity and specificity for pyrazinamide (PZA) resistance detection for each of up to 3 tNGS solutions

  Outcomes 1.1 to 1.5 will be evaluated on the PP population. Point estimates (with 95% CI) of sensitivity and specificity will be derived based on pooled data for all sites. In order to assess whether there is an association between the results and the clinical site from where the samples were collected, the estimates of sensitivity and specificity for each site will be compared with each other by use of a Pearson's chi-squared test, at a significance level of 5%, adjusted by Bonferroni correction for the total number of tests performed. A random effect model will be used if it is believed that a high site-effect is present: this will be assessed by the evaluation of heterogeneity using Cochran's Q (with a significance level set at 0.1) and the I2 statistics (with a value \>0.5).

  January 2021 - March 2021

Secondary Outcomes (4)

• Point estimates, with 95% confidence intervals, of sensitivity and specificity for additional second-line resistance detection (bedaquiline, linezolid, clofazimine, streptomycin) for up to 3 tNGS solutions.

  January 2021 - March 2021

• Comparison of drug-specific point estimates of sensitivity and specificity (with 95% confidence intervals) for up to 3 tNGS solutions against Hain MTBDRplus/sl drug-specific results.

  January 2021 - March 2021

• Comparison of overall test success rate (defined as the total number of full profiles i.e. calls across all drug targets) in up to 3 tNGS solutions against success rate in Xpert MTB/RIF and Hain MTBDRplus/sl.

  January 2021 - March 2021

• Summary of technical performance characteristics in up to 3 tNGS solutions including invalid and indeterminate rates, ease of use metrics, and other operational characteristics

  January 2021 - March 2021

Interventions

targeted Next Generation Sequencing (tNGS) DIAGNOSTIC_TEST

The index tests used in this trial will include up to three end-to-end, targeted next generation sequencing (tNGS) solutions for diagnosis of DR-TB. Each solution will include all of the equipment, reagents, and software necessary for handling the entire sequencing workflow, including DNA extraction from processed sputum samples (i.e. sediment), library preparation, sequencing, and data analysis/interpretation for clinical result reporting.

Eligibility Criteria

• Age: 18 Years+
• Sex: all
• Healthy Volunteers: No
• Age Groups: Adult (18-64), Older Adult (65+)
• Sampling Method: Probability Sample

Study Population

Adults with pulmonary TB, confirmed by Xpert MTB/RIF or Ultra, who are also at risk for or proven to have drug resistant TB, will be invited to participate in the trial. Interested individuals meeting these criteria will be referred to study personnel for screening. Both HIV-positive individuals and HIV-negative individuals will be included in this study. Depending on the sites individuals may be recruited at outpatient clinic settings as well as inpatient hospital settings.

You may qualify if:

• A TB-positive result by Xpert MTB/RIF OR Xpert MTB/RIF Ultra (i.e. "MTB DETECTED") at or prior to enrollment, AND
• At risk for drug resistant TB based on at least one of the following risk factors:
• A. A positive RIF-resistance result by Xpert MTB/RIF OR Xpert MTB/RIF Ultra (i.e."RIF resistance DETECTED") OR B. Not responding TB treatment with positive sputum smear or culture after ≥ 3 months of standard TB treatment. OR C. Previously diagnosed with Rif-resistant/MDR-TB and failed TB treatment with positive sputum smear or culture after ≥ 3months of a standard MDR-TB regimen OR D. Previously received \>1 month of treatment for a prior TB episode OR E. Close contact with a known drug-resistant TB case AND
• Willing to provide sputum AND
• years of age and older (or legal adult age corresponding to the site) AND
• Provision of signed informed consent

You may not qualify if:

• Have started treatment for current TB episode more than 7 days prior to date of enrolment (i.e. must have been on treatment for less than 7 days for this TB treatment episode at enrolment) OR
• Institutionalized or imprisoned

Sponsors & Collaborators

• Foundation for Innovative New Diagnostics, Switzerland: lead

Study Sites (3)

National Center for Tuberculosis and Lung Diseases

Tbilisi, 380060, Georgia

Location

Hinduja Hospital and Medical Research Centre

Mumbai, Maharashtra, 40016, India

Location

National Institute for Communicable Diseases & Wits Health Consortium

Johannesburg, Sandringham, 2192, South Africa

Location

Related Publications (2)

• Miotto P, Colman RE, Cabibbe AM, Rancoita PMV, Di Marco F, De la Rossa A, Hoogland C, Uplekar S, Laurent S, Cirillo DM, Rodrigues C, Kambli P, Tukvadze N, Maghradze N, Omar SV, Joseph L, Suresh A, Rodwell TC. Clinical evaluation of a commercial culture-free targeted next-generation sequencing test for diagnosis of drug-resistant tuberculosis. Microbiol Spectr. 2025 Dec 12:e0303525. doi: 10.1128/spectrum.03035-25. Online ahead of print.

  PMID: 41384933 DERIVED

• Georghiou SB, Tukvadze N, Rodrigues C, Omar SV, Cabibbe AM, Seifert M, Uplekar S, Ismail N, Ruhwald M, Suresh A, Colman RE. Targeted next-generation sequencing for drug-resistant tuberculosis diagnosis: implementation considerations for bacterial load, regimen selection and diagnostic algorithm placement. BMJ Glob Health. 2025 Nov 4;10(11):e019135. doi: 10.1136/bmjgh-2025-019135.

  PMID: 41192929 DERIVED

Biospecimen

Retention: SAMPLES WITH DNA

No patient genetic information will be collected, analyzed or recorded in this study. The proposed genetic sequencing and molecular analysis protocols are only intended to include TB pathogen-specific sequences and will be limited to analysis of MTB bacteria genomes.

MeSH Terms

Conditions

Tuberculosis, Multidrug-Resistant

Condition Hierarchy (Ancestors)

Tuberculosis; Mycobacterium Infections; Actinomycetales Infections; Gram-Positive Bacterial Infections; Bacterial Infections; Bacterial Infections and Mycoses; Infections

Study Design

• Study Type: observational
• Observational Model: COHORT
• Time Perspective: CROSS SECTIONAL
• Sponsor Type: OTHER
• Responsible Party: SPONSOR

Study Record Dates

• First Submitted: January 20, 2020
• First Posted: January 27, 2020
• Study Start: April 16, 2021
• Primary Completion: January 31, 2023
• Study Completion: June 30, 2023
• Last Updated: October 4, 2023

Record last verified: 2023-10

Locations

GE (1); IN (1); ZA (1)