MTB Drug Resistance in India: Why Genomic Surveillance and Smarter Analysis Tools Matter
October 10, 2026 · 6 min read
India carries about a quarter of the world's tuberculosis (TB) burden and nearly a third of its drug-resistant TB. Counting cases is no longer enough. To end TB, laboratories and programmes need to know which drugs still work for each patient and where resistant Mycobacterium tuberculosis (MTB) strains are spreading. Whole-genome sequencing (WGS), backed by a reliable MTB drug resistance tool, can turn that question into a routine, data-driven answer.
India's TB Burden at a Glance
According to the WHO Global Tuberculosis Report 2025, an estimated 10.7 million people developed TB worldwide in 2024. India accounted for about 25% of these cases, roughly 2.7 million people, and about 28% of TB deaths among HIV-negative people.
There is real progress. Incidence fell from 237 per lakh population in 2015 to 187 per lakh in 2024, a 21% decline against a global fall of 12%. Mortality came down from 28 to 21 per lakh over the same period. India notified 26.18 lakh TB patients in 2024, and treatment success under the National Tuberculosis Elimination Programme (NTEP) reached 90%, above the global average of 88%.
Yet the WHO End TB milestone called for a 50% fall in incidence by 2025, and India reached 21%. Closing that gap depends heavily on how well the country detects and manages drug resistance.
Fall in TB incidence, 2015–2024
Table 1. Key TB statistics for India, 2024
| Indicator | India | Context |
|---|---|---|
| Share of global TB cases | 25% (~27 lakh) | 10.7 million cases worldwide |
| TB incidence (per lakh) | 187 | Down from 237 in 2015 (-21%) |
| TB mortality (per lakh) | 21 | Down from 28 in 2015 |
| Patients notified | 26.18 lakh | Against ~27 lakh estimated |
| Treatment success | 90% | Global average 88% |
| Share of global MDR/RR-TB | 32% (~1.25 lakh) | China and Philippines 7.1% each |
Source: WHO Global Tuberculosis Report 2025; Ministry of Health and Family Welfare.
Drug-Resistant TB: Where India Stands Out
WHO estimates that about 390,000 people developed MDR/RR-TB worldwide in 2024. India accounted for 32%, roughly 1.25 lakh estimated cases, far ahead of China and the Philippines at 7.1% each. India also holds 33% of the global gap between people who developed MDR/RR-TB and those enrolled on treatment.
Share of global MDR/RR-TB cases, 2024
Resistance is not limited to patients who failed earlier treatment. The First National Anti-TB Drug Resistance Survey (2014-2016), which enrolled 5,280 patients, found that close to 23% of new cases were resistant to at least one drug, with MDR-TB in about 3%. Isoniazid resistance was the most common. Resistance walks in with newly diagnosed patients, not just with treatment failures.
Where Conventional TB Drug Resistance Testing Falls Short
For years the programme protocol tested only rifampicin up front. A patient can be rifampicin-sensitive and still carry isoniazid or pyrazinamide resistance, and the regimen never learns about it. The gap widens with newer drugs: bedaquiline and linezolid now anchor shorter DR-TB regimens, and a rifampicin result says nothing about them.
Culture-based phenotypic drug susceptibility testing (DST) remains important, but it takes weeks and needs specialised laboratory capacity. Rapid molecular tests such as cartridge-based nucleic acid amplification tests and line probe assays detect selected mutations quickly, yet cover a limited set of targets. Reporting is a further constraint: many peripheral health units lack reliable computers and internet, which slows data flow through Ni-kshay. Resistance data that never gets pooled cannot guide policy.
How Sequencing Changes MTB Drug Resistance Detection
Next-generation sequencing (NGS) reads many resistance genes, or the entire genome, in a single run. Two approaches are most relevant:
- Targeted NGS (tNGS) examines selected resistance-associated regions and, depending on the assay, can work directly from suitable clinical specimens. WHO introduced tNGS recommendations for DR-TB diagnosis in 2023-2024 and incorporated them into its 2025 diagnostic guidance.
- Whole-genome sequencing (WGS) examines most of the bacterial genome, revealing resistance-associated mutations, lineage and the genetic relationships between isolates needed to investigate transmission.
India's InTGS: Building National Genomic Surveillance
The Indian Tuberculosis Genomic Surveillance Consortium (InTGS), part of the Department of Biotechnology's DARE2ERAD TB initiative launched in March 2022, aims to sequence about 32,200 clinical MTB strains and build a central strain repository. Its goals include mapping the genetic diversity of Indian MTB, identifying known and emerging resistance mutations, linking lineages to treatment outcomes and studying household transmission. According to the DBT Annual Report 2024-25, 6,694 strains had been sequenced at the reported stage.
InTGS whole-genome sequencing progress
Sequencing thousands of genomes produces large datasets that must be processed, quality-checked and interpreted consistently. That is where bioinformatics becomes the bottleneck. Our launch announcement explains why ClariSeq Analytics built a platform for exactly this step.
From Raw Reads to a Drug Resistance Report
A typical WGS-based TB analysis workflow includes:
- Quality control: assessing read quality and flagging low-quality data.
- Read alignment: mapping reads to an appropriate reference genome.
- Coverage assessment: confirming that key genomic regions have adequate depth.
- Variant detection: identifying single-nucleotide variants, insertions and deletions.
- Resistance interpretation: evaluating variants against curated evidence such as the WHO catalogue.
- Lineage assignment: characterising ancestry using established genomic markers.
- Reporting: presenting interpretable results with quality indicators and limitations.
Low depth, contamination, mapping errors and repetitive regions can all distort variant calls, so resistance interpretation must weigh both mutation evidence and data quality. A catalogue alone does not help a lab; someone has to turn raw variant calls into a report a clinician or programme officer can act on. That step is where most labs get stuck.
ClariSeq TB: An MTB Drug Resistance Tool Built for Sequencing Labs
ClariSeq TB, developed by ClariSeq Analytics LLP, is a bioinformatics platform that turns mycobacterial whole-genome sequencing data into clear, usable results within a single analysis environment:
- MTB/NTM species identification: confirms whether an isolate belongs to the M. tuberculosis complex or is a nontuberculous mycobacterium, which needs a different treatment path.
- Drug resistance prediction: interprets resistance-associated variants against the WHO mutation catalogue across first-line and second-line drugs.
- Lineage and spoligotyping: places each isolate on the lineage tree so clusters and transmission links can be tracked.
- Quality metrics and genome visualisation: shows the coverage and sequencing quality behind every call.
- Insights dashboard: pools results across samples and sites to reveal resistance patterns by drug and lineage over time.
The idea is simple. A lab should not need an on-site bioinformatics team to get from a sequencer run to a report, and a programme should not wait for a periodic survey to learn what is circulating. Genomic predictions complement, rather than replace, clinical judgement and phenotypic DST, and should be interpreted within validated workflows and applicable guidelines.
Want to see what a report looks like? Take the virtual tour of the dashboard, or contact our team to talk through your sequencing workflow.
Frequently Asked Questions
What is MTB drug resistance?
It is the ability of Mycobacterium tuberculosis to survive one or more anti-TB medicines, most often due to specific genetic mutations. MDR-TB, resistant to both isoniazid and rifampicin, is the most closely tracked form.
Can whole-genome sequencing detect TB drug resistance?
Yes. WGS identifies resistance-associated mutations across first-line and second-line drugs in one run. Results are interpreted against curated evidence such as the WHO mutation catalogue and should be read alongside quality metrics and applicable guidelines.
How does an MTB drug resistance tool like ClariSeq TB help?
It automates the bioinformatics, from quality control to variant calling and catalogue-based interpretation, and delivers species, lineage and resistance results in a single report, so labs without in-house bioinformaticians can act on sequencing data faster.
Explore ClariSeq TB
See how ClariSeq TB handles whole-genome sequencing analysis, MTB/NTM identification, drug resistance interpretation and genomic data visualisation. Start your free trial of ClariSeq TB today.
- Explore the ClariSeq TB product page
- Take the virtual tour
- Start a free trial, or sign in to your account
- Contact us with questions about your lab's workflow
Scientific information provided for educational and research purposes. Genomic resistance predictions require appropriate validation and must be interpreted according to applicable clinical and laboratory guidelines.
References
- World Health Organization. Global Tuberculosis Report 2025. https://www.who.int/teams/global-programme-on-tuberculosis-and-lung-health/tb-reports/global-tuberculosis-report-2025
- World Health Organization. Global Tuberculosis Report 2025: Drug-resistant TB. https://www.who.int/teams/global-programme-on-tuberculosis-and-lung-health/tb-reports/global-tuberculosis-report-2025/tb-disease-burden/1-3-drug-resistant-tb
- Ministry of Health and Family Welfare. TB incidence in India drops by 21% from 2015 to 2024. PIB, 12 November 2025. https://www.pib.gov.in/PressReleasePage.aspx?PRID=2189415
- Central TB Division and ICMR. First National Anti-TB Drug Resistance Survey, 2014-2016.
- World Health Organization. Catalogue of Mutations in Mycobacterium tuberculosis Complex and Their Association with Drug Resistance, 2nd ed., 2023. https://www.who.int/publications/i/item/9789240082410
- World Health Organization. The Use of Next-Generation Sequencing for the Surveillance of Drug-Resistant Tuberculosis: An Implementation Manual, 2023. https://www.who.int/publications/i/item/9789240078079
- World Health Organization. Consolidated Guidelines on Tuberculosis, Module 3: Diagnosis, updated 2025. https://tbksp.who.int/sites/default/files/2025-08/9789240110991-eng.pdf
- Department of Biotechnology. Annual Report 2024-25. https://dbtindia.gov.in/sites/default/files/DBT%20Annual%20Report%202024-25.pdf
- Indian Tuberculosis Genomic Surveillance Consortium. InTGS Portal. https://intgs.nii.ac.in/InTGS/
See it on your own sequencing data
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