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Infectious disease specialists refer Next-Generation Sequencing (NGS) to assess bacterial resistance, enabling quick treatment access in tuberculosis (TB). Integrating NGS into India’s TB elimination strategy represents a forward-thinking approach aligned with global best practices.
As access to genomic testing grows, it offers a valuable option to reduce the gaps in how it can improve upon conventional TB diagnostics. Research institutions are working towards integrating NGS into national TB programmes, making this technology available to more patients. Additionally, studies on TB meningitis have shown promising results using whole genome sequencing on cerebrospinal fluid samples, which is critical for diagnosing difficult-to-detect forms of TB, stated Dr Gunisha Pasricha, Principal Scientist, Infectious Disease Expert, MedGenome.
Annually, India records nearly 2.7 million TB cases which is 25% of the global burden. While conventional TB diagnostic measures remain the foundation, this often do not identify drug resistant strains of causing treatment failures and continuing transmission. NGS is beginning to evolve TB diagnostics by giving a comprehensive understanding of resistance of the bacterial organism and allowing for faster treatment decisions that are more targeted.
Limitations of conventional TB testing like sputum smear microscopy and bacterial culture detects only acid-fast bacilli and does not give information about the presence of drug resistance. Culture-based methods are more descriptive; but take weeks, delaying necessary treatment decisions. The existing tests often do not detect resistance to second line drugs, which is important to identify for the identification of multi-drug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB) cases. When resistance is not identified, the patient is treated without an effective medication, which sees TB spreading.
A case study illustrates a patient originally diagnosed with TB lymphadenitis with standard tests did not respond to first-line treatment. GeneXpert and smear microscopy were negative for TB, but the infection lingered. Only when tested with whole genome sequencing, resistance mutations for rifampicin, isoniazid, and ethambutol, as well as hetero-resistance for pyrazinamide were detected. This genomic information allowed doctors to change the patient over to an MDR-TB regimen, incorporating bedaquiline, with resultant clinical improvement and resolution of lymph nodes, said Dr Gunisha.
Unlike traditional methods focus on specific genetic regions. NGS analyzes the entire TB genome. By sequencing millions of DNA fragments simultaneously, it identifies mutations linked to resistance against both first and second-line drugs. This detailed genetic profiling enables clinicians to detect novel mutations and mixed infections, which conventional tests often overlook, she said.
NGS-based TB tests are high in accuracy. Whole genome sequencing can provide comprehensive drug resistance predictions for multiple TB drugs within 14 days, significantly reducing the time needed for treatment adjustments compared to traditional methods. NGS serves as a powerful epidemiological tool. By analysing TB strains across regions, public health officials can track transmission patterns, identify emerging resistance trends, and implement targeted interventions. This surveillance capability is crucial in densely populated areas were TB spreads rapidly. In large-scale studies, genomic sequencing has demonstrated advantages over conventional drug susceptibility and Line Probe Assays in detecting drug-resistant TB cases.
By combining advanced diagnostics with healthcare infrastructure and community-driven initiatives, India can more effectively combat drug-resistant TB. With sustained innovation and investment, the country moves closer to its goal of a TB-free future.
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