Rohit Kumar had lost all hope. All anti-tuberculosis drugs had stopped giving results for the 23-year-old from Delhi. As a last resort, his doctor asked him to undergo genome testing. Kumar (name changed) was found to be multi-drug resistant (MDR). Fortunately, he had not reached the extensive drug-resistant stage. He was immediately put on a new drug regime and is now on the road to recovery. Like Kumar, there are several TB patients who are benefiting from genome sequencing, which helps to make the right diagnosis at the right time.
“Genomics is the future of effective tuberculosis diagnosis,” says Gunisha Pasricha, principal scientist, infectious disease expert, MedGenome, a genomics research and drug development organisation. “With advanced techniques like culture-free, whole genome sequencing (WGS), we are gradually progressing towards overcoming the challenges around accurate and timely diagnosis of tuberculosis.” As per a paper titled, ‘WGS of Mycobacterium TB Isolates from India’, published in Frontiers in Microbiology, “WGS of mycobacterium tuberculosis (MtB) has been constructive in understanding its evolution, genetic diversity and the mechanisms involved in drug resistance.” The study highlighted the immense significance of employing WGS in diagnosis as well as treatment.
Numbers, too, merit attention and call for timely interventions to stymie the endemic. As the world celebrated World TB Day on March 24, nearly 10 million people were estimated to have developed tuberculosis globally. In 2022, 1.5 million people died from it. India has the world’s highest TB burden, with an estimated 26 lakh people contracting the disease and approximately 4 lakh people dying from the disease every year, as per the Union government figures. In 2022, India accounted for the highest number of TB cases in the world, representing a whopping 27 per cent of the global burden, revealed the World Health Organization's Global Tuberculosis Report 2023.
A growing body of scholarship underscores that wrong dosage, poor quality of drugs and delay in diagnosis have precipitated India’s MDR TB epidemic. Out of 1.1 lakh cases, 63,801 were diagnosed with the MDR variant. Understandably, therefore, in recent times, experts have advocated the use of molecular diagnostics to treat the contagious disease, especially in the backdrop of MDR emerging as a major concern. The WHO, too, recommends molecular tests. The latest India-TB report, however, shows that the traditional culture-based sputum test continues to be the predominant method across the country.
Vinod Scaria, senior consultant, genome informatics and computational biology, Vishwanath Cancer Care Foundation, told THE WEEK that both diagnosis and treatment need to be kept in mind. “Tuberculosis is an endemic, but when it becomes active infection the problem arises and the big issue is resistance to drugs,” he said. “The culture-based (microscopic) methods are no doubt the gold standard around the world. But, there are limitations in the sense that they may or may not detect infections that are called extra-pulmonary in case of TB.” Scaria, who was part of Indian SARS-CoV2 genomic sequencing (INSACOG) project during his stint with CSIR Institute of Genomics and Integrative Biology, added that the solution to this problem was meta genome sequencing, which can identify and make information available holistically. “When it comes to treatment, in case of TB the conventional ways may miss the drug resistance markers available, delaying the diagnosis and the treatment,” he said. “By sequencing the entire genome, all markers will be covered and the exact causes can be learnt in much less time.”
Pasricha concurs. “The conventional techniques like liquid culture or solid culture will take more time to give results,” she said. “The molecular methods, on the other hand, sequence the whole genome and we have validated the tests within 14 days.” She further explained that culture-based WGS had proven effective in predicting drug resistance and providing insights into the genetic makeup of TB strains. However, culture-based WGS takes 10-12 weeks to determine the drug resistance susceptibility results of the sample. “WGS from direct sputum/clinical samples offers a solution,” she said. “Advancements in genomics have helped us address these issues, and today we have technologies like SPITSEQ, a culture-free WGS method that comes with 100 per cent sensitivity, 98.4 per cent accuracy in resistance variant profiling and 97.7 per cent accuracy with phenotypic drug susceptibility tests for at least six anti-tuberculosis drugs.” She admitted that although culture-based microscopic methods are the gold standard, the world is increasingly recognising the importance of next-generation sequencing. “We get a regular inflow of requests by doctors to perform WGS using new technologies,” she said.
The government also acknowledges the gaps. A senior official in the department of biotechnology, the nodal organisation sequencing more than 30,000 TB strains, told THE WEEK that there are at least two challenges in the current methods of surveillance of drug resistance in MtB. “Existing genetic testing for drug resistance picks only the known genes/mutations and because of the long doubling time of Mtb, traditional drug sensitivity tests are time-consuming,” he said. He added that this necessitates the development of novel technologies for rapid detection of drug resistance and identification of novel mutations. Developments in WGS technologies make it an extremely useful tool to address both these issues.
The government has initiated a slew of measures to combat TB. The campaign got a renewed push with the launch of Pradhan Mantri TB-Mukt Bharat Abhiyan in September 2022 which aims to eradicate TB by 2025. In fact, the reported increase in TB cases the same year were attributed to enhanced surveillance. According to the India TB report 2023, published by central TB division in the ministry of health and family welfare, the year 2022 marked a “milestone year for TB surveillance efforts in India, with a record high notification of 24.2 lakh cases, a 13 per cent increase from 2021”. This means a case notification rate of approximately 172 cases per lakh population. The highest notification was seen in Delhi (546 per lakh population) and the lowest in Kerala (67 per lakh population). Ni-kshay Mitras, Ni-kshay Poshan Yojana, TB Vijetas and TB Champions are some other initiatives of the government focusing on generating awareness on TB prevention.
To provide impetus to molecular testing, there was another initiative called the Indian TB Genomic Surveillance Consortium (InTGS) launched under the government's DARE2ERAD TB (data-driven research to eradicate TB) umbrella in March 2023. It was modelled on the lines of INSACOG, to monitor the genomic variations in MtB through a multi-laboratory network. The partners of this consortium are CSIR and the Indian Council of Medical Research (ICMR). As part of the initiative, the department of biotechnology plans to perform whole genome sequencing of 32,200 clinical strains from active TB patients.
Acknowledging the importance of WGS in TB, Union minister for science and technology Dr Jitendra Singh had said: “In order to fully understand the biological characteristics of MtB and the effect of the mutations on transmission, treatment and disease severity, analysing the genomic data of the organism is essential.” Singh admitted that WGS is increasingly gaining traction as an important molecular tool for TB surveillance. “InTGS is a first pan-India initiative at such scale to fully understand the biological characteristics and could lay the groundwork for use of modern technology such as WGS for TB diagnosis and surveillance in future,” said Singh.
Dr Rajendra P. Joshi, deputy director general, central TB division, wrote in the 2023 India TB report that under the national tuberculosis elimination programme, 4,960 nucleic acid amplification test machines have been deployed across the country for rapid molecular diagnosis of TB to ensure early and complete case finding.
However, observers feel that the pace at which India is performing WGS on TB strains may not be enough to achieve the TB-mukt target by 2025. The numbers attest to the pessimism. In March 2023, the Union minister declared the commencement of the pilot phase of InTGS with successful completion of whole genome sequencing of 182 strains isolated from TB patients. In nearly a year since then, the sequencing has been completed for only 513 strains, as per the recent data provided to THE WEEK by the department of biotechnology.
“The reason behind the slow progress is the reluctance of the government to rope-in the private sector,” said an expert, on condition of anonymity. “While the government may take years to perform WGS of 32,200 TB strains, the private sector is capable of doing the job within 3-4 months. In case of Covid-19, the government opened up the testing of RT-PCR by the private players. This resulted not only in reduced cost of the test but also in availability of early reports. The molecular tests were extensively used for Covid-19 detection and they can be re-purposed for TB diagnostics to eradicate the disease by 2025. It is surprising why the government is not doing it.” The apprehension of experts is not misplaced. The organisations chosen for the execution of InTGS are all government agencies. Whereas sequencing will be performed together by BRIC-National Institute of Biomedical Genomics, Kalyani, CSIR-Centre for Cellular & Molecular Biology, Hyderabad, and ICMR-National Institute for Research in Tuberculosis, Chennai, a bio-repository for TB strains is being established at International Centre for Genetic Engineering and Biotechnology, New Delhi.
For data analysis and storage, National Institute of Immunology, New Delhi, and Indian Biological Data Centre, Faridabad, have been given the responsibility, respectively.
The chorus is growing for strengthening access to WGS TB services, improving surveillance and drug resistance management besides investing heavily in R&D, as explained in a recent paper titled, ‘Genomic revolution: Transforming TB diagnosis and treatment with the use of WGS’ published in the Indian Journal of Tuberculosis.
For India to be TB-mukt by 2025, it will have to make rapid strides in using whole genome sequencing to its full potential. Said Pasricha: “Public private partnership is very important so that all go hand-in-hand to eradicate TB from India.”