Mutations in tuberculosis bacteria make it resistant to drugs, say researchers

The scientists have discovered several mutations in the genes of TB bacteria causing drug resistance. The results of the four-year research were published in the latest issue of Frontiers in Microbiology, a scientific journal.

The team comprised researchers from the Institute of Bioinformatics, Bengaluru; Indian Council of Medical Research (ICMR), National Jalma Institute of Leprosy and other Mycobacterial Diseases, Agra; and Yenepoya University, Mangaluru. It was funded by the Department of Biotechnology (DBT), Infosys Foundation and Yenepoya University.

The researchers performed whole genome sequencing of mycobacterium tuberculosis (MTB) strains collected between 2010 and 2014 at the National Jalma Institute of Leprosy and Other Mycobacterial Diseases at Agra.

“We analysed 200 MTB strains from different categories such as sensitive to first-line drugs, rifampicin mono-resistant, isoniazid mono-resistant, streptomycin mono-resistant, MDR (multi-drug resistant) and pre-extensively drug-resistant (pre-XDR)," T.S. Keshava Prasad, professor at Yenepoya University, and faculty scientist, Institute of Bioinformatics, said in an interview.

The research team identified several novel genetic variations and novel genotypes in clinical strains from north India, which might potentially be associated with drug resistance.

“At least 20% of the strains were also co-infected with non-tuberculous mycobacteria species along with MTB. We identified a total of over 12,000 novel genetic variations in MTB isolates (strains), including 343 novel single nucleotide variations (SNVs) in 38 genes, which are known to be associated with drug resistance. A large majority of these SNVs are not currently used in the diagnostic protocols for detection of drug-resistant TB," said D.S. Chauhan, senior scientist and head of Jalma Institute’s microbiology department, under whose supervision the MTB cultures were grown and maintained. “The results are not surprising. We have always suspected that there may be co-infections and our tools are not adequate to detect organisms and drug-resistance accurately," he added.

Other members of the team were Renu Verma, Jayshree Advani, and Oishi Chatterjee, involved in culturing MTB and analysing data.

For TB treatment, the first-line anti-tuberculosis drugs used are isoniazid, rifampicin, ethambutol, and pyrazinamide. The second-line anti-tuberculosis drugs are moxifloxacin, high dose levofloxacin (fluoroquinolones) and linezolid, delamanid, and bedaquiline.

Of these, bedaquiline is the latest drug with increased evidence of success against MTB. The Rv0678 gene in the TB causing bacteria is known to be associated with bedaquiline resistance. Bedaquiline is commonly used by the Union health ministry for treating TB. The researchers also found a genetic variation in the Rv0678 gene in some of the MTB isolates sequenced.

“Keeping in mind that bedaquiline is a fairly new anti-TB drug, the identification of SNVs in this gene suggests the dynamic and rapid evolution of MTB clinical strains. Our study identified several novel genetic variations that were not previously reported in MTB," said Prasad. “Among these were several novel genetic variations in the genes that are known to confer drug resistance."

The emerging drug resistance is a serious global threat and possesses a significant challenge to public health. India alone accounted for 24% of global MDR TB incidence and 27% of global TB incidence among HIV-negative individuals.