Bacterial DNA Sequencing Predicts Susceptibility to First-Line TB Drugs

By Marilynn Larkin

October 03, 2018

NEW YORK (Reuters Health) - Sequencing bacterial DNA can predict drug resistance and susceptibility to first-line TB drugs, including isoniazid, rifampin, pyrazinamide and ethambutol, according to a new study.

"Treatment of tuberculosis requires concomitant use of multiple drugs in order to avoid the development of bacterial drug resistance," Dr. Helen Cox of the Wellcome Centre for Infectious Diseases Research in Africa in Cape Town, South Africa, told Reuters Health by email.

"Detailed drug susceptibility testing is required for clinicians to be able to tailor a specific multi-drug treatment regimen for each patient," said Dr. Cox, who coauthored an editorial that accompanied the study.

Dr. Timothy Walker of John Radcliffe Hospital in Headington, Oxford, UK and colleagues obtained whole-genome sequences for 10,209 TB isolates from 16 countries across six continents. For each isolate, they identified mutations associated with drug resistance and susceptibility across nine genes, and predicted individual phenotypes and complete susceptibility profiles.

Profiles were categorized as "pansusceptible" if they were predicted to be susceptible to isoniazid and other TB drugs.

As reported online September 26 in the New England Journal of Medicine, the largest proportion of phenotypes were predicted for rifampin (94.5%) and the smallest for ethambutol (89.8%).

Resistance to isoniazid, rifampin, ethambutol and pyrazinamide was predicted correctly, with sensitivities of 97.1%, 97.5%, 94.6% and 91.3%, respectively. Susceptibility also was predicted correctly, with specificities of 99.0%, 98.8%, 93.6% and 96.8%.

Of the 7,516 isolates (74%) with complete phenotypic susceptibility profiles, (78%) had complete genotypic predictions, among which 89.5% were correctly predicted.

Among the 4,037 (69%) pansusceptible profiles, 97.9% were correctly predicted.

Currently, said Dr. Cox, "bacterial DNA sequencing relies on first culturing the TB bacteria in order to obtain sufficient DNA. Unfortunately, TB bacteria are slow growing organisms and it can take a minimum of two weeks to grow enough to be able to sequence the whole genome."

"The next step," she said, "would be to optimize laboratory techniques to be able to sequence DNA directly from sputum samples. This would enable rapid determination of resistance to all TB drugs, and therefore rapid initiation of effective TB treatment for all TB patients."

In email to Reuters Health, Dr. Walker also noted that for the approach to work in countries where TB is widespread, "first we need to get better at making DNA from TB in sputum samples, and at sequencing in portable devices. It's coming..."

"Our findings are relevant to first-line drugs only," he said. "More work (needs to be done) on the other (TB) drugs, including new and repurposed drugs."

Dr. Cox added, "There will be considerable logistical hurdles and health system constraints to be overcome for this approach to be used to tailor treatment for most TB patients who reside in resource-constrained countries."

"However," she said, "if we are to effectively tackle the current global epidemic of drug-resistant TB, then the provision of more effective treatment that avoids the development of resistance to new TB drugs such as bedaquiline is paramount across all high-burden settings."

"We believe that we should strive to provide the same standard of care for all TB patients, regardless of where they reside," she concluded.


N Engl J Med 2018.