Pyrosequencing Detects Tuberculosis Drug Resistance and Improves Management

Myobacterium Tuberculosis
Myobacterium Tuberculosis
Pyrosequencing may benefit clinical decision making and reduce time to start of effective treatment in patients with drug-resistant tuberculosis.

Pyrosequencing may benefit clinical decision making and reduce time to start of effective treatment in patients with drug-resistant tuberculosis (TB), according to study results published in Clinical Infectious Diseases.

The emergence and spread of multidrug-resistant TB (MDR-TB) is a barrier to TB elimination and a threat to TB control. MDR-TB is resistant to the most effective first-line medications, including isoniazid and rifampin, and was reported in approximately 1.8% of patients with TB in California in 2017. Rapid diagnosis of drug-resistant TB is critical to the initiation of an effective treatment regimen. Culture-based phenotypic methods usually require >4 weeks, which results in delayed diagnosis, treatment with ineffective drugs, poor treatment outcomes, and spread of drug-resistant TB. In addition, culture-based phenotypic methods may miss mutations that confer low-level rifampin resistance. Rapid molecular drug susceptibility testing for TB is an important tool for detecting mutations associated with resistance.

In 2012, the California Department of Public Health began offering a molecular drug susceptibility assay using pyrosequencing for the detection of mutations associated with resistance to isoniazid, rifampin, quinolones, and injectable drugs in the Mycobacterium tuberculosis complex. As pyrosequencing provides sequence results, it goes a step further than previous molecular tests by providing the precise sequence of mutation since not all mutations confer drug resistance and mutations can confer different levels of resistance. Therefore, this study evaluated the effect of the pyrosequencing assay on the initiation of MDR treatment and how pyrosequencing might influence clinicians’ decisions regarding the management of TB patients in California.

TB surveillance and laboratory data for specimens submitted between 2012 and 2016 were analyzed to determine time to effective treatment initiation. A survey of clinicians was used to analyze how pyrosequencing results were influencing clinical decision making.

The results demonstrated that in patients with MDR-TB effective treatment was initiated 5 weeks earlier when pyrosequencing was used and that the use of pyrosequencing influenced clinical decisions in a substantial number of cases. The pyrosequencing turnaround time for results was a median of 1 day, but the time from specimen collection to receipt date was >1 week. Therefore, optimization of the gap between specimen collection and submission for pyrosequencing would provide significant improvement for the test. In patients who had no changes in their treatment regimen, nearly one-fifth of providers indicated that pyrosequencing was a reason for choosing the regimen, meaning that pyrosequencing was used to confirm susceptibility of drugs. In more than one-third of patients with changes to their drug regimen, pyrosequencing was indicated as a reason for the change. Further, survey results confirmed that pyrosequencing results triggered additional testing and consultation in many patients, particularly patients with a resistance mutation.

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Overall, the findings show that pyrosequencing lessens the time to effective treatment initiation in patients with MDR-TB and helped tailor patients’ drug regimens to optimize their effectiveness. The study authors concluded that, “Nevertheless, further improvement can be made to reduce the time to initiate MDR-TB treatment by recognizing MDR-TB risks and submitting smear negative sputa rapidly for [pyrosequencing].”


Lowenthal P, Lin SYG, Desmond E, Shah N, Flood J, Barry PM. Evaluation of the impact of a sequencing assay for detection of drug resistance on the clinical management of tuberculosis [published online November 1, 2018]. Clin Infect Dis. doi:10.1093/cid/ciy937/5154873