New Method for Genome Analysis of Drug Resistant Tuberculosis Bacteria Directly from Patient Samples

A European research consortium has developed a test for the detection of drug resistant strains of the tuberculosis (TB) bacterium Mycobacterium tuberculosis, which yields results within a few days rather than the period of weeks that is required by current methods.

The new procedure allows whole gene sequencing of M. tuberculosis in samples of patients' sputum. Whole genome sequencing provides comprehensive data on resistance mutations and strain typing for monitoring transmission, but unlike conventional molecular tests, this has only previously been achievable from M. tuberculosis after a long period of growth in culture.

Investigators working in the framework of the PATHSEEK project, which includes researchers at University College London (United Kingdom), Erasmus Medical Center (Rotterdam, The Netherlands), and the biotech companies CLC bio (Aarhus, Denmark) and Oxford Gene Technology (Oxford, United Kingdom), have described a method for enriching M. tuberculosis DNA directly from patient sputum samples.

The technique utilizes biotinylated RNA baits, designed specifically for M. tuberculosis DNA, to capture full M. tuberculosis genomes directly from infected sputum samples, allowing whole genome sequencing without the requirement of culture. The investigators used this method to analyze 24 smear-positive sputum samples, collected from the United Kingdom and Lithuania where a matched culture sample was available, and two samples that had failed to grow in culture.

M. tuberculosis sequencing data was obtained directly from all 24 smear-positive culture-positive sputa, of which 20 were high quality. Results were compared with conventional molecular and culture-based methods, and high levels of concordance were observed between phenotypical resistance and predicted resistance based on genotype. High quality sequence data was obtained from one smear positive culture negative case.

“Using the conventional methods, patients with resistant TB would need to wait for up to six weeks for antibiotic resistance testing,” said senior author Dr. Judith Breuer professor of virology at University College London. “In that time, they may be taking drugs that are suboptimal or suffer unnecessary and unpleasant treatment side effects. Our technique and the associated software could reduce testing for antimicrobial resistance to a few days, allowing doctors to give precise antimicrobial treatment earlier than is currently possible.”

Dr. John Anson, executive vice president at Oxford Gene Technology, said, “It is a privilege to be involved with the PATHSEEK project, which is yielding such fruitful results, and to play an active role in developing new techniques for the rapid detection and characterization of such important diseases.”

Details of the new method were published in the May 13, 2015, online edition of the Journal of Clinical Microbiology.

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University College London
Erasmus Medical Center
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