Faster identification of resistant tuberculosis

A team led by University College London (UCL) has reduced the time needed to genetically sequence the bacteria causing tuberculosis (Mycobacterium tuberculosis, M. tb) from patient samples from weeks to days. The team’s method has been published in the Journal of Clinical Microbiology.

Tuberculosis (TB) disease rates in some parts of London are as high as in Sub-Saharan Africa, and drug-resistant strains are becoming increasingly common. These require specific treatments, and if doctors know that a bug is resistant they can start therapy earlier.

Whole genome sequencing reveals the complete genetic sequence of an M. tb sample, in many cases pinpointing drug resistance mutations so that appropriate treatments can be given. However, this process currently takes weeks because samples need to be grown in the laboratory before there is enough genetic material to measure.

“Using the conventional methods, patients with resistant TB would need to wait for up to six weeks for antibiotic resistance testing,” said senior author Professor Judith Breuer. “In that time, they may be taking drugs that are suboptimal or suffer unnecessary and unpleasant treatment side effects.”

The researchers’ technique and associated software allowed them to enrich M. tb DNA directly from patient sputum (mucus) samples. This means that the samples can be sequenced and analysed within a few days, said Professor Breuer, avoiding the need to spend weeks growing them in the lab.

To extract M. tb from sputum samples, the researchers used probes made of RNA molecules, engineered to bind to M. tb DNA. The method was tested on 24 routine samples taken from patients in London and Lithuania, and the sequencing results from sputum matched perfectly with those from the relevant cultured isolates.

“As well as delivering personalised treatments to patients, the tests could also be used to precisely track the spread of TB,” said co-lead author Dr Josephine Bryant. “With rapid sequencing available, it would be possible to trace TB infections in communities, or to identify a few highly infectious people, sometimes called ‘super-spreaders’. If public health officials can identify these individuals faster and stop them from spreading the disease, control and prevention of future outbreaks could be improved.”

The technique has also been applied to other infections - including chlamydia, HIV, hepatitis, herpes, influenza A, norovirus and cytomegalovirus - which are becoming resistant to antimicrobials. The team hope to make the technique cheaper and simpler so it could be used in countries with less economically rich healthcare systems where drug-resistant TB is common.

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