UK moves to whole genome sequencing for identifying TB strains

Infectious diseases

By Anna Sayburn

8 Dec 2017

England will be the first country in the world to conduct whole genome sequencing (WGS) on all tuberculosis (TB) samples in 2018, delegates attending the BTS Winter meeting have heard.

In January, the London-based national mycobacterium reference service (NMRS) laboratory will join the Birmingham-based service, which has been using WSG for the past year.

Dr Eliza Alexander, from Public Health England, announced the plan at a TB symposium at the British Thoracic Society Winter Meeting.

Current systems for identifying strains of TB, with drug sensitivity information and typing, can take eight weeks. WSG, said Dr Alexander, can give results in seven days.

“It’s also cheaper; it’s one test and gives us timely information for improving patient care, especially around drug resistance.”

She said it can also provide better understanding of transmission routes, by allowing speedy analysis of whether outbreaks are linked to each other and the direction of travel.

Susceptibility to drugs is a key issue, given the widespread nature of multi-drug resistant TB. Dr Alexander said unpublished data suggested WSG demonstrated very high positive predictive values for identifying strains of TB susceptible to the most commonly used drugs, isoniazid and rifampicin.

Compared to the currently used MIRU-VNTR process for typing TB, WGS is “much more discriminatory and selective” which can help to focus publish health work, she said.

It can also guide patient management in contact tracing and drug selection. She said the laboratories plan to phase out phenotypic sensitivity testing for the most commonly used drugs.

Some clinicians attending the meeting reacted nervously to the news, asking whether this did not risk missing unknown variants or strains. Dr Alexander said they would continue to sequence anything phenotypically resistant, and that the phasing out process would be done over time.

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