Rapid test co-developed by Sanger Institute could help save lives claimed by the tropical disease melioidosis

A new rapid test co-developed by the Wellcome Sanger Institute could help save some of the 89,000 lives lost each year to a neglected tropical disease.

Melioidosis affects an estimated 165,000 people worldwide annually and is caused by the bacterium Burkholderia pseudomallei, which lives in soil and water in tropical and subtropical regions and can enter the body through skin abrasions, ingestion or inhalation.

Many of those affected die before they diagnosis.

Diagnosis is complicated because the symptoms vary, from localised abscess or pneumonia to acute septicaemia, or it can present as a chronic infection.

This, and the fact that it typically affects isolated, rural communities, means the disease is hugely underreported and many patients due before being diagnosed.

Now a new test that uses CRISPR gene editing technology enables diagnosis within hours, rather than the three to four days it currently takes using bacterial culture methods.

This means patients could be given the correct antibiotics much faster, saving lives.

The test, called CRISPR-BP34, has 93 per cent sensitivity to a genetic target specific to the bacterium, compared to 66.7 per cent using current methods.

Results are available in four hours with urine, pus or sputum samples, and within one day for blood samples.

It was developed by researchers at the Mahidol-Oxford Tropical Medicine Research Unit (MORU), Chiang Mai University, Vidyasirimedhi Institute of Science and Technology (VISTEC) in Thailand and the Wellcome Sanger Institute at Hinxton.

Prof Nick Thomson, senior author and head of parasites and microbes at the Wellcome Sanger Institute, said: “This research is a testament to international collaboration and how the application of genomics at scale leads to clinical intervention. Using a genetic target mined from a bank of thousands of bacterial genomes, the team was able to produce an incredibly sensitive test that is specific to the bacterium behind melioidosis. I look forward to seeing the clinical impacts of this research.”

The researchers analysed more than 3,000 B. pseudomallei genomes, most of which were sequenced at the Sanger Institute, to search for conserved regions of the genome.

Screening the targets against other pathogens and human host genomes, they ensured the chosen target was specific to B. pseudomallei.

The test ruptures bacterial cells and uses a recombinase polymerase amplification reaction to amplify the bacterial target DNA for increased sensitivity.

A CRISPR reaction is also used to provide specificity and cases are confirmed via a simple lateral flow ‘dipstick’ read-out.

It was tested on samples from patients with and without the disease in Thailand, where about 40 per cent of those with melioidosis die, many of them within a day or two of being admitted to hospital while they await diagnosis. The results were published in Lancet Microbe.

While there is no licensed vaccine for melioidosis, patients can be effectively treated with intravenous antibiotics – ceftazidime or carbapenem – during the initial intensive phase of treatment.

However, currently patients are often initially treated with a range of unnecessary antibiotics to target the various symptoms presenting, wasting time and resources.

Prof Nick Day, senior author and Director of the Mahidol-Oxford Tropical Medicine Research Unit (MORU), Thailand, and the Wellcome Trust Thailand Asia and Africa Programme, said: “Melioidosis has been neglected despite its high mortality rate and high incidence in many parts of Asia. Early diagnosis is essential so that the specific treatment required can be started as soon as possible. The new rapid diagnostic tool developed through this collaboration has the potential to be a game-changer.”

The team are now designing randomised clinical trials to show the test’s effectiveness in a hospital and some of them are beginning to investigate the role of human genetics in susceptibility and immune response to melioidosis infection.

Dr Claire Chewapreecha, co-lead author at the Mahidol-Oxford Tropical Medicine Research Unit (MORU), Thailand, and Wellcome Sanger Institute international fellow, said: "Working in rural Thailand has many limitations. But we have shown that limitations breed innovation, and what succeeds here can succeed anywhere. I am so proud of the team behind this new, robust rapid diagnostic test for melioidosis, and hope that it can potentially be used anywhere in the world to get the right treatments to patients faster, ultimately saving lives."

Dr Somsakul Wongpalee, co-lead author at Chiang Mai University, Thailand, added: "We carefully designed the rapid diagnostic test based on CRISPR-BP34, with a robust algorithm, and tested its performance in vitro. We are thrilled that the CRISPR-BP34 test demonstrates outstanding diagnostic efficacy when tested on clinical samples, showcasing its potential to significantly impact patient outcomes and potentially save lives in the near future."