A quick, easy-to-use diagnostic test could save more lives from melioidosis

Globally, more than half of patients die after infection with the neglected tropical disease, meliodosis, often before they are diagnosed. A new rapid test could save lives by diagnosing patients in hours, rather than the several days required by current bacterial culture methods, meaning they get the right antibiotics faster.

The test uses CRISPR to detect a genetic target that is specific Burkholderia pseudomallei, the bacterium that causes melioration, with 93 percent sensitivity. It was developed by researchers at Mahidol-Oxford Tropical Medicine Research Unit (MORU), Chiang Mai University, Vidyasirimedhi Institute of Science and Technology (VISTEC) in Thailand and the Wellcome Sanger Institute in the UK.

The results, published today (March 14) on Lancet Microbmeans that more lives could be saved from melioidosis, with a quick, easy-to-use diagnostic test that could be rolled out worldwide.

Melioosis is a neglected tropical disease that affects an estimated 165,000 people worldwide each year, of which 89,000 die from the disease. It is caused by the bacterium, Burkholderia pseudomalleiwhich lives in soil and water in tropical and subtropical regions and enters the human body through inoculation through skin abrasions, ingestion or inhalation.

It is difficult to diagnose melioidosis as symptoms vary from local abscess or pneumonia to acute sepsis or may present as a chronic infection. As a result of this, and the locations of isolated communities in rural areas that it affects most, the disease remains highly under-reported.

Currently, melioidosis is diagnosed in patients after culturing bacterial samples, which takes three to four days. In Thailand, about 40 percent of melioidosis patients die, many of whom die within the first to two days of being admitted to the hospital while waiting for a diagnosis.

There is no approved vaccine for melioidosis, but patients can be effectively treated with intravenous antibiotics – ceftazidime or carbapenem – during the first intensive phase of treatment. However, current practices often involve initially treating patients with a series of unnecessary antibiotics to target the various symptoms the disease produces, which can waste time and resources.

In a new study, the team set out to develop a new rapid test to reduce the time needed to correctly diagnose and treat meliodosis patients.

Researchers identified a genetic target specifically for B. pseudomallei with analyzing over 3,000 B. pseudomallei genomes, most of which were sequenced at the Sanger Institute. They searched for conserved regions of the genome and screened the targets against other pathogens and human host genomes to ensure that their chosen target was specific for B. pseudomallei.

Their test, called CRISPR-BP34, involves rupturing bacterial cells and using a recombinant polymerase amplification reaction to amplify the target bacterial DNA for increased sensitivity. In addition, a CRISPR reaction is used to provide specificity and a simple “dipstick” lateral flow readout is used to confirm cases of alleles.

To assess the effectiveness of the test, the team collected clinical samples from 114 patients with melioidosis and 216 patients without the disease at Sunpasitthiprasong Hospital, a hospital in northeastern Thailand where melioidosis is endemic. The CRISPR-BP34 assay was then applied to these samples.

The new test showed an increased sensitivity of 93 percent, compared to 66.7 percent in bacterial culture methods. It also gave results in less than four hours for urine, pus and sputum samples and within a day for blood samples. This is a significant improvement over the current diagnostic method of bacterial culture, which typically takes three to four days.

This new rapid diagnostic test will allow healthcare professionals to prescribe the right antibiotics faster, meaning fewer patients will die waiting for a diagnosis. While saving valuable time, the new test will also save resources and money, with fewer unnecessary antibiotics being prescribed and less time for patients in hospital.

In the next steps for the team, they are currently planning randomized clinical trials to show the effectiveness of these tests in hospital settings. Additionally, team members will begin investigating the role of human genetics in susceptibility and immune response to melioid 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, powerful rapid diagnostic test for melioidosis and hope it can 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, said: “We carefully designed the CRISPR-BP34-based rapid diagnostic test with a robust algorithm and tested its performance in vitro. We are excited that the CRISPR-BP34 test demonstrates excellent diagnostic efficacy when tested in clinical samples, demonstrating its potential to significantly impact patient outcomes and save lives in the near future.”

This research is a testament to international collaboration and how applying 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 for the bacterium behind melioidosis. I look forward to seeing the clinical implications of this research.”

Professor Nick Thomson, senior author and Head of Parasites and Microbes at the Wellcome Sanger Institute

Professor 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: “Meliosis has been neglected despite its high mortality and incidence in many parts of Asia. Early diagnosis is essential in order to initiate the specific treatment required as soon as possible. The new rapid diagnostic tool developed through this collaboration has the potential to be a game changer.”