CREDIT: Thom Leach
Credit: Thom Leach

A new test uses CRISPR to detect Burkholderia pseudomallei, the bacterium that causes melioidosis, in hours rather than the typical three to four days currently needed. It also has 93 percent sensitivity compared to 66.7 percent for current tests. This could be a critical advance, since many patients die of this infection because it takes so long to determine which antibiotics will work for them. More than 165,000 cases of Melioidosis are estimated to occur annually, mainly in Southeast Asia and in northern Australia.

The work appears in Lancet Microbe, and the lead author is Sukripong Pakdeerat of the University of Bangkok. The test was developed by researchers in Thailand and the Wellcome Sanger Institute in the U.K.

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, “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 identified a genetic target specific to B. pseudomallei by 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 their chosen target was specific to B. pseudomallei.

Their test, called CRISPR-BP34, ruptures bacterial cells and uses a recombinase polymerase reaction to amplify the bacterial target DNA. A CRISPR reaction is then used and a simple lateral flow ‘dipstick’ read-out is employed to confirm cases of melioidosis.

There is no vaccine for melioidosis. Intravenous antibiotics—ceftazidime or carbapenem— are effective during the first intensive phase of treatment. However, with current bacterial culture-based diagnostics, many patients receive a range of ineffective antibiotics first. It’s estimated that about 40 percent die, many before it’s known which antibiotic they actually need.

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

The team will next study how the test works in clinical settings. They will also begin investigating the role of human genetics in susceptibility and immune response to melioidosis infection.

Professor 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.”

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