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.”
Reference
Benchmarking CRISPR-BP34 for point-of-care melioidosis detection in low-income and middle-income countries: a molecular diagnostics study. Lancet Microbe 2024; 5: e379–89. Published Online March 13, 2024 https://doi.org/10.1016/ S2666-5247(23)00378-6.
Background
Melioidosis is a neglected but often fatal tropical disease. The disease has broad clinical manifestations, which makes diagnosis challenging and time consuming. To improve diagnosis, we aimed to evaluate the performance of the CRISPR-Cas12a system (CRISPR-BP34) to detect Burkholderia pseudomallei DNA across clinical specimens from patients suspected to have melioidosis.
Methods
We conducted a prospective, observational cohort study of adult patients (aged ≥18 years) with melioidosis at Sunpasitthiprasong Hospital, a tertiary care hospital in Thailand. Participants were eligible for inclusion if they had culture-confirmed B pseudomallei infection from any clinical samples. Data were collected from patient clinical records and follow-up telephone calls. Routine clinical samples (blood, urine, respiratory secretion, pus, and other body fluids) were collected for culture. We documented time taken for diagnosis, and mortality at day 28 of follow-up. We also performed CRISPR-BP34 detection on clinical specimens collected from 330 patients with suspected melioidosis and compared its performance with the current gold-standard culture-based method. Discordant results were validated by three independent qualitative PCR tests. This study is registered with the Thai Clinical Trial Registry, TCTR20190322003.
Findings
Between Oct 1, 2019, and Dec 31, 2022, 876 patients with culture-confirmed melioidosis were admitted or referred to Sunpasitthiprasong Hospital, 433 of whom were alive at diagnosis and were enrolled in this study. Median time from sample collection to diagnosis by culture was 4·0 days (IQR 3·0–5·0) among all patients with known survival status at day 28, which resulted in delayed treatment. 199 (23%) of 876 patients died before diagnosis and 114 (26%) of 433 patients in follow-up were treated, but died within 28 days of admission. To test the CRISPR-BP34 assay, we enrolled and collected clinical samples from 114 patients with melioidosis and 216 patients without melioidosis between May 26 and Dec 31, 2022. Application of CRISPR-BP34 reduced the median sample-to-diagnosis time to 1·1 days (IQR 0·7–1·5) for blood samples, 2·3 h (IQR 2·3–2·4) for urine, and 3·3 h (3·1–3·4) for respiratory secretion, pus, and other body fluids. The overall sensitivity of CRISPR-BP34 was 93·0% (106 of 114 samples [95% CI 86·6–96·9]) compared with 66·7% (76 of 114 samples [57·2–75·2]) for culture. The overall specificity of CRISPR-BP34 was 96·8% (209 of 216 samples [95% CI 93·4–98·7]), compared with 100% (216 of 216 samples [98·3–100·0]) for culture.
Interpretation
The sensitivity, specificity, speed, and window of clinical intervention offered by CRISPR-BP34 support its prospective use as a point-of-care diagnostic tool for melioidosis. Future development should be focused on scalability and cost reduction.
Funding
Chiang Mai University Thailand and Wellcome Trust UK.