CRISPR/Cas13a Assay Detects Salmonella in Under 60 Minutes Across Large Clinical Cohorts
A CRISPR/Cas13a-based assay combined with recombinase polymerase amplification detected Salmonella spp. with 87.5% sensitivity and 98.8% specificity in hospitalised diarrhoea patients, and showed over 98.7% concordance with culture across three prospective cohorts totalling over 2,000 subjects. The 60-minute turnaround and 100 fg/uL detection limit make it a practical rapid alternative to time-consuming broth enrichment culture.
The original study
Application of CRISPR/Cas13a system on the rapid detection of Salmonella spp.
- Authors
- Huang Y, Liang W, Huang M, Deng Y, Huang Z, Ai C, et al.
- Journal
- PLoS neglected tropical diseases
- PMID
- 41871065
Original abstract
BACKGROUND: Salmonella spp. infections can manifest in various clinical symptoms, from asymptomatic carriage to gastroenteritis, and even severe sepsis. Given the rapid progression of the disease and its potential to cause severe outcomes or trigger cluster outbreaks, making the detection of Salmonella spp. critically important. Although broth enrichment culture is considered the gold standard, it is time-consuming and involves multiple steps, making it difficult to meet urgent diagnostic needs. Hence, prompt and precise detection of Salmonella spp. is crucial not only for early diagnosis and effective treatment, but also for preventing transmission, controlling outbreaks, and screening asymptomatic Salmonella carrier. METHODS: This study developed a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) -SE assay that integrated the advantages of the recombinase polymerase amplification (RPA) and CRISPR/Cas13a system for detecting Salmonella spp. The clinical performance of CRISPR/Cas13a-SE assay was evaluated by a cohort of 94 inpatients with diarrhea and three prospective studies. RESULTS: The CRISPR/Cas13a-SE assay can be completed within 60 minutes, and its limit of detection was 100 fg/μL. Compared to the broth enrichment culture, the CRISPR/Cas13a-SE assay demonstrated a sensitivity of 87.5% and a specificity of 98.8% in a cohort of 94 inpatients with diarrhea. In our prospective studies involved three distinct cohorts: 1,662 food handlers, 211 outpatients with diarrhea, and 154 inpatients with Gram-negative bacteremia. Compared with broth enrichment culture, CRISPR/Cas13a-SE assay had a high concordance rate of 98.79% (1642/1662), 99.52% (210/211)., and 100.00% (154/154) respectively. CONCLUSIONS: We demonstrated that the CRISPR/Cas13a-SE system showed excellent detection performance for infectious diarrhea caused by Salmonella spp. The combined use of CRISPR/Cas13a-SE with the blood culture method enhances the rapid diagnosis of invasive salmonellosis, which is crucial for early target-based therapy. Additionally, screening of asymptomatic Salmonella carrier will be benefit for disease prevention and control.