Rapid, Amplification-free, RNA-based Uropathogen Detection With LbuCas13a

Expeditious identification of bacterial infection remains an important challenge in an emergency department. Bacterial cultures remain the gold standard, though they take 24-72 hours to result. Polymerase chain reaction-based diagnostics are emerging but take several hours to get a result. Here, we report a rapid bacterial RNA detection platform based on Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology with urine-to-result time within 1 hour.

All CRISPR experiments were conducted as an open format plate reader assay with fluorescent readouts. In derivation studies, Escherichia coli 16s rRNA was spiked in commercially purchased human urine to determine assay compatibility and limit of detection. In validation studies, previously collected, patient-derived raw urine was used to examine the assay concordance with urinary tract infection (UTI) diagnosis (N = 14).

The lower limit of detection of our CRISPR assay was ∼10⁶ copies/µL in human urine. In validation studies, the overall sensitivity was 75% for Gram-negative and Gram-positive UTIs combined. When performed postanalytically to conventional urinalysis, the combined diagnostic schema had 100% specificity and positive predictive value. Overall urine-to-result time was less than 1 hour.

We demonstrated the feasibility to adopt an amplification-free CRISPR assay for the purpose of rapid uropathogen detection. To our knowledge, this is the first demonstration of an RNA-based tool for detecting uropathogens. Our assay may be used postanalytically to conventional urinalysis for improved specificity to diagnose UTIs. Future research may focus on improving the sensitivity and discriminating uropathogen versus bacterial contaminant, which is beyond the scope of the current study.