CRISPR-Cas12a enables portable detection of antibiotic resistance genes

Antimicrobial resistance (AMR) is a growing public health concern across clinical, veterinary, and environmental settings, yet current surveillance tools are often limited by cost, infrastructure requirements, or turnaround times. The C12a toolbox was created to address these gaps by targeting three markers of particular One Health relevance: blaCTX-M-15, conferring resistance to β-lactams; floR, conferring resistance to amphenicols; and the Class 1 integron integrase gene intI1, a recognised proxy for multidrug resistance dissemination.

The system works by first amplifying the target DNA by PCR, after which a crRNA-guided Cas12a complex recognises the sequence and triggers non-specific trans-cleavage of a fluorescent reporter probe, producing a detectable signal within 20 minutes. Limits of detection reached 70 attomolar for blaCTX-M-15 and 50 attomolar for floR in purified DNA, and below 200 CFU/mL in bacterial culture – 10 to 100 times more sensitive than standard gel electrophoresis of PCR products.

The toolbox performed consistently whether read out via fluorescence microplate reader, direct blue-light visualisation, or lateral flow assay strips, making it adaptable to resource-constrained settings. Detection of intI1 in 17 of 18 ARG-positive isolates adds weight to its proposed role as a marker of multidrug resistance. The authors, however, caution that it cannot replace direct ARG detection for specific surveillance purposes.

The study was conducted by Maryhory Vargas-Reyes, Roberto Alcántara and Pohl Milon at Universidad Peruana de Ciencias Aplicadas. It was published on 1 March 2026 in Scientific Reports.