Applications and Challenges of CRISPR-Cas Technology for the Detection of Antimicrobial Resistance Genes

Wenting Tang,1,* Ninglei Yang,2,* Meijia Shi1 1Department of Laboratory Medicine, Jiaxing Second Hospital, Jiaxing, Zhejiang, People’s Republic of China; 2Department of Laboratory Medicine, Shanghai First Rehabilitation Hospital, Shanghai, People’s Republic of China*These authors contributed equally to this workCorrespondence: Meijia Shi, Department of Laboratory Medicine, Jiaxing Second Hospital, Jiaxing, Zhejiang, People’s Republic of China, Email [email protected]: The global rise of antimicrobial resistance (AMR) demands rapid and precise diagnostic tools capable of providing actionable results at the point of care. Traditional methods, including bacterial culture and PCR, face critical limitations: culture-based approaches require days to weeks for results, potentially delaying life-saving treatment decisions, while PCR-based methods, though faster, require expensive instrumentation, trained personnel, and are typically confined to centralized laboratory settings. CRISPR-Cas systems offer a promising approach for detecting bacterial drug resistance genes with high specificity, speed, and sensitivity. By utilizing Cas enzymes (eg, Cas12 and Cas13) and guide RNAs, CRISPR enables targeted recognition of resistance markers, typically requiring upstream nucleic acid amplification (eg, recombinase polymerase amplification or loop-mediated isothermal amplification) to achieve clinically relevant sensitivity. Platforms such as SHERLOCK and DETECTR facilitate rapid identification of markers associated with pathogens like MRSA and CRE directly from clinical samples, supporting point-of-care use. Integration with microfluidics and AI further expands its potential for personalized therapy and AMR surveillance. Despite ethical and regulatory challenges, CRISPR-Cas technology holds significant promise for advancing antimicrobial stewardship and public health responses to AMR.Keywords: CRISPR-Cas systems, antimicrobial resistance, molecular diagnostics, resistance gene markers, point-of-care testing