Programmable CRISPR-Cas diagnostic platforms for rapid detection of uropathogens and antimicrobial resistance.

Urinary tract infections (UTIs) represent a global burden, impacting more than 150 million individuals annually, and are a major contributor to the antimicrobial resistance (AMR) crisis because of the rampant empirical use of antibiotics. Although microbial culture remains the gold standard of diagnosis, its long turnaround time (48–72 h) limits timely, actionable decision-making for effective antimicrobial stewardship. This review is a critical analysis of the development of CRISPR-Cas biosensing as a better analytical platform to detect uropathogens in a rapid and point-of-care (POC) format. The diagnostic mechanisms of Class II Cas effectors (Cas12, Cas13, and Cas14) are discussed in detail, including programmable collateral trans-cleavage activity that allows programmable attomolar sensitivity and single-nucleotide specificity in the identification of specific resistance markers. New engineering advancements that have brought these assays from the bench to the bedside are heavily emphasized, particularly the integration of isothermal pre-amplification techniques (LAMP/RPA) into streamlined one-pot systems that lower the risk of contamination. Additionally, the review assesses the advancement of instrument-free formats, e.g., lyophilized reagents, paper-based microfluidics, and smartphone-based colorimetric readouts that would be suitable in resource-constrained environments. Lastly, the manuscript discusses important analytical issues, including sample preparation in complicated urine samples and multiplexing. It concludes that next-generation CRISPR diagnostics, when satisfying the requirements of the World Health Organization in its category of REASSURED, can fill the gap between molecular accuracy and decentralized patient care, and this will provide a powerful answer to the global AMR threat.