A CRISPR/Cas12a-Based System for Sensitive Detection of Antimicrobial-Resistant Genes in Carbapenem-Resistant <i>Enterobacterales</i>

oleh: Jiyong Shin, Sei Rim Kim, Zifan Xie, Yong-Su Jin, Yi-Cheng Wang

Format: Article
Diterbitkan: MDPI AG 2024-04-01

Deskripsi

Antimicrobial-resistant (AMR) bacteria pose a significant global health threat, and bacteria that produce New Delhi metallo-β-lactamase (NDM) are particularly concerning due to their resistance to most β-lactam antibiotics, including carbapenems. The emergence and spread of NDM-producing genes in food-producing animals highlight the need for a fast and accurate method for detecting AMR bacteria. We therefore propose a PCR-coupled CRISPR/Cas12a-based fluorescence assay that can detect NDM-producing genes (bla<sub>NDM</sub>) in bacteria. Thanks to its designed gRNA, this CRISPR/Cas12a system was able to simultaneously cleave PCR amplicons and ssDNA-FQ reporters, generating fluorescence signals. Our method was found to be highly specific when tested against other foodborne pathogens that do not carry bla<sub>NDM</sub> and also demonstrated an excellent capability to distinguish single-nucleotide polymorphism. In the case of bla<sub>NDM</sub>-<sub>1</sub> carrying <i>E. coli</i>, the assay performed exceptionally well, with a detection limit of 2.7 × 10<sup>0</sup> CFU/mL: 100 times better than conventional PCR with gel electrophoresis. Moreover, the developed assay detected AMR bacteria in food samples and exhibited enhanced performance compared to previously published real-time PCR assays. Thus, this novel PCR-coupled CRISPR/Cas12a-based fluorescence assay has considerable potential to improve current approaches to AMR gene detection and thereby contribute to mitigating the global threat of AMR.