Chemiluminescent Probes Allow for the Rapid Identification of Colibactin-Producing Bacteria

The pks (or clb) gene cluster, which produces the genotoxic natural product colibactin, is encoded by human gut Enterobacteriaceae, including many commensal strains of E. coli. Colibactin cross-links DNA and is implicated in colorectal cancer development, highlighting the importance of identifying colibactin-producing gut bacteria within biological samples. In this study, we develop phenoxy-dioxetane chemiluminescent probes that selectively react with a critical colibactin biosynthetic enzyme, the serine peptidase ClbP. We show that these chemiluminescent probes have superior sensitivity, speed, and detection capabilities compared with previously reported fluorescent ClbP probes. Furthermore, we employ these chemiluminescent probes to detect pks ⁺ E. coli directly in complex stool suspensions. These probes will enable multiple applications requiring the detection of colibactin-producing bacteria, including the identification of ClbP inhibitors and the screening of clinical samples.