Engineered bacteria detect tumor DNA

Advances in bacterial engineering have catalysed the development of living cell diagnostics and therapeutics, including microbes that respond to diseases such as gut inflammation, intestinal bleeding, pathogens and hypoxic tumors. Bacteria can easily access the entire gastrointestinal tract via oral administration, and they can produce outputs that can be noninvasively measured in stool or urine. Cellular memory, such as bistable switches or genomic rearrangement, has been used to allow bacteria to store information over time. However, living biosensors have not yet been engineered to detect specific DNA sequences or mutations from outside the cell. Here, we engineer naturally competent Acinetobacter baylyi to detect donor DNA from the genomes of colorectal cancer (CRC) cells and organoids. We characterize the functionality of the biosensors in vitro with co-culture assays and then validate in vivo with sensor bacteria delivered orally or rectally into mice injected with orthotopic donor CRC organoids. We observe horizontal gene transfer from the tumor to the sensor bacteria in vivo, allowing their detection in stool. The sensor bacteria achieved 100% discrimination between mice with and without CRC using both delivery methods. Our findings establish a framework for biosensing applications that require the detection of mutations or organisms within environments that are difficult to sample. In addition, the platform can be readily expanded to include in situ production and delivery of therapeutic payloads at the detection site.