Genetic sequences that are as reliable as fingerprints when it comes to identifying different strains of E. coli.
Professors and students in Cal Poly's Biological Sciences, Chemistry and Biochemistry, and Computer Science departments are working together with the university's Center for Applications in Biotechnology (CAB) (formerly the Environmental Biotechnology Institute/EBI) to develop a searchable, online library of E. coli "pyroprints" – genetic sequences that are as reliable as fingerprints when it comes to identifying different strains of E. coli. This common bacterium with hundreds of variations is found in the intestines of mammals and birds. Several of different E. coli strains can severely sicken humans. These pathogenic strains are usually spread by fecal contamination: bird, deer, and cattle droppings as well as human feces.
Cal Poly's developing E. coli database is named CPLOP. It's a punny name that stands for the Cal Poly Library of Pyroprints. Right now it contains 2,400 pyroprints from the DNA of unique E. coli strains collected, cultured and analyzed at Cal Poly; another 2,871 E. coli strains are isolated in the Biological Sciences department freezers, waiting to be cultured and categorized. Right now it holds digital pyroprints of 2,400 identified E. coli bacteria, and information about which host animal species they come from.
Pyroprinting & The Center for Applications in Biotechnology
Chris Kitts, the CAB's director, hopes to build the Cal Poly Library of Pyroprints into a lower-cost resource for the county, the region, the state and beyond. "There are plenty of places where people need to know 'Who's pooping in this water?'" Kitts said. Currently, one private lab in Seattle is the only facility in the Western United States that offers E. coli "fingerprint" matching to confirm the sources of contamination in recreational waters -- at $100 per strain, Kitts said. "If you need to fingerprint 1000 strains, which is not uncommon when you're investigating the source of water pollution, the bill is $100,000," Kitts said. "Our method will cost about a third of that."
More grant funding or private donations would help speed up the process of analyzing the E. coli samples currently in the department's freezer, and getting them into the CPLOP database. Grants and private funding would also enable the CAB to hire students to work during non-class time identifying and pyroprinting E. coli strains to enter into the library. Grants or donations could also be used to pay computer science students for non-class time needed to complete the digital matching function of the CPLOP database, Kitts said.
UC Davis (which is also looking for toxic E. coli strains throughout California) is collaborating with the CAB by sending wildlife fecal samples to Cal Poly to be documented, cultured, pyroprinted and added to the CPLOP library. The CAB is also working with Pacific Wildlife Care to get additional samples into the database. The Morro Bay non-profit group rescues and rehabilitates injured wild animals.
To find out more about the Cal Poly Laboratory of Pyroprints, contact Dr. Rafael Jimenez-Flores at firstname.lastname@example.org.