Microbial source tracking by molecular fingerprinting

To date, microbial source tracking (MST), i.e. determining the source of microbial contamination based on the specific strains observed in environment, is done using methods that are time-consuming, expensive and not always reliable. The biology department at Cal Poly, San Luis Obispo has developed a new method for MST called pyroprinting. Pyroprints are a result of pyrosequencing replicates of intergenic transcribed spacer (ITS) regions in a target bacterial genome. E. coli pyroprints can be used as DNA fngerprints of individual E. coli strains in identifying sources of fecal contamination and studying bacterial patterns in host animals. The MST method consists of two parts: the pyroprinting process and a database of sequenced pyroprints. The actual source tracking is achieved by comparing a newly obtained pyroprint to the pyroprints of known provenance from a database. In this paper, we describe the design and implementation of Cal Poly Library of Pyroprints (CPLOP). The CPLOP database provides storage and essential analysis of pyroprints for strain identification. Our current implementation contains pyroprints of bacterial isolates of E. coli , obtained by students and researchers from known hosts and from the environment. Users of CPLOP are able to organize pyroprints into groups, run analyses to find similarities between bacterial isolates, and cluster isolates into bacterial strains.