Cephid microfluidic technology
Primers amplify groups of organisms using conserved regions of gene sequences. Specific members of the group are detected using internal probes in unique regions
Our research objective is to develop PCR-based direct detection methods for pathogens in environmental samples using two human pathogens as model organisms: Salmonella enteritis in surface water and Mycobacterium avium in drinking water. Initial experiments will focus on detecting Escherichia coli in environmental samples, which is found in contaminated water at sufficiently high levels so that it may be detected by PCR techniques.
These organisms have been chosen as model organisms because their ubiquitous, yet parsimonious distribution in water. Salmonella enteritis is the most common pathogen within the Salmonella group and has been detected in surface water in the Milwaukee River Basin, which drains to Lake Michigan. Mycobacterium avium has only recently been recognized as a human pathogen for immunocompromised individuals; this organism is resistant to chlorine and has been detected in drinking water distribution systems in other studies (USEPA, unpublished data).
Through using model organisms that occur frequently in the environments under study, detection methods can be optimized and adapted for detection of other pathogenic agents through modifying the genetic target. Many genetic targets for pathogens have been characterized; the challenge is detection of these targets in complex water samples. This project will focus on three important aspects of testing:
Sample collection: integrated sampling; need highly sensitive methods due to parsimonious distribution of pathogens
Sample concentration: problems include attachment to particles, PCR inhibitors, high biomass from natural community of organisms
Sample preparation: microfluidic technology integrated with real-time PCR will allow for automation in the field