Testing the Efficacy of PCR for DNA Fingerprinting Avian Isolates of E. coli from Trout Lake using the rpoS Gene

The DNA fingerprinting technique using the rpoS gene product was investigated. DNA fingerprints for various samples of E. coli isolated from gull, duck and unknown sources were generated by creating customized primers for two distinct but adjoining regions within the rpoS gene to study the quantitative presence of the gene within different hosts by PCR. Optimization needed to be done at numerous steps of the PCR protocol, involving variables such as dNTP concentration, dilutions, duration of steps and annealing temperatures, as well as other procedural details such as centrifugation and agarose content in gels. Though the results improved progressively after incorporating various changes in protocol, a lot more optimization needs to be done before results can be studied quantitatively to differentiate between gene expression in various host-specific strains.