BIOL40241 - Microbiological Techniques for the Diagnosis of Bacterial Infections

Assignment Task

Assessment Requirements

After a series a Bioinformatics workshops (weeks 12-14), you should be able to identify unique genes that could be used as targets for a PCR based diagnostic test for strain of E. coli that cause urinary tract infections (known as UPEC: Uropathogenic E. coli ). You should download genome sequences for:

One uropathogenic (UPEC) strain of E. coli (strain CFT073).

Accession number: NC004431

One enterohaemorrhagic (EHEC) strain of E. coli (strain EDL933)

Accession number: NC002655

One commensal strain of E. coli (strain MG1655)

Accession number: NC000913

Using the same techniques as you used in the bioinformatics workshops in weeks 12-14 (Virulence finder, CARD and BLAST), find the genes that are unique to the UPEC strain. Assess their suitability to be used as a target for a PCR based diagnostic test, by testing their presence or absence by BLASTing a larger collection of strains (10 UPEC strains, 10 non-UPEC strains, the accession numbers of which will be provided for you), and after choosing a single best gene, design primers to ampligy this gene by means of primer3 and OligoAnalyzer

This assessment is a 2500-word (maximum) report on how bioinformatics analysis has led you to choose your locus for further investigation as targets for a PCR based diagnostic test for UPEC. The report should contain an introduction and discussion, as well as a temporal account of how you worked through the data to come to your final choice of loci. You can make use of screenshots but these should be informative and annotated and help the reader to replicate the methodology.

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