1. Bad hygiene or bad bug??? A case-based bioinformatics exercise for biology/microbiology students

3. In this activity students will: Investigate a current epidemiological case about an alarming outbreak of Clostridium difficile in Canada and U.S. Using web-based bioinformatics tools, students will explore the following questions: What makes C. difficile pathogenic? What might cause increased pathogenicity in C. difficile? How does C. difficile regulate genes involved in pathogenicity? Can a genetic mutation affect its pathogenic ability? What types of mutations would you predict? Can you test your predictions with information about DNA sequence???

4. Potential audiences: Biology course: 1 st year non-majors and above Microbiology: allied health, general microbiology, etc.

5. Problem space: Background information and websites about opportinists pathogens of GI tract, exotoxins, C. difficile. Tutorial information about operon model in bacterial chromosomes Sequences of C. difficile toxins A and B and regulator genes from patients involved in outbreak as well as control (historical) samples. (We will be including comprehensive sample set from MacDonald study identifying outbreak origins and toxin differences). Links to appropriate bioinformatics tools. CaseIt activities simulating researchers’ approach to studying the outbreak

6. Sample Investigative Activity: Identification of tcdC gene variant as putative reason for high pathogenicity Once students have identified tcdC gene mutation as a causative factor, they can compare sequences among patients. How similar are gene sequences among patients in Quebec, UK, and Europe?

7. Steps in bioinformatic analysis Obtain sequences –What sequences? Provide data set, or Student-driven GenBank search Upload into Workbench ClustalW alignment and tree Case It! activities interwoven

8. Deletion Mutation? Alignment of tcdC negative regulator genes

9. Quebec U.K. Italy tcdC negative regulator genes

10. Published PCR analysis of toxA and toxB genes from C. difficile

11. Case It! simulation of PCR analysis

12. PFGE analysis of C. difficile strains

13. PFGE and Southern blot of C. perfringens

14. Case It! simultation of PFGE analysis and Southern blot

15. Case It! simultation of PFGE analysis

17. Summary Student engaged in investigation of a current medical issue Motivation to use a variety of bioinformatics tools Adaptable for different types of courses/student populations Integration with labs or lab simulation

18. References: Eggerston, Laura. 2006. Quebec strain of C. difficile in 7 provinces. CMAJ 174 (5). doi:10.1503/cmaj.060105. Pechine S, Janoir C, Collignon A. 2005. Quebec strain of C. difficile in 7 provinces. J Clin Microbiol. 2005 Oct;43(10):5018-25. Rupnik et. Al. 2005. Revised nomenclature of Clostridium difficile toxins and associated genes. J Med Microbiol 54 (2005), 113-117. Loo et. al., A Predominantly Clonal Multi-Institutional Outbreak of Clostridium difficile–Associated Diarrhea with High Morbidity and Mortality. Volume 353:2442- 2449, Number 23 Cohen, et. al. 2000. Analysis of the Pathogenicity Locus in Clostridium difficile Strains. The Journal of Infectious Diseases, volume 181 (2000), pages 659– 663