bad hygiene or bad bug??? a case-based bioinformatics exercise for biology/microbiology students
TRANSCRIPT
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Bad hygiene or bad bug???
A case-based bioinformatics exercise for biology/microbiology
students
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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???
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Potential audiences:
Biology course: 1st year non-majors and above
Microbiology: allied health, general microbiology, etc.
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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
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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?
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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
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DeletionMutation?
Alignment of tcdC negative regulator genes
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Quebec
U.K.
Italy
tcdC negative regulator genes
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Published PCR analysis of toxA and toxB genes from C. difficile
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Case It! simulation of PCR analysis
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PFGE analysis of C. difficile strains
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PFGE and Southern blot of C. perfringens
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Case It! simultation of PFGE analysis and Southern blot
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Case It! simultation of PFGE analysis
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Case It! simultation of PFGE analysis
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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
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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