Bad hygiene or bad bug???

A case-based bioinformatics exercise for biology/microbiology

students

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???

Potential audiences:

Biology course: 1st year non-majors and above

Microbiology: allied health, general microbiology, etc.

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

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?

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

DeletionMutation?

Alignment of tcdC negative regulator genes

Quebec

U.K.

Italy

tcdC negative regulator genes

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

Case It! simulation of PCR analysis

PFGE analysis of C. difficile strains

PFGE and Southern blot of C. perfringens

Case It! simultation of PFGE analysis and Southern blot

Case It! simultation of PFGE analysis

Case It! simultation of PFGE analysis

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

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