LMP1208H: Molecular clinical microbiology and infectious diseases

Who can attend

Students must be registered in our Laboratory Medicine and Pathobiology (LMP) graduate program (PhD or MSc) to attend this course.

Or - non-LMP students enrolled in similar programs may attend but must have approval from the module coordinator to register for the course.

Students with an interest in public health microbiology and/or genomic epidemiology are encouraged to enroll in this course.

Students at any stage of their graduate studies are welcome.  

Course description

This course covers foundational topics in public health practice such as laboratory diagnostics, genomic epidemiology, antimicrobial resistance, and emerging modelling approaches. It consists of lectures from specialists in each topic.

The goal is to provide you with the scientific basis to understand how laboratory techniques and innovative applications help us elucidate the epidemiology of infectious diseases, their current impact on human medicine, and their role in the detection and characterization of etiologic agents causing diseases.

The major course objectives are to:

• review the microbiology of common pathogens and their current diagnostic methods.
• understand how genomics and proteomics have been applied to the diagnosis, infection control, and management of infectious diseases.
• provide knowledge of both practical and theoretical aspects of the specialist area of medical microbiology and the necessary skills to undertake individual and collaborative research in this field.
• be introduced to recently developed and constantly improving techniques such as next generation sequencing and emerging applications such as phylodynamics and machine learning, and how they can impact our understanding and control of important infectious diseases.

Course coordinators

Dr. Venkata Duvvuri

• venkata.duvvuri@oahpp.ca

Dr. Tom Braukmann

• tom.braukmann@oahpp.ca

lmp.grad@utoronto.ca for administrative queries.

Timings and location

This course is offered every year in the Winter term.

Course dates for 2025: January 8 – March 26

Wednesdays 9:30 am - 12:30 pm (two lectures per session)

Location: Public Health Ontario

661 University Ave, Boardroom 1923
Toronto ON, M5G 1M1

Sign in is required in Suite 1701

Evaluation methods

Research proposal (40% of the final mark)

You will write an original five-page proposal which includes:

• a literature review and rationale that serves as a background in identifying major gaps in knowledge on the specific topic under study
• a proposed hypothesis
• specific aims and experimental approaches to carry out the proposed aims
• incorporation of the principles of equity, diversity, and inclusion (EDI) in data acquisition, analysis and interpretation.

The final research proposal will be due by 5:00 pm on the day of the second last class to the coordinators

Oral presentation of a scientific paper (30% of the final mark)

Oral presentations will occur after each lecture.

The paper will be assigned one week in advance and it will be related to the topic of the lecture.

Oral presentations should include necessary background to contextualise the focus of the paper, a description of the methods used, a review of the data and major findings, and an overall critique of the paper (strength and limitations). Whenever possible, student should suggest additional experiments and highlight/propose future directions.

Oral presentations will be evaluated on the quality of slides and content and effective communication.  

Group written assignment (20% of the final mark)

The group written assignment will focus on designing a public health genomic surveillance program for a pathogen of interest using what you have learned in the course.

Groups should be established by the 4th week of class. The final assignment is due by the last day of class.

Participation (10% of the mark)

Participation will be evaluated based on the following:

• A short introductory description of your graduate research project to the group
• Meaningful participation in general discussion and critiques of papers
• Evaluation of oral presentations
• Attendance and punctuality
• Professional behaviour

We expect all submitted assignments to be original work produced by the student. The use of artificial intelligence (eg. ChatGPT) and reproduction of other written material, including their own work, is not acceptable. The course coordinators will use AI content detectors and plagiarism-checking software (eg. turnitin.com) if necessary.

Schedule

A lecture takes place at 9:30 am and at 11:00 am in each session. Please note the topics and lecturers may differ from the current course offering.