LMP1208H: Molecular clinical microbiology and infectious diseases

Who can attend

You must be registered in our graduate program (PhD or MSc) to attend this course.

Non-LMP students enrolled in similar programs must seek approval from the module coordinator to register for the course.

You should be familiar with concepts pertaining to basic microbiology and molecular biology principles and techniques for understanding various contemporary areas of research in clinical microbiology and their applications.

Course description

This course provides an introduction to medical bacteriology, virology, mycology, and parasitology, including its crucial role in public health practice.

It consists of lectures from specialists in each topic, and discussions on selected papers.

The goal is to provide students with the scientific basis for how new laboratory techniques help us understand 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.
  • To understand how genomics and proteomics have been applied to the diagnosis, control, and management of infectious diseases.
  • To 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.
  • To 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. Vanessa Tran

Dr. Tom Braukmann

Dr. Venkata Duvvuri

lmp.grad@utoronto.ca for administrative queries.

Timings and location

This course is offered every year in the Winter term.

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

Location: Public Health Ontario

Evaluation methods

Please note: For all submitted assignments, the expectation is that this is 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.

Research proposal (40% of the final mark)

You will write an original five-page proposal single-spaced (excluding front page, references, tables, and figures; Times New Roman size 12 has to be used) 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.

You will use high-quality up-to-date references to develop the content of the report.

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 scientific papers (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.

Take-home written assignment (20% of the final mark)

A take-home written assignment will be given on a topic related to the course material. The assignment will be due two weeks after it is assigned.

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


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.



January 12, 2022

9:30 am: Introduction

January 19, 2022

9:30 am: Genomics and bioinformatics in public health microbiology

  • Dr. Justin Schonfeld

11 am: Use of Microbial Genomics in Public Health 

January 26, 2022

9:30 am: New generation sequencing strategies applied to pathogen discovery

11 am: Genomics applied to the study of bacterial epidemics

February 2, 2022

9:30 am: Molecular testing in routine clinical microbiology laboratories: an epidemiologist’s perspective

11 am: The pulmonary microbiota and human health

February 9, 2022

9:30 am: Responding to emerging infectious diseases on a public health level

11 am: Challenges associated with real-time PCR testing for SARS-CoV-2

February 16, 2022

9:30 am: The pulmonary microbiota and human health

  • Dr. Rupert Kaul

11 am: Abstract presentations

  • Students

February 23, 2022

9:30 am: Hepatitis

11 am: COVID-19 serology

March 2, 2022

9:30 am: Molecular Methods In a Hospital Microbiology Laboratory

11 am: TBD

  • Dr. Melissa Richard- Greenblatt

March 9, 2022

9:30 am: Molecular approaches to medical parasitology

  • Dr. Antoine Corbeil

11 am: Molecular and proteomic applications in clinical mycology

March 16, 2022

9:30 am: Discovery of new antimicrobial agents

  • Dr. Gerry Wright

11 am: Molecular dissemination of antibiotic resistance

March 23, 2022

9:30 am: Using sero-epidemiology to measure population immunity to infectious diseases

11 am: Understanding vaccine effectiveness using lab data: focus on influenza

  • Dr. Sarah Buchan

March 30, 2022

9:30 am: Molecular microbiology and vaccine development

  • Dr. Scott Gray-Owen

11 am: Vaccine development and formulation: an industrial perspective 

  • Dr. Fernando Ausar