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.

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 learn the common microorganisms associated with specific clinical diseases.
  • 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 new generation sequencing and high-resolution proteomics and how they can impact our understanding and control of important infectious diseases.

Course coordinators

Dr. Nahuel Fittipaldi

Dr. Vanessa Tran

Dr. Melissa Greenblatt


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: TBA

Evaluation methods

Take-home research proposal (40% of the final mark)

You will be assigned a topic selected by the instructor in the first week of the course.

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 comprehensive rationale literature review that serves as a background in identifying major gaps in knowledge on the specific topic under study.
  • based on that, you will propose a hypothesis
  • followed by the aims of the study and innovative research strategies and experimental approaches that can be designed and carried out to fill the proposed aims.

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

You will present an abstract to the class (oral and written, 300 words) on week 6 and submit the final report as a PDF email attachment on week 11 (March 23, 2022 by 5:00 pm) to the coordinators. Late submission will be penalized 2 marks out of 40 per day late. Submissions exceeding 5 pages will be penalized at 5 marks out of 40 per each extra page started.

Presentation of scientific papers (30% of the final mark)

You will receive the paper one week in advance and are expected to start with a background to the field, describe the methods used, and carefully analyze data (from specific experiments to overall meaning of findings/major advances).

Whenever possible, you should identify limitations, suggest additional required experiments, and highlight/propose future directions.

You are also expected to prepare high-quality PowerPoint slides (no for critiques) to ensure effective communication of material to faculty and peers and you will be evaluated on the quality of the presentation. 

Written critiques of scientific papers discussed in lectures (20% of the final mark)

Same considerations as the presentations. They have to be presented in a maximum three-page report.

Participation (10% of the mark)

You will be evaluated on your involvement in the general discussion and punctuality.


A lecture takes place at 9:30 am and at 11:00 am in each session.



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