University of Ottawa - Medical Microbiology - Ottawa


Program Director

Dr. Peter Jessamine


Program Administrator

Nadia Sant

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The Medical Microbiology training program at the University of Ottawa is done in collaboration with the Adult & Pediatric Infectious Disease training programs. Microbiology is now fully regionalized for 16 hospitals within eastern Ontario, with samples coming to the Regional Microbiology Reference Laboratory at The Ottawa Hospital (TOH), General Campus (aerobic and anaerobic Bacteriology, Mycology and Mycobacteria) and the Children’s Hospital of Eastern Ontario (CHEO) (Virology, COVID). A sophisticated molecular suite is present at both sites for advanced diagnostics, and we are frontrunners in total laboratory automation with the introduction in 2017 of the BD Kiestra platform. We provide full Mycology and Mycobacteriology work up, and have worked tirelessly to maintain a high degree of expertise in those subspecialties in order to supply optimal diagnostic microbiology services to the numerous specialty infectious disease clinics found at TOH. Further linkages with the Ottawa Health Department, Public Health Ontario Laboratories and the Public Health Agency of Canada make our training program desirable as it provides a complete diagnostic picture from the individual patient to the community.

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Medical Microbiology PGY-1

As per the Royal College requirements the first year is designed to give the trainee a broad base of clinical training to support an understanding of Medical Microbiology in the hospital and the community. The resident must do blocks of General Internal Medicine and General Pediatrics. The remaining blocks are selected to complete a broad exposure and therefore will include rotations in Family Medicine, Cardiology, General Surgery, Obstetrics, Emergency Medicine, Adult Infectious Disease, Intensive Care, Respirology, Oncology, and Hematology. The final block is in the Microbiology laboratory. This broad exposure will assist the trainee in the successful completion of their MCCQE Part II examination and provide a solid foundation for the additional years of training.

Medical Microbiology PGY-2 to 4

The second year is the first year of the core microbiology training, however ongoing clinical exposure is provided to maintain the trainee's understanding of the role of the Microbiology laboratory in clinical medicine. At the University of Ottawa, it is our belief that Infectious Diseases offers the best opportunity for a broad clinical exposure. Microbiology in Eastern Ontario has become regionalized to the General Campus of The Ottawa Hospital (TOH), where Bacteriology, Mycology and Mycobacteria are performed. This regionalization was made possible with the laboratory working 24/7, and the purchase of the BD Kiestra Total Laboratory Automation System. In addition, a broad range of molecular diagnostics related to bacterial drug resistance and pathogen identification is performed. Virology is regionalized to the Children’s Hospital of Eastern Ontario where molecular diagnostics has replaced viral culture. During their training, the trainee is expected to participate in a research project that is to be presented at the annual Pathology and Laboratory Medicine Research Day and at a National Conference (AMMI/CACMID). The Infectious Disease clinical training will also include clinics in general Infectious Diseases, HIV, travel and tropical medicine, TB, Non TB Mycobacteria, Hepatitis, transplant infectious diseases, and STDs. The STD rotations are done at the Regional Sexual Health Centre. The core microbiology training will provide 48 weeks of bacteriology, 12 weeks of virology, 8 weeks of mycology, 8 weeks of mycobacteriology, 4 weeks of parasitology, and 8 weeks of infection control / antimicrobial stewardship. It is expected that the trainee will acquire skills that permit progressive responsibility to be part of all their rotations.

Research blocks are built in to the rotation, and are designed to be flexible to support the opportunities that develop or emerge over the course of the training. Research projects may be linked to outbreaks and are therefore linked to Infection Prevention & Control or the Infectious Disease consult service. Rotations with the Ottawa Health Department are also done to demonstrate the linkage of Microbiology and Public Health.

The training program is designed to give the trainee a broad lab and clinical exposure so that they are capable of working in a community or tertiary care / academic health centre.

The faculty is a group of dedicated personnel with a strong commitment to the program so that the training of the individual is optimized.

Medical Microbiology PGY-5:

The final year of training is flexible and planned according to the needs and interests of the resident to provide further experience in microbiology and to provide the trainee with a greater level of responsibility. It may consist of a mixture of clinical, laboratory, or basic microbiology rotations. Electives may be taken at other centres in this year, and may also be taken in earlier years, provided the core requirements are met over the 5-year period. Elective time away from the home program site are limited in the final year. All electives are to be approved by the RPC.