Medical Microbiology Residency Training Program.

Residency program overview

Program curriculum


This year consists of 16 weeks of Medicine/Medical Specialties, 4 weeks of Surgery, 4 weeks of Pediatrics, 4 weeks of Emergency Medicine, 4 weeks of Obstetrics & Gynecology, 4 weeks of Family Medicine, 4 weeks of Psychiatry, and 4 weeks of Microbiology.

a group of students posing for a picture

PGY-2 to 4

Medical microbiology is a five year program with the first year structured for successful completion of MCCQE Part II. The second year is the first year of Microbiology laboratory training, and is combined with 6 months of Infectious Disease training. Microbiology in the Champlain LHIN is now consolidated at the General Campus of The Ottawa Hospital (TOH). Virology remains at the Children’s Hospital of Eastern Ontario, and rotations occur in PGY 3 & 4 years. The Microbiology laboratory at TOH has the Kiestra installed and the lab is ion the process of completing the implementations of this instrument and how it will impact clinical care as it relates to Infectious Diseases. The Kiestra in itself has created numerous opportunities for applied research activities and resident education.
In the PGY 3 year the plan is complete the resident’s bench training and this will include Mycobacteriology, Mycology, Molecular diagnostics and Virology. The resident will then start the transition from the bench worker to bench resource, and then take on call responsibilities. The resident will also do 6 months of Infectious Diseases as well. Once the resident has demonstrated a competence and level of comfort related to lab work, there will be an opportunity to be involved in a continuity clinic, which will allow the resident to have a better understanding of the progression of disease, or better yet the response to therapy. Involvement in laboratory committees will also start during this time.
The PGY 4 year the resident will comprise more of what was happening in the PGY 3 year, but the resident is encouraged to examine other laboratories during elective periods. More time in Infectious Diseases is included with rotation at the Children’s Hospital of Eastern Ontario. Call will continue with continuous exposure to committees and opportunities to visit community hospitals that are associated with the consolidated Microbiology lab. Lab management issues is included during this time and extends into the final year.


The PGY 5 year is a time to refine and consolidate knowledge and prepare for exams in the spring. The trainee will be transitioning to a junior attending. Flexibility is built into the program to support further areas of training and specialization.


The research interests of members of the Division of Microbiology and the Division of Infectious Diseases are diverse and include: molecular diagnostics, laboratory detection and molecular epidemiology of antimicrobial resistant bacteria, epidemiology of hospital-acquired infections, viral pathogenesis and vaccine development, hepatitis, basic and clinical aspects of HIV/AIDS, tropical diseases, etc. Residents are strongly encouraged to participate in research activities and to present and publish their results. Support is available for residents to attend meetings and present their research.

Research within Medical Microbiology will also examine the application of new technologies and it impact on clinical care. The laboratory has recently had the Kiestra Total Laboratory Automation installed and this will provide great experience for all trainees.

a researcher looking in a microscope


Eastern Ontario Regional Laboratory (at the Ottawa Hospital - General Campus)

  • General bacteriology
  • Kiestra TLA
  • Mycobacteriology
  • Molecular diagnostics
  • Clostridium difficile testing
  • Mycology

Regional Virology Laboratory

  • Molecular virology
  • Rapid diagnostics
  • Viral culture

The EORLA laboratory at The Ottawa Hospital (TOH) is a modern laboratory, 24/7 operation and the main reference laboratory for Eastern Ontario. It was opened in 2006. The laboratory provides diagnostic microbiology services for the General and Civic Campuses which have approximately 1000 inpatient beds, and extensive outpatient clinics. Transplant services at The Ottawa Hospital include allogeneic and autologous bone marrow and renal transplants. The University of Ottawa Heart Institute is also served by this laboratory and it performs heart transplants and also uses the artificial heart and left ventricular device as a bridge to transplantation. Outpatient clinics of particular microbiologic interest at TOH include the Tuberculosis, Cystic Fibrosis, Travel & Tropical Medicine, HIV, Hepatitis and Non Tuberculous Mycobacterial Clinics. The Civic Campus has an active outpatient antibiotic therapy clinic. The General Campus provides high risk pregnancy care to the region, which includes eastern Ontario and western Quebec. The General Campus has a 24 bed level 3 Neonatal Intensive Care Unit, while the Civic Campus has a 19 bed Special Care Nursery.

The clinical spectrum of disease seen at TOH is diverse and the diagnostic requirements are extensive. The TOH EORLA laboratory has a rich array of resources that includes the standard CL2 laboratory space for work up of all specimen types for bacteria and fungi as well as a Containment Level 3 laboratory for mycobacterial culture and identification. The new Bactec blood culture system has been installed and provides the rapid detection of bacterial pathogens, and along with the Bruker MALDI-TOF, or mass spectrometer, for rapid identification of bacterial and mycobacterial pathogens. Nucleic acid amplification tests may be done on conventional and real time instruments that are used as part of organ donor screening and detection of resistance genes which facilitates tailored antimicrobial therapy.  Most importantly, the lab staff is are committed to providing quality microbiologic services to the patients served by the laboratory, are also the most important resource for teaching of the Medical Microbiology and other trainees.

The TOH EORLA laboratory also provides diagnostic services to Ottawa Hospital Cancer Program, the Rehabilitation Centre and 16 community hospitals within the Champlain LHIN, which includes the CHEO, Montfort and Queensway Carleton Hospitals.
Residents rotating at TOH EORLA have access to a teaching microscope that is connected to a digital camera that can be used to create images for teaching and study, and also for plate round presentations as it is linked to a LED monitor.

The future plans for the EORLA laboratories are bright with the implementation of the Beckton-Dickinson Kiestra instrument for total laboratory automation at the EORLA TOH site, which will include smart incubators, digital imaging with stored images that are archived.. The Regional Virology Laboratory at CHEO provides regional diagnostic services for CHEO and the TOH. The RVL provides diagnostic services using molecular diagnostics and limited culture backup. The RVL provides diagnostic and therapeutic services that include HCV, HBV, CMV & HIV viral loads.

Residents working within the laboratory have designated work space in the laboratory and also a study area that includes individual computers with internet access and updated text books. Off-site access to electronic resources is possible both through the university and hospital.