Do You Have What It Takes to Be a Clinical Microbiologist?

Scientist who helped decode SARS-CoV-2 in Canada shares what it takes to be a clinical microbiologist during a pandemic

María Carla Rosales Gerpe, MSc, PhD

María Rosales Gerpe, MSc, PhD, is a freelance scientific writer with more than a decade of research experience in molecular biology and gene therapy. She's also a reporter for Metroland...

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Published:Jan 23, 2023
|Updated:Jan 31, 2023
|6 min read

For Robert Andrew Kozak, PhD, a clinical microbiologist at Sunnybrook Health Sciences Centre in Toronto, Canada, and an assistant professor at the University of Toronto, his first position as a clinical microbiologist landed him in the middle of a pandemic, where he was part of the team that isolated SARS-CoV-2 in Canada. Just before the pandemic, while conducting research at the National Microbiology Lab, he also found himself dealing with another dangerous pathogen: the Ebola virus, during one of its biggest outbreaks. 

Today’s Clinical Lab sat down with Kozak to chat about why he likes to find himself in dangerous situations—just kidding. Kozak shared with us how and why he became a clinical microbiologist.

“I've scared my niece and nephew by telling them that, ‘yeah, uncle Rob went all the way to grade 27,’” says Kozak about his lengthy career path. Kozak spent six years pursuing doctoral studies and another nine as a postdoctoral researcher and clinical microbiology residency fellow. “It was a bit of a long haul,” he laughs. “I tell my trainees that I got my first real job at age 37.” His real job’s first task—isolating SARS-CoV-2, the virus responsible for the COVID-19 pandemic—required just that: extensive and diverse training.

A long yet enjoyable road: Experience is an asset to clinical research

However long the road, Kozak says those years of experience paid off during the COVID-19 pandemic. Having experience with many different pathogens was critical to studying emerging pathogens such as SARS-CoV-2. “From bacteriology to virology,” he says, “I’ve worked on hep C, influenza, Ebola, and other zoonotic diseases.” And he has found that such knowledge is often transferrable between pathogens and essential for developing diagnostics, and even therapeutics, in times of need.

"Knowledge is often transferrable between pathogens and essential for developing diagnostics, and even therapeutics, in times of need."

In his current work as a clinical microbiologist and researcher, Kozak focuses on emerging and reemerging pathogens, with a particular interest in viruses. Recently, this has involved researching the transmission of viral hemorrhagic fevers during the West African Ebola outbreak in 2016. He has also worked on Zika virus, Bundibugyo ebolavirus, Crimean-Congo hemorrhagic fever, and hantaviruses during his postdoctoral work at the Public Health Agency of Canada’s Special Pathogens Program at the National Microbiology Lab in Winnipeg.

As Kozak began working as a clinical microbiologist at Sunnybrook in May 2019, having studied the link between viral load in Ebola virus disease and patient outcomes during the West African outbreak proved to be essential training for working with SARS-CoV-2 as the pandemic unfolded in real time.

Baptism by fire: Working as a clinical microbiologist during a pandemic 

As the COVID-19 pandemic evolved in early 2020 in Canada, Kozak began collaborating with many scientists to better understand the disease. In March 2020, he was part of the team that isolated the SARS-CoV-2 virus in Canada. Isolating the Canadian strain of the virus was key for Canadian scientists developing vaccines, therapeutics, and diagnostics for COVID-19. Kozak used these viral samples to further probe the virus’s pathogenesis, conduct pre-clinical testing with collaborators at the University of Toronto, pursue vaccine research alongside other collaborators at the Universities of Guelph and Laval, as well as assess point-of-care testing using the isolated virus as a positive control. 

"The team also relied on informal networks within the microbiology and infectious disease community that were working toward similar goals."

The team isolating SARS-CoV-2 was led by Samira Mubareka, MD, PhD, a Sunnybrook and University of Toronto clinician-researcher, and included collaborators from McMaster University: Karen Mossman, PhD, a professor of pathology and molecular medicine, and Arinjay Banerjee, PhD, a scientist at the Vaccine and Infectious Disease Organization in Canada who was a postdoc in Mossman’s lab at the time.

“I don’t think any of us imagined the scope and scale that this disease would have,” says Kozak about COVID-19. He still finds it surreal that he started working as a clinical microbiologist at such a pivotal time. The work was very fast paced, and we had to learn many things on the fly, he says. “But I reminded myself that people working in the ICU and emergency were dealing with more stressful things than I was. I also had a really good team.” Kozak says the team also relied on informal networks within the microbiology and infectious disease community that were working toward similar goals.

This rapid nationwide collaboration proved fruitful—Canada outperformed other G10 countries with its response to COVID-19, reporting fewer infections and deaths.

A day in the life: Clinical microbiology in a hospital setting

As the COVID-19 pandemic continues, “a big challenge of the job [remains] encountering so many emerging and/or reemerging pathogens,” says Kozak. “A few months ago, there was a report of acute flaccid paralysis due to vaccine-derived polio in the US. So all of a sudden, that's on our radar.” Having to adapt and pivot his work is “both a challenge and a reward of the job,” he says. 

“The technologists are the most valuable people in the clinical lab. They are the ones who may conduct 10,000 Gram stains over their career, so I fully trust their judgment.” 

According to Kozak, the microbiology lab is not just a place where tests are analyzed, but is also the site where researchers and clinicians meet to interrogate diseases for the benefit of patients. As a clinical microbiologist at Sunnybrook, Kozak is involved in the day-to-day operations, including managing lab staff to whom he says he feels indebted: “The technologists are the most valuable people in the clinical lab. They are the ones who may conduct 10,000 Gram stains over their career, so I fully trust their judgment.” 

Aside from interpreting test results, consulting with clinicians is a daily conversation involving many disciplines and departments at the hospital. Kozak is often called in to discuss recommendations for testing so clinicians can pinpoint the cause of a disease and select an appropriate treatment. In essence, Kozak’s job is to be a trusted resource for clinicians, so they can make the right call for their patients. 

Because he works at an academic teaching hospital, he must also ensure that medical students and incoming clinical microbiology fellows are trained and ready for the current and future clinical landscape. Finally, he conducts ongoing research to ensure his lab remains up-to-date with the latest advances to save time and reduce costs, which ultimately benefits the public.

Looking ahead: The future of clinical microbiology

Kozak notes that his lab currently relies on considerable automation, something that the pandemic expedited. “If a robot can do it, then that frees up a technologist to work on something else,” he says. “We have also implemented whole genome sequencing at a clinical level, which we didn't see as much of pre-pandemic.” 

His lab has also started evaluating the use of artificial intelligence (AI) for curbing antimicrobial resistance, which remains the main public health priority worldwide. The test uses chromogenic agar, which can be used to visualize bacteria through a color change. AI algorithms are then trained to associate different colors to types of bacteria and even their antimicrobial resistance, so it can later identify bacterial species and whether or not they are resistant to a specific antibiotic. 

Using this AI-based test in the lab could drastically decrease unnecessary prescriptions of antibiotics and allow clinicians to administer more efficient treatments. “We're definitely going to keep using AI, so we can integrate lots of data like a patient’s biochemistry,” says Kozak.

"Because of the recent shortage of postdoctoral fellows and the great resignation, he says it’s ever more pressing to ensure that trainees understand the full value of research."

The future of clinical laboratory graduates

Kozak attributes his dedication to his work as a clinical microbiologist to the mentors he had throughout his education. Because of the recent shortage of postdoctoral fellows and the great resignation, he says it’s ever more pressing to ensure that trainees understand the full value of research. “Many people who go through grad school miss out on the fact that PhD training can prepare you for so many things,” he says. “One of the many reasons I like clinical microbiology is because, although you're able to do research, and in many instances, it's encouraged, the main job is to provide diagnostic services for patients.” 

To ensure a bright future in clinical microbiology for his trainees, Kozak highlights the many training and career options available to them and works on fostering their career interests. “Trainees come to graduate school to do research and experiments,” he says, “but that training should also prepare them for the next step of their careers.” Being empowered by his mentors to tackle the different projects that sparked his curiosity as a trainee led Kozak to becoming a clinical microbiologist. He hopes he can do the same to encourage his trainees to embrace their individual career paths too.

CLINICAL MICROBIOLOGY TRAINING SNAPSHOT

YEAR

TRAINING

FOCUS

2004PhD in microbiology and immunology at McGill UniversityThe role of RD2 and NOD2 in host-pathogen interactions of the BCG vaccine
2010First post-doctoral position at McGill University, National Hepatitis C Research Training ProgramInvestigating replication and drug resistance of hepatitis C virus
2012Second post-doctoral position at the University of Guelph, Department of Pathobiology at the Ontario Veterinary CollegeVaccine development for avian influenza (H5N1) via adenovirus, and oncolytic virus research leveraging fowl adenoviruses including Newcastle disease virus
2015Third post-doctoral position at Public Health Agency of Canada, Special Pathogens Program at the National Microbiology LaboratoryInvestigation into pathogenesis of emerging threats Ebola, Zika, and Bundibugyo viruses
2016Clinical Microbiology Fellowship at the University of TorontoInfection control, clinical case rounds, clinician consultations, microbiology training for clinical residents

CLINICAL MICROBIOLOGY WORK SNAPSHOT

YEAR

ROLE

2019–presentCLINICAL MICROBIOLOGIST at Sunnybrook Hospital and Health Sciences Center
  • Isolating and decoding of SARS-CoV-2; COVID-19 infection control
  • Emerging and re-emerging diseases infection control (e.g., polio)
  • Clinician consultations
  • Microbiology training for clinical residents
2020–presentASSISTANT PROFESSOR at University of Toronto
  • Research interests: Emerging zoonotic diseases and oncolytic viruses
Top Image:
In his current work as a clinical microbiologist and researcher, Kozak focuses on emerging and reemerging pathogens, with a particular interest in viruses.
Courtesy of Robert Andrew Kozak, PhD and Sunnybrook-Health-Sciences-Centre