A Look Inside the Public Health Microbiology Lab

One crucial aspect of Newfoundland and Labrador’s response to, and management of, the COVID-19 epidemic is continued testing. To date, over 20,000 people in this province have been tested for SARS-CoV-2, the virus that causes COVID-19. And although swabbing patients at testing centres is becoming a routine practice, there’s much work that happens between the swab and the lab result.

With that in mind, we caught up with Public Health Informatician Laura Gilbert and Hedy Dalton-Kenny, regional manager of Eastern Health’s Public Health Microbiology Lab (PHML), at the Dr. L.A. Miller Centre in St. John’s, to learn more about the COVID-19 testing process and the other important work completed by the PHML.

Public Health Microbiology staff (l-r): Sandy Hookey, medical laboratory technologist – Molecular; Robert Needle, research scientist; Jason Meeboer, medical laboratory technologist – lab; Caitlin Gosse, medical laboratory technologist; Maddison Decker, medical laboratory technologist (student)- Bacteriology

What kind of work takes place at the PHML?
The PHML is an integral component of Newfoundland and Labrador’s clinical care services and public health system. Critically linked to all sectors of the public health infrastructure such as disease control and prevention, environmental health, epidemiology, emergency preparedness and response, the PHML provides early detection of health risks associated with infectious agents, compiles data in support of outbreak investigations and identifies causative agents of infections and diseases to aid in treatment and prevention. As providers of essential services and leadership in the development of programs and policies, the PHML offers the science and resources needed to promote and protect the health of our communities.

The mandate of the PHML is at both the clinical bacteriological level and the population health level – supporting, protecting and promoting the health and well-being of Newfoundlanders and Labradorians. The PHML responds to emerging threats from any community within our province to proactively monitor and coordinate outbreak support, and to generate critical surveillance data. The PHML also provides specialized testing services for diseases to ensure equitable access for all communities throughout the province to sophisticated laboratory technology.

PHML plays an important role in the surveillance, treatment, control and prevention of infections. The job of the clinical microbiology laboratory is to test specimens from patients for microorganisms that are, or may be, a cause of the illness and to provide information (when appropriate) about the in vitro activity of antimicrobial drugs against human pathogens identified. The microbiological processing of patient specimens is fundamental to the everyday diagnosis, treatment and management of patients with infectious diseases.

How many people work there?
Right now, 61 people work at the PHML. Our staff includes medical lab assistants (MLAs) and medical laboratory technologists (MLTs), clerical staff, storekeepers, the regional operations manager, the division chief and director, medical and clinical microbiologists, the research and development scientist, and a public health informatician.

What does an average day look like for the team?
Our days can be really varied. For medical lab assistants (MLAs) and medical laboratory technologists (MLTs), days involve processing specimens, setting up and running tests, completing quality control checks and processes and, of course, reporting results. Additionally, some staff may be involved in various development projects, writing policies and procedures and maintaining safety in our laboratory.

Our clerical team ensure data is entered efficiently and accurately, from ordering specimens to information control. They have a critical role to ensure information enters and leaves the PHML according to quality standards.

Storekeepers keep all of our supplies ready at hand, ready and prepared. Additionally, these professionals ensure that specimen collection devices and equipment are distributed to our stakeholders and partners.

Our microbiologists ensure accurate and timely communication and clinical perspectives to the health-care professionals in our province. They are also involved in development, validation of new methods and updating procedures to meet national and international best practices.

Other members of our leadership team are involved in day-to-day operations, planning and capacity building, outbreak investigation, and molecular epidemiology, to name just a few!

We are a very diverse team and each of our members is critical, valuable and instrumental to meet our goals and fulfill our role.

(L-r): Maria Hibbs, MLT – COVID-19 testing; Samantha Slaney, MLT- Water testing; Kristie Sullivan, MLT – Serology

How is the COVID-19 sample analysed – how does that process work?
Once the PHML receives specimens, all orders are checked for accuracy. For COVID-19 specimens, there is an extraction step that takes any potential SARS-CoV-2 (the virus that causes COVID-19) RNA and purifies it from the original swab specimen. This needs to be done extremely carefully to avoid contamination and ensure high quality specimens. The actual tests that get performed at the PHML are called molecular reverse transcription real time polymerase chain reactions (RT-qPCR). Ultimately, it measures the amount of specific RNA by amplifying any RNA present. Probes are used that produce a fluorescent signal when specimens are heated and cooled repeatedly. Once the process is complete, trained MLTs review the curves produced by the fluorescence and report the results. This is a highly sensitive method that is very good at picking up whatever RNA might be in the specimen. This is why some patients may test positive, repeatedly, for a long time.

Is PPE required for the analysis?
PPE is required, including use of biological safety cabinets (BSCs), breathing protection, rear closing gowns, and gloves, as well as standard laboratory safe handling processes. Every process in the lab is reviewed during development and an assessment is completed regarding safety procedures. We follow national and international biosafety recommendations and guidelines. This is instrumental given our licensing under the federal Human Pathogens and Toxins Act.

The process is quite safe when handling procedures and PPE are worn. Laboratory staff have a relatively contained specimen with containment equipment.

Additionally, federal and internal recommendations provide minimal levels of recommendations which are built on the individual institutions. At the PHML we have erred on the side of caution and are also involved in national discussions and working groups on the topic so we are always able to see what our peers are doing across the country and adjust as more is learned about this emergent virus.

How has the COVID-19 pandemic affected your work?
While certain areas of our lab were always 24/7 operations, given the urgency and need for test results during the COVID-19 global pandemic, this model has been extended to most other areas. This, combined with social distancing and, initially, maintaining a pod system, has led to a decrease in the number of staff while demand and expectations have only increased. It has been a challenging time, but our staff and colleagues have handled it with complete professionalism and grace.

What’s the most fulfilling part of your job?
The most fulfilling part of working at the Public Health Microbiology Laboratory is the ability to provide health-care providers with vital information needed for patient care and to assist in times of public health crisis; from outbreaks, to pandemics, to public health emergencies. These are times that are critical to the safety and well-being of the general population.

Although our roles may be less visible in normal circumstances, it is incredibly fulfilling to research, prepare and plan to meet the needs of the clinical teams and the Department of Health and Community Services. The results and data produced by the PHML are critical to policy makers and our government. They have a direct impact on the decisions being made. We are proud of our work and the role that we play in ensuring the health and well-being of Newfoundlanders and Labradorians.■

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