National Microbiology Laboratory

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The National Microbiology Laboratory (NML) is a division of the Public Health Agency of Canada, the agency of the Government of Canada that is responsible for public health, health emergency preparedness and response, and infectious and chronic disease control and prevention. NML is primarily located in the Canadian Science Centre for Human and Animal Health (CSCHAH) in Winnipeg, Manitoba, also home to the Canadian Food Inspection Agency’s National Centre for Foreign Animal Disease. This modern state-of-the-art infectious disease laboratory facility houses the only Containment Level 4 (also known as Biosafety Level 4) operational laboratories in Canada. With maximum containment, scientists are able to work safely with pathogens ranging from the most common to the most serious including Ebola, Marburg and Lassa fever.

The NML aims to advance human health through laboratory leadership, scientific excellence, and public health innovation, through the identification, investigation, control and prevention of infectious disease.

NML’s role involves five main activities. On a day-to-day basis, NML staff are confirming provincial diagnostic results and sub-typing samples to monitor for resistance and determine the specific strains that are circulating. They are studying how pathogens infect cells and developing vaccines against the world’s most problematic viruses. They are leading national and international laboratory networks that enhance the standardization and quality of testing, augment training, and provide connections that can be relied on during outbreaks. All of this day-to-day work is interspersed with larger outbreaks such as SARS, H1N1 and listeriosis for which NML must maintain a constant state of readiness in order to respond to emerging threats. These examples of reference services, surveillance, research, leadership and emergency response demonstrate the five core activities through which NML accomplishes its mission. The first four activities are always ongoing and are essential for ensuring the technical capacity and scientific knowledge base required to effectively respond to emergency situations and emerging issues.


The National Microbiology Laboratory was preceded by the Bureau of Microbiology which was originally part of the Laboratory Centre for Disease Control of Health Canada in Ottawa. In the 1980s, Health Canada identified both the need to replace existing laboratory space that was reaching the end of its lifespan and the need for Containment Level 4 space in the country. Around the same time, Agriculture Canada (prior to the Canadian Food Inspection Agency being formed) also identified the need for new laboratory space including high-containment. Numerous benefits were identified for housing both laboratories in one building and Winnipeg was chosen as the site; an announcement was made in October 1987.

After some debate, the spot chosen for the site was a city works yard near to the Health Sciences Centre (a major teaching hospital), the University of Manitoba’s medical school, and other life science organizations. Construction of the facility that came to be named the Canadian Science Centre for Human and Animal Health (often referred to locally as “the Virology Lab”) began with an official groundbreaking in December 1992. The joint venture design team of Toronto-based Dunlop Architects and Winnipeg-based Smith Carter Architects and Engineers Inc. visited 30 laboratories to seek best practices in containment and design. Construction finished toward the end of 1997 with the first programs beginning in the spring of 1998 and all laboratories coming on line after that. The official opening took place in 1999.[1]

Following the SARS outbreak in 2003, the Public Health Agency of Canada (PHAC) was formed in 2004 [2] to provide a stronger focus on public health and emergency preparedness in the country. It is a member of the federal Health Portfolio (along with Health Canada, the Canadian Institute of Health Research, and other organizations). NML is part of the Infectious Disease Prevention and Control branch of PHAC.


Human pathogens are classified into risk groups.[3] The criteria to determine the group includes the level of risk to the health of a person or to public health, as well as the likelihood that the human pathogen will actually cause disease in a human, and whether treatment and preventative measures are available. It can depend on the type of work being done as to which level of containment is needed for pathogens from specific risk groups; as an example, culturing (or growing) a virus or bacterium requires higher containment than some diagnostic tests.

NML operates Containment Level 2, 3 and 4 laboratories. In human health infectious disease laboratories, the design and construction of the facility, the engineering controls, and the training and techniques of staff are all focused on protecting lab workers, containing the pathogens, and preventing contamination of materials to ensure accurate diagnosis and research. All of these factors vary depending on the level of containment.

The vast majority (87.7%) of NML’s lab space is Containment Level 2 (CL2). This is the same type of laboratory found in doctor’s offices, hospitals and universities. In a Level 2 lab, work with infectious materials is done inside a biosafety cabinet (BSC) and appropriate personal protective gear is worn relative to activities (gloves, eye protection, lab coats, gowns, etc.). Risk Group 2 pathogens worked with in Level 2 can cause disease but are not a serious hazard and they are often circulating in the community. Environmental contamination must be minimized by the use of hand washing sinks and decontamination facilities such as autoclaves. Examples include E-coli; whooping cough; and seasonal influenza.

NML also has Containment Level 3 (CL3) laboratories (8.6% of lab space). Risk Group 3 pathogens may be transmitted by the airborne route, often need only a low infectious dose to produce effects, and can cause serious or life-threatening disease. CL3 emphasizes additional primary and secondary barriers to minimize the release of infectious organisms into the immediate laboratory and the environment. Additional features to prevent transmission of CL3 organisms are appropriate respiratory protection, HEPA filtration of exhausted laboratory air and strictly controlled laboratory access. Examples include tuberculosis; West Nile virus; and pandemic H1N1 influenza.

A small percentage of laboratory space (3.6%) is devoted to Containment Level 4 (CL4) at NML. These agents have the potential for aerosol transmission, often have a low infectious dose and produce very serious and often fatal disease; there is no licensed treatment or vaccine available. This level of containment represents an isolated unit independent of other areas. CL4 emphasizes maximum containment of the infectious agent by completely sealing the facility perimeter with confirmation by negative pressure testing; isolation of the researcher from the pathogen by an enclosed positive pressure suit; and decontamination of air and all other materials. Examples include Ebola; Nipah; Marburg; and 1918 pandemic influenza.


NML programs are housed in two facilities in proximity to each other in Winnipeg: The Canadian Science Centre for Human and Animal Health on Arlington Street and the J.C. Wilt Infectious Diseases Research Centre on Logan Avenue.

NML is divided into four main laboratory divisions which are supported by scientific and administrative services. The primary NML divisions are:

Bacteriology and Enterics - focussing on bacterial diseases, such as tuberculosis and meningitis, along with food and water-borne pathogens including E. coli and Salmonella, antibiotic resistant organisms and infections affecting the human nervous system.

Viral Diseases - addressing a range of viral diseases, including hepatitis and other blood-borne pathogens, respiratory viruses and viral exanthemata, such as measles.

Zoonotic Diseases and Special Pathogens - dealing with viral, bacterial and rickettsial zoonoses (diseases transmitted to humans from other species), such as West Nile Virus and Lyme disease, along with risk group 4 agents such as Ebola, Marburg and Lassa fever viruses.

HIV and Retrovirology - providing a comprehensive range of laboratory services and scientific expertise relating to HIV and emerging retroviruses.

The Science Technology Core and Services Division works closely with these divisions to provide cutting-edge technological approaches, including genomics, proteomics and bioinformatics.

These science-based divisions are complemented and supported by numerous other programs and services such as Business Operations, Scientific Informatics Services, NML Program Support and Services, Intellectual Property Management and Business Development, Surveillance and References Services, and the Real Property, Safety and Security team who ensure safe, secure and suitable facilities for the scientific work to take place in. Outside of the two main facilities, NML also funds the National Reference Centre for Parasitology in Montreal and has a Laboratory Liaison Technical Officer in each provincial lab.


NML employs a wide range of professionals, some of the best in their respective fields. This includes scientists (MD, PhD, and DVM), biologists, and laboratory technicians, of course, but it also includes informatics specialists, biosafety experts, specialized operations and maintenance staff, and administrative staff, among others. In total, there were approximately 450 staff members as of 2012.


NML is renowned for its work on a broad spectrum of infectious diseases from seasonal influenza to Ebola and its accomplishments are too many to detail.

Some recent examples of the caliber of work by NML include the response to the 2009 H1N1 influenza pandemic. In April 2009, the Mexican national lab approached NML for assistance with identifying a respiratory virus that was causing outbreaks in Mexico. NML was able to quickly identify the new virus and recognize that it matched the virus that was beginning to circulate in the U.S. As the lead laboratory in Canada, NML rapidly developed diagnostic tests and equipped provincial labs to be able to test for the new virus. NML also assisted Mexico by providing additional testing and sent staff to their lab to help them set up their own testing protocols.

In the international laboratory sector, NML is well regarded for its unique mobile laboratory capacity. NML has developed three types of mobile labs: a CL3 lab-truck, CL2 lab-trailer and a “lab in a suitcase”. The lab-truck is generally used for in-country deployments at high-profile events such as the 2010 Olympics, the lab-trailer is used for international large-scale events where there may be a threat of bio-terrorism or other deliberate acts involving infectious agents, and the lab in a suitcase is frequently used in remote areas of the world with little available infrastructure. An example would be the multiple deployments over the years to combat outbreaks of Ebola in Africa.

NML has also had significant success in the area of vaccine and treatment development, particularly for the most serious diseases in the world including Ebola, Marburg and Lassa fever viruses. Promising candidate vaccines have been developed that have been extremely effective in pre-clinical trials. Work is now taking place to move them into safety trials with the hope that they will eventually reach the market and be of use during outbreaks to protect contacts and health care workers.

As a leader in the field, NML houses the secretariats for both the Canadian Public Health Laboratory Network (CPHLN) and the Global Health Security Action Group – Laboratory Network (GHSAG-LN). The role of CPHLN is to provide a forum for public health laboratory leaders to share knowledge. The CPHLN leverages its combined strength to champion efforts in order to provide rapid and coordinated nationwide laboratory response to emerging and re-emerging communicable disease threats. The GHSAG-LN network’s goals are to coordinate the diagnostic capabilities of all participants and contribute to disease surveillance around the world.

The Canadian Network for Public Health Intelligence (CNPHI) is an innovation developed by NML staff. It is a secure web-based system that compiles information from various surveillance systems and issues alerts to users. More than 4,000 public health officials across Canada now subscribe to it. CNPHI tools assist in determining the existence or extent of an outbreak through the recognition of related cases across jurisdictions.


Dr. Frank Plummer has been the Scientific Director General of NML since 2000. He is also the Chief Science Advisor for the Public Health Agency of Canada, a distinguished professor at the University of Manitoba and a Canada Research Chair.

Dr. Plummer is recognized in Canada and abroad for his work in public health and science, having received numerous honours, including most recently his investiture in the Order of Manitoba, appointment as Officer to the Order of Canada and induction into the Royal Society of Canada; being named Canada’s Health Researcher of the year by the Canadian Institutes of Health Research (the Michael Smith Award); and receiving a grant from the Grand Challenges in Global Health initiatives of the Bill & Melinda Gates Foundation for his HIV research. Other awards include the Rh Institute Award; an Achievement Award from the American Venereal Disease Association; Fellowship, Scholarship, Scientist and Senior Scientist awards from the Medical Research Council of Canada; the I.S. Ravidin Award in the Basic Sciences from the American College of Surgeons; the St. Boniface Hospital Research Foundation International Award for work on HIV/AIDS in Africa.

In 2001, he was named Canada Research Chair of the Canadian Institutes of Health Research. He has also been elected to the American Society of Clinical Investigation and the Association of American Physicians, has served as an advisor to the National Academy of Sciences in the US, and as a consultant to the World Bank, the World Health Organization, and the Governments of Kenya, India and Lesotho.

Dr. Plummer received his medical degree from the University of Manitoba in 1976 and trained in internal medicine and infectious diseases at the University of Southern California, the University of Manitoba, the University of Nairobi, and the Centers for Disease Control in Atlanta. He joined the University of Manitoba faculty in 1984 and is currently Distinguished Professor at that University of Manitoba, as well as Professor of Medical Microbiology and Community Health Sciences.

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