ARCHIVED: Chapter 6: Learning from SARS: Renewal of public health in Canada – Strengthening the role of laboratories in public health and public health emergencies
- 6A. Key Activities of Laboratories
- 6A.1 Diagnosis of Infections
- 6A.2 Characterization of Micro-organisms
- 6A.3 Reference Microbiology
- 6A.4 Support to Epidemiologic Surveillance
- 6A.5 Laboratory Surveillance
- 6A.6 Environmental Surveillance
- 6A.7 Chronic Disease Surveillance
- 6A.8 Emergency Preparedness and Response
- 6A.9 Applied Research
- 6A.10 Fundamental Research
- 6B. The Public Health Laboratory System in Canada
- 6C. Analysis of the Laboratory Response to SARS
- 6D. The Ideal Public Health Laboratory System for Canada
- 6E. Recommendations
- Appendix 6.1 - Canadian Public Health Laboratory Network (CPHLN) Draft Terms of Reference
Laboratory issues were highlighted in briefs received from the Canadian Association of Medical Microbiologists, the Canadian Infectious Diseases Society, the Canadian Society for Medical Laboratory Science, and the Ontario Association of Medical Laboratories. The SARS experience has clearly illustrated the central role that public health laboratories play in both public health and the health care system. Serving sometimes as first-line testing facility when a novel agent emerges, and at other times as a reference centre or 'court of last resort' to standardize and improve testing procedures for unusual pathogens, public health laboratories are a key resource in infectious disease diagnosis, surveillance, and epidemic response. Public health laboratories also have potential functions in chronic disease surveillance and diagnosis that could grow in the years ahead as more links are established between apparently non-communicable diseases and a variety of pathogens.
6A. Key Activities of Laboratories
Canada has a wide variety of medical laboratories, organized variously under the ownership and management of investor-owned corporations, non-profit hospitals and health regions, or various levels of government in the form of public health laboratories. The list of activities below applies particularly to a public health laboratory, but other types of laboratories carry out some of these functions:
- Diagnosis of infections
- Characterization of micro-organisms
- Reference services
- Support to epidemiologic surveillance and epidemic investigation
- Participating in, conducting or coordinating laboratory surveillance of infectious diseases
- Environmental surveillance
- Emergency preparedness and response
- Applied research and development
- Fundamental research
While discharging these functions, public health laboratories are integrated with the wider public health team. They play important roles in providing information for public health policy, training health human resources, and public health research.
A brief description of each of the key functions may provide the reader with a better understanding and appreciation of the role of laboratories in public health.
6A.1 Diagnosis of Infections
There is a public health dimension to all communicable diseases and to some related infectious disease issues (e.g., nosocomial infections and antimicrobial resistance). In Canada, diagnostic services for infectious diseases can be provided by private laboratories, hospital laboratories, provincial laboratories or national laboratories. The most frequent infectious diseases, such as lower urinary tract infections (cystitis), skin infections (impetigo, carbuncles, cellulitis), typical community-acquired pneumonias, and upper respiratory tract infections (pharyngitis, laryngitis, sinusitis), are all diagnosed using microbiological techniques available in private laboratories or hospital laboratories. The role of private laboratories varies widely. In some provinces, they mainly provide diagnostic services to community-based physicians. In others, they also have a significant role in providing services to hospitals, and major hospitals have developed public-private partnerships with investor-owned laboratory service providers.
Less common infections are diagnosed in laboratories at either the provincial or national levels. In cases of new diseases such as West Nile virus and SARS, or rare diseases such as Hantavirus and Ebola virus, the National Microbiology Laboratory [NML] at times takes on the role of front-line diagnostic laboratory. This occurs when the NML receives specimens for testing directly from health care institutions, a situation that arises when it is the only laboratory in the country able to provide the required testing for reasons of economy of scale or requirements for high levels of containment. In many instances, this is a time-limited role as other laboratories become proficient in testing for these rare or dangerous agents, or tests become commercially available. The NML may also play a role in facilitating the adoption of new testing technology by hospital or provincial public health laboratories.
6A.2 Characterization of Micro-organisms
Detailed characterization of organisms is a frequent function of public health laboratories. There are many important reasons for characterizing organisms associated with infection. These include gaining an understanding of a class of organisms' susceptibility to treatments so that appropriate treatment choices can be made, understanding the relatedness of organisms of the same class and thus possible common sources of infection, and determining how an organism is causing disease and predicting risks of infectious disease outbreaks. Different types of characterization are generally performed by different types of laboratories in the health care or public health system. As with other areas of public health, this function has suffered from a lack of coordination and problems with data sharing.
6A.3 Reference Microbiology
Reference microbiology includes activities such as confirmation of the identification of rarer organisms, organizing and coordinating quality assurance, and proficiency testing programs. All laboratories require some kind of reference function. Provincial public health laboratories may provide this function for laboratories in their jurisdiction and the NML provides reference microbiology services to all provincial laboratories as well as some international reference activities. In the absence of resources for developmental work at provincial laboratories, reference microbiology has been provided by some academic hospital laboratories. Thus, Canadian reference laboratory systems are ad hoc and not well-coordinated.
6A.4 Support to Epidemiologic Surveillance
Almost all infectious disease surveillance involves a laboratory test at some stage, as clinical diagnosis in and of itself is seldom deemed definitive. In Canada, national surveillance systems for different infectious diseases have evolved independently of each other, and are largely stand-alone. The type of laboratory testing required for a given surveillance system determines where testing can be done. For some infections (meningitis, Creutzfeldt-Jakob Disease [CJD]), all specimens are tested at the national level. For others such as influenza, initial isolation is performed at the provincial level and a sample is referred to the National Microbiology Laboratory for sub-typing. This practice extends to many areas such as surveillance of vaccine adverse events (now being planned), vaccine failures or antiviral drug treatment failures.
At times, the sampling frame for surveillance is systematic and at other times it is not. For some diseases, a laboratory result generated on the front line or in provincial laboratories becomes part of an epidemiologic report and contributes to a deeper understanding of a particular emerging disease or outbreak. New techniques have allowed 'molecular finger-printing' of organisms to establish their epidemiologic relationships, as in different strains of the SARS virus. These techniques can also be important in linking severity of infections to subtle differences in viruses or bacteria that otherwise appear to be part of the same family.
Unfortunately, these types of activities are again not wellcoordinated; Canada continually loses opportunities to advance knowledge or improve its own management of infectious diseases by failing to aggregate these data in a coherent laboratory-linked surveillance system. As a corollary, while there is considerable laboratory input into infectious disease surveillance systems, closer links are needed to surveillance in general. The case for better integration of laboratory and epidemiologic activities in Canada was highlighted by multiple stakeholders, including the Canadian Society for Medical Laboratory Science, the Canadian Infectious Disease Society, Canadian Association of Medical Microbiologists, and the Ontario Association of Medical Laboratories. As well, it is clear that better standardization of laboratory testing would improve the comparability of results, and mitigate either uncertainty or the need for repeat testing.
6A.5 Laboratory Surveillance
Some types of surveillance are primarily laboratory-based. West Nile virus is one example. The National Microbiology Laboratory performed all testing of dead birds and mosquitoes over the first three years; testing has since largely devolved to provincial laboratories. Other types of surveillance that are primarily laboratory-based include molecular finger-printing of foodborne organisms, and determination of antimicrobial resistance.
Most laboratory surveillance systems are passive, that is, they rely on submitted biologic material to make inferences. If patients with signs of a particular infection are not tested, or if they are tested in laboratories that are not part of a surveillance network, then information is lost. Epidemiologists regard passive surveillance as flawed in that it lacks a systematic sampling frame, clear definition of denominators, and assurance that laboratory information can be integrated with standardized epidemiologic and clinical information. The outputs of a passive surveillance system have limited utility. Canada needs more active laboratory surveillance with known sampling frames and better denominator data to strengthen our ability to anticipate, detect and respond to infectious disease threats.
More timely and sensitive laboratory surveillance for many infectious diseases is entirely feasible by marrying advances in information technology with advances in molecular typing of organisms.
Consider the current sequence of events for a reportable disease of national interest: a patient with a particular clinical syndrome presents to a physician. The physician orders a laboratory test. The test is performed by a local private laboratory, or perhaps in a hospital laboratory. The laboratory reports the test to the attending physician, who in turn reports the case to local public health, and this in turn is reported provincially and ultimately nationally. This system can take from a few days up to several weeks before case counts cumulate to the national level, and it is particularly weak for timely recognition of multi-jurisdictional outbreaks.
More timely detection can only be achieved through linking laboratories. The Canadian Public Health Laboratory Network [CPHLN] is putting such a network in place for enteric diseases, bioterrorism and other events. Although it is several years behind the United States' PulseNet, the enteric disease surveillance system, PulseNet Canada is close to being operational.
It is ultimately possible for all provincial laboratories and some major academic medical centres to use common technology platforms and typing procedures, and then be linked in real time over the Internet to provide surveillance information on key infectious diseases. Multiple stakeholders encouraged the creation of this type of integrated information platform. Persuading laboratory stakeholders to participate in these types of systems is a matter of finding the right inducements or mutual advantages. As discussed below, a private US company, Focus Technologies, was able to gain participation of many Canadian hospitals in a system to monitor antimicrobial resistance simply by providing continuous feedback to the hospital laboratories from a shared databank. Similar inducements could foster the creation of a national public health laboratory system that would serve as an integral part of a seamless national public health system.
6A.6 Environmental Surveillance
Food and water safety monitoring are key parts of the laboratory surveillance system, as the Walkerton and North Battleford outbreaks have reminded us. This part of the system is delivered very differently in different jurisdictions. Water testing is often devolved to the local level and responsibility is spread through different ministries. Similarly, food safety testing is spread across provincial and federal agencies including Health Canada and the Canadian Food Inspection Agency.
In general, food and water safety surveillance in Canada is at a fairly rudimentary state of development. The BSE situation in Alberta has forcefully demonstrated that failure to adequately monitor food safety can be economically catastrophic for national industries. For environmental monitoring, public health laboratories must be able not only to detect infectious agents, but also unusual toxins from non-infectious sources that may or may not be food- or water-borne.
6A.7 Chronic Disease Surveillance
While the public health laboratory system is largely concerned with infectious diseases, there are some well established chronic disease surveillance systems - screening for phenylketonuria and hypothyroidism, for instance - that may be performed by provincial public health laboratories. In other jurisdictions, these functions are provided by individual hospital laboratories.
The role of public health laboratories in chronic disease surveillance is likely to change in the near term. Two decades ago, few physicians would have imagined that peptic ulcer disease was integrally linked to infection with Helicobacter pylori. More and more chronic diseases now seem to be caused by infections or at least have infectious cofactors. Human papillomavirus has been linked to cervical cancer, and hepatitis viruses are major causes of hepatic cancer. At the same time, strong genetic risk factors for chronic diseases have been identified (Brca genes for breast cancer). What may emerge is a new integrative approach to preventing chronic diseases. For example, instead of cytological screening for cervical cancer with Pap smears, physicians and nurse practitioners may test for Human papillomavirus and genetic factors that predispose to progression to cervical cancer in the face of a chronic infection. Prions may turn out to be involved in various chronic diseases. These developments again highlight the need for a laboratory system that is integrated with the goals of both public health and clinical care.
Unfortunately, Canada has undertaken no national planning for these types of novel programs and there is virtually no federal presence in these cutting-edge fields. The current window of opportunity will close quickly, as a variety of local screening programs and market-driven testing strategies appear. Ample room must be left for pluralism and innovation, but Canada should move ahead to develop a public health strategy that can anticipate and channel these new surveillance opportunities.
6A.8 Emergency Preparedness and Response
Public health laboratories are tasked with preparedness and response to any infectious disease emergency or large epidemic. Related activities include participation in planning for emergencies (Viral Hemorrhagic Fever Emergency Response Plan, Pandemic Influenza Plan, Smallpox Plan), exercises, development of diagnostics, training and equipping other laboratories, stockpiling of reagents, coordination of laboratory networks, provision of surge capacity to other laboratories and participation in biologic terrorism preparedness at special events (G8 Summit in Kananaskis and World Youth Day in Toronto) and finally front-line response to infectious disease in Canada and elsewhere. Many of these activities - e.g., bioterrorism, West Nile virus, SARS - are new mandates for public health laboratories. And very often the new mandate is an unfunded one.
The Canadian Association of Medical Microbiologists and Canadian Society for Medical Laboratory Science both emphasized the need for advance planning that would provide the required capacity and funding for laboratories to deal effectively with infectious outbreaks, bioterrorism, or other workload surges.
6A.9 Applied Research
As technology changes and new infectious diseases emerge, an increasingly important role for public health laboratories is applied research on the diagnosis and detection of infectious diseases. This includes evaluation of new commercially-available diagnostic tests, development of in-house diagnostics, and research aimed at answering specific public health questions. As discussed in detail in Chapter 10, the capacity for research in public health laboratories has been weak for many years and has, if anything, eroded further in the last decade. This must be remedied.
6A.10 Fundamental Research
Fundamental research is a key activity for public health laboratories for several reasons. First, fundamental research has merit in its own right. Absent investments in fundamental research capacity, Canada would not have had the technology and expertise required to isolate and sequence the SARS coronavirus so rapidly. Second, public health laboratories have unique resources and their research facilities can answer important scientific questions of relevance to the health of Canadians. Third, the excitement of research opportunities will unquestionably help to draw talent to public health laboratories. And, as the SARS experience has so vividly illustrated, maintaining cutting-edge scientific expertise is important in the response to emergencies.
Significant involvement in fundamental curiosity-driven research is a public health laboratory function that has withered. Most public health laboratories view basic science research as someone else's job. Within Health Canada, this kind of research was actively discouraged until research became a clear part of the mandate of Health Canada scientists with realignment in June 2000. These mandates must be protected and expanded in the new Canadian Agency for Public Health.
6B. The Public Health Laboratory System in Canada
As noted, four levels of laboratories form the public health laboratory system in Canada. These are private, local and hospital laboratories, provincial public health laboratories, national laboratories and international laboratory networks. In some provinces, hospital and provincial laboratories are integrated. These different levels of laboratories function as a hierarchy, although there are no formal reporting relationships or requirements. Usually, the sophistication and breadth of diagnostic capacity and scientific expertise increases at higher levels in the system. In an epidemic or an emergency, these different levels of laboratories may be supplemented or complemented by laboratories that are primarily based in academic institutions and whose primary role is research. This was clearly the case in the Toronto SARS outbreak, where, as noted in Chapter 2, teaching hospital laboratories took on the task of polymerase chain reaction [PCR] testing to offload the Central Provincial Public Health Laboratory.
The role of the different laboratory levels in surveillance and response to an epidemic is dynamic, varying with the disease or stage of an epidemic and with the state of development of diagnostics. For instance, for very common diseases, diagnostics are usually available at the first contact laboratory while for rare diseases diagnostic testing may only be available at one laboratory. Commercially available diagnostic testing is more likely to be used at the local or hospital level while in-house diagnostics are more likely to be used farther up in the hierarchy.
6B.1 Front-line Laboratories (Private, Local and Hospital Laboratories)
First-contact or front-line laboratories, which may be private, local or hospital-based, function primarily to diagnose infections and are not technically part of the formal public health system. However, there are public health obligations on them for the reporting of notifiable diseases. The use of notifiable disease legislation is a major mechanism for provincial laboratories and epidemiology programs to obtain data from front-line laboratories. In addition, hospital laboratories are a key part of the response to institutional outbreaks of infection. In front-line laboratories, specimens are mainly derived from ill patients and are submitted for a battery of specific diagnostic tests. In general, these diagnostics focus on bacterial diseases and in many instances traditional technologies are used. However, the testing technology varies with the interest, expertise and resources of the individual laboratories. Some front-line laboratories perform a considerable amount of viral diagnostics as well.
Many front-line laboratory services for infectious diseases have been privatized to achieve cost savings. This has created some problems since private laboratories are reluctant to perform many labour-intensive, low-profit-margin tests. Privatization may also make it more difficult to perform certain kinds of surveillance given the scope of new federal privacy legislation (see Chapter 9).
Front-line laboratories normally have a complement of one or at most a few professional laboratory scientists and a number of technologists. In major teaching hospitals, these laboratories are larger and may play a major academic role in training and research. In smaller centres, these laboratories may be supervised by general pathologists with very little training in microbiology.
Although local and hospital laboratories initially identify many infectious disease outbreaks, their involvement in national surveillance systems is generally through their respective provincial laboratories. The hierarchical system where biologic material is moved from one level in the system to the next for more comprehensive testing is very cumbersome and slow. The closer to the front line that an infection can be diagnosed, the more timely the detection of infectious disease threats will be.
As already indicated, these front-line laboratories could play a much greater role in infectious disease surveillance and outbreak detection. They could be a part of a mechanism for real-time sensing of infectious disease threats, and also play a key role in epidemic response. SARS was primarily a nosocomial outbreak, but patients come from and return to communities; infection control cannot stop at the hospital's walls. A further reason for greater integration of front-line laboratories into the public health sphere is that, in major academic centres, these laboratories have significant expertise that is essential for creating a seamless public health network.
Any move to achieve better integration and a more functional laboratory system will raise issues of standardized testing methods, information technology, data sharing and funding. These issues must be faced and can be managed. As one example of the necessary alignment of incentives, Focus Technologies Inc. successfully gained the participation of several Canadian hospital laboratories in monitoring antimicrobial resistance by a data-sharing scheme. Hospital laboratories provided data on anti-microbial resistance to the company at no charge but were then able to view their institution's antimicrobial resistance patterns in comparison to others. The company later marketed the overall data. Focus is no longer active in Canada, but the precedent is important. Public health authorities and health care administrators must work together to create the necessary incentives for institutional participation in regional, provincial, and national programs.
A start has been made on integrating front-line laboratories into the public health system, specifically in the area of monitoring antimicrobial resistance, through the establishment of networks for surveillance of antimicrobial resistance. Health Canada's Nosocomial and Occupational Infections Section has been successful in building close links with leading specialists and institutions; further networking is possible and has already been identified as a priority for action and funding in Chapter 5. As well, the CPHLN plans to integrate local and hospital laboratories into an envisioned three-tiered bioterrorism response network, with local and hospital laboratories playing a key 'sensor' role. Thus far, these activities have progressed slowly because of a lack of resources. The funding programs of the Canadian Agency for Public Health (especially the Communicable Disease Control Fund) and the proposed F/P/T Network for Communicable Disease Control are both mechanisms to accelerate these initiatives.
6B.2 Provincial Laboratories
All provinces have provincial public health laboratories with the exception of New Brunswick. In New Brunswick, the functions of a provincial laboratory are performed by two different hospital laboratories. Provincial laboratories operate within the realm of public health, but there are many different models. In British Columbia, the provincial laboratory is part of the British Columbia Centre for Disease Control [BC CDC] with integrated infectious disease epidemiology and laboratory programs. In Nova Scotia and Alberta, the provincial laboratories are merged with a hospital laboratory. In Manitoba, Saskatchewan, Quebec, Ontario and Newfoundland, organizationally and physically separate laboratories exist. Some provincial laboratories have multiple sites within the province. These smaller laboratories would typically have a few professional microbiologists whose involvement in research and development is relatively limited.
In every province, there are different relationships with local academic institutions and hospital laboratories. In this "system", the functions and services provided by provincial laboratories vary considerably. Among the functions provided are reference services for local laboratories within their jurisdiction, and primary diagnosis for certain infections (often viral disease diagnostics are centralized). The territories are served by provincial laboratories under contract arrangements with Nunavut being served by Ontario, the Northwest Territories by Alberta, and Yukon by the BC CDC.
Provincial laboratories face a number of challenges. Their relationship with hospital and private laboratories across the country is variable; it ranges from a quasi-regulatory oversight role in Quebec to collaborative relationships or even competitive positioning in other jurisdictions. One reason for strained relationships is that, whether owing to budget cuts to public health laboratories or advances in technology, hospital laboratories are now undertaking more and more testing activities that were once fulfilled only by public health laboratories. This has led, in some circles, to a negative spiral as decision makers infer that public health laboratories can indeed be safely downsized. However, the resulting loss of capacity to respond to emerging infectious diseases is not replaceable by private or hospital laboratories in the absence of a whole series of prior agreements with these entities.
The Committee's view is that strong provincial laboratories remain an essential component of the public health system. The Communicable Disease Control Fund and F/P/T Network for Communicable Disease Control offer mechanisms for coordinated upgrading of these laboratories, with clearer definition of their roles in the referral hierarchy.
6B.3 National Laboratories and National Laboratory Networks
Within Health Canada, a number of laboratories are involved in infectious diseases. The primary laboratories are the National Microbiology Laboratory [NML] in Winnipeg, the Laboratory for Foodborne Zoonoses [LFZ] in Guelph and the National Laboratory for Retroviruses in Ottawa. These laboratories all reside within the Population and Public Health Branch and would be part of the new Canadian Agency for Public Health.
These laboratories serve multiple functions including front-line diagnostics (for new or rare diseases), reference microbiology (confirming test results and quality assurance), support to epidemiologic surveillance, conducting and coordinating laboratory surveillance, emergency preparedness and response, and applied and fundamental research.
The LFZ in Guelph focuses on the animal side of foodborne zoonotics, while the Retrovirology Laboratory specifically deals with HIV and related viruses. The LFZ also has laboratories in St.Hyacinthe, Quebec and Lethbridge, Alberta.
These laboratories have testing capacity that is generally more sophisticated than the provincial laboratories, and are staffed by a significant number of PhD or MD trained scientists. In addition to the operations in Winnipeg, the NML provides modest support to six national reference centres based mainly in provincial laboratories. These reference centres have developed for a variety of reasons over the years; they provide specialized services not available at the NML and have developed significant expertise in selected areas. For instance, the Alberta provincial laboratory provides national reference services for streptococcal infections. This model of shared F/P/T expertise is entirely consistent with both the vision for the distributed functions of the Canadian Agency for Public Health set out in Chapter 4 and the anticipated workings of the new F/P/T Network for Communicable Disease Control.
As part of its role, the NML plays a key role in a cluster of federal and provincial laboratories that are part of Canada's bioterrorism response. Because of the need to provide surge capacity to the provinces and front-line response anywhere in the world, two multidisciplinary laboratory response teams have been established at the NML and equipped with portable laboratories capable of performing routine and molecular diagnostics in high containment. One team is on call at all times and a team can be on the way to the field in as little as three hours. The Canadian Association of Medical Microbiologists highlighted the importance of such rapid response teams, particularly if they can combine laboratory and epidemiologic expertise. The NML teams have been fully deployed only three times - once to New Brunswick, once to Kananaskis, and once to Hong Kong to assist in the investigation of the Metropole Hotel and Amoy Gardens clusters of SARS cases.
Provincial and hospital laboratories have their own unique strengths, but do look to the NML for national leadership in laboratory issues related to infectious diseases. The NML provides coordination on a number of aspects of laboratory surveillance across the country. A key development over the last two years is the establishment of a new working relationship with provincial laboratories through the CPHLN. The CPHLN's draft terms of reference are attached in Appendix 6.1. This body is made up of the directors of the provincial laboratories; the Scientific Directors of the NML, the LFZ, and the National Retrovirus Laboratory; as well as leaders of the federal Centre for Infectious Disease Prevention and Control [CIDPC] and the Centre for Surveillance Coordination and Response. It is functioning increasingly as a national coordinating body, reflecting the modus operandi that the Committee hopes can be achieved more widely in the Network for Communicable Disease Control and beyond. Not only has F/P/T collaboration in the CPHLN been strong, but its importance was endorsed by non-governmental stakeholder submissions.
For provincial laboratory directors, the CPHLN offers opportunities both to provide input to Health Canada's programs and to share expertise in a national peer-to-peer network. For the NML, the CPHLN provides a useful mechanism for communicating with and learning from provincial laboratories, drawing on expertise that it does not necessarily have and implementing national programs. If CPHLN continues to be successful, ultimately it could be a single point of contact between federal and provincial public health laboratories for all work on issues pertaining to infectious diseases.
The NML houses and funds the CPHLN, but importantly, it is chaired by a provincial laboratory director. The CPHLN is gradually beginning to coordinate federal-provincial laboratory programming in a number of areas, key ones being bioterrorism, real-time molecular fingerprinting of E.coli and Salmonella, and food and water safety. As all jurisdictions move forward to strengthen the fabric of the nation's public health systems, the CPHLN should in turn be strengthened and expanded. Supported by new federal funds and linked to the new F/P/T Network for Communicable Disease Control, it should serve as another exemplar for how national programs can be planned and implemented in Canada's complex multi-jurisdictional environment.
6B.4 International Laboratory Networks
Several international laboratory networks have arisen from the need for combined firepower and rapid communication among scientists in epidemic situations. Canada's national laboratories have extensive links to their counterparts in other countries.
Strong links to the US CDC exist for virtually all programs. This has been enormously important over the years in developing Canadian capacity. Canada, through the NML and Defence R&D Canada at Suffield, Alberta, is a member of the US CDC-led Laboratory Response Network, charged with responding to the threat posed by biological and chemical weapons and related terrorist activities. The NML is also a member of the US CDC-based PulseNet, a molecular typing network for enteric pathogens. As noted above, PulseNet Canada is moving forward steadily. Recently, it was agreed that the NML and the CIDPC should create a formal liaison with the US CDC's National Center for Infectious Diseases; this is underway.
Canada also participates in several different virology networks including the European Viral Diseases Network and the International High Security Laboratory Network. The latter includes the level 4 laboratory programs from Canada, the USA, Germany, France, Italy, the UK, South Africa, Australia, Japan, and Russia. After September 11, 2001, the Ministers/Secretaries of Health of the G7 countries and Mexico established the Global Health Security Action Group, which includes a laboratory network chaired by Canada, to respond to bioterrorism. This network's ambit has now been expanded to include pandemic influenza.
Although the World Health Organization itself has no laboratories, it organized an international network of more than ten laboratories responding to SARS, including all affected countries plus experts from some other countries. The network led to unprecedented, extensive, and generous sharing of data and procedures. This resulted in very rapid progress on the laboratory front. The international laboratory network exemplifies some of the best practices and precedents from the SARS experience internationally.
6C. Analysis of the Laboratory Response to SARS
The laboratory response to identifying the causative agent of SARS was one of the most visible parts of the epidemic response in Canada. The informal hierarchy identified above has not yielded a public health laboratory system, and the extant arrangements were not well-structured for investigating and responding to an outbreak. Instead, Canadian biomedical laboratories are structured to support the diagnosis of infection in individuals. However, the system was able to adapt to the different demands of the SARS outbreak. The inner workings of the NML likewise were not designed for an epidemic response, and changes in the way the NML operated were required for the national laboratory to respond effectively.
The 'discovery' phase of the laboratory response consisted of ruling out known agents as the cause of SARS and identifying the causative agent. In doing this through the CPHLN, agreement on the types of specimens to be obtained and specimen shipping protocols was reached very quickly. The network agreed that testing for known agents would be performed at the provincial laboratories, mainly Ontario and British Columbia, allowing the NML to focus on unknown agents. The CPHLN was also able to provide useful advice to scientists at the NML in directions for research. These steps were taken extremely rapidly; within two weeks, the SARS coronavirus had been identified and the laboratory role shifted to one of diagnosis of coronavirus infection, development of diagnostic tests, and research on the agent.
As the laboratory response developed, investigations into the cause of SARS were highly centralized at the NML. The centralization of biologic material and laboratory results yielded a clearer picture of all the data on causation, notwithstanding the disappointing lack of associated clinical and epidemiologic data. A further advantage of unified leadership was that laboratory studies were readily coordinated, avoiding duplication and directing maximum effort at the most important issues. However, predictably, moving specimens through the hierarchy from hospital laboratory to provincial laboratory to national laboratory slowed down investigations. On occasion, specimens were received at the NML two to four weeks after they were first obtained. For other individuals with probable SARS, reference specimens were never received at the NML.
During the early phases of the SARS epidemic there were several significant impediments to an effective laboratory response. The two most important were inadequate data management and the lack of clinical and epidemiologic data.
Data management: The NML had no laboratory-wide laboratory information system. In spite of many years spent in developing a Laboratory Data Management System by Health Canada, the extant system could not serve the epidemic response needs. A new database had to be created from scratch, and was made accessible to laboratories in the CPHLN over the Internet. This experience highlights the need for software platforms that are agile, modular, and rapidly modifiable for special purposes. More often than not, grand and purpose-built architectural designs in software development are overtaken by faster-moving and smaller platforms that can be customized to the changing needs of users. The challenge, as always, is to balance considerations of flexibility, economy, integration, and interoperability. For the future, laboratory databases that can communicate with one another must be established in public health laboratories across the country. If a global system cannot be achieved, then at a minimum a common information management system for outbreak responses should be established.
The lack of integration of epidemiologic and laboratory data: As Chapters 2 and 5 have already highlighted, laboratory data were not well-integrated with epidemiologic data during the SARS outbreak in Canada. This objective has still not been fully achieved, with severe adverse effects on research that will be further reviewed in Chapter 10. An integrated laboratory and epidemiologic data management system is indeed achievable, at least for outbreak response. Such a system should have been in place before SARS, and must now be established as soon as possible. This shortcoming points to the general need for greater integration of laboratory and epidemiologic sciences in a renewed public health system.
Once the potential causative link to the new coronavirus became clear, the role of the NML shifted to performing diagnostic testing, development of further diagnostic tests, supporting provincial and other laboratories with their own diagnostics, and reporting results. The NML initially provided coronavirus PCR primer sequence information to the CPHLN and engineered a positive control for PCR testing. The plan of the CPHLN was to rapidly devolve testing capacity to provincial laboratories. However, at the same time, provincial, hospital and academic laboratories began developing their own testing based on published sequences of the coronavirus and material obtained from ill patients. This resulted in some chaos and duplication as individual scientists and laboratories went their own way.
For example, several coronavirus genes from the same Tor2 isolate have been cloned and expressed multiple times and are now being used in diagnostic tests across the country. On the positive side, the agile response of hospitals and provincial laboratories is important and encouraging. On the negative side, the development of multiple diagnostics is somewhat wasteful and has led to the proliferation of diagnostic tests that, notwithstanding a common genetic platform, may not have equal sensitivity and specificity. Perhaps more importantly, when multiple laboratories are providing testing in an uncoordinated manner without sharing data, the ability to see the whole picture of the epidemic is lost. If this development had been anticipated, mechanisms for coordination and reduction of duplication could have been put in place, along with a centralized database for all laboratory results.
This is yet another lesson from SARS. For the future, better coordination of efforts must be achieved through extension of the CPHLN membership to major hospital laboratories, the development of stronger provincial networks of laboratories, or both.
Once laboratory results of coronavirus testing became available, there were some new issues around reporting of results. Although results of testing were available, the release of results to physicians and public health units was at times delayed in the Ontario Ministry of Health and Long-Term Care [OMHLTC]. We have not determined the extent or duration of these delays. The Committee leaves it to the Campbell Investigation to determine the impact of these delays, if any, on the second wave of SARS in Toronto.
A related difficulty arose from the fact that 172 individuals, primarily from Ontario, tested positive for the SARS coronavirus, but were not classified as probable or suspect SARS. As of mid-August it is still not known if these individuals actually had some form of the infection, how they acquired it, and if they produced additional chains of transmission. Collaborative work is currently underway with the OMHLTC to pursue the matter. This information was and remains critical to determining whether there was hidden community transmission of the SARS coronavirus and describing the full spectrum of disease caused by the virus.
The reporting of results to individual physicians was also problematic. For hospitalized patients who were discharged or died, results of laboratory tests were sent directly to medical records and in some instances were not seen by the physicians who cared for the patient. This illustrates the inadequacies not only of laboratory information systems, but also the weak interface between public health and the health care system. In effect, no system exists to pull important information together into a coherent picture of an outbreak. This situation again illustrates that the data systems and business processes in place for managing day-to-day infectious disease problems are ill-suited to responding to epidemics. Different operational procedures need to be put in place urgently for an effective outbreak or epidemic response.
6D. The Ideal Public Health Laboratory System for Canada
Ideally, Canada should have a fully coordinated and integrated national public health laboratory system that delivers timely surveillance for infectious disease threats, is an active participant in infectious disease prevention programs, and responds effectively and quickly to infectious disease outbreaks.
Achieving this vision depends on strong regional or provincial public health laboratories that are closely linked to front-line laboratories and other organizations involved in public health through funding streams, collaborative agreements, common or related testing procedures, shared or interoperable information systems and common programming. Such a configuration would help to bring public health back into the health care system. These laboratories should be integrated with epidemiologic components of public health in regional or provincial agencies, helping to reinforce the secondline of defence against public health hazards. As such, they should be supported by the new Communicable Disease Control Fund in the Canadian Agency for Public Health and linked together through both the CPHLN and the new F/P/T Network for Communicable Disease Control. These laboratories should also be closely tied to scientists in academic institutions. Testing for important infectious disease agents must be performed through common testing procedures at the lowest level possible within the integrated laboratory system, with results of interest reported to the regional and ultimately the national level in real time through integrated information management systems.
Whenever possible, the regional laboratory would take on leadership, coordination, and research roles in the network rather than performing high volumes of testing on site. Expertise and innovation capacity should be distributed across the network, with each regional laboratory developing national expertise in given areas, as outlined earlier. The laboratory elements in the Canadian Agency for Public Health would be an integral part of the network. In particular, the new federal agency must itself maintain world-class laboratory science capacity, and its laboratory leaders in turn should have a mandate to build regional public health capacity and play a major role in coordinating national surveillance and epidemic responses.
To achieve this vision, significant inducements need to be identified for front-line laboratories to become part of regional laboratory networks and for provincial public health laboratories to develop programs that fit into an integrated national system. The Communicable Disease Control Fund described in Chapter 5 would support these aims, and the proposed F/P/T Network for Communicable Disease Control would lend momentum to the integration of laboratory and epidemiologic functions.
The SARS experience has highlighted the importance of public health laboratories in surveillance for infectious disease and the central role of these laboratories in the response to epidemics. In some respects, the laboratory response to SARS went well. Its relative success was a function of significant capacity at the national level, effective F/P/T laboratory working relationships, pre-existing functional networks, and a culture of mutual respect and assistance among the provincial and national laboratories. These prerequisites for success should be emulated in other parts of the public health system. We have identified a number of challenges and issues in Canada's public health laboratory system. The Committee accordingly recommends that:
- 6.1 The F/P/T Conference of Deputy Ministers of Health should urgently launch an expedited review to ensure that the public health laboratories in Canada have the appropriate capacity and protocols to respond effectively and collaboratively to the next serious outbreak of infectious disease. The review could be initiated through the Canadian Public Health Laboratory Network and engage with the new F/P/T Network for Communicable Disease Control as soon as the latter is operational.
- 6.2 Health Canada, in collaboration with the relevant provincial/territorial authorities, should urgently initiate the development of a laboratory information system capable of meeting the information management needs of a major outbreak or epidemic. The laboratory information system must be designed in such a way as to address the functional needs of laboratories, be readily integrated with epidemiologic information, and be aligned with data-sharing agreements across jurisdictions and institutions.
- 6.3 The F/P/T Conference of Deputy Ministers of Health should launch a full review of the role of laboratories in national infectious disease surveillance systems, with the aim of creating a more efficient, timely, and integrated platform for use of both public and private laboratories in surveillance.
- 6.4 The Government of Canada, through the Canadian Agency for Public Health, should invest in the expansion of the Canadian Public Health Laboratory Network to integrate hospital and community-based laboratories. This includes alignment of incentives and clarification of roles and responsibilities for infectious disease control. The relevant monies could flow from the Public Health Partnerships Program or the Communicable Disease Control Fund (see Chapter 5).
- 6.5 The Canadian Agency for Public Health should give priority to strengthening the capacity of provincial/territorial laboratories as regards testing for infectious diseases. The Agency should provide incentives to increase the participation of provincial public health laboratories in national programs. It should support provincial/ territorial public health laboratories in the creation of provincial laboratory networks equivalent to the Canadian Public Health Laboratory Network; these would connect in turn to the national network. The relevant monies would flow from the Communicable Disease Control Fund.
- 6.6 The Canadian Agency for Public Health should support participation and leadership in international laboratory networks by our national laboratories, thereby building on the success of the international collaboration in the response to SARS.
- 6.7 Health Canada, in collaboration with provincial/territorial authorities, should sponsor a process that will lead to a shared vision for the development, incorporation, and evaluation of leading-edge technology in the public health laboratory system. Among the issues that require elucidation are the role of national systems for the real-time surveillance of infectious disease through molecular fingerprinting of micro-organisms, toxicology capacity to detect illnesses caused by the poisoning of natural environments and occupational hazards, and the potential for linking genetic testing and infectious disease surveillance in novel programs that would target cofactors associated with the development of chronic diseases.
- 6.8 A national report card of performance and gap assessment for public health laboratories should be developed through the Canadian Public Health Laboratory Network and/or the F/P/T Network for Communicable Disease Control, allowing comparative profiling of various provincial and national laboratories against international standards.
The Committee also takes note of human resource shortfalls in the laboratory sphere, as outlined in multiple stakeholder submissions. We discuss human resource matters in Chapter 7.
Appendix 6.1 - Canadian Public Health Laboratory Network (CPHLN)
Draft Terms of Reference
The Canadian Public Health Laboratory Network (CPHLN) was organized in 2001 in an effort by provincial health laboratory directors who recognized a void in interprovincial communication and in communication with the National Microbiology Laboratory following the demise of TAC, and was coincidental to the terrorism of September 11, 2001 and to the subsequent anthrax threats. In addition to addressing concerns regarding increased frequency and potential lethality of bioterrorism agents, the scope of the Network was expanded to include other aspects of public health such as food and water safety in response to water quality problems in Walkerton, Ontario and North Battleford, Saskatchewan. At present, the Network is in the initial stages of its development and is currently determining how best to provide leadership in the development of a proactive network of public health laboratories that will serve to protect the health of Canadians. It is also considering how to positively influence and support the broader Canadian health care renewal initiative. The Network's current mandate is to develop and implement strategies to:
- Coordinate pathogen detection, infectious disease prevention and control;
- Conduct laboratory-based surveillance including the development of early warning systems to monitor and detect emerging pathogens, antibiotic resistant organisms and outbreaks; and
- Counter bioterrorist threats.
The benefits envisioned by the CPHLN include:
- A coordinated national laboratory response network;
- National standardization of laboratory procedures and quality assurance methods leading to greater consistency of results;
- Expanded training available to Network participants regarding protocols, best practices and emerging technologies;
- Enhanced national capability regarding the detection of emerging pathogens, antibiotic resistant organisms and outbreaks, and the prevention and control of infectious diseases;
- Reduced duplication of effort; and
- Enhanced support for laboratories through increased collaboration.
2.0 Mission, Vision and Guiding Principles
- 2.1 The mission of the CPHLN is to provide leadership in public health laboratory functions through the development of a proactive network of public health laboratories to protect the health of Canadians.
- 2.2 The vision of the CPHLN is to become an actionoriented national microbiology network providing value-added advice and services in direct support of the broader Public Health System.
- 2.2.1 The CPHLN's guiding principles are:
- integrated management;
- value of public health surveillance and early detection; and
- best practic
3.0 Strategic Orientation
The following provides a graphical overview of the CPHLN strategic orientation. For more details concerning strategic priorities and strategic goals, refer to the CPHLN Strategic Plan.
4.0 Guidelines/Operating Principles
- 4.1 The CPHLN shall work within the context of the CPHLN Strategic Plan and reporting structure.
- 4.2 The CPHLN shall respect the mandates and roles of all partners and work together in a way that will enhance their efforts.
- 4.3 Where appropriate and feasible the CPHLN shall collaborate with international, federal, provincial, and territorial agencies with a bioterrorism response or public health mandate, and participate on and/or communicate with related committees.
- 4.4 The CPHLN will facilitate the coordination of existing public health committees by clearly understanding the roles and mandates of the various organizations involved in bio-terrorism response and other public health protection activities.
- 5.1.1 The CPHLN shall be composed of no less than 13 and no more than 25 members, including the chairs.
- 5.1.2 Members shall include the medical or scientific directors from the public health laboratories in each province, except Ontario which lacks a Medical Director for the Ontario Public Health Laboratories and will be allowed two representatives, Health Canada stakeholders, the Department of Defense Research and Development Canada, and the Canadian Council of Chief Medical Officers of Health as follows:
- The Laboratory Director or designate of each Provincial or Territorial Public Health Laboratory (maximum thirteen designates)
- The National Microbiology Laboratory (NML), the Scientific Director General or designate, plus designates from each of the following five NML reference centers: Bacteriology, Zoonotic Diseases and Special Pathogens, Host Genetics and Prion Diseases, Enteric Pathogens, and Viral Diagnostics). (Six representatives)
- The Department of Defense Research and Development Canada (one representative)
- The Centre for Emergency Preparedness and Response (one representative)
- The Laboratory for Foodborne Zoonosis, Guelph (one representative)
- The Centre for Infectious Disease Prevention and Control, Ottawa (one representative)
- The Canadian Council of Chief Medical Officers of Health (one representative)
- 5.1.3 Members shall be appointed by their respective organizations for a term of three years. The term is renewable for an additional term of two years at the unanimous discretion of the chair and vice-chair.
- 5.1.4 In the event that a member resigns during his or her term, a replacement for the balance of the term shall be appointed by the representative organization.
- 5.1.5 Members shall make a commitment to be actively involved in the work of the CPHLN, to make attendance at meetings a priority and commit to furthering the objectives of the CPHLN as defined by the strategic plan.
- 5.1.6 Members shall arrange to have a designate to attend meetings in the event that they are unavailable to attend.
- 5.1.7 Due to the responsibilities of the CPHLN to contribute to the minimization bioterrorism threats to the health and safety of Canadian, all members will be required to have Level II Secret Clearance to maintain membership in the CPHLN.
- 5.1.8 Any designate who attends a CPHLN meeting in the place of a member must have Level II Secret Clearance.
- 5.1.9 Outside individuals are not permitted to attend CPHLN meetings except at the invitation of the Chair and with appropriate consideration for security clearance requirements.
- 5.1.10 Loss of membership can occur by a vote by the CPHLN membership where the consensus of the voting members results in a vote to revoke a particular membership. Reinstatement may occur following a formal written request and a subsequent consensus vote by the CPHLN membership.
5.2 CPHLN Leadership
- 5.2.1 The CPHLN shall be chaired by one CPHLN member in good standing. The term of the chair is one year. The vice-chair from the previous year will be automatically appointed chair for the following year.
- 5.2.2 The CPHLN shall have a vice-chair held by one CPHLN member in good standing. CPHLN members shall appoint the vice-chair for a term of one year at which point the vice-chair takes the position of chair for one additional term of one year.
- 5.2.3 In the event that a chair should resign the vice-chair will assume the position of chair and the CPHLN will appoint a new vice-chair.
- 5.2.4 In the event that a vice-chair should resign the CPHLN will appoint a new vice-chair.
- 5.2.5 The chair or, in his/her absence, the vice-chair shall preside over CPHLN meetings.
- 5.2.6 The chair and vice-chair shall participate as appropriate in the delivery of CPHLN submissions to the Council of Deputy Ministers of Health and/or other jurisdictional bodies with a bioterrorism response or public health mandate.
- 5.2.7 The chair and vice-chair shall work closely with the Network Manager and, through the Secretariat staff to further the goals and objectives of the CPHLN according to the strategic plan.
5.3 CPHLN Subcommittees
- 5.3.1 The CPHLN shall create committees and subcommittees as required, to address important public health laboratory issues.
- 5.3.2 Subcommittee members shall be nominated and approved by the CPHLN for a term of three years (renewable). Where a subcommittee member resigns during that term, a replacement for the balance of the term shall be appointed by the Subcommittee and approved by the CPHLN.
- 5.3.3 Subcommittee members shall have laboratory expertise in the particular area of focus of the subcommittee and shall represent federal, provincial, territorial or regional laboratories. Subcommittees will attempt representation from each jurisdiction and geographic region.
5.4 CPHLN Secretariat
- 5.4.1 A dedicated Secretariat shall be established at the NML in Winnipeg, to administer and facilitate the work of the CPHLN.
- 5.4.2 The Secretariat will consist of a Network Manager and a Scientific Information Officer and Standards Officer who shall report to the Network Manager. Other staff may be hired as required to the Secretariat based on the advice of the Network Manager, endorsement by the CPHLN membership and availability of the required funds.
- 5.4.3 The Secretariat shall report to the CPHLN chair and be administered on a day-to-day basis by the Scientific Director General of the NML or his/her designate.
- 5.4.4 The Secretariat shall be funded by Health Canada through the NML until such time as permanent operational funds are established for the CPHLN.
- 5.4.5 The Secretariat will provide support to and participate in CPHLN meetings as required but will not function as a voting member of the CPHLN.
- 5.4.6 CPHLN meeting agendas shall be prepared by the Secretariat, in consultation with the chair, and issued at least one week prior to meetings.
- 5.4.7 Minutes of CPHLN meetings shall be prepared by the Secretariat and distributed to Network members, and other clients and partners as appropriate, within two weeks of the meeting date.
5.5 CPHLN Meetings
- 5.5.1 The CPHLN shall hold semi-annual meetings to discuss and address business related to strategic priorities, goals, objectives and initiatives; current issues; communication flow; member relations; and funding and resource requirements, including annual budget and operating plans).
- 5.5.2 Quorum for meetings shall be attendance by a simple majority of members.
- 5.5.3 Decisions shall be made by consensus where consensus is defined as general agreement, either verbal or by poll. When consensus cannot be reached, decisions shall be made by a simple majority of the members present. Each member receives one vote.
- 5.5.4 No decision by the CPHLN is legally binding in anyway as the CPHLN is not established as a legal entity.
- 5.5.5 Minutes will be recorded by the Secretariat and distributed to members.
- 5.5.6 Agenda items should be forwarded to the Secretariat no later than one month prior to the meeting.
- 5.5.7 The agenda and required material will be circulated at least one week in advance of the meeting.
6.0 CPHLN Terms of Reference
- 6.1 Minor amendments to the Terms of Reference may be made by the Chair subject to ratification by the members at the next meeting of the CPHLN.
- 6.2 The Terms of Reference may be amended at any meeting of the CPHLN by consensus or by vote.
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