Laboratory Training for Field Epidemiologists Planning a Strategy for Laboratory Investigations Adapted sample taking May 2007

Laboratory Training for Field Epidemiologists Learning objectives At the end of the presentation, participants should understand : Strategies for laboratory analysis Rationale to engage the laboratory early How to formulate objectives for laboratory analysis

Laboratory Training for Field Epidemiologists Planning an Epidemiologic Investigation Formulate Objectives Plan Data Analysis Develop Data Collection Instruments and Sampling Strategy Collect Data Analyze Data Interpret Data Draw Conclusions

Laboratory Training for Field Epidemiologists Planning a Laboratory Investigation Formulate Objectives Plan Laboratory Analysis Determine Sampling Strategy Collect Specimens Analyze Specimens Interpret Tests Draw Conclusions

Laboratory Training for Field Epidemiologists Planning a Collaborative Investigation Formulate Objectives Plan Prepare Analyse Interpret Results and Draw Conclusions Collect Data needs Instruments and Sampling Strategy Data Lab needs Sampling strategy Specimens

Laboratory Training for Field Epidemiologists Why Plan? Laboratory requirements relate to investigation objectives confirm a diagnosis to document an infection? document a common source? provide information to help clinical management (antibiotic resistance)? What laboratory tests help answer the objective(s)? What specimens are required for the laboratory test(s)? What’s the sampling strategy?

Laboratory Training for Field Epidemiologists Planning the laboratory Investigation Formulate Objectives Plan Laboratory Analysis Determine Sampling Strategy Collect Specimens Analyze Specimens Interpret Tests Draw Conclusions

Laboratory Training for Field Epidemiologists Define objectives Consider the scope public health intervention (e.g. surveillance, outbreak) research (e.g. serological survey) Identify investigative objective test a hypothesis (e.g. diagnostic test) (Qualitative) – fewer specimens needed measure (e.g. incidence) (Quantitative) – may require specimens from all subjects (e.g. cohort study)

Laboratory Training for Field Epidemiologists Confidentiality and Consent Public health investigations vs Research Studies public health investigation: designed to understand a health event in order to make immediate control and prevention recommendations Considerations: type of specimens required (consider invasiveness) need for ethical committee review (time consuming) usually not required for public health investigations type of consent (verbal, written) (adults, children) labelling of specimens (nominal, unique identifiers) personal identifiers (how will link to epidemiologic data)

Laboratory Training for Field Epidemiologists Ethical considerations Investigating a case of acute flaccid paralysis in a polio endemic area public health intervention nominal specimen (confidentiality) verbal consent (no ethics review committee clearance needed) Investigating possible polio-virus shedding among immunosuppressed subjects in Europe research study use of unique (non-nominal) identifiers ethics review committee required, written informed consent

Laboratory Training for Field Epidemiologists Planning the laboratory investigation Formulate Objectives Plan Laboratory Analysis Determine Sampling Strategy Collect Specimens Analyze Specimens Interpret Tests Draw Conclusions

Laboratory Training for Field Epidemiologists Laboratory Involvement in the Field Presence in the field ideal Can provide timely input based on direct involvement and observation time consuming, expensive most useful in complex investigations, unusual clinical presentations, unknown pathogens, Remote participation as part of outbreak team (more common) optimal value if involved early need to exchange appropriate, sufficient information efficient for routine investigations (known, common pathogens)

Laboratory Training for Field Epidemiologists Communicating with the Laboratory Share initial information early time, place and person characteristics suspect pathogens Ensure on-going communication identify focal person, obtain contact information generate outbreak number provide updates send epidemiological report for input/revisions

Laboratory Training for Field Epidemiologists Planning the laboratory investigation Formulate Objectives Plan Laboratory Analysis Determine Sampling Strategy Collect Specimens Analyze Specimens Interpret Tests Draw Conclusions

Laboratory Training for Field Epidemiologists Which specimens to collect? 1. What are the suspected pathogens? 2. What tests are available to identify the suspected pathogens?

Laboratory Training for Field Epidemiologists Which specimens to collect? 1. What are the suspected pathogens? what is the clinical syndrome? what are the epidemiological characteristics? what are the macroscopic characteristics of the specimen? what infections are endemic in the geographical area?

Laboratory Training for Field Epidemiologists Which specimens to collect? 2. What tests are available to identify the suspected pathogens? what specimens are required for these tests? consult the laboratory review guides and references which laboratory can do the test? consider bio-level, geography, timelines consult the laboratory activate the network

Laboratory Training for Field Epidemiologists Typical scenario Typical clinical syndrome most cases meet a classical case definition Typical epidemiological characteristics transmission pattern (e.g. incubation period) compatible with clinical picture Typical macroscopic appearance of the specimen cloudy cerebro-spinal fluid, rice water diarrhoea Endemic area cholera in Bengal, meningitis in the Sahel

Laboratory Training for Field Epidemiologists Sampling strategy: typical scenario Seeking laboratory confirmation one or few key laboratory tests one key specimen measles virus IgM on serum cholera culture on rectal swab Use routine procedures standard collection and transport procedures first level laboratory know your counterparts in the laboratory

Laboratory Training for Field Epidemiologists Unusual scenario Atypical presentation severe cases (e.g. fatal influenza-like illness) Unusual epidemiological characteristics unknown or unusual mode of transmission Non-compatible macroscopic appearance of the specimen Non-endemic area cholera in Latin America in early 1990’s

Laboratory Training for Field Epidemiologists Sampling strategy: Unusual scenario Look for a wide range of pathogens - seek advice from laboratory Short-list pathogens on the basis of: clinical picture epidemiological characteristics geographical location macroscopic appearance of the specimen Consider more than one type of test (e.g. culture, serology)

Laboratory Training for Field Epidemiologists Sampling strategy: Unusual scenario Examine more than one type of specimen (e.g. blood, urine, stools) pathogen might be present in an apparently unaffected organ (e.g. Legionella requires a urine sample) Get help plan for storage, packaging and transport use reference laboratories

Laboratory Training for Field Epidemiologists Assess the situation Unusual situations may be due to: unusual presentation of an common pathogen emerging pathogen not usually seen in the area emergence of new pathogens SARS, avian influenza, hantavirus Balance need for simplicity with risk of missing serious events seek input from all disciplines for decision-making

Laboratory Training for Field Epidemiologists Cluster of febrile rash* (Middle East) Suspect pathogenMeasles Virus Possible testsMeasles IgM ELISA virus isolation? Specimens neededacute serumurine sample? Laboratories to usedistrict laboratoryreference laboratory? *consistent with measles case definition

Laboratory Training for Field Epidemiologists Cluster of febrile neurological syndrome (Uttar Pradesh, India) Suspect pathogensBacterial meningitisJapanese encephalitis Enterovirus encephalitis Proposed testsCSF - bacteriologyserologyserology (serum, CSF) culture (stool, CSF) Specimens neededCSFacute and convalescent serum stool and CSF Laboratories to usedistrict laboratorystate laboratory national laboratory

Laboratory Training for Field Epidemiologists How to select the laboratory Location Referral protocols Capacity Biosafety level Quality, accreditation or certification (e.g., Polio) Credibility, track record Costs

Laboratory Training for Field Epidemiologists Planning the laboratory investigation Formulate Objectives Plan Laboratory Analysis Determine Sampling Strategy Collect Specimens Analyze Specimens Interpret Tests Draw Conclusions

Laboratory Training for Field Epidemiologists Who to sample? Cases “typical” cases cases likely to carry the pathogen (e.g. children) untreated patients (e.g. without antibiotics) outliers (e.g. demographic, geographic) Controls laboratory controls to check that the test is indeed negative controls from a case-control study to check to confirm diagnosis (not infected) All subjects or a representative sample?

Laboratory Training for Field Epidemiologists When to sample? Once acute or convalescent phase depends on disease blood culture first, then serology (typhoid) depends on symptoms fever spikes (e.g. malaria, septicaemia) Twice acute and convalescent serum

Laboratory Training for Field Epidemiologists How many specimens to collect? Ensure sufficient number of specimens (at least 20) avoid sampling error obtain reliable results Repeat sampling acute and convalescent sera intermittent shedding (e.g. stool microscopy for parasites, bacterial endocarditis) explore chronic carriage unknown etiology Avoid overwhelming the laboratory

Laboratory Training for Field Epidemiologists Rule of thumb: cholera outbreak 10 samples to confirm the outbreak Five samples per week during the outbreak Samples at the end to confirm that the outbreak is over Source: WHO

Laboratory Training for Field Epidemiologists Planning the laboratory investigation Formulate Objectives Plan Laboratory Analysis Determine Sampling Strategy Collect Specimens Analyze Specimens Interpret Tests Draw Conclusions

Laboratory Training for Field Epidemiologists Analyze specimens Based on epidemiological information, objectives and laboratory consults determine ideal testing algorithms select tests: screening confirmatory

Laboratory Training for Field Epidemiologists Testing algorithm Standardizes and documents the approach and is: essential for quantitative studies defines what to count adapted to the investigation objectives agreed upon by epidemiologists and the laboratory Takes into account the need for information need to optimize resources (cost, staff time) Must be flexible for qualitative studies

Laboratory Training for Field Epidemiologists Testing algorithm: Hepatitis B Virus outbreak

Laboratory Training for Field Epidemiologists Testing Algorithm: HBV Outbreak Variations are possible to explore: vaccine-induced reactions fulminant infection with negative HBsAg test Final decisions are a consensus between epidemiologists laboratory The algorithm may help case management

Laboratory Training for Field Epidemiologists Source: WHO Testing Algorithm: HIV

Laboratory Training for Field Epidemiologists Planning the laboratory investigation Formulate Objectives Plan Laboratory Analysis Determine Sampling Strategy Collect Specimens Analyze Specimens Interpret Tests Draw Conclusions

Laboratory Training for Field Epidemiologists Reporting results Need to clarify from the start: When will the results be ready? Who will help interpret the results? Who will produce the report? Who is the lead? How will sensitive information will be handled? To whom will the results will be reported and not reported? careful with media-sensitive issues (e.g. cholera) Who will sign-off the final report?

Laboratory Training for Field Epidemiologists Integrating laboratory data Epidemiologic debrief should include the laboratory enables interpretation of epidemiological results in light of the laboratory evidence Review should include: interpretation - what can be concluded limitations – explains why some things cannot be concluded

Laboratory Training for Field Epidemiologists A multi-state outbreak of Hepatitis A among school children, USA 1997: Results StateEpidemiological resultsLaboratory results MichiganTwo clusters in two cities Hepatitis associated with consumption of frozen strawberries in two epidemiological studies Indistinguishable Hepatitis A virus MaineCases scattered in the state Borderline association between hepatitis and consumption of frozen strawberries Hepatitis A virus indistinguishable from the Michigan virus ArizonaHandful of cases having eaten frozen strawberries Hepatitis A virus indistinguishable from the Michigan and Maine virus

Laboratory Training for Field Epidemiologists A multi-state outbreak of Hepatitis A among school children, USA 1997: Conclusions This multi-state outbreak was caused by the consumption of the same frozen strawberries among school children Michigan - the epidemiological information is sufficient to conclude this Maine - the laboratory evidence supports the less conclusive epidemiological evidence Arizona - few cases; only the laboratory evidence allows this conclusion The smaller number of cases in Maine and Arizona may reflect a lower level of contamination of the product distributed in these two states

Laboratory Training for Field Epidemiologists Take home messages Frame objectives with the end (public health action) in mind Engage the laboratory early Create sampling strategy consistent with your objectives Collect only as many specimens as you need – don’t overdo it Create the analytical strategy Put all laboratory and epidemiology pieces together to draw conclusions

Laboratory Training for Field Epidemiologists Adapted sample taking Developed by the Department of Epidemic and Pandemic Alert and Response of the World Health Organization with assistance from: European Program for Intervention Epidemiology Training Canadian Field Epidemiology Program Thailand Ministry of Health Institut Pasteur

Laboratory Training for Field EpidemiologistsReferences Slide 37 Source: Rapid HIV tests: Guidelines for use in HIV testing and counselling services in resource- constrained settings WHO 2004