Adapted sample taking
Planning a Strategy
for
Laboratory Investigations
May 2007
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
A N D
R E S P O N S E
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
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Laboratory Training for FieldEEpidemiologists
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Planning an Epidemiologic
Investigation
Formulate
Objectives
Interpret Data
Draw Conclusions
Plan Data Analysis
Analyze Data
Develop Data
Collection Instruments
and Sampling Strategy
Collect Data
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
A N D
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Planning a Laboratory
Investigation
Formulate
Objectives
Interpret Tests
Draw Conclusions
Plan Laboratory Analysis
Analyze Specimens
Determine Sampling
Strategy
Collect Specimens
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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Planning a Collaborative Investigation
Formulate
Objectives
Interpret Results and
Draw Conclusions
Plan
Analyse
Lab needs
Data needs
Prepare
Instruments and
Sampling Strategy
Specimens
Data
Collect
Sampling
strategy
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Laboratory Training for FieldEEpidemiologists
Data
A N D
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Specimens
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?
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
A N D
R E S P O N S E
Planning the laboratory
Investigation
Formulate
Objectives
Interpret Tests
Draw Conclusions
Plan Laboratory Analysis
Analyze Specimens
Determine Sampling
Strategy
Collect Specimens
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
A N D
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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)
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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)
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Laboratory Training for FieldEEpidemiologists
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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
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
A N D
R E S P O N S E
Planning the laboratory
investigation
Formulate
Objectives
Interpret Tests
Draw Conclusions
Plan Laboratory Analysis
Analyze Specimens
Determine Sampling
Strategy
Collect Specimens
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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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)
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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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
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
A N D
R E S P O N S E
Planning the laboratory
investigation
Formulate
Objectives
Interpret Tests
Draw Conclusions
Plan Laboratory Analysis
Analyze Specimens
Determine Sampling
Strategy
Collect Specimens
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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Which specimens to collect?
1.
What are the suspected pathogens?
2.
What tests are available to identify the suspected
pathogens?
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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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?
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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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
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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
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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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
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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
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Laboratory Training for FieldEEpidemiologists
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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)
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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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
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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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
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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Cluster of febrile rash*
(Middle East)
Suspect pathogen
Possible tests
Measles Virus
Measles IgM ELISA
virus isolation?
Specimens needed
acute serum
urine sample?
Laboratories to use
district laboratory
reference laboratory?
*consistent with measles case definition
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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Cluster of febrile neurological syndrome
(Uttar Pradesh, India)
Suspect pathogens
Proposed tests
Bacterial meningitis
Japanese
encephalitis
Enterovirus
encephalitis
CSF - bacteriology
serology
serology
(serum, CSF)
culture
(stool, CSF)
Specimens needed
CSF
acute and
convalescent
serum
acute and
convalescent
serum
stool and
CSF
Laboratories to use
district laboratory
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Laboratory Training for FieldEEpidemiologists
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state
laboratory
R E S P O N S E
national
laboratory
How to select the laboratory
•
Location
•
Referral protocols
•
Capacity
•
Biosafety level
•
Quality, accreditation or certification (e.g., Polio)
•
Credibility, track record
•
Costs
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
A N D
R E S P O N S E
Planning the laboratory
investigation
Formulate
Objectives
Interpret Tests
Draw Conclusions
Plan Laboratory Analysis
Analyze Specimens
Determine Sampling
Strategy
Collect Specimens
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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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?
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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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
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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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
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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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
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
A N D
R E S P O N S E
Planning the laboratory
investigation
Formulate
Objectives
Interpret Tests
Draw Conclusions
Plan Laboratory Analysis
Analyze Specimens
Determine Sampling
Strategy
Collect Specimens
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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Analyze specimens
•
Based on epidemiological information, objectives and
laboratory consults
• determine ideal testing algorithms
• select tests:
• screening
• confirmatory
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Laboratory Training for FieldEEpidemiologists
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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
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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Testing algorithm:
Hepatitis B Virus outbreak
Total Anti-HBc
(Test for exposure to HBV)
Positive
Negative
HBsAg
(Test for current infection)
Positive
Negative
IgM anti-HBc
(Test for recent infection)
Positive
Recent infection
Absence of infection
Natural immunity
Negative
Chronic infection
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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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
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Laboratory Training for FieldEEpidemiologists
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Testing
Algorithm:
HIV
Source: WHO
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
A N D
R E S P O N S E
Planning the laboratory
investigation
Formulate
Objectives
Interpret Tests
Draw Conclusions
Plan Laboratory Analysis
Analyze Specimens
Determine Sampling
Strategy
Collect Specimens
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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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?
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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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
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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A multi-state outbreak of Hepatitis A among
school children, USA 1997: Results
State
Michigan
Epidemiological results
Two clusters in two cities
Hepatitis associated with
consumption of frozen
strawberries in two
epidemiological studies
Maine
Cases scattered in the state
Borderline association
between hepatitis and
consumption of frozen
strawberries
Arizona
Handful of cases having eaten
frozen strawberries
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Laboratory results
Indistinguishable Hepatitis A
virus
Hepatitis A virus
indistinguishable from the
Michigan virus
Hepatitis A virus
indistinguishable from the
Michigan and Maine virus
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
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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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
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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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
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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References
Slide 37
• Source: Rapid HIV tests: Guidelines for use in HIV
testing and counselling services in resourceconstrained settings WHO 2004
P I D E M I C A L E R T
Laboratory Training for FieldEEpidemiologists
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