laboratory training for field epidemiologists planning a strategy for laboratory investigations...

E P I D E M I C A L E R T A N D R E S P O N S E Laboratory Training for Field Epidemiologists

Planning a Strategy for

Laboratory Investigations

Adapted sample taking

May 2007


Learning objectivesLearning 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


Planning an Epidemiologic Planning an Epidemiologic InvestigationInvestigation

Formulate Objectives

Plan Data Analysis

Develop Data

Collection Instruments and Sampling Strategy

Collect Data

Analyze Data

Interpret Data Draw Conclusions


Planning a Laboratory InvestigationPlanning a Laboratory Investigation


Plan Laboratory Analysis

Determine Sampling Strategy

Collect Specimens

Analyze Specimens

Interpret Tests Draw Conclusions


Planning a Collaborative InvestigationPlanning a Collaborative Investigation


Plan

Prepare

Analyse

Interpret Results and Draw Conclusions

Collect

Data needs

Instruments and Sampling Strategy

Data

DataLab needs

Sampling strategy

Specimens

Specimens


Why Plan?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?


Planning the laboratory InvestigationPlanning the laboratory Investigation




Collect Specimens

Analyze Specimens



Define objectives 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)


Confidentiality and ConsentConfidentiality 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)


Ethical considerations 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


Planning the laboratory investigationPlanning the laboratory investigation




Collect Specimens

Analyze Specimens



Laboratory Involvement Laboratory Involvement in the Field 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)


Communicating with the Laboratory 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






Collect Specimens

Analyze Specimens



Which specimens to collect?Which specimens to collect?

1. What are the suspected pathogens?

2. What tests are available to identify the suspected pathogens?



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?



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


Typical scenarioTypical 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


Sampling strategy: typical scenarioSampling 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


Unusual scenarioUnusual 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


Sampling strategy: Unusual scenario 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)


Sampling strategy: Unusual scenarioSampling 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


Assess the situation 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


Cluster of febrile rash* Cluster of febrile rash* (Middle East)(Middle East)

Suspect pathogen Measles Virus

Possible tests Measles IgM ELISA virus isolation?

Specimens needed acute serum urine sample?

Laboratories to use district laboratory reference laboratory?

*consistent with measles case definition


Cluster of febrile neurological syndrome Cluster of febrile neurological syndrome (Uttar Pradesh, India)(Uttar Pradesh, India)

Suspect pathogens Bacterial meningitis Japanese encephalitis

Enterovirus encephalitis

Proposed tests 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 state laboratory

national laboratory


How to select the laboratoryHow to select the laboratory

• Location

• Referral protocols

• Capacity

• Biosafety level

• Quality, accreditation or certification (e.g., Polio)

• Credibility, track record

• Costs






Collect Specimens

Analyze Specimens



Who to sample?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?


When to sample?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


How many specimens to collect?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


Rule of thumb: cholera outbreakRule 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






Collect Specimens

Analyze Specimens



Analyze specimensAnalyze specimens

• Based on epidemiological information, objectives and laboratory consults

• determine ideal testing algorithms

• select tests:

• screening

• confirmatory


Testing algorithm 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


Testing algorithm: Testing algorithm: Hepatitis B Virus outbreak Hepatitis B Virus outbreak

Recent infection

Positive

Chronic infection

Negative

IgM anti-HBc(Test for recent infection)

Positive

Natural immunity

Negative

HBsAg(Test for current infection)

Positive

Absence of infection

Negative

Total Anti-HBc(Test for exposure to HBV)


Testing Algorithm: HBV OutbreakTesting 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


Source: WHO

Testing Testing Algorithm: HIVAlgorithm: HIV






Collect Specimens

Analyze Specimens



Reporting resultsReporting resultsNeed 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?


Integrating laboratory dataIntegrating 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


A multi-state outbreak of Hepatitis A among school A multi-state outbreak of Hepatitis A among school children, USA 1997: Resultschildren, USA 1997: Results

State Epidemiological results Laboratory results

Michigan Two clusters in two cities

Hepatitis associated with consumption of frozen strawberries in two epidemiological studies

Indistinguishable Hepatitis A virus

Maine Cases scattered in the state

Borderline association between hepatitis and consumption of frozen strawberries

Hepatitis A virus indistinguishable from the Michigan virus

Arizona Handful of cases having eaten frozen strawberries

Hepatitis A virus indistinguishable from the Michigan and Maine virus


A multi-state outbreak of Hepatitis A among school A multi-state outbreak of Hepatitis A among school children, USA 1997: Conclusionschildren, 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


Take home messagesTake 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


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


ReferencesReferences

Slide 37

• Source: Rapid HIV tests: Guidelines for use in HIV testing and counselling services in resource-constrained settings WHO 2004

laboratory training for field epidemiologists planning a strategy for laboratory investigations...

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laboratory tests

laboratory investigations

laboratory analysis

laboratory requirements

laboratory analysis

sampling strategy specimens

investigation objectives