Interpretation of laboratory and epidemiological evidence

Yvan Hutin and Aftab Jasir

Conducting a collaborative epidemiology-laboratory investigation

Formulating the objectives

Planning

Preparing

Analysing

Drawing conclusions

Collecting

Data analysis

Instruments Data

DataLab analysis

Sampling strategy

Specimens

Specimens

When faced with the need to interpret evidence, bear in mind why the investigation was conduced

Dictionary definition of the verb: Interpret

“Explain the meaning of…”

Description and interpretation in neurophysiology

• Occipital cortex, visual zone: I see concentric circles

• Pre-visual zone: This is a TARGET!

Description and interpretation in a relationship

Description • S/he did not call back

Interpretation• S/he is angry

• S/he is shy

• S/he is too in love

• There is someone else

• I said something wrong

• S/he lost my number

• I was too insistent

• The parents disagree

• Horoscopes do not match

Probably not enough data to conclude….

Description and interpretation in clinical practice

Situation Description Interpretation

Chest X-ray •Alveolar opacity•Systematized, lobar opacity

•Consolidation (Pneumonia?)

Dermatology •Copper papules•Soles and palms•Desquamation

•Secondary syphilis

Language and interpretation

(1) Describe and (2) interpret: What is this?

Pay attention to the language you used

• If you used the word “ear” you make it a rabbit

• If you used the word “beak”, you make it a duck

Jastrow

Interpretation of descriptive epidemiological data to generate

hypotheses

Narrow epidemic curve

Cluster of cases @ public tap

Case patients used the tap

Time

Place

Person

Hypothesis:The public tap was contaminated for a brief duration and caused the outbreak

Interpretation of analytical epidemiological data and additional

investigations to test an hypothesis

Strong association water drinking / illness

High attributable fraction

Water positive for S. Typhi

OR

AFP

Wateranalysis

Epidemiological evidence supported the hypothesis of the tap as the source of the outbreak

X-contamination sewage / water supply

Sanitaryassessment

Sewage contaminated the tap with S. Typhi and caused the outbreak

Elements to consider before interpreting association as causation

? Chance? Bias? Confounding factor? Causation

? Strength of the association? Dose response? Consistency? Biological plausibility? Exposure/ outcome sequence

Casting the net and pulling it up

Descriptive epidemiological data

generates hypotheses

Analytical epidemiological data

tests hypotheses

Can you guess why two different fishermen?

Language used for data description and data interpretation

Description: Results• Cases started to occur at

5AM, peaked at 7AM and decreased with a last case at 10AM

• Cases clustered around cooling tower A

• Malaria rates were high in all age groups

• Cases were more likely than controls to lack health insurance

Interpretation: Discussion

• The shape of the epidemic curve suggested a point source outbreak

• We suspected that tower A was the source of outbreak

• Unstable transmission does not lead to population immunity

• Access to health care may increase the risk of illness

Interpretation of data in a discussion section of a paper

+

=

Example of integration of various pieces of evidence into an

interpretation• Outbreak of cutaneous anthrax • Beef slaughter in West Bengal, India

• Cohort study • Contact with meat is a risk factor

• Null hypothesis: Eating meat does not cause cutaneous

anthrax

Attack rate of anthrax by exposures, Sarkarpara, Murshidabad, WB, India,

2007

Exposures  AR in exposed (%)AR in unexposed

(%)

Association

RR 95% CI Age > 20 18 11 1.6 0.9-3

Female sex 17 14 1.2 0.7-2

Slaughter 83 9 8.7 6-13

Handling 26 10 2.6 2-4

Carry skins 100 15 6.7 5- 9

Eating 17 0 Undefined

All case-patients who had eaten meat had also other exposures

Other elements of evidence beyond epidemiological data

• Elements available before the outbreak– Heat inactivate spores

– Infected meat causes intestinal disease

– Meat involved in intestinal outbreakswas poorly cooked (e.g., Kebabs)

• Elements from the outbreak investigation– The beef meat was boiled

Testing the hypothesis that eating meat could cause cutaneous anthrax

+

=

Always consider other hypotheses

✘Avoid: We found that… This could be due to... [this real

phenomenon]

Prefer: The results are … Two possibilities

• This could be due to this real phenomenon• This could be an artifact of the study

Examine both options See what the data support and conclude

Dealing with an un-expected finding

• One unexpected exposure is associated with outcome

• Absence of context No other studies No biological rationale

• Treat as a hypothesis generation: This association should be examined in other studies

• Do not force an explanation/ rationalization✘ “This may be due to…”

Risk factors for post-traumatic stress disorder (PTSD), Indian Tsunami,

2005• Unexpected effect modification:• Single woman more PTSD than married This may be due to the fact that they are alone…

• Coding error: It’s the converse that is true!• Married women have more PTSD

This may be due to the fact that they have to deal with their whole family…

✘ Do not force interpretations Propose further studies to look into it

Take home message

• Interpretation has a subjective component– Requires a careful, documented approach

• We raise hypotheses with descriptive epidemiology and test them with analytical epidemiology

• Findings acquire a meaning in the context of what was known before

Conducting a collaborative epidemiology-laboratory investigation

Formulating the objectives

Planning

Preparing

Analysing

Drawing conclusions

Collecting

Data analysis

Instruments Data

DataLab analysis

Sampling strategy

Specimens

Specimens

When faced with the need to interpret evidence, bear in mind why the investigation was conduced

Possible objectives of joint laboratory epidemiology investigations

• Test a hypothesis (Qualitative outcome)– Test a hypothesis

• About an etiologic agent(e.g., Is West Nile virus the cause of the outbreak?)

• About the relatedness of isolates(e.g., Are the cases caused by an identical pathogen?)

• Measure a quantity (Quantitative outcome)– Estimate a quantity

• Prevalence

• Incidence

Using laboratory evidence to confirm a diagnosis during an outbreak

• Short list potential etiologic agents (Hypothesis generating) according to:– Epidemiological characteristics

– Clinical characteristics

– Setting

• Test for agents short listed (Hypothesis testing)– Positive test

– Negative test

• Use predictive values positive and negatives

Case scenario 1Viral Hemorrhagic Fever (VHF)

• Fever

• Bleeding disorders

• Progress to high fever

• Shock

• High case fatality

Virus families causing VHF sensitive or specific?

Short listing?

Diverse group of animal and human illnesses that may be caused by five distinct families of RNA viruses

• Arenaviridae, (Lymphocytic choriomeningitis virus, Lassa virus, Argentine, Bolivian, Brazilian and Venezuelan hemorrhagic fevers viruses)

• Filoviridae (Ebola virus and Marburg virus)

• Bunyaviridae (Hantaviruses, Crimean-Congo hemorrhagic fever)

• Flaviviridae (dengue, yellow fever, WNV)

• Rhabdoviridae (Lyssavirus)

Interpreting positive tests results during an outbreak

• Use the predictive value positive that depends upon:– The frequency of the disease

– The specificity of the test +++

• Elements that support the hypothesis of a true positive– The disease is frequent (GAS)

– The test is specific ( emm typing)

• Elements that support the hypothesis of a false positive– The disease is rare (WNV)

– The test is not sufficiently specific (CFT)

Interpreting negative tests results during an outbreak

• Use the predictive value negative that depends upon:– The frequency of the disease

– The sensitivity of the test +++

• Elements that support the hypothesis of a true negative– The disease is rare (WNV)

– The test is sensitive (IgM ELISA)

• Elements that support the hypothesis of a false negative– The disease (condition) is common (GAS, Q fever)

– The test is not sufficiently sensitive(Gram staining/PCR)

A test was negative only for the pathogens that were looked for

• If the culture on a specific medium was not done, the test cannot be interpreted as negative for the specific pathogen

• If you did not ask for Campylobacter culture, the “negative” stool culture is not really “negative” for Campylobacter

Host-pathogen relationship

• Presence of an organism may have different interpretation according to the context

• Immune system– Immunocompetent patient

• Opportunistic pathogens may be innocent

– Immunocompromised patient

• Opportunistic pathogens may be the cause of the infection

• Age (pertussis)

• Physiological status (e.g., Urinary infection in pregnancy)

Possible objectives of joint laboratory epidemiology investigations

• Test a hypothesis (Qualitative outcome)– Test a hypothesis

• About an etiologic agent(e.g., Is West Nile virus the cause of the outbreak?)

• About the relatedness of isolates(e.g., Are the cases caused by an identical pathogen?)

• Measure a quantity (Quantitative outcome)– Estimate a quantity

• Prevalence

• Incidence

Using laboratory evidence to confirm the relatedness of isolates

• Generate hypotheses using epidemiological evidence– Studies allowing the use of statistical tests (Large sample size)

– Studies not allowing the use of statistical tests (Small sample size)

• Test hypotheses using laboratory evidence– Use typing technique adapted to:

• Hypothesis

• Pathogen

Nosocomial IGAS infections,Skåne, Southern Sweden, 2012

• 43 cases of invasive Group A Streptococcus (iGAS) between 9 January and 29 April 2012

• 27 cases between 3 January and 24 April 2011

• Thirteen of the 43 cases in 2012 were treated in an Intensive Care Unit. One case, a 84 year old already hospitalised prior to iGAS diagnosis, died

• Hospital rejects the hypothesis of nosocomial infections

IGAS cases typing results, Skåne, Sweden, 2012

Typing(EMM/PFGE)

N %

emmst1 / P7 20 47%emmst3 / P1 15 35%emmst28 / P6 2 5%emmst81 / P2 2 5%emmst89 / P5 2 5%emmst4 / P3 1 2%emmst1 / P4 1 2%

Cases of IGAS by date of onset, Skåne, Sweden, 2012

Toxin (superantigen) pattern, IGAS, Skåne, Sweden, 2012

PHASE 1 emmst3 / P1

PHASE 2 emmst1 / P7

other subtypes Total

# (n=15) % #(n=20) % # (n=8) % # (n=43) %

SPE_A 15 100% 20 100% 1 13% 36 84%

SPE_B 15 100% 20 100% 8 100% 43 100%

SPE_C 15 100% 20 100% 3 38% 38 88%

SPE_F 15 100% 20 100% 8 100% 43 100%SPE_G 14 93% 19 95% 7 88% 40 93%SPE_H 5 33% 19 95% 5 63% 29 67%SPE_I 0 0% 0 0% 0 0% 0 0%SPE_J 7 47% 3 15% 3 38% 13 30%

SSA 15 100% 20 100% 1 13% 36 84%

Possible objectives of joint laboratory epidemiology investigations

• Test a hypothesis (Qualitative outcome)– Test a hypothesis

• About an etiologic agent(e.g., Is West Nile virus the cause of the outbreak?)

• About the relatedness of isolates(e.g., Are the cases caused by an identical pathogen?)

• Measure a quantity (Quantitative outcome)– Estimate a quantity

• Prevalence

• Incidence

Interpreting prevalence and incidence

• A study estimating the frequency of a disease on the basis of a laboratory test (e.g., serological survey) must be interpreted according to:– Predictive value positive

– Predictive value negative

• These will depend upon:– The test used (sensitivity and specificity)

– The frequency of the disease

Be careful about what the manufacturer may say about the predictive values

• The manufacturer may report values of – Sensitivity

– Specificity

• These probably come from panel testing

• Be careful with values of predictive values positive and negative reported by manufacturers – These values depends upon specific prevalence settings

– They may come from a combination of a positive and negative panels that generate an artificial prevalence of 50%

Take home message: Interpret epidemiological and laboratory

evidence as a team • Positive tests are likely to rule in the diagnosis if the

test is specific and the disease is common

• Negative tests are likely to rule out the diagnosis if the test is sensitive and the disease is uncommon

• Emergent pathogens are discovered in the laboratory and assessed according to additional studies

• Laboratory investigations of relatedness must be based on hypotheses developed on the basis of the epidemiology

• Interpret incidence and prevalence indicators according to predictive values positive and negative