1 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases Special

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Food and Agriculture Organization of the United Nation

Regional Office for Asia and the Pacific

Emergency Center for Transboundary Animal Diseases

Special Concern for Animal Outbreak Investigation & Herd Factors

Field Epidemiology in Action14 September 2009, Khonkaen

Pawin Padungtod Regional Project Coordinator, ECTAD - RAP

[email protected]

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Unit of Analysis• Country• Province• Village/Farm• House/Flock• Animal

Herd

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• Factors related to disease spreading– Between herds : Herd level source of infection– Within a herd : Reproductive number

• Factors related to investigation result– Factors affecting validity– Factors affecting precision

Herd factors in animal disease outbreak investigation

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Herd level source of infection

• Neighboring farms

• Introduction

• Resurgence

Disease-freefarm

Animals

Humans Vehicles

Animalproducts

Wind Water

Neighbour

B. Dufour, P. Hendrikx. 2009.Epidemiological surveillance in animal health. OIE publication www.oie.int

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Herd level source of infection:Neighboring farm/country• Health status• Distance • Cross farm/border activities

Nicoline DeHaan and Jonathan Rushton. 2009.FAO

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Herd level source of infection:Introduction• Prevalence in the area

– Individual Prevalence (Animal)– Aggregate Prevalence (Farm/Village)

M. Gilbert et al. 2006. EID 12(2) : 227

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Herd level source of infection:Resurgence• Time period from last outbreak

• Agent survival

T,Tiensin et al. 2005. EID. 11(11) : 1164

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Transmission within a herd

• Transmissibility of the pathogen (SAR)• The extent of receptivity of the host• Animal husbandry

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Source of infection within a herd

• Reservoir - Receptive but not susceptible

• Carrier - Receptive and susceptible

National geographic magazine

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Source of infection within a herd

Time

Incubatorycarrier

Convalescencecarrier

Chroniccarrier

Inte

nsity

of

tran

smis

sion

Incubation RecoveryClinical sign

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Basic reproductive number (R0)• Number of new case arise from an index case in naïve population.

• R0 = b * k * d

– b = Probability of transmission per contact (case /contact)

– k = Frequency of contact (contact / time)

– d = Duration of shedding (time)

National geographic magazine

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Basic reproductive number (R0 = 1)

Day 1 2 3 4 5 6 7 8

New Cases 1 1 1 1 1 1 1 1

All Cases 1 2 3 4 5 6 7 8

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Basic reproductive number (R0)Day New

Cases

All

Cases

1 1 1

2 2 3

3 4 7

4 8 15

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Basic reproductive number (R0)

• R0 < 1 Disease subside

• R0 = 1 Endemic

• R0 > 1 Disease outbreak

• FMD R0 = 60

Time

Nu

mb

er

of

new

cases

R0=0.9

R0=1

R0=1.1

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Basic reproductive number and herd immunity

Disease cannot spread if certainProportion of the animals are not susceptible

Disease spread freely if allAnimals are susceptible

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Factors Affecting R0

• Addition of susceptible• Die-off or departure• Vector abundance• Population density• Individual mobility

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R0 exampleFMD in pigs Transmission rate

(b*k)

Infectious period

(D)

R0

Non-vaccinated 6.1 6.5 40

Vaccinated 2.0 5.3 11

Vaccinated

(4-fold dose)

0.4 2.3 1.0

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Factors Affecting Investigation Result :Validity & Precision

Validity (bias, systematic variation)

Yes No

Precision(variance,

random variation)

Yes

No

P P

P P

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Factors Affecting Precision• Sample size

– Number of population (N)– Expected number of disease animal/herds

(prevalence*N)– Confidence level

Population

Sample

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Effect of sample size on precision

Cow Herd Within Herd

n 1200 50 20

Expected prevalence 40% 10% 80%

Required sample size 283 37 19

Actual sample size 20 20 5

Absolute error 21.3% 10.2% 30.4%

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Validity• Internal validity

– Free from systematic error (bias)

0

20

40

60

80

100

treatment control

bias

variance

outcome

0

20

40

60

80

100

treatment control

bias

variance

outcome

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Validity

PopulationSimple random sampling Multi-stages sampling

Cluster1

Cluster2

Farm1

Farm2

Farm3

Farm1

Farm2

Farm3

Animal Animal Animal Animal Animal Animal

Animal

1st stage

2nd stage

3rd stage

• External validity– Good representation of the population – sampling method

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Factors Affecting Validity• Diagnostic test

characteristic– Sensitivity : P(T+|D+)– Specificity : P(T-|D-)

Infected

(D+)

Not infected

(D-)

Test positive

(T+)

90 30

Test negative

(T-)

10 870

Total 100 900

Sensitivity (SE)

Specificity (SP)

= 90 / 100 = 870 / 900

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Aggregate (pooled) testing• To determine the infection status at group level instead of

an individual– A pool of cloacal swabs from 20 chickens in a village – 10 pools, each pool contains 5 individual samples– Bulk milk tank test for antibiotic residues– Individual fecal culture from 30 cows in a herd

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Herd-level sensitivity (HSe)• Probability of obtaining at least one positive

result from an infected herd• HSe = 1 – [1 – (f * Se)]A

– f = sampling fraction– Se = individual sensitivity– A = number of infected animal

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Herd-level sensitivity (HSe)

0.00

0.20

0.40

0.60

0.80

1.00

0.1 0.3 0.5 0.7 0.9

Sampling fraction

He

rd s

en

sit

ivit

y

0.99

0.8

0.6

HSe = 1 – [1 – (f * Se)]A

A=4

f=0.2HSe0.590.500.40

f=0.6HSe0.970.930.83

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Herd-level specificity (HSp) • Probability of obtaining only negative results

from a test applied to every individual in a non-infected herd

• HSp = Spn

– Sp = Individual specificity– n = number of animals tested

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Herd-level specificity (HSp)

0.00

0.20

0.40

0.60

0.80

1.00

5 10 15 20 25 30 35 40 45 50

Number of animal tested

Herd

sp

ecif

icit

y

0.999

0.99

0.9

HSp = SpnHSp0.990.900.35 HSp

0.960.670.01

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Summary• Factors affecting transmission of diseases

– Between herd• Neighboring farms/villages• Prevalence in the area• Agent survival

– Within herd (R0)• b = Probability of transmission per contact (case /contact)• k = Frequency of contact (contact / time)• d = Duration of shedding (time)

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Summary

• Factors related to investigation result– Factors affecting precision

• Sample size

– Factors affecting validity• Diagnostic test characteristics

– HSe– HSp

• Sampling method– Simple random– Multi stages sampling

Documents

1 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases Special