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Special Concern for Animal Outbreak Investigation & Herd Factors Field Epidemiology in Action 14 September 2009, Khonkaen Pawin Padungtod Regional Project Coordinator, ECTAD - RAP Pawin.padungtod@fao.org Unit of Analysis Country Province Village/Farm House/Flock Animal Herd

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special concern for animal outbreak investigation herd factors

Special Concern for Animal Outbreak Investigation & Herd Factors

Field Epidemiology in Action

14 September 2009, Khonkaen

Pawin Padungtod

Regional Project Coordinator, ECTAD - RAP

Pawin.padungtod@fao.org

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

Herd

slide3

Herd factors in animal disease outbreak investigation

  • 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 level source of infection
Herd level source of infection

Neighboring farms

Introduction

Resurgence

Neighbour

Wind

Water

Disease-free

farm

Animals

Animal

products

Humans

Vehicles

B. Dufour, P. Hendrikx. 2009.Epidemiological surveillance in animal health.

OIE publication www.oie.int

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

Nicoline DeHaan and Jonathan Rushton. 2009.FAO

herd level source of infection introduction
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

herd level source of infection resurgence
Herd level source of infection:Resurgence
  • Time period from last outbreak
  • Agent survival

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

transmission within a herd
Transmission within a herd

Transmissibility of the pathogen (SAR)

The extent of receptivity of the host

Animal husbandry

source of infection within a herd
Source of infection within a herd

Reservoir - Receptive but not susceptible

Carrier - Receptive and susceptible

National geographic magazine

source of infection within a herd10
Source of infection within a herd

Incubation

Clinical sign

Recovery

Intensity of

transmission

Time

Incubatory

carrier

Convalescence

carrier

Chronic

carrier

basic reproductive number r 0
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

basic reproductive number r014
Basic reproductive number (R0)

R0< 1 Disease subside

R0= 1 Endemic

R0> 1 Disease outbreak

FMD R0 = 60

basic reproductive number and herd immunity
Basic reproductive number and herd immunity

Disease spread freely if all

Animals are susceptible

Disease cannot spread if certain

Proportion of the animals are not

susceptible

factors affecting r 0
Factors Affecting R0

Addition of susceptible

Die-off or departure

Vector abundance

Population density

Individual mobility

factors affecting precision
Factors Affecting Precision

Sample size

Number of population (N)

Expected number of disease animal/herds (prevalence*N)

Confidence level

Population

Sample

validity
Internal validity

Free from systematic error (bias)

Validity
validity22
External validity

Good representation of the population – sampling method

Population

Multi-stages sampling

Simple random sampling

Cluster

1

Cluster

2

1st stage

Farm

1

Farm

2

Farm

3

Farm

1

Farm

2

Farm

3

2nd stage

3rd stage

Animal

Animal

Animal

Animal

Animal

Animal

Animal

Validity
factors affecting validity
Factors Affecting Validity
  • Diagnostic test characteristic
    • Sensitivity : P(T+|D+)
    • Specificity : P(T-|D-)
aggregate pooled testing
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

herd level sensitivity hse
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

herd level sensitivity hse26
Herd-level sensitivity (HSe)

f=0.6

HSe

0.97

0.93

0.83

HSe = 1 – [1 – (f * Se)]A

A=4

f=0.2

HSe

0.59

0.50

0.40

herd level specificity hsp
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

herd level specificity hsp28
Herd-level specificity (HSp)

HSp

0.99

0.90

0.35

HSp = Spn

HSp

0.96

0.67

0.01

summary
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)
summary30
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