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1 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 Action 14 September 2009, Khonkaen Pawin Padungtod Regional Project Coordinator, ECTAD - RAP Pawin.padungtod@fao.org
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2 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases Unit of Analysis Country Province Village/Farm House/Flock Animal Herd
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3 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 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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4 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 4 Herd level source of infection Neighboring farms Introduction Resurgence Disease-free farm Animals HumansVehicles Animal products WindWater Neighbour B. Dufour, P. Hendrikx. 2009.Epidemiological surveillance in animal health. OIE publication www.oie.intwww.oie.int
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5 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 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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6 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 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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7 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 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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8 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 8 Transmission within a herd Transmissibility of the pathogen (SAR) The extent of receptivity of the host Animal husbandry
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9 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 9 Source of infection within a herd Reservoir - Receptive but not susceptible Carrier - Receptive and susceptible National geographic magazine
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10 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 10 Source of infection within a herd Time Incubatory carrier Convalescence carrier Chronic carrier Intensity of transmission IncubationRecoveryClinical sign
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11 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 11 Basic reproductive number (R 0 ) Number of new case arise from an index case in naïve population. R 0 = 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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12 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 12 Basic reproductive number (R 0 = 1) Day 12345678 New Cases 11111111 All Cases 12345678
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13 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 13 Basic reproductive number (R0) DayNew Cases All Cases 111 223 347 4815
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14 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 14 Basic reproductive number (R0) R 0 < 1 Disease subside R 0 = 1 Endemic R 0 > 1 Disease outbreak FMD R 0 = 60
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15 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 15 Basic reproductive number and herd immunity Disease cannot spread if certain Proportion of the animals are not susceptible Disease spread freely if all Animals are susceptible
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16 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 16 Factors Affecting R 0 Addition of susceptible Die-off or departure Vector abundance Population density Individual mobility
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17 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 17 R 0 example FMD in pigsTransmission rate (b*k) Infectious period (D) R0R0 Non-vaccinated6.16.540 Vaccinated2.05.311 Vaccinated (4-fold dose) 0.42.31.0
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18 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases Factors Affecting Investigation Result : Validity & Precision Validity (bias, systematic variation) YesNo Precision (variance, random variation) Yes No P P PP
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19 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 19 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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20 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases Effect of sample size on precision CowHerdWithin Herd n12005020 Expected prevalence40%10%80% Required sample size2833719 Actual sample size20 5 Absolute error21.3%10.2%30.4%
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21 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases Validity Internal validity –Free from systematic error (bias)
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22 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases Validity Population Simple random sampling Multi-stages sampling Cluster 1 Cluster 2 Farm 1 Farm 2 Farm 3 Farm 1 Farm 2 Farm 3 Animal 1 st stage 2 nd stage 3 rd stage External validity –Good representation of the population – sampling method
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23 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases Factors Affecting Validity Diagnostic test characteristic –Sensitivity : P(T+|D+) –Specificity : P(T-|D-) Infected (D+) Not infected (D-) Test positive (T+) 9030 Test negative (T-) 10870 Total100900 Sensitivity (SE) Specificity (SP) = 90 / 100= 870 / 900
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24 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 24 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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25 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 25 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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26 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 26 Herd-level sensitivity (HSe) HSe = 1 – [1 – (f * Se)] A A=4 f=0.2 HSe 0.59 0.50 0.40 f=0.6 HSe 0.97 0.93 0.83
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27 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 27 Herd-level specificity (HSp) Probability of obtaining only negative results from a test applied to every individual in a non- infected herd HSp = Sp n –Sp = Individual specificity –n = number of animals tested
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28 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 28 Herd-level specificity (HSp) HSp = Sp n HSp 0.99 0.90 0.35 HSp 0.96 0.67 0.01
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29 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases Summary Factors affecting transmission of diseases –Between herd Neighboring farms/villages Prevalence in the area Agent survival –Within herd (R 0 ) b = Probability of transmission per contact (case /contact) k = Frequency of contact (contact / time) d = Duration of shedding (time)
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30 Food and Agriculture Organization of the United Nation Regional Office for Asia and the Pacific Emergency Center for Transboundary Animal Diseases 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
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