Estimating patterns and drivers of infection prevalence and intensity when detection is imperfect and sampling error occurs

David A.W. Miller, Brooke L. Talley, Karen R. Lips, Evan H. Campbell Grant

Research output: Contribution to journalArticle

42 Citations (Scopus)

Abstract

Epidemiological studies are crucial for understanding the distribution and dynamics of emerging infectious diseases. To accurately assess infection states in wild populations, researchers need to account for observational uncertainty. We focus on two sources of uncertainty when estimating epidemiological parameters: nondetection of infection in sampled individuals and sampling error when quantifying infection intensity for infected individuals. We developed new analytical methods to simultaneously estimate prevalence and the distribution of infection intensities based on repeated sampling of individuals in the wild. The methods are an extension of those used for occupancy estimation and address both sources of observation error. At the same time, we account for heterogeneity in detection probability that results from individual variation in infection intensity. We use two estimation approaches to account for detection. The first is to use the complete likelihood in a hierarchical Bayesian model and fit using Markov chain Monte Carlo sampling. The second is to estimate the detection relationship using a mark-recapture abundance estimator and use those results to calculate weighted estimates for prevalence and mean infection intensities. We use data from a field survey of Batrachochytrium dendrobatidis in Illinois amphibians to test these methods. We show that detection probability using quantitative PCR is strongly related to infection intensity, measured in zoospore equivalents. Sites in the study varied greatly in estimated prevalence and to a lesser extent in mean infection intensities of infected individuals. We did not find evidence of a relationship of snout-vent-length to infection intensity or prevalence. Naïve estimates of prevalence that do not account for detection were less than estimates for either of our methods, which yielded similar prevalence values for most sites. Uncertainty when assessing disease state is a characteristic of most diagnostic tests. The estimators presented here account for this uncertainty and thus can improve accuracy when assessing the relationship of ecological factors to prevalence and infection intensity.

Original languageEnglish (US)
Pages (from-to)850-859
Number of pages10
JournalMethods in Ecology and Evolution
Volume3
Issue number5
DOIs
StatePublished - Oct 1 2012

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sampling
infection
uncertainty
detection
emerging diseases
zoospores
individual variation
infectious disease
Markov chain
wild population
diagnostic techniques
amphibian
epidemiological studies
field survey
analytical methods
amphibians
analytical method
quantitative polymerase chain reaction
researchers
methodology

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Ecological Modeling

Cite this

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abstract = "Epidemiological studies are crucial for understanding the distribution and dynamics of emerging infectious diseases. To accurately assess infection states in wild populations, researchers need to account for observational uncertainty. We focus on two sources of uncertainty when estimating epidemiological parameters: nondetection of infection in sampled individuals and sampling error when quantifying infection intensity for infected individuals. We developed new analytical methods to simultaneously estimate prevalence and the distribution of infection intensities based on repeated sampling of individuals in the wild. The methods are an extension of those used for occupancy estimation and address both sources of observation error. At the same time, we account for heterogeneity in detection probability that results from individual variation in infection intensity. We use two estimation approaches to account for detection. The first is to use the complete likelihood in a hierarchical Bayesian model and fit using Markov chain Monte Carlo sampling. The second is to estimate the detection relationship using a mark-recapture abundance estimator and use those results to calculate weighted estimates for prevalence and mean infection intensities. We use data from a field survey of Batrachochytrium dendrobatidis in Illinois amphibians to test these methods. We show that detection probability using quantitative PCR is strongly related to infection intensity, measured in zoospore equivalents. Sites in the study varied greatly in estimated prevalence and to a lesser extent in mean infection intensities of infected individuals. We did not find evidence of a relationship of snout-vent-length to infection intensity or prevalence. Na{\"i}ve estimates of prevalence that do not account for detection were less than estimates for either of our methods, which yielded similar prevalence values for most sites. Uncertainty when assessing disease state is a characteristic of most diagnostic tests. The estimators presented here account for this uncertainty and thus can improve accuracy when assessing the relationship of ecological factors to prevalence and infection intensity.",
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Estimating patterns and drivers of infection prevalence and intensity when detection is imperfect and sampling error occurs. / Miller, David A.W.; Talley, Brooke L.; Lips, Karen R.; Campbell Grant, Evan H.

In: Methods in Ecology and Evolution, Vol. 3, No. 5, 01.10.2012, p. 850-859.

Research output: Contribution to journalArticle

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