Occupancy modeling for improved accuracy and understanding of pathogen prevalence and dynamics

PloS One
Michael E ColvinCarl B Schreck

Abstract

Most pathogen detection tests are imperfect, with a sensitivity < 100%, thereby resulting in the potential for a false negative, where a pathogen is present but not detected. False negatives in a sample inflate the number of non-detections, negatively biasing estimates of pathogen prevalence. Histological examination of tissues as a diagnostic test can be advantageous as multiple pathogens can be examined and providing important information on associated pathological changes to the host. However, it is usually less sensitive than molecular or microbiological tests for specific pathogens. Our study objectives were to 1) develop a hierarchical occupancy model to examine pathogen prevalence in spring Chinook salmon Oncorhynchus tshawytscha and their distribution among host tissues 2) use the model to estimate pathogen-specific test sensitivities and infection rates, and 3) illustrate the effect of using replicate within host sampling on sample sizes required to detect a pathogen. We examined histological sections of replicate tissue samples from spring Chinook salmon O. tshawytscha collected after spawning for common pathogens seen in this population: Apophallus/echinostome metacercariae, Parvicapsula minibicornis, Nanophyetus sal...Continue Reading

References

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Citations

Jun 10, 2018·Parasites & Vectors·Julie Alice SimonMarie-Lazarine Poulle
Jun 7, 2018·Frontiers in Veterinary Science·Shelly Lachish, Kris A Murray
Jan 23, 2020·Journal of Aquatic Animal Health·Carson F H WhiteWendy A Monk

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Methods Mentioned

BETA
PCR
enzyme linked immunosorbent assay
ELISA

Software Mentioned

R
R2WinBUGS
WinBUGS

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