Occupancy Modeling for Improved Accuracy and Understanding of Pathogen Prevalence and Dynamics

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 salmincola/ metacercariae, and Renibacterium salmoninarum. A hierarchical occupancy model was developed to estimate pathogen and tissue-specific test sensitivities and unbiased estimation of host- and organ-level infection rates. Model estimated sensitivities and host- and organ-level infections rates varied among pathogens and model estimated infection rate was higher than prevalence unadjusted for test sensitivity, confirming that prevalence unadjusted for test sensitivity was negatively biased. The modeling approach provided an analytical approach for using hierarchically structured pathogen detection data from lower sensitivity diagnostic tests, such as histology, to obtain unbiased pathogen prevalence estimates with associated uncertainties. Accounting for test sensitivity using within host replicate samples also required fewer individual fish to be sampled. This approach is useful for evaluating pathogen or microbe community dynamics when test sensitivity is <100%.     

Elevated intra-rumen pressure and secondary rumen contractions in sheep (Ovis aries)

1. Sheep rumens were insufflated with nitrogen to 5, 10, 15, and 20 cm water pressure and sustained at each pressure for 10 min. 2. Measurements included rumen motility, reticulorumen myoelectric activity, eructation frequency and volume, changes in tracheal pressure and rumen contraction amplitude. 3. As intra-rumen pressure increased, contractions designated as special secondary contractions appeared. 4. At a pressure of approximately 15 cm water, most of the special secondary contractions became regular secondaries; therefore, the special secondaries were called pro-secondary contractions. 5. Increased intra-rumen pressure was associated with respiratory distress. The recovery phase following, rumen insufflation was accompanied by hyperpnea.     

Salmonella spp. in nestling common barn-owls (Tyto alba) from southwestern New Jersey

The prevalence of Salmonella spp. in nestling common barn-owls was investigated in southwestern New Jersey during the summer of 1985. Of 94 owls sampled by swabbing the cloaca, eight (8.5%) were found to harbor Salmonella spp. Three serotypes--S. thompson, S. tuindorp, and S. typhimurium--were identified. Five (20%) of the 25 nest sites examined (all of them in or near farm buildings or dwellings) contained Salmonella-positive owls.