Inferring pathogen presence when sample misclassification and partial observation occur

1. Surveillance programmes are essential for detecting emerging pathogens and often rely on molecular methods to make inference about the presence of a target disease agent. However, molecular methods rarely detect target DNA perfectly. For example, molecular pathogen detection methods can result in misclassification (i.e. false positives and false negatives) or partial detection errors (i.e. detections with ' ambiguous ', ' uncertain ' or ' equivocal ' results). Then, when data are to be analysed, these partial observations are either discarded or censored; this, however, disregards information that could be used to make inference about the true state of the system. There is a critical need for more direction and guidance related to how many samples are enough to declare a unit of interest ' pathogen free '. 2. Here, we develop a Bayesian hierarchal framework that accommodates false negative, false positive and uncertain detections to improve inference related to the occupancy of a pathogen. We apply our modelling framework to a case study of the fungal pathogen Pseudogymnoascus destructans (Pd) identified in Texas bats at the invasion front of white-nose syndrome. To improve future surveillance programmes, we provide guidance on sample sizes required to be 95% certain a target organism is absent from a site. 3. We found that the presence of uncertain detections increased the variability of resulting posterior probability distributions of pathogen occurrence, and that our estimates of required sample size were very sensitive to prior information about pathogen occupancy, pathogen prevalence and diagnostic test specificity. In the Pd case study, we found that the posterior probability of occupancy was very low in 2018, but occupancy probability approached 1 in 2020, reflecting increasing prior probabilities of occupancy and prevalence elicited from the site manager. 4. Our modelling framework provides the user a posterior probability distribution of pathogen occurrence, which allows for subjective interpretation by the decision-maker. To help readers apply and use the methods we developed, we provide an interactive RShiny app that generates target species occupancy estimation and sample size estimates to make these methods more accessible to the scientificcommunity(https://rmummah.shinyapps.io/ambigDetect_sampleSize). This modelling framework and sample size guide may be useful for improving inferences from molecular surveillance data about emerging pathogens, non-native invasive species and endangered species where misclassifications and ambiguous detections occur.

Automated summary

Surveillance programmes rely on molecular methods to detect emerging pathogens, but these methods often result in misclassifications or ambiguous detections. This study develops a Bayesian framework to improve inference and provides guidance on sample sizes for better surveillance programmes.