Detecting Leishmania in dogs: A hierarchical-modeling approach to investigate the performance of parasitological and qPCR-based diagnostic procedures

Abstract

Background Domestic dogs are primary reservoir hosts of Leishmania infantum, the agent of visceral leishmaniasis. Detecting dog infections is central to epidemiological inference, disease prevention, and veterinary practice. Error-free diagnostic procedures, however, are lacking, and the performance of those available is difficult to measure in the absence of fail-safe “reference standards”. Here, we illustrate how a hierarchical-modeling approach can be used to formally account for false-negative and false-positive results when investigating the process of Leishmania detection in dogs. Methods/Findings We studied 294 field-sampled dogs of unknown infection status from a Leishmania-endemic region. We ran 350 parasitological tests (bone-marrow microscopy and culture) and 1,016 qPCR assays (blood, bone-marrow, and eye-swab samples with amplifiable DNA). Using replicate test results and site-occupancy models, we estimated (a) clinical sensitivity for each diagnostic procedure and (b) clinical specificity for qPCRs; parasitological tests were assumed 100% specific. Initial modeling revealed qPCR specificity < 94%; we tracked the source of this unexpected result to some qPCR plates having subtle signs of possible contamination. Using multi-model inference, we formally accounted for suspected plate contamination and estimated qPCR sensitivity at 49–53% across sample types and dog clinical conditions; qPCR specificity was high (95–96%), but fell to 81–82% for assays run in plates with suspected contamination. The sensitivity of parasitological procedures was low (~12–13%), but increased to ~33% (with substantial uncertainty) for bone-marrow culture in seriously-diseased dogs. Leishmania-infection frequency estimates (~49–50% across clinical conditions) were lower than observed (~60%). Conclusions We provide statistical estimates of key performance parameters for five diagnostic procedures used to detect Leishmania in dogs. Low clinical sensitivies likely reflect the absence of Leishmania parasites/DNA in perhaps ~50–70% of samples drawn from infected dogs. Although qPCR performance was similar across sample types, non-invasive eye-swabs were overall less likely to contain amplifiable DNA. Finally, modeling was instrumental to discovering (and formally accounting for) possible qPCR-plate contamination; even with stringent negative/blank-control scoring, ~4–5% of positive qPCRs were most likely false-positives. This work shows, in sum, how hierarchical site-occupancy models can sharpen our understanding of the problem of diagnosing host infections with hard-to-detect pathogens including Leishmania.