Roberts, E. K. | bioRxiv Science

bioRxiv2022

Prospecting for zoonotic pathogens using targeted DNA enrichment

There are over 60 zoonoses linked to small mammals, including some of the most devastating pathogens in human history. Meanwhile, millions of museum-archived tissues are available to understand natural history of these pathogens. Our goal is to maximize the value of museum collections for pathogen-based research using targeted sequence capture. To this end, we have generated a probe panel that includes 39,916, 80bp RNA probes targeting 32 pathogen groups, including bacteria, helminths, fungi, and protozoans. Lab generated, mock control samples show that we are capable of enriching targeted loci from pathogen DNA 2,882 to 6,746-fold. Further, we were able to identify bacterial species in museum-archived samples, including Bartonella, a known human zoonosis. These results show that probe-based enrichment of pathogens is a highly customizable and efficient method for identifying pathogens from museum-archived tissues.

genomics↗

bioRxiv2022

A Non-invasive, Biomarker Assay for Detecting Chronic Wasting Disease Pathology in White-tailed Deer

We describe a blood test that exploits differences in the abundance of diagnostic miRNA biomarkers associated with prion infections in cervids. Using sera from 93 pen-raised white-tailed deer euthanized after unintentional exposure to Chronic Wasting Disease (CWD), quantification of candidate reference and diagnostic miRNAs revealed sensitivity of the q-RT-PCR method to interference from sample degradation, requiring exclusion of 60 specimens that exhibited excessive hemolysis or yielded poor amplification of reference or diagnostic miRNAs. Subsequent quantification of three potentially diagnostic and two control miRNAs in the 33 remaining, minimally degraded sera established diagnostic criteria congruent (100% sensitivity, 92.3% specificity, 93.9% accuracy) with results from standard CWD diagnosis by microscopic detection of immunoreactivity in obex and/or medial retropharyngeal lymph nodes (conducted by the National Veterinary Services Laboratory, NVSL, Ames, IA). Overall, the miRNA assay proved to be at least as accurate and sensitive as other CWD testing alternatives to immunohistochemical diagnosis, albeit supported by data from relatively few animals owing to the challenge of acquiring usable specimens from animals euthanized in a mass depopulation. Nevertheless, for sera acquired antemortem, this biomarker-based test may represent a useful new resource for managing spread of CWD that offers the advantages of being rapid, sensitive, non-invasive, and amenable to high throughput scaling.

molecular biology↗