Emerging Infectious Diseases (Aug 2023)

Prospecting for Zoonotic Pathogens by Using Targeted DNA Enrichment

  • Egie E. Enabulele,
  • Winka Le Clec’h,
  • Emma K. Roberts,
  • Cody W. Thompson,
  • Molly M. McDonough,
  • Adam W. Ferguson,
  • Robert D. Bradley,
  • Timothy J. C. Anderson,
  • Roy N. Platt

DOI
https://doi.org/10.3201/eid2908.221818
Journal volume & issue
Vol. 29, no. 8
pp. 1566 – 1579

Abstract

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More than 60 zoonoses are linked to small mammals, including some of the most devastating pathogens in human history. Millions of museum-archived tissues are available to understand natural history of those pathogens. Our goal was to maximize the value of museum collections for pathogen-based research by using targeted sequence capture. We generated a probe panel that includes 39,916 80-bp RNA probes targeting 32 pathogen groups, including bacteria, helminths, fungi, and protozoans. Laboratory-generated, mock-control samples showed that we are capable of enriching targeted loci from pathogen DNA 2,882‒6,746-fold. We identified bacterial species in museum-archived samples, including Bartonella, a known human zoonosis. These results showed that probe-based enrichment of pathogens is a highly customizable and efficient method for identifying pathogens from museum-archived tissues.

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