Targeted Metagenomics for Clinical Detection and Discovery of Bacterial Tick-Borne Pathogens

J Clin Microbiol. 2020 Oct 21;58(11):e00147-20. doi: 10.1128/JCM.00147-20. Print 2020 Oct 21.


Tick-borne diseases, due to a diversity of bacterial pathogens, represent a significant and increasing public health threat throughout the Northern Hemisphere. A high-throughput 16S V1-V2 rRNA gene-based metagenomics assay was developed and evaluated using >13,000 residual samples from patients suspected of having tick-borne illness and >1,000 controls. Taxonomic predictions for tick-borne bacteria were exceptionally accurate, as independently validated by secondary testing. Overall, 881 specimens were positive for bacterial tick-borne agents. Twelve tick-borne bacterial species were detected, including two novel pathogens, representing a 100% increase in the number of tick-borne bacteria identified compared to what was possible by initial PCR testing. In three blood specimens, two tick-borne bacteria were simultaneously detected. Seven bacteria, not known to be tick transmitted, were also confirmed to be unique to samples from persons suspected of having tick-borne illness. These results indicate that 16S V1-V2 metagenomics can greatly simplify diagnosis and accelerate the discovery of bacterial tick-borne pathogens.

Keywords: Lyme disease; anaplasmosis; human granulocytic ehrlichiosis; metagenomics; tick-borne bacteria; vector-borne diseases.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Bacteria / genetics
  • Ehrlichiosis*
  • Humans
  • Metagenomics
  • RNA, Ribosomal, 16S / genetics
  • Tick-Borne Diseases* / diagnosis
  • Ticks*


  • RNA, Ribosomal, 16S