Targeted Metagenomics for Clinical Detection and Discovery of Bacterial Tick-Borne Pathogens
Luke C. Kingry, Sarah W. Sheldon, Stephanie Oatman, Bobbi S. Pritt, Melissa Anacker, Jenna Bjork, David F. Neitzel, Anna K. Strain, Jon Berry, Lynne M. Sloan, Laurel Respicio-Kingry, Elizabeth A. Dietrich, Karen C. Bloch, Abelardo C. Moncayo, Ganesh Srinivasamoorthy, Bin Hu, Alison F. Hinckley, Paul S. Mead, Kiersten J. Kugeler, Jeannine M. Petersen
Abstract
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.