Development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens

Sci Rep. 2021 Jun 11;11(1):12384. doi: 10.1038/s41598-021-91956-z.

Abstract

Inadequate sensitivity has been the primary limitation for implementing high-throughput sequencing for studies of tick-borne agents. Here we describe the development of TBDCapSeq, a sequencing assay that uses hybridization capture probes that cover the complete genomes of the eleven most common tick-borne agents found in the United States. The probes are used for solution-based capture and enrichment of pathogen nucleic acid followed by high-throughput sequencing. We evaluated the performance of TBDCapSeq to surveil samples that included human whole blood, mouse tissues, and field-collected ticks. For Borrelia burgdorferi and Babesia microti, the sensitivity of TBDCapSeq was comparable and occasionally exceeded the performance of agent-specific quantitative PCR and resulted in 25 to > 10,000-fold increase in pathogen reads when compared to standard unbiased sequencing. TBDCapSeq also enabled genome analyses directly within vertebrate and tick hosts. The implementation of TBDCapSeq could have major impact in studies of tick-borne pathogens by improving detection and facilitating genomic research that was previously unachievable with standard sequencing approaches.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Babesia microti / genetics*
  • Babesia microti / pathogenicity
  • Babesiosis / diagnosis
  • Babesiosis / microbiology*
  • Borrelia burgdorferi / genetics*
  • Borrelia burgdorferi / pathogenicity
  • Genome, Bacterial
  • Genotyping Techniques / methods*
  • Genotyping Techniques / standards
  • Humans
  • Lyme Disease / diagnosis
  • Lyme Disease / microbiology*
  • Mice
  • Molecular Diagnostic Techniques / methods*
  • Molecular Diagnostic Techniques / standards
  • Sensitivity and Specificity
  • Sequence Analysis, DNA / methods*
  • Sequence Analysis, DNA / standards
  • Ticks / microbiology