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

Scientific Reports
Komal JainRafal Tokarz

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.

References

Mar 31, 1983·The New England Journal of Medicine·J L BenachR A Kaslow
Dec 6, 2000·Proceedings of the National Academy of Sciences of the United States of America·J E Purser, S J Norris
Jul 16, 2005·Clinical Microbiology Reviews·Maria E Aguero-RosenfeldGary P Wormser
Sep 11, 2008·The Journal of Infectious Diseases·Gary P WormserIra Schwartz
Jan 29, 2011·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·C W AngT Herremans
Feb 1, 2011·Bioinformatics·Robert Schmieder, Robert Edwards
Mar 1, 2012·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·V SeriburiG P Wormser
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
May 11, 2012·Diagnostic Microbiology and Infectious Disease·Dionysios LiverisGary P Wormser
Sep 4, 2014·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Brian A FallonCarl Brenner
May 23, 2015·Infectious Disease Clinics of North America·Adriana R Marques
Sep 24, 2015·Genome Research·Todd N WylieGregory A Storch
Oct 28, 2015·BMC Infectious Diseases·Camilo E KhatchikianGary P Wormser
Nov 14, 2015·Ticks and Tick-borne Diseases·Neeta P ConnallyJames I Meek
Apr 27, 2016·JAMA : the Journal of the American Medical Association·Edgar SanchezLinden T Hu
May 14, 2016·MMWR. Recommendations and Reports : Morbidity and Mortality Weekly Report. Recommendations and Reports·Holly M BiggsMarc S Traeger
Jul 23, 2016·Emerging Infectious Diseases·Samia N NaccacheCharles Y Chiu
Feb 9, 2017·Archives of Pathology & Laboratory Medicine·Robert SchlabergUNKNOWN Microbiology Resource Committee of the College of American Pathologists
Feb 13, 2018·European Journal of Internal Medicine·Michael SamarkosOlga Kampouropoulou
Oct 26, 2018·Annual Review of Pathology·Wei GuCharles Y Chiu
Feb 6, 2019·Nature Biotechnology·Hayden C MetskyChristian B Matranga
Apr 27, 2019·Ticks and Tick-borne Diseases·Rafal TokarzW Ian Lipkin
Dec 11, 2019·Journal of Proteome Research·Bryna L FitzgeraldJohn T Belisle
Jul 28, 2020·Parasites & Vectors·Rafal TokarzAdriana R Marques
Oct 23, 2020·Journal of Clinical Microbiology·Michael R MoselJohn N Aucott

❮ Previous
Next ❯

Software Mentioned

TBDCapSeq
Geneious
EasyMag
Bowtie2 mapper
BlastN
Bowtie2
Megablast
BLASTX
Cutadapt
FastQC

Related Concepts

Related Papers

Journal of Medical Entomology
Rafal Tokarz, W Ian Lipkin
Schweizerische Rundschau für Medizin Praxis = Revue suisse de médecine Praxis
T Rufli
© 2021 Meta ULC. All rights reserved