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

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 co...

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Autores principales: Komal Jain, Teresa Tagliafierro, Adriana Marques, Santiago Sanchez-Vicente, Alper Gokden, Brian Fallon, Nischay Mishra, Thomas Briese, Vishal Kapoor, Stephen Sameroff, Cheng Guo, Luis A. Marcos, Linden Hu, W. Ian Lipkin, Rafal Tokarz
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Publicado: Nature Portfolio 2021
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Acceso en línea:https://doaj.org/article/dbd846340ea64ae88cdea56825636c91
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spelling oai:doaj.org-article:dbd846340ea64ae88cdea56825636c912021-12-02T17:34:30ZDevelopment of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens10.1038/s41598-021-91956-z2045-2322https://doaj.org/article/dbd846340ea64ae88cdea56825636c912021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-91956-zhttps://doaj.org/toc/2045-2322Abstract 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.Komal JainTeresa TagliafierroAdriana MarquesSantiago Sanchez-VicenteAlper GokdenBrian FallonNischay MishraThomas BrieseVishal KapoorStephen SameroffCheng GuoLuis A. MarcosLinden HuW. Ian LipkinRafal TokarzNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Komal Jain
Teresa Tagliafierro
Adriana Marques
Santiago Sanchez-Vicente
Alper Gokden
Brian Fallon
Nischay Mishra
Thomas Briese
Vishal Kapoor
Stephen Sameroff
Cheng Guo
Luis A. Marcos
Linden Hu
W. Ian Lipkin
Rafal Tokarz
Development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens
description 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.
format article
author Komal Jain
Teresa Tagliafierro
Adriana Marques
Santiago Sanchez-Vicente
Alper Gokden
Brian Fallon
Nischay Mishra
Thomas Briese
Vishal Kapoor
Stephen Sameroff
Cheng Guo
Luis A. Marcos
Linden Hu
W. Ian Lipkin
Rafal Tokarz
author_facet Komal Jain
Teresa Tagliafierro
Adriana Marques
Santiago Sanchez-Vicente
Alper Gokden
Brian Fallon
Nischay Mishra
Thomas Briese
Vishal Kapoor
Stephen Sameroff
Cheng Guo
Luis A. Marcos
Linden Hu
W. Ian Lipkin
Rafal Tokarz
author_sort Komal Jain
title Development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens
title_short Development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens
title_full Development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens
title_fullStr Development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens
title_full_unstemmed Development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens
title_sort development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens
publisher Nature Portfolio
publishDate 2021
url https://doaj.org/article/dbd846340ea64ae88cdea56825636c91
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