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...
Guardado en:
Autores principales: | , , , , , , , , , , , , , , |
---|---|
Formato: | article |
Lenguaje: | EN |
Publicado: |
Nature Portfolio
2021
|
Materias: | |
Acceso en línea: | https://doaj.org/article/dbd846340ea64ae88cdea56825636c91 |
Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
id |
oai:doaj.org-article:dbd846340ea64ae88cdea56825636c91 |
---|---|
record_format |
dspace |
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 |
work_keys_str_mv |
AT komaljain developmentofacapturesequencingassayforenhanceddetectionandgenotypingoftickbornepathogens AT teresatagliafierro developmentofacapturesequencingassayforenhanceddetectionandgenotypingoftickbornepathogens AT adrianamarques developmentofacapturesequencingassayforenhanceddetectionandgenotypingoftickbornepathogens AT santiagosanchezvicente developmentofacapturesequencingassayforenhanceddetectionandgenotypingoftickbornepathogens AT alpergokden developmentofacapturesequencingassayforenhanceddetectionandgenotypingoftickbornepathogens AT brianfallon developmentofacapturesequencingassayforenhanceddetectionandgenotypingoftickbornepathogens AT nischaymishra developmentofacapturesequencingassayforenhanceddetectionandgenotypingoftickbornepathogens AT thomasbriese developmentofacapturesequencingassayforenhanceddetectionandgenotypingoftickbornepathogens AT vishalkapoor developmentofacapturesequencingassayforenhanceddetectionandgenotypingoftickbornepathogens AT stephensameroff developmentofacapturesequencingassayforenhanceddetectionandgenotypingoftickbornepathogens AT chengguo developmentofacapturesequencingassayforenhanceddetectionandgenotypingoftickbornepathogens AT luisamarcos developmentofacapturesequencingassayforenhanceddetectionandgenotypingoftickbornepathogens AT lindenhu developmentofacapturesequencingassayforenhanceddetectionandgenotypingoftickbornepathogens AT wianlipkin developmentofacapturesequencingassayforenhanceddetectionandgenotypingoftickbornepathogens AT rafaltokarz developmentofacapturesequencingassayforenhanceddetectionandgenotypingoftickbornepathogens |
_version_ |
1718379970393276416 |