Metagenomic surveillance for bacterial tick-borne pathogens using nanopore adaptive sampling
Abstract Technological and computational advancements in the fields of genomics and bioinformatics are providing exciting new opportunities for pathogen discovery and genomic surveillance. In particular, single-molecule nucleotide sequence data originating from Oxford Nanopore Technologies (ONT) seq...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-07-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-37134-9 |
| _version_ | 1797784637414572032 |
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| author | Evan J. Kipp Laramie L. Lindsey Benedict Khoo Christopher Faulk Jonathan D. Oliver Peter A. Larsen |
| author_facet | Evan J. Kipp Laramie L. Lindsey Benedict Khoo Christopher Faulk Jonathan D. Oliver Peter A. Larsen |
| author_sort | Evan J. Kipp |
| collection | DOAJ |
| description | Abstract Technological and computational advancements in the fields of genomics and bioinformatics are providing exciting new opportunities for pathogen discovery and genomic surveillance. In particular, single-molecule nucleotide sequence data originating from Oxford Nanopore Technologies (ONT) sequencing platforms can be bioinformatically leveraged, in real-time, for enhanced biosurveillance of a vast array of zoonoses. The recently released nanopore adaptive sampling (NAS) strategy facilitates immediate mapping of individual nucleotide molecules to a given reference as each molecule is being sequenced. User-defined thresholds then allow for the retention or rejection of specific molecules, informed by the real-time reference mapping results, as they are physically passing through a given sequencing nanopore. Here, we show how NAS can be used to selectively sequence DNA of multiple bacterial tick-borne pathogens circulating in wild populations of the blacklegged tick vector, Ixodes scapularis. |
| first_indexed | 2024-03-13T00:42:44Z |
| format | Article |
| id | doaj.art-9b6968d7117e448da6fa315ff7f390e9 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-13T00:42:44Z |
| publishDate | 2023-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-9b6968d7117e448da6fa315ff7f390e92023-07-09T11:13:32ZengNature PortfolioScientific Reports2045-23222023-07-0113111210.1038/s41598-023-37134-9Metagenomic surveillance for bacterial tick-borne pathogens using nanopore adaptive samplingEvan J. Kipp0Laramie L. Lindsey1Benedict Khoo2Christopher Faulk3Jonathan D. Oliver4Peter A. Larsen5Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota—Twin CitiesDepartment of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota—Twin CitiesDivision of Environmental Health Sciences, School of Public Health, University of Minnesota—Twin CitiesDepartment of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota—Twin CitiesDivision of Environmental Health Sciences, School of Public Health, University of Minnesota—Twin CitiesDepartment of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota—Twin CitiesAbstract Technological and computational advancements in the fields of genomics and bioinformatics are providing exciting new opportunities for pathogen discovery and genomic surveillance. In particular, single-molecule nucleotide sequence data originating from Oxford Nanopore Technologies (ONT) sequencing platforms can be bioinformatically leveraged, in real-time, for enhanced biosurveillance of a vast array of zoonoses. The recently released nanopore adaptive sampling (NAS) strategy facilitates immediate mapping of individual nucleotide molecules to a given reference as each molecule is being sequenced. User-defined thresholds then allow for the retention or rejection of specific molecules, informed by the real-time reference mapping results, as they are physically passing through a given sequencing nanopore. Here, we show how NAS can be used to selectively sequence DNA of multiple bacterial tick-borne pathogens circulating in wild populations of the blacklegged tick vector, Ixodes scapularis.https://doi.org/10.1038/s41598-023-37134-9 |
| spellingShingle | Evan J. Kipp Laramie L. Lindsey Benedict Khoo Christopher Faulk Jonathan D. Oliver Peter A. Larsen Metagenomic surveillance for bacterial tick-borne pathogens using nanopore adaptive sampling Scientific Reports |
| title | Metagenomic surveillance for bacterial tick-borne pathogens using nanopore adaptive sampling |
| title_full | Metagenomic surveillance for bacterial tick-borne pathogens using nanopore adaptive sampling |
| title_fullStr | Metagenomic surveillance for bacterial tick-borne pathogens using nanopore adaptive sampling |
| title_full_unstemmed | Metagenomic surveillance for bacterial tick-borne pathogens using nanopore adaptive sampling |
| title_short | Metagenomic surveillance for bacterial tick-borne pathogens using nanopore adaptive sampling |
| title_sort | metagenomic surveillance for bacterial tick borne pathogens using nanopore adaptive sampling |
| url | https://doi.org/10.1038/s41598-023-37134-9 |
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