Metagenomic surveillance for bacterial tick-borne pathogens using nanopore adaptive sampling.

Autor: Kipp EJ; Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota-Twin Cities, St. Paul, MN, USA. kipp0046@umn.edu., Lindsey LL; Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota-Twin Cities, St. Paul, MN, USA., Khoo B; Division of Environmental Health Sciences, School of Public Health, University of Minnesota-Twin Cities, Minneapolis, MN, USA., Faulk C; Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota-Twin Cities, St. Paul, MN, USA., Oliver JD; Division of Environmental Health Sciences, School of Public Health, University of Minnesota-Twin Cities, Minneapolis, MN, USA., Larsen PA; Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota-Twin Cities, St. Paul, MN, USA.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2023 Jul 07; Vol. 13 (1), pp. 10991. Date of Electronic Publication: 2023 Jul 07.
DOI: 10.1038/s41598-023-37134-9
Abstrakt: 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.
(© 2023. The Author(s).)
Databáze: MEDLINE
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