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

oleh: Evan J. Kipp, Laramie L. Lindsey, Benedict Khoo, Christopher Faulk, Jonathan D. Oliver, Peter A. Larsen

Format: Article
Diterbitkan: Nature Portfolio 2023-07-01

Deskripsi

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.