RT Journal Article
SR Electronic
T1 Enabling metagenomic surveillance for bacterial tick-borne pathogens using nanopore sequencing with adaptive sampling
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.08.17.456696
DO 10.1101/2021.08.17.456696
A1 Evan J. Kipp
A1 Laramie L. Lindsey
A1 Benedict S. Khoo
A1 Christopher Faulk
A1 Jonathan D. Oliver
A1 Peter A. Larsen
YR 2021
UL http://biorxiv.org/content/early/2021/08/17/2021.08.17.456696.abstract
AB Technological and computational advancements in the fields of genomics and bioinformatics are providing exciting new opportunities for pathogen discovery and 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) pipeline facilitates immediate mapping of individual nucleotide molecules (i.e., DNA, cDNA, and RNA) to a given reference as each molecule is 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 entire genomes of bacterial tick-borne pathogens circulating in wild populations of the blacklegged tick vector, Ixodes scapularis. The NAS method provided a two-fold increase in targeted pathogen sequences, successfully enriching for Borrelia (Borreliella) burgdorferi s.s.; Borrelia (Borrelia) miyamotoi; Anaplasma phagocytophilum; and Ehrlichia muris eauclairensis genomic DNA within our I. scapularis samples. Our results indicate that NAS has strong potential for real-time sequence-based pathogen surveillance.Competing Interest StatementThe authors have declared no competing interest.