PT  - JOURNAL ARTICLE
AU  - Evan J. Kipp
AU  - Laramie L. Lindsey
AU  - Benedict S. Khoo
AU  - Christopher Faulk
AU  - Jonathan D. Oliver
AU  - Peter A. Larsen
TI  - Enabling metagenomic surveillance for bacterial tick-borne pathogens using nanopore sequencing with adaptive sampling
AID  - 10.1101/2021.08.17.456696
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.08.17.456696
4099  - http://biorxiv.org/content/early/2021/08/17/2021.08.17.456696.short
4100  - http://biorxiv.org/content/early/2021/08/17/2021.08.17.456696.full
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.