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

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.

Automated summary

Technological and computational advancements in genomics and bioinformatics are being utilized to enhance pathogen discovery and genomic surveillance. The use of single-molecule nucleotide sequence data from ONT sequencing platforms allows for real-time bioinformatic analysis for monitoring various animal-origin zoonotic diseases. The NAS strategy enables immediate mapping of nucleotide molecules to a reference genome, allowing for selective sequencing of DNA from multiple bacterial tick-borne pathogens in wild populations of the blacklegged tick vector, Ixodes scapularis.