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Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
Published on: August 25, 2018
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Metagenomic surveillance for bacterial tick-borne pathogens using nanopore adaptive sampling
Evan J Kipp1, Laramie L Lindsey2, Benedict Khoo3
1Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota-Twin Cities, St. Paul, MN, USA. kipp0046@umn.edu.
Scientific Reports
|July 7, 2023
Summary
Nanopore adaptive sampling (NAS) enables real-time selective sequencing of DNA from pathogens. This technology enhances genomic surveillance of tick-borne diseases in wildlife populations.
Area of Science:
- Genomics
- Bioinformatics
- Pathogen Discovery
Background:
- Genomic and bioinformatics advancements offer new tools for pathogen discovery and surveillance.
- Single-molecule sequencing data from Oxford Nanopore Technologies (ONT) can be used for real-time biosurveillance of zoonotic diseases.
Purpose of the Study:
- To demonstrate the utility of nanopore adaptive sampling (NAS) for targeted sequencing of bacterial pathogens.
- To showcase NAS's application in studying pathogens within wild tick populations.
Main Methods:
- Utilized nanopore adaptive sampling (NAS) for real-time selective sequencing.
- Applied NAS to DNA from Ixodes scapularis ticks.
- Bioinformatically mapped sequencing reads to references during real-time sequencing.
Main Results:
- NAS successfully enabled selective sequencing of multiple bacterial tick-borne pathogens.
- Demonstrated the feasibility of targeting specific DNA molecules as they are sequenced.
- Showcased the application in a wildlife vector population.
Conclusions:
- Nanopore adaptive sampling (NAS) is a powerful tool for enhancing genomic surveillance of tick-borne pathogens.
- NAS facilitates targeted sequencing, improving efficiency in pathogen discovery and monitoring.
- This method has significant implications for understanding pathogen dynamics in wildlife.
