Journal
BMC GENOMICS
Volume 16, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s12864-015-1634-x
Keywords
Hybrid capture; Whole-genome sequencing; SNPs; Tick-borne pathogens; Lyme disease
Funding
- National Science Foundation/National Institutes of Health Ecology and Evolution of Infectious Diseases Program [R01 GM105246-01]
- Gaylord Donnelley Postdoctoral Environmental Fellowship (the Yale Institute for Biospheric Studies)
- NIH [5T32AI007404-23]
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Background: Rapid and accurate retrieval of whole genome sequences of human pathogens from disease vectors or animal reservoirs will enable fine-resolution studies of pathogen epidemiological and evolutionary dynamics. However, next generation sequencing technologies have not yet been fully harnessed for the study of vector-borne and zoonotic pathogens, due to the difficulty of obtaining high-quality pathogen sequence data directly from field specimens with a high ratio of host to pathogen DNA. Results: We addressed this challenge by using custom probes for multiplexed hybrid capture to enrich for and sequence 30 Borrelia burgdorferi genomes from field samples of its arthropod vector. Hybrid capture enabled sequencing of nearly the complete genome (similar to 99.5 %) of the Borrelia burgdorferi pathogen with 132-fold coverage, and identification of up to 12,291 single nucleotide polymorphisms per genome. Conclusions: The proprosed culture-independent method enables efficient whole genome capture and sequencing of pathogens directly from arthropod vectors, thus making population genomic study of vector-borne and zoonotic infectious diseases economically feasible and scalable. Furthermore, given the similarities of invertebrate field specimens to other mixed DNA templates characterized by a high ratio of host to pathogen DNA, we discuss the potential applicabilty of hybrid capture for genomic study across diverse study systems.
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