Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi

• DOI: 10.1186/s12864-015-1634-x
• Publication Date: 2015-06-05T14:05:55Z
• Authors: Giovanna Carpi; Katharine S. Walter; Stephen J. Bent; Anne Gatewood Hoen; Maria Diuk-Wasser; Adalgisa Caccone
• Keywords: 0301 basic medicine; 570; 572; 610; Polymorphism, Single Nucleotide; 630; 03 medical and health sciences; 1311 Genetics; Genetics; Animals; Humans; Lyme disease; Whole-genome sequencing; 0303 health sciences; Hybrid capture; Tick-borne pathogens; Methodology Article; Arthropod Vectors; High-Throughput Nucleotide Sequencing; Sequence Analysis, DNA; whole-genome sequencing; Borrelia burgdorferi; FOS: Biological sciences; 1305 Biotechnology; Communicable diseases--Epidemiology; tick-borne pathogens; Nucleotide sequence; Genome, Bacterial; SNPs; Biotechnology

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 (~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. Keywords: Hybrid capture Whole-genome sequencing SNPs Tick-borne pathogens Lyme disease