title: Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi.
abstract: 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.
authors.affiliation: Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA. giovanna.carpi@yale.edu.
authors.forename: Giovanna
authors.initials: G
authors.lastname: Carpi
authors.affiliation: Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA. katharine.walter@yale.edu.
authors.forename: Katharine S
authors.initials: KS
authors.lastname: Walter
authors.affiliation: Robinson Research Institute, University of Adelaide, 5005, Adelaide, SA, Australia. Stephen.bent@adelaide.edu.au.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Bent
authors.affiliation: The Geisel School of Medicine, Dartmouth College, 03755, Hanover, NH, USA. Anne.G.Hoen@dartmouth.edu.
authors.forename: Anne Gatewood
authors.initials: AG
authors.lastname: Hoen
authors.affiliation: Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA. mad2256@columbia.edu.|Department of Ecology, Evolution and Environmental Biology, Columbia University, 10027, New York, NY, USA. mad2256@columbia.edu.
authors.forename: Maria
authors.initials: M
authors.lastname: Diuk-Wasser
authors.affiliation: Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA. adalgisa.caccone@yale.edu.|Department of Ecology and Evolutionary Biology, Yale University, 06520, New Haven, CT, USA. adalgisa.caccone@yale.edu.
authors.forename: Adalgisa
authors.initials: A
authors.lastname: Caccone
mesh_terms: D000818:Animals; D001179:Arthropod Vectors / Q000382:microbiology*; D025065:Borrelia burgdorferi / Q000235:genetics*; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics / Q000379:methods; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000191:economics / Q000379:methods