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Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi
- Source :
- BMC Genomics
- Publication Year :
- 2015
- Publisher :
- BioMed Central, 2015.
-
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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1634-x) contains supplementary material, which is available to authorized users.
- Subjects :
- Population
Human pathogen
Genome
Polymorphism, Single Nucleotide
DNA sequencing
Genetics
Lyme disease
Animals
Humans
Borrelia burgdorferi
education
Whole genome sequencing
education.field_of_study
Whole-genome sequencing
Hybrid capture
Tick-borne pathogens
biology
Methodology Article
Arthropod Vectors
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA
biology.organism_classification
FOS: Biological sciences
Communicable diseases--Epidemiology
DNA microarray
Nucleotide sequence
Arthropod Vector
Genome, Bacterial
Biotechnology
SNPs
Subjects
Details
- Language :
- English
- ISSN :
- 14712164
- Volume :
- 16
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- BMC Genomics
- Accession number :
- edsair.doi.dedup.....0b2d380916acbbc5828df3f83c38ccfb