Selective whole genome amplification and sequencing of Coxiella burnetii directly from environmental samples.

Autor: Cocking JH; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America; School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States of America. Electronic address: Jill.Cocking@nau.edu., Deberg M; School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States of America., Schupp J; Pathogen and Microbiome Division, TGen North, Flagstaff, AZ, United States of America. Electronic address: jschupp@tgen.org., Sahl J; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America. Electronic address: Jason.Sahl@nau.edu., Wiggins K; Pathogen and Microbiome Division, TGen North, Flagstaff, AZ, United States of America. Electronic address: kwiggins@tgen.org., Porty A; Department of Biology, Laurentian University, Sudbury, Ontario, Canada. Electronic address: APorty@laurentian.ca., Hornstra HM; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America. Electronic address: Heidie.Hornstra-ONeill@nau.edu., Hepp C; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America; School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States of America. Electronic address: Crystal.Hepp@nau.edu., Jardine C; Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada. Electronic address: cjardi01@uoguelph.ca., Furstenau TN; School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States of America. Electronic address: Tara.Furstenau@nau.edu., Schulte-Hostedde A; Department of Biology, Laurentian University, Sudbury, Ontario, Canada. Electronic address: aschultehostedde@laurentian.ca., Fofanov VY; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America; School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States of America. Electronic address: Viacheslav.Fofanov@nau.edu., Pearson T; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America. Electronic address: Talima.Pearson@nau.edu.
Jazyk: angličtina
Zdroj: Genomics [Genomics] 2020 Mar; Vol. 112 (2), pp. 1872-1878. Date of Electronic Publication: 2019 Oct 31.
DOI: 10.1016/j.ygeno.2019.10.022
Abstrakt: Whole genome sequencing (WGS) is a widely available, inexpensive means of providing a wealth of information about an organism's diversity and evolution. However, WGS for many pathogenic bacteria remain limited because they are difficult, slow and/or dangerous to culture. To avoid culturing, metagenomic sequencing can be performed directly on samples, but the sequencing effort required to characterize low frequency organisms can be expensive. Recently developed methods for selective whole genome amplification (SWGA) can enrich target DNA to provide efficient sequencing. We amplified Coxiella burnetii (a bacterial select agent and human/livestock pathogen) from 3 three environmental samples that were overwhelmed with host DNA. The 68- to 147-fold enrichment of the bacterial sequences provided enough genome coverage for SNP analyses and phylogenetic placement. SWGA is a valuable tool for the study of difficult-to-culture organisms and has the potential to facilitate high-throughput population characterizations as well as targeted epidemiological or forensic investigations.
Competing Interests: Declaration of Competing Interest The authors declare that they have no competing interests.
(Copyright © 2019. Published by Elsevier Inc.)
Databáze: MEDLINE
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