@article{c2afa7971aa448f7888a9100a03063b7,
title = "Selective whole genome amplification and sequencing of Coxiella burnetii directly from environmental samples",
abstract = "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.",
keywords = "Coxiella burnetii, Selective whole genome amplification, Whole genome sequencing",
author = "Cocking, {Jill Hager} and Michael Deberg and Jim Schupp and Jason Sahl and Kristin Wiggins and Ariel Porty and Hornstra, {Heidie M.} and Crystal Hepp and Claire Jardine and Furstenau, {Tara N.} and Albrecht Schulte-Hostedde and Fofanov, {Viacheslav Y.} and Talima Pearson",
note = "Funding Information: This work was funded under the State of Arizona Technology and Research Initiative Fund (TRIF), administered by the Arizona Board of Regents, through Northern Arizona University, the National Institute On Minority Health And Health Disparities under the National Institutes of Health award numbers U54MD012388, The Centre of Excellence in Goat Research and Innovation, and by the Canada Research Chair in Applied Evolutionary Ecology. The University of Guelph - OMAFRA Partnership (Emergency Management program) provided funding to support sample collection in Canada. The funders had no role in determining the content of this work. Funding Information: This work was funded under the State of Arizona Technology and Research Initiative Fund (TRIF), administered by the Arizona Board of Regents, through Northern Arizona University, the National Institute On Minority Health And Health Disparities under the National Institutes of Health award numbers U54MD012388 , The Centre of Excellence in Goat Research and Innovation , and by the Canada Research Chair in Applied Evolutionary Ecology . The University of Guelph - OMAFRA Partnership (Emergency Management program) provided funding to support sample collection in Canada. The funders had no role in determining the content of this work. Publisher Copyright: {\textcopyright} 2019",
year = "2020",
month = mar,
doi = "10.1016/j.ygeno.2019.10.022",
language = "English (US)",
volume = "112",
pages = "1872--1878",
journal = "Genomics",
issn = "0888-7543",
publisher = "Academic Press Inc.",
number = "2",
}