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

Jill Hager Cocking, Michael Deberg, Jim Schupp, Jason Sahl, Kristin Wiggins, Ariel Porty, Heidie M. Hornstra, Crystal Hepp, Claire Jardine, Tara N. Furstenau, Albrecht Schulte-Hostedde, Viacheslav Y. Fofanov, Talima Pearson

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
JournalGenomics
DOIs
StateAccepted/In press - Jan 1 2019

Fingerprint

Coxiella burnetii
Genome
Metagenomics
DNA
Livestock
Single Nucleotide Polymorphism
Bacteria
Population

Keywords

  • Coxiella burnetii
  • Selective whole genome amplification
  • Whole genome sequencing

ASJC Scopus subject areas

  • Genetics

Cite this

Selective whole genome amplification and sequencing of Coxiella burnetii directly from environmental samples. / Cocking, Jill Hager; Deberg, Michael; Schupp, Jim; Sahl, Jason; Wiggins, Kristin; Porty, Ariel; Hornstra, Heidie M.; Hepp, Crystal; Jardine, Claire; Furstenau, Tara N.; Schulte-Hostedde, Albrecht; Fofanov, Viacheslav Y.; Pearson, Talima.

In: Genomics, 01.01.2019.

Research output: Contribution to journalArticle

Cocking, JH, Deberg, M, Schupp, J, Sahl, J, Wiggins, K, Porty, A, Hornstra, HM, Hepp, C, Jardine, C, Furstenau, TN, Schulte-Hostedde, A, Fofanov, VY & Pearson, T 2019, 'Selective whole genome amplification and sequencing of Coxiella burnetii directly from environmental samples', Genomics. https://doi.org/10.1016/j.ygeno.2019.10.022
Cocking, Jill Hager ; Deberg, Michael ; Schupp, Jim ; Sahl, Jason ; Wiggins, Kristin ; Porty, Ariel ; Hornstra, Heidie M. ; Hepp, Crystal ; Jardine, Claire ; Furstenau, Tara N. ; Schulte-Hostedde, Albrecht ; Fofanov, Viacheslav Y. ; Pearson, Talima. / Selective whole genome amplification and sequencing of Coxiella burnetii directly from environmental samples. In: Genomics. 2019.
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