Rapid typing of Coxiella burnetii

Heidie M. Hornstra, Rachael A. Priestley, Shalamar M. Georgia, Sergey Kachur, Dawn N. Birdsell, Remy Hilsabeck, Lauren T. Gates, James E. Samuel, Robert A. Heinzen, Gilbert J. Kersh, Paul Keim, Robert F. Massung, Talima Pearson

Research output: Contribution to journalArticle

51 Citations (Scopus)

Abstract

Coxiella burnetii has the potential to cause serious disease and is highly prevalent in the environment. Despite this, epidemiological data are sparse and isolate collections are typically small, rare, and difficult to share among laboratories as this pathogen is governed by select agent rules and fastidious to culture. With the advent of whole genome sequencing, some of this knowledge gap has been overcome by the development of genotyping schemes, however many of these methods are cumbersome and not readily transferable between institutions. As comparisons of the few existing collections can dramatically increase our knowledge of the evolution and phylogeography of the species, we aimed to facilitate such comparisons by extracting SNP signatures from past genotyping efforts and then incorporated these signatures into assays that quickly and easily define genotypes and phylogenetic groups. We found 91 polymorphisms (SNPs and indels) among multispacer sequence typing (MST) loci and designed 14 SNP-based assays that could be used to type samples based on previously established phylogenetic groups. These assays are rapid, inexpensive, real-time PCR assays whose results are unambiguous. Data from these assays allowed us to assign 43 previously untyped isolates to established genotypes and genomic groups. Furthermore, genotyping results based on assays from the signatures provided here are easily transferred between institutions, readily interpreted phylogenetically and simple to adapt to new genotyping technologies.

Original languageEnglish (US)
Article numbere26201
JournalPLoS One
Volume6
Issue number11
DOIs
StatePublished - Nov 2 2011

Fingerprint

Coxiella burnetii
Single Nucleotide Polymorphism
Assays
genotyping
assays
Genotype
Phylogeography
Real-Time Polymerase Chain Reaction
Genome
Technology
genotype
phylogeny
Pathogens
phylogeography
Polymorphism
Cell culture
quantitative polymerase chain reaction
Genes
genetic polymorphism
genomics

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Hornstra, H. M., Priestley, R. A., Georgia, S. M., Kachur, S., Birdsell, D. N., Hilsabeck, R., ... Pearson, T. (2011). Rapid typing of Coxiella burnetii. PLoS One, 6(11), [e26201]. https://doi.org/10.1371/journal.pone.0026201

Rapid typing of Coxiella burnetii. / Hornstra, Heidie M.; Priestley, Rachael A.; Georgia, Shalamar M.; Kachur, Sergey; Birdsell, Dawn N.; Hilsabeck, Remy; Gates, Lauren T.; Samuel, James E.; Heinzen, Robert A.; Kersh, Gilbert J.; Keim, Paul; Massung, Robert F.; Pearson, Talima.

In: PLoS One, Vol. 6, No. 11, e26201, 02.11.2011.

Research output: Contribution to journalArticle

Hornstra, HM, Priestley, RA, Georgia, SM, Kachur, S, Birdsell, DN, Hilsabeck, R, Gates, LT, Samuel, JE, Heinzen, RA, Kersh, GJ, Keim, P, Massung, RF & Pearson, T 2011, 'Rapid typing of Coxiella burnetii', PLoS One, vol. 6, no. 11, e26201. https://doi.org/10.1371/journal.pone.0026201
Hornstra HM, Priestley RA, Georgia SM, Kachur S, Birdsell DN, Hilsabeck R et al. Rapid typing of Coxiella burnetii. PLoS One. 2011 Nov 2;6(11). e26201. https://doi.org/10.1371/journal.pone.0026201
Hornstra, Heidie M. ; Priestley, Rachael A. ; Georgia, Shalamar M. ; Kachur, Sergey ; Birdsell, Dawn N. ; Hilsabeck, Remy ; Gates, Lauren T. ; Samuel, James E. ; Heinzen, Robert A. ; Kersh, Gilbert J. ; Keim, Paul ; Massung, Robert F. ; Pearson, Talima. / Rapid typing of Coxiella burnetii. In: PLoS One. 2011 ; Vol. 6, No. 11.
@article{72dd54905e354c4fafb64397f0369021,
title = "Rapid typing of Coxiella burnetii",
abstract = "Coxiella burnetii has the potential to cause serious disease and is highly prevalent in the environment. Despite this, epidemiological data are sparse and isolate collections are typically small, rare, and difficult to share among laboratories as this pathogen is governed by select agent rules and fastidious to culture. With the advent of whole genome sequencing, some of this knowledge gap has been overcome by the development of genotyping schemes, however many of these methods are cumbersome and not readily transferable between institutions. As comparisons of the few existing collections can dramatically increase our knowledge of the evolution and phylogeography of the species, we aimed to facilitate such comparisons by extracting SNP signatures from past genotyping efforts and then incorporated these signatures into assays that quickly and easily define genotypes and phylogenetic groups. We found 91 polymorphisms (SNPs and indels) among multispacer sequence typing (MST) loci and designed 14 SNP-based assays that could be used to type samples based on previously established phylogenetic groups. These assays are rapid, inexpensive, real-time PCR assays whose results are unambiguous. Data from these assays allowed us to assign 43 previously untyped isolates to established genotypes and genomic groups. Furthermore, genotyping results based on assays from the signatures provided here are easily transferred between institutions, readily interpreted phylogenetically and simple to adapt to new genotyping technologies.",
author = "Hornstra, {Heidie M.} and Priestley, {Rachael A.} and Georgia, {Shalamar M.} and Sergey Kachur and Birdsell, {Dawn N.} and Remy Hilsabeck and Gates, {Lauren T.} and Samuel, {James E.} and Heinzen, {Robert A.} and Kersh, {Gilbert J.} and Paul Keim and Massung, {Robert F.} and Talima Pearson",
year = "2011",
month = "11",
day = "2",
doi = "10.1371/journal.pone.0026201",
language = "English (US)",
volume = "6",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "11",

}

TY - JOUR

T1 - Rapid typing of Coxiella burnetii

AU - Hornstra, Heidie M.

AU - Priestley, Rachael A.

AU - Georgia, Shalamar M.

AU - Kachur, Sergey

AU - Birdsell, Dawn N.

AU - Hilsabeck, Remy

AU - Gates, Lauren T.

AU - Samuel, James E.

AU - Heinzen, Robert A.

AU - Kersh, Gilbert J.

AU - Keim, Paul

AU - Massung, Robert F.

AU - Pearson, Talima

PY - 2011/11/2

Y1 - 2011/11/2

N2 - Coxiella burnetii has the potential to cause serious disease and is highly prevalent in the environment. Despite this, epidemiological data are sparse and isolate collections are typically small, rare, and difficult to share among laboratories as this pathogen is governed by select agent rules and fastidious to culture. With the advent of whole genome sequencing, some of this knowledge gap has been overcome by the development of genotyping schemes, however many of these methods are cumbersome and not readily transferable between institutions. As comparisons of the few existing collections can dramatically increase our knowledge of the evolution and phylogeography of the species, we aimed to facilitate such comparisons by extracting SNP signatures from past genotyping efforts and then incorporated these signatures into assays that quickly and easily define genotypes and phylogenetic groups. We found 91 polymorphisms (SNPs and indels) among multispacer sequence typing (MST) loci and designed 14 SNP-based assays that could be used to type samples based on previously established phylogenetic groups. These assays are rapid, inexpensive, real-time PCR assays whose results are unambiguous. Data from these assays allowed us to assign 43 previously untyped isolates to established genotypes and genomic groups. Furthermore, genotyping results based on assays from the signatures provided here are easily transferred between institutions, readily interpreted phylogenetically and simple to adapt to new genotyping technologies.

AB - Coxiella burnetii has the potential to cause serious disease and is highly prevalent in the environment. Despite this, epidemiological data are sparse and isolate collections are typically small, rare, and difficult to share among laboratories as this pathogen is governed by select agent rules and fastidious to culture. With the advent of whole genome sequencing, some of this knowledge gap has been overcome by the development of genotyping schemes, however many of these methods are cumbersome and not readily transferable between institutions. As comparisons of the few existing collections can dramatically increase our knowledge of the evolution and phylogeography of the species, we aimed to facilitate such comparisons by extracting SNP signatures from past genotyping efforts and then incorporated these signatures into assays that quickly and easily define genotypes and phylogenetic groups. We found 91 polymorphisms (SNPs and indels) among multispacer sequence typing (MST) loci and designed 14 SNP-based assays that could be used to type samples based on previously established phylogenetic groups. These assays are rapid, inexpensive, real-time PCR assays whose results are unambiguous. Data from these assays allowed us to assign 43 previously untyped isolates to established genotypes and genomic groups. Furthermore, genotyping results based on assays from the signatures provided here are easily transferred between institutions, readily interpreted phylogenetically and simple to adapt to new genotyping technologies.

UR - http://www.scopus.com/inward/record.url?scp=80355129294&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=80355129294&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0026201

DO - 10.1371/journal.pone.0026201

M3 - Article

VL - 6

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 11

M1 - e26201

ER -