Rapid Typing of Coxiella burnetii
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...
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| Format: | Online |
| Language: | English |
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Public Library of Science
2011
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3206805/ |
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pubmed-3206805 |
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pubmed-32068052011-11-09 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 Research Article 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. Public Library of Science 2011-11-02 /pmc/articles/PMC3206805/ /pubmed/22073151 http://dx.doi.org/10.1371/journal.pone.0026201 Text en This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. https://creativecommons.org/publicdomain/zero/1.0/ This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
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 |
| spellingShingle |
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 |
| author_facet |
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 |
| author_sort |
Hornstra, Heidie M. |
| title |
Rapid Typing of Coxiella burnetii
|
| title_short |
Rapid Typing of Coxiella burnetii
|
| title_full |
Rapid Typing of Coxiella burnetii
|
| title_fullStr |
Rapid Typing of Coxiella burnetii
|
| title_full_unstemmed |
Rapid Typing of Coxiella burnetii
|
| title_sort |
rapid typing of coxiella burnetii |
| description |
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. |
| publisher |
Public Library of Science |
| publishDate |
2011 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3206805/ |
| _version_ |
1611485217367785472 |