Rapid typing of Coxiella burnetii

Hornstra, Heidie M. and Priestley, Rachael A. and Georgia, Shalamar M. and Kachur, Sergey and Birdsell, Dawn N. and Hilsabeck, Remy and Gates, Lauren T. and Samuel, James E. and Heinzen, Robert A. and Kersh, Gilbert J. and Keim, Paul and Massung, Robert F. and Pearson, Talima (2011) Rapid typing of Coxiella burnetii. PLoS ONE, 6 (11). e26201. ISSN 1932-6203

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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.

Item Type:	Article
ID number or DOI:	10.1371/journal.pone.0026201
Keywords:	Coxiella burnetii; phylogeography; variant genotypes; genotyping; sequence alignment; genomic databases; phylogenetics; DNA signatures; Q fever;
Subjects:	Q Science > QR Microbiology
NAU Depositing Author Academic Status:	Faculty/Staff
Department/Unit:	Research Centers > Center for Microbial Genetics and Genomics
Date Deposited:	16 Oct 2015 20:10
URI:	http://openknowledge.nau.edu/id/eprint/1720

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