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Open Access Research article

Genotyping of Brucella species using clade specific SNPs

Jeffrey T Foster1*, Lance B Price2, Stephen M Beckstrom-Sternberg13, Talima Pearson1, William D Brown1, Danika M Kiesling1, Christina A Allen1, Cindy M Liu12, James Beckstrom-Sternberg3, Frank F Roberto4 and Paul Keim12

Author Affiliations

1 Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011-4073, USA

2 Translational Genomics Research Institute, Flagstaff, AZ, 86001, USA

3 Translational Genomics Research Institute, Phoenix, AZ, 85004, USA

4 Idaho National Laboratory, Idaho Falls, ID, 83415, USA

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BMC Microbiology 2012, 12:110  doi:10.1186/1471-2180-12-110

Published: 19 June 2012

Abstract

Background

Brucellosis is a worldwide disease of mammals caused by Alphaproteobacteria in the genus Brucella. The genus is genetically monomorphic, requiring extensive genotyping to differentiate isolates. We utilized two different genotyping strategies to characterize isolates. First, we developed a microarray-based assay based on 1000 single nucleotide polymorphisms (SNPs) that were identified from whole genome comparisons of two B. abortus isolates , one B. melitensis, and one B. suis. We then genotyped a diverse collection of 85 Brucella strains at these SNP loci and generated a phylogenetic tree of relationships. Second, we developed a selective primer-extension assay system using capillary electrophoresis that targeted 17 high value SNPs across 8 major branches of the phylogeny and determined their genotypes in a large collection ( n = 340) of diverse isolates.

Results

Our 1000 SNP microarray readily distinguished B. abortus, B. melitensis, and B. suis, differentiating B. melitensis and B. suis into two clades each. Brucella abortus was divided into four major clades. Our capillary-based SNP genotyping confirmed all major branches from the microarray assay and assigned all samples to defined lineages. Isolates from these lineages and closely related isolates, among the most commonly encountered lineages worldwide, can now be quickly and easily identified and genetically characterized.

Conclusions

We have identified clade-specific SNPs in Brucella that can be used for rapid assignment into major groups below the species level in the three main Brucella species. Our assays represent SNP genotyping approaches that can reliably determine the evolutionary relationships of bacterial isolates without the need for whole genome sequencing of all isolates.