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

Additional files

Additional file 1 Figure S1.:

Brucellaphylogeny using maximum parsimony developed using 777 single nucleotide polymorphisms. Letters on branches refer to phylogenetic locations of CUMA assays developed in this work. Stars on branches represent phylogenetic locations of species or clade specific assays from Foster et al. 2008. In this figure we rooted with B. neotomae because it is the most basal taxon in the Brucella phylogeny for these taxa tested (unpubl. data). (PDF 284 kb).

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Additional file 2 Table S3.:

List of BrucellaDNA samples tested with CUMA. DNA samples came from the following institutions, Louisiana State University (LSU), California Department of Health Services (CDHS), U.S. Armed Forces Institute of Pathology (AFIP), Alaska Public Health Laboratory (APHL), Brigham Young University (BYU), U.S. Centers for Disease Control (CDC), USDA-National Animal Disease Center (NADC), and the Arizona Department of Health Services (ADHS). Samples with a species name in the branch column were genotyped as that species using assays in (Foster et al. 2008) but gave all ancestral SNP alleles in our assays. Assays for B. abortus in blue B. melitensis in pink, and B. suis/canis in green, which correspond to the branches in Figure 1. The 85 samples also run in the MIP assay have an asterisk, except for 3 samples not run on CUMA. Samples likely mislabeled, due to incorrect branch assignment based on species/biovar, are highlighted in yellow. (PDF 135 kb).

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Additional file 3 Table S1.:

List of 28 whole genomes used forin silicocomparisons to SNP alleles from MIP assay. (PDF 62 kb).

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Additional file 4 Table S2.:

List ofBrucellaisolates used in 17 CUMA assays, including isolate name, species, and biovar when known or applicable and the SNP allele for each assay. (PDF 44 kb).

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