This locus is specific to ST20 where allele G indicates ST20 and allele A excludes ST20. b Samples failed to be genotyped with the ST20 specific locus Cox56bp10, find more likely C646 due to low levels of DNA. However, other loci were used to determine groups of likely sequence types and ST20 was not able to be excluded. c Samples genotyped as allele C at locus Cox51bp67. This locus is specific to sequence type 8 where allele C indicates ST8 and allele T excludes ST8. d All SNP assays failed to amplify either

allele. Temporal sampling Using the IS1111 assay [26], C. burnetii DNA was detected in every bovine milk sample (n = 340) representing five commercial brands (each from a different processing plant) that were purchased biweekly (every two weeks) for 32 months (May 2010 through December 2012) (Figure 1 and Table 3). For the bovine milk samples collected across the entire USA, the genotype Nutlin-3a of all samples was likely to be exclusively ST20. There were 14 samples where the allele for the ST20-specific locus could not be amplified (Table 3), but even in these cases, results from other SNP assays placed the samples in clades that included ST20. Only six samples contained too little DNA for any genotyping.

Table 3 Genotyping results of Coxiella burnetii DNA from bovine and caprine milk sampled every-other week Brand ID Bottling state Species Samples ST20 a Possible ST20 b ST8 c Possible ST8 d Other STs Unable to genotype e A Arizona Bovine 68 67 1 0 0 0 0 B Arizona Bovine 68 63 3 0 0 0 2 C California Bovine

68 59 6 0 0 0 3 D Colorado Bovine 68 65 2 0 0 0 1 E Idaho Bovine 68 66 2 0 0 0 0 F California Caprine 60 2 0 28 10 2 18     TOTALS 400 322 14 28 10 2 24 a Samples genotyped as allele G at locus Cox56bp10. This locus is specific to sequence type 20 where allele G indicates ST20 and allele A excludes ST20. b Samples failed to be genotyped with the ST20 specific locus Cox56bp10, likely due to low levels of DNA. However, other loci were used to determine groups of likely sequence types and ST20 was never excluded. c Samples genotyped selleckchem as allele C at locus Cox51bp67. This locus is specific to sequence type 8 where allele C indicates ST8 and allele T excludes ST8. d Samples failed to be genotyped with the ST8 specific locus Cox51bp67, likely due to low levels of DNA. However, other loci were used to determine groups of likely sequence types and ST8 was never excluded. e All SNP assays failed to amplify either allele. Caprine milk from a single brand and processing plant was also sampled biweekly for 28 months (September 2010 through December 2012).