For each herd, only one isolate representing a distinct ribotype

For each herd, only one isolate representing a distinct ribotype was typed using MLST. N2 = Number of isolates from milking machine rubber liners or bulk tank milk. ST = sequence type. CC = clonal complex. 1 Isolated from milking machine rubber liners. 2 Isolated from bulk tank milk. * Isolate contains plasmid (see text). Table 2 Isolate diversity indices and summary statistics EGFR assay   n-RT RT RT-h n-ST ST ST-h θ π plasmid All 83 17 0.90 46 16 0.76 0.0127 0.0111 15 Bovine* 56 4 0.67 19 3 0.49 0.0089 0.0127 7 Canine 26 13 0.88 26 14

0.90 0.0139 0.0094 7 Feline 1 1   1 1       1 n-RT = number of isolates ribotyped. n-ST = number of isolates sequence typed. RT = number of ribotypes. RT-h = ribotype (gene) diversity. ST = number of STs. ST-h = ST (gene) diversity. θ = population parameter theta (per site). π = nucleotide diversity. plasmid = number of strains containing the plasmid. *The bovine isolates represent 18 distinct herds (farms). With one exception a single ST was obtained from each herd (two STs were obtained from one herd) (see Methods). Examination of evolutionary relationships GSK2126458 clinical trial among STs using a Bayesian phylogenetic approach

(ClonalFrame, [68]) produced a well-supported phylogeny (Figure 3), with three independent runs of the Markov chain all producing congruent topologies. Repeating the runs without the recombination model (we assume no recombination) had no affect on the topology, but branch lengths did vary (Figure 4). The average total Olopatadine branch length for the three phylogenies, not accounting for recombination (15.9 coalescent time units), was slightly larger than the average length of the three phylogenies that did account for recombination (14.2 coalescent time units). Figure 3 ClonalFrame 75% majority-rule consensus phylogeny (node posterior probabilities are at least 0.75). Posterior probabilities for major lineages are shown at nodes. Dashed circles

show each clonal complex (CC) and grey shading shows isolates assigned to the two clusters (A and B) determined by the Structure analysis. Taxa labels are colored as follows: red = canine isolate, blue = bovine isolate, green = feline isolate. The first number in the label shows isolate ID. For canine isolates, tissue source follows the isolate ID, which is followed by the ST. Tissue source abbreviations are as follows: thr = throat, vag = vaginal, uri = urine, der = OSI-906 ic50 dermis, wou = wound exudate. For bovine and feline isolates, the ID is followed by the geographic location of collection (ITA = Italy, BEL = Belgium, NY = New York state, USA). Strain 227.NY.1 (underlined) is the strain who’s genome was sequenced in this study. Circles with white centers indicate those strains that contained the plasmid discussed in the text. The strain shaded in dark grey (166.thr.7) was grouped with CC4 members based on ClonalFrame analysis but it was not contained within CC4 based on eBURST.

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