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emi12111-sup-0001-suppdoc1.docx2363K

Supplementary document 1. Predictive mPCR design.

emi12111-sup-0002-suppdata4.xlsx15K

Supplementary data 4. Subclade prediction algorithm.

emi12111-sup-0003-ts1.pdf341K

Table S1.C. jejuni strains. C. jejuni isolates analysed in this study listed in order present in the phylogram from cluster C6 to C9ii, strain name gives full strain designation (some names abridged on figure), study indicates if data were from novel or from Champion and colleagues (2005), source indicates whether this isolate was considered human, livestock or wildlife and water associated, notes indicate animal source or any known clinical symptoms.

emi12111-sup-0004-ts2.pdf304K

Table S2. Multilocus sequence typing (MLST) data. MLST data were generated for 132/270 C. jejuni isolates listed in order present in the phylogram from cluster C6 to C9ii. ST, sequence type; CC, clonal cluster.

emi12111-sup-0005-ts3.pdf1560K

Table S3. Identification of variable regions. Comparative genomic hybridization data were used to score CDSs as present or absent (variable) and the percentage of isolates within a cluster that were scored present was calculated. CDS = C. jejuni 11168 defined coding sequences used for microarray reporter design, variable regions refer to hypervariable plasticity regions PR1-PR7 (Pearson et al., 2003), hypervariable regions HR01-16 (Taboada et al., 2004), regions of divergence PH01-15 (Hepworth et al., 2011) and variable regions VR1-2 (this study). Group indicates which group of the phylogram, C6-B6 and C7-C9ii indicate cluster, parenthesis indicates the number of strains within a cluster.

emi12111-sup-0006-fs1.pdf542K

Fig. S1. Distribution of MLST CC in the comparative phylogeny tree. Isolates are coloured according to clonal complex; ST-21 (red), ST-45 (green), ST-353 (blue), ST-257 (pink), ST-206 (orange), other CC (dark brown, CC ST in parenthesis), unassigned (black, bold) and untyped (black, unbold).

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