3.2 [74]. The number of clusters K was estimated by calculating the ad hoc statistic ΔK[76]. ΔK was calculated for K = 1 through 10 using 5 Markov chains for each value of K. The simulations of Evanno et al. [76] showed that the highest value for ΔK reliably identified the optimum selleck inhibitor value of K. Chains were run for 500,000 steps following an initial
burn-in of 100,000 steps, using the admixture ancestry and correlated allele frequency models. Once the optimum value of K was identified, strains were assigned to clusters using assignment coefficients (proportion of cluster membership) generated from an additional run utilizing the linkage ancestry and correlated allele frequency models. A study of recombinant bacterial populations showed the linkage model of ancestry to produce the most accurate assignment scores in situations where there are multiple linked loci along contiguous sections of DNA [75]. The model assumes these sections, which could be recombinant, to be discrete units of inheritance. Markov chains were run selleck screening library for 2,000,000 steps following an initial burn-in of 500,000 steps. Acknowledgements We would like to thank staff from Cornell
University’s Quality Milk Production Services and Animal Health Diagnostic Centre for their contribution to sample and isolate collection. This study made use of PathogenTracker 2.0 ( http://www.microbtracker.net), developed by Martin Wiedmann. This work was supported by the National Institute of Allergy and Infectious Disease, U.S.
National Institutes of Health, under Grant No. AI073368 awarded to M.J.S. Electronic supplementary material Additional file 1: Streptococcus RefSeq genome summary statistics. (DOC 102 KB) Additional file 2: S. canis annotation. (XLS 540 KB) Additional file 3: Additional Streptococcus genomes. (XLS 30 KB) Additional file 4: Insertion sites of putative integrative plasmid. (DOC 58 KB) Additional file 5: S. canis isolate MLST allele data. (DOC 87 KB) Additional file 6: Ln P(D) scores for Structure analysis. (DOC 206 MycoClean Mycoplasma Removal Kit KB) Additional file 7: MLST PCR primer details. (DOC 118 KB) Additional file 8: Putative integrative plasmid PCR primer details. (XLS 24 KB) References 1. Devriese LA, Hommez J, Kilpper-Balz R, Schleifer KH: Streptococcus canis sp. nov.: a species of group G streptococci from animals. Int J Syst Bacteriol 1986,36(3):422–425.CrossRef 2. Vandamme P, Pot B, Falsen E, Kersters K, Devriese LA: Taxonomic study of Lancefield streptococcal groups C, G, and L ( Streptococcus dysgalactiae ) and proposal of S. dysgalactiae subsp. equisimilis subsp. nov. Int J Syst Bacteriol 1996,46(3):774–781.PubMedCrossRef 3. Murase T, Morita T, Sunagawa Y, Sawada M, Shimada A, Sato K, Hikasa Y: Isolation of Streptococcus canis from a Japanese raccoon dog with fibrinous pleuropneumonia. Vet Rec 2003,153(15):471–472.PubMedCrossRef 4.