Fig. 1

ML tree of C. fetus core genome and mammalian associated C. fetus recombination regions. Cft 03-427 was excluded from the visualization. Tree branches are labeled with the clade numbers, serotype and MLST STs of the C. fetus strains. Subspecies identification (genotype and phenotype), H₂S production test results (+ positive, − negative), the presence of the putative cysteine transporter (+ present, − absent) and the Gubbins predicted recombination regions in the mammalian associated C. fetus core genome are shown, with on the right side a zoomed ML tree of clade 5. Gene flgE2 encodes a flagellar hook protein and cjeI a type II R-M system protein. Scale bar at the bottom left represents the nucleotide substitutions per site