Fig. 4

Phylogenetic tree based on the core-genome SNPs of S. Welikade strains, constructed with maximum likelihood according to the K3Pu + F + I model. Consensus tree was obtained after 3,000 bootstraps. SNP tree branch lengths were corrected taking in account the recombination events predicted by the ClonalFrame ML tool. The tree is rooted on the historical strain 839 K. The SNP average carried out on branches is noted in blue. Bootstrap values greater than 80% are noted with blue dots on nodes. The strains implicated in the goat’s cheese outbreak that occurred in France in 2016 are highlighted in the purple box. The blue box highlights the epidemic Gallus gallus cluster. The heatmap shows the presence (in black) or absence (in beige) of the phages. The accession numbers of each phage are: CTC2A [NC_ 030949], 186 [NC_001317], AA91 [NC_022750], Haemop_HP2 [ NC_003315], KO2 [NC_005857], 118970_sal3 [NC_031940], Fels-1 [NC_010391], Fels-2 [NC_010463], SEN34_[NC_028699], ST64B [NC_004313], Sf6 [NC_005344], X29 [NC_024369], F108 [NC_008193], RE-2010 _[NC_019488], Gifsy-1 _[NC_010392], Gifsy-2 _[NC_010393], GF-2 _[NC_026611], I2_2 _[NC_001332], P88 _[NC_026014], PsP3 _[NC_005340], and Mu _[NC_000929]