The evolutionary history of INF isolates of ST2 was inferred using the Maximum Likelihood method based on the General Time Reversible model. Evolutionary analyses were conducted with RaxML-NG [118,119]. The tree with the highest log-likelihood is shown (S3 Fig). A bootstrap of 1000 replicates was performed, and values above 70 are shown[120]. The initial tree for the heuristic search was randomly generated. A discrete Gamma distribution was used to model evolutionary rate differences among sites with four categories. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis based on a ’Mugsy’ alignment [121]. All positions containing gaps and missing data were eliminated. There were a total of 2288372 positions in the final dataset. Isolates BPH0662 (GCA_900086615.2) and IRL01 (GCA_009685135.1) were included as references for the two major ST2 lineages [15].

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