Fig. S1. A neighbour-joining tree based on the concatenated sequences of the six housekeeping genes. The tree shows the phylogenetic relationships of the 250 STs Aeromonas STs and the 11 clades identified.

Fig. S2. A diagram showing the clonal relationships among the 250 Aeromonas STs evaluated in this study obtained by the goeBURST algorithm in PHILOViZ software. Each circle corresponds to an ST, and ST numbers are given inside the circles. The lines between STs indicate clonal relationships and are represented as plain black, dashed black and plain grey depending on the number of allelic mismatches between profiles (1, 2 and 3, respectively).

Fig. S3. A tree produced by ClonalFrame showing the relationships within the 250 ST analysed in this study. Red dots indicate the recombination events found to be significantly supported. The species clades identified by the neighbour-joining phylogeny were shown with the same numbering as reported in Fig. S1.

Fig. S4. Admixture analysis performed by BAPS software in the Aeromonas population. (A) BAPS analysis of the 250 STs: each column represents a single ST and is coloured according to the proportion of genetic variation assigned to each cluster. (B) A gene flow network, identified in the Aeromonas population. Arrows indicate the average fraction of DNA transferred via gene flow from the source cluster to the target cluster. Circular loops indicate the fraction of DNA estimated as belonging to the cluster itself.

Fig. S5. Maximum likelihood phylogeny obtained by AdaptML software showing the strain designations.

Table S1. Origins and typing data of the Aeromonas strains analysed in the present study.

Table S2. List of the RTE food products analysed in this study.

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