Unrooted maximum-likelihood tree based on concatenated sequences of the seven housekeeping gene fragments (3993 nt). The tree shows the structure of the studied Aeromonas spp. population, and the relative placement of human (red font), non-human animal (black font) and environmental (blue font) strains was indicated. The horizontal lines represent genetic distance, with the scale bar indicating the number of substitutions per nucleotide position. The numbers at the nodes are support values estimated with 100 bootstrap replicates. Only bootstrap values > 70 are indicated on the tree. The roots of the clades defined in 1 are represented by bold lines. MLPA clusters of strains sharing identical STs or grouped into CCs sharing at least 4 identical alleles at the 7 loci are indicated by frames (red frames for clusters of human strains, grey frames for clusters of non-human animal strains and uncolored frames for clusters of strains of various origins). In these frames, the following characteristics are indicated from left to right: (i) the strain’s clinical involvement when applicable as Inf for infection and Col for colonization; (ii) the SwaI pulsotype of the strains, with strains of identical pulsotypes designated by the same letter, strains with pulsotypes sharing more than 85% of their DNA fragments by A, A1, A2, … and strains with pulsotypes sharing no more than 70% of their DNA fragments by distinct letters, i.e., A, B, C, …; (iii) the names of STs shared by several strains; (iv) the names of CCs sharing at least 5 identical alleles at the 7 loci; and (v) the names of CCs sharing at least 4 identical alleles at the 7 loci. These ST and CC names are indicated to the right of the brackets grouping the strains with identical STs or belonging to the same CC and are followed by the bootstrap value (indicated in parentheses) supporting the corresponding MLPA cluster. (*) indicates that the relative position of the corresponding branch varied according to the method used. ND, not determined.
Roger et al. BMC Microbiology 2012 12:62 doi:10.1186/1471-2180-12-62