Fig. 3: Resistance and virulence gene analysis.

a Midpoint rooted maximum likelihood phylogenetic tree based on 1275 core gene sequences of 1305 S. maltophilia complex strains. The coloured shading of the lineages represents the groups found by Bayesian clustering, with lineage names given. Hundred percent branch support is indicated by red dots. The pattern of gene presence (blue coloured line) or absence (white) is displayed in columns next to the tree, showing, from left to right, selected efflux pump genes: resistance-nodulation-cell-division (RND)-type efflux pumps, smeU2 as part of the five-gene RND efflux pump operon smeU1-V-W-U2-X, tetACG, emrA of the major facilitator superfamily (MFS), emrE and sugE of the small-multidrug-resistance (SMR) efflux pump family, norM of the MATE family; the aminoglycoside acetyltransferase aac and phosphotransferase aph, clpA, htpX, the β-lactamases blaL1 and blaL2, the sul1 and sul2 genes encoding dihydropteroate synthases, catB, and the virulence genes smoR, pilU, stmPr1 and katA. b Variable correlation plot of a multiple correspondence analysis (MCA) visualising nine resistance and virulence genes as active variables in red and three supplementary variables region, origin and groupin blue. c Factor individual biplot map of phylogenetic lineages, indicated by their 99% confidence intervals (ellipses) across the first two MCA dimensions. The five highest contributing active variables are shown in red with 0 denoting absence and 1 presence of this variable. d Factor individual biplot map of the isolation source as indicated in the coloured legend. Source data are provided as Source Data file.