Fig. 2: Evolutionary history of qacA-harbouring ST45 MRSA.

a Maximum clade credibility tree of 385 ST45 S. aureus isolates. The heatmaps provide additional annotations regarding country/region of isolation, methicillin resistance determined by mecA carriage, and the presence or absence of additional AMR determinants, including qacA, aac(6’)-aph(2”), emrC, and tetK. The black arrow indicates the predicted time for qacA acquisition (median node age = 1998, 95% HPD = 1996 to 1999). These isolates were divided into seven subclades based on qacA carriage and geographic origin. b GMRF Bayesian skyride plot. EPS of the major qacA-positive C2B (light green) subclade was compared with those of the qacA-negative C4 (navy blue) and C6 (light blue) subclades. The solid black line indicates the median EPS, and the coloured boundary indicates the 95% HPD. c The chromosomal region surrounding qacA in AUSMDU00020487. Each CDS (grey arrow) in this region was assigned a positional number, and CDSs of the same ortholog groups are linked by black solid lines. ISs (orange), plasmid replication initiator gene repA (blue), and AMR genes, including blaZ (red), aac(6’)-aph(2”) (green), and qacA (black), are highlighted. Boundaries of Tn552 and TN4001 are depicted by the brackets. Fragmented genes are flagged with an asterisk. d Comparison of gene content surrounding qacA between the major subclades. Percentages of gene presence are displayed in the heatmap, with dark blue indicating the presence of the gene among all isolates within a given subclade, while yellow indicates the absence of the gene. A summary of gene functionality, dosage, and synteny can be accessed in Supplementary Data 3.