Fig. 4: The distribution of.

A Antimicrobial resistance genes, B virulence factor genes that are variably present in the clones, and C plasmids across the BAPS clones. Bubble sizes correspond to relative frequency, with numbers indicating relative frequencies within each clone. The tree is the same as in Fig. 1. For the detection of virulence factor genes and antimicrobial resistance genes, SRST2 pipeline with a threshold of 90% for identity and coverage was used. The shaded squares in (A) indicate the genes that were significantly overrepresented in each clone compared to other clones, as determined by a one-sided proportion test with a significance level of 0.01. For plasmids in (C), short reads for each strain were mapped against one of the plasmid backbones from each cluster presented in Fig. S3A, using a cutoff of 90% coverage to determine the presence of the plasmid. Genome IDs on the x-axis in (C) correspond to the isolate from which the reference plasmid genome was obtained. For IncC plasmid, the shortest IncC plasmid backbone in the population was used as reference. The labels “chr” and “Cl.” denote “chromosomal” and “cluster” indicating the genomic context of the gene on chromosomal or plasmid, respectively. “Unk” denotes “unknown,” indicating cases where the genomic context could not be resolved due to either the absence of the genome in the collection or fragmented contigs.