FIGURE 5.

Phylogenetic relationships and flanking genetic environments of 10 cfr-positive isolates. A core genome single-nucleotide polymorphism (SNP)-based maximum-likelihood phylogenetic tree was constructed for 50 cfr-positive isolates. Due to limitations of short-read sequencing, 40 isolates exhibited substantial loss of cfr-flanking regions and were therefore excluded from detailed comparative analysis. Ten isolates with relatively complete genome assemblies and intact cfr-flanking sequences were selected for combined phylogenetic and genomic context visualization. Metadata including isolation source, geographic origin, host, collection year, and strain ID are indicated alongside the phylogenetic tree. The genetic environments surrounding the cfr gene are shown on the right, with arrows representing open reading frames colored according to gene function. The orientation and arrangement of genes illustrate both conserved and variable cfr-associated genetic structures among phylogenetically related and unrelated isolates.