FIG 1.

Phylogenetic tree of USA300 incarceration isolates annotated with prediction concordance or discordance. A recombination-masked whole-genome alignment was used to make a maximum likelihood phylogeny of USA300 clinical isolates from incarcerated individuals. The tree is midpoint rooted and annotated with resistance or susceptibility to clindamycin and levofloxacin. Tree tips are labeled with prediction discordance (resistance to both clindamycin and levofloxacin) or prediction concordance (susceptibility to clindamycin, levofloxacin, or both). Clustering of isolates discordant with the prediction rule is observed, indicating circulation of dual clindamycin-levofloxacin-resistant USA300.