Figure 6

Exclusion of epidemiologically linked pairs based on phylogenetic position. Red indicates primary case isolate, blue is the secondary case isolate. A: excluded pair 1. B: excluded pair 2. C: Excluded pair with SNP difference of 149. N09501026 shares a deletion with an isolate in a different study [36]. D: Example of expected phylogenetic positioning of direct transmission pairs, brackets indicate paired isolates.