FIG 3 .

Core genome tree data confirming close intrahost relatedness of the 19 CF P. aeruginosa isolates. A core genome single nucleotide polymorphism (SNP) tree was created based on read mapping to the PAO1 reference genome. Additional P. aeruginosa reference genomes PA14 (wild type, non-CF), PA356 (CF), and PA381 (CF) are included in the tree. Each patient is represented by a designation consisting of a capital “P” followed by a number, and different isolates from the same patient are labeled with the letters A, B, and C.