Phylogenetic analyses of AS-PCR amplicon and bulk sequences.

<p>Genetic relationships between pre-existing minority drug resistance populations and majority-level drug resistant populations that subsequently arose were analyzed by Maximum Likelihood phylogeny inferred by MEGA6. Numbers next to each symbol indicates the collecting point IDs of each patient (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135941#pone.0135941.s004" target="_blank">S4 Table</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135941#pone.0135941.s005" target="_blank">S5 Table</a>). Italic numbers at the tree-nodes indicate bootstrap values of the taxa analyzed. (A) Analysis of K103N populations in Individual 3: Solid and open circles indicate K103N positive and negative bulk sequence results, respectively. A solid triangle indicates K103N-positive amplicon at ID 9. ID 9 samples are highlighted with red. (B) Analysis of T215I populations in Individual 3: Solid and open circles indicate T215I positive and negative bulk sequence results, respectively. Two solid triangles indicate T215I-positive AS-PCR amplicon from ID 17 and 21 samples. ID17 and 21 are highlighted with red. (C) Analysis of K103N populations in Individual 4: Solid and open circles indicate K103N positive and negative bulk sequence results, respectively. A solid triangle indicates sequence data of K103N-positive amplicon derived from ID 2 sample. Red letters; ID 2 samples are highlighted with red.