FIG 3.

Neighbor-joining phylogenetic tree of P. jirovecii clinical isolates from San Francisco. Repeat samples from the same clinical episode produced an identical genotype (SF45-1 and -2 and SF46-1 and -2). The other paired samples were genetically similar between samples but not identical. The other points represent isolates from patients from which a single sample is available. Very few samples had identical genotypes, suggesting that the six-microsatellite array will have a high discriminatory power between isolates.