Utility of Whole-Genome Sequencing to Ascertain Locally Acquired Cases of Coccidioidomycosis, Washington, USA

Abstract

Coccidioidomycosis is an emerging fungal infection in Washington, USA, and the epidemiology of the disease in this state is poorly understood. We used whole-genome sequencing to differentiate locally acquired cases in Washington on the basis of the previously identified phylogeographic population structure of Coccidioides spp. Clinical isolates from coccidioidomycosis cases involving possible Washington soil exposure were included. Of 17 human infections with epidemiologic evidence of possible local acquisition, 4 were likely locally acquired infections and 13 were likely acquired outside Washington. Isolates from locally acquired cases clustered within the previously established Washington clade of C. immitis. Genetic differences among these strains suggest multiple environmental reservoirs of C. immitis in the state.

Keywords: Coccidioides; United States; Washington; coccidioidomycosis; fungal infections; fungi; public health; surveillance; valley fever; whole-genome sequencing.

Figure

Genetic relationships among Coccidioides immitis isolates. A) Isolates from patients in Washington, USA, compared with isolates from other locations. B) Genetic relationships among C. immitis isolates from the Washington clade; single-nucleotide polymorphism numbers are shown above the branches. Dark blue indicates previously described environmental and human isolates (13) from Washington, light blue indicates isolates from new cases that were likely acquired in Washington, and orange indicates isolates from cases that were likely acquired outside Washington. Isolates from patients with the documented travel histories are indicated as Traveler. Travel history is detailed in the Table. Isolates with SJV names are from the San Joaquin Valley, California, as described (20). Bootstrap values shown in green circle indicate 100% support. Scale bars indicate nucleotide substitutions per site. CDC, Centers for Disease Control and Prevention; Env, environment.