title: Next-generation sequencing of Coccidioides immitis isolated during cluster investigation.
abstract: Next-generation sequencing enables use of whole-genome sequence typing (WGST) as a viable and discriminatory tool for genotyping and molecular epidemiologic analysis. We used WGST to confirm the linkage of a cluster of Coccidioides immitis isolates from 3 patients who received organ transplants from a single donor who later had positive test results for coccidioidomycosis. Isolates from the 3 patients were nearly genetically identical (a total of 3 single-nucleotide polymorphisms identified among them), thereby demonstrating direct descent of the 3 isolates from an original isolate. We used WGST to demonstrate the genotypic relatedness of C. immitis isolates that were also epidemiologically linked. Thus, WGST offers unique benefits to public health for investigation of clusters considered to be linked to a single source.
authors.affiliation: Translational Genomics Research Institute, Phoenix, Arizona, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Engelthaler
authors.forename: Tom
authors.initials: T
authors.lastname: Chiller
authors.forename: James A
authors.initials: JA
authors.lastname: Schupp
authors.forename: Joshua
authors.initials: J
authors.lastname: Colvin
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Beckstrom-Sternberg
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: Driebe
authors.forename: Tracy
authors.initials: T
authors.lastname: Moses
authors.forename: Waibhav
authors.initials: W
authors.lastname: Tembe
authors.forename: Shripad
authors.initials: S
authors.lastname: Sinari
authors.forename: James S
authors.initials: JS
authors.lastname: Beckstrom-Sternberg
authors.forename: Alexis
authors.initials: A
authors.lastname: Christoforides
authors.forename: John V
authors.initials: JV
authors.lastname: Pearson
authors.forename: John
authors.initials: J
authors.lastname: Carpten
authors.forename: Paul
authors.initials: P
authors.lastname: Keim
authors.forename: Ashley
authors.initials: A
authors.lastname: Peterson
authors.forename: Dawn
authors.initials: D
authors.lastname: Terashita
authors.forename: S Arunmozhi
authors.initials: SA
authors.lastname: Balajee
mesh_terms: D016000:Cluster Analysis; D003045:Coccidioides / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D003047:Coccidioidomycosis / Q000175:diagnosis / Q000453:epidemiology / Q000382:microbiology*; D004271:DNA, Fungal / Q000032:analysis / Q000235:genetics; D016681:Genome, Fungal / Q000235:genetics*; D005838:Genotype; D006801:Humans; D017720:Molecular Epidemiology; D016533:Mycological Typing Techniques / Q000379:methods*; D016377:Organ Transplantation / Q000009:adverse effects*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity
chemical_list: D004271:DNA, Fungal