Next-Generation Sequencing of C. immitis | CDC EID

EID Journal Home > Volume 17, Number 2–February 2011

Volume 17, Number 2–February 2011
Research
Next-Generation Sequencing of Coccidioides immitis Isolated during Cluster Investigation
David M. Engelthaler, Tom Chiller, James A. Schupp, Joshua Colvin, Stephen M. Beckstrom-Sternberg, Elizabeth M. Driebe, Tracy Moses, Waibhav Tembe, Shripad Sinari, James S. Beckstrom-Sternberg, Alexis Christoforides, John V. Pearson, John Carpten, Paul Keim, Ashley Peterson, Dawn Terashita, and S. Arunmozhi Balajee

Author affiliations: Translational Genomics Research Institute, Phoenix, Arizona, USA (D.M. Engelthaler, J.A. Schupp, J. Colvin, S.M. Beckstrom-Sternberg, E.M. Driebe, T. Moses, W. Tembe, S. Sinari, A. Christoforides, J.V. Pearson, J. Carpten, P. Keim); Centers for Disease Control and Prevention, Atlanta, Georgia, USA (T. Chiller, S.A. Balajee); Northern Arizona University, Flagstaff, Arizona, USA (S.M. Beckstrom-Sternberg, J.S. Beckstrom-Sternberg, P. Keim); and Los Angeles County Department of Public Health, Los Angeles, California, USA (A. Peterson, D. Terashita)

Suggested citation for this article

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.

Genotyping of microorganisms typically relies on comparison of genomic features (e.g., fragment size, repeats, single-nucleotide polymorphisms [SNPs]) between strains and/or against a database of feature profiles (e.g., PulseNET and mlst.net) for a population of the microbe of interest. Such genotyping tools are useful for molecular epidemiologic studies, microbial forensics, and phylogenetic applications. Molecular epidemiology methods may differ in genotyping specificity in linking cases to sources in an epidemiologic investigation; may be less than optimal (e.g., use of pulse-field gel electrophoresis to identify sources of foodborne outbreak often includes nontarget isolates); may not be sensitive enough to detect minor mutations in closely related strains in a forensic investigation (e.g., identifying markers in nearly identical strains of Bacillus anthracis); or may not have the resolution necessary to clearly elucidate population structure (e.g., use of nonphylogenetically informative characters such as amplified fragment-length polymorphism fragments or variable-number tandem repeats to establish clades of organisms).

Next-generation sequencing technology (next gen) provides rapid, relatively cost-effective whole-genome sequence typing (WGST). Although these technologies are relatively novel, they are quickly being adapted for use in the fields of genomics, transcriptomics, and phylogenetics and have been highly successful for resequencing, gene expression, and genomic profiling projects (1). Recently, next gen sequencing has been described as a viable genotyping tool in the fields of infectious disease epidemiology and microbial forensics (2,3).

Coccidioidomycosis is an invasive fungal infection caused by the dimorphic fungus Coccidioides spp. and is endemic to the southwestern United States (4). Organ donor–transmitted coccidiodomycosis was first reported almost 5 decades ago and is a rare but serious complication of solid organ transplantation; death rate associated with disseminated disease in this patient population is high (72%) (5). In these cases, donor-transmitted coccidioidomycosis was recognized because recipients underwent transplantation in a coccidioidomycosis-nonendemic area and had no prior travel history to a coccidioidomycosis-endemic area. No genotyping methods were used to confirm the genetic relationship between isolates recovered from the donor and recipient in any of these studies.

We describe the use of WGST to genotypically link C. immitis isolates recovered from a transplant-related cluster of coccidioidomycosis in an area to which it is endemic. Results show that isolates recovered from the transplantation patients were essentially genetically indistinguishable, thereby identifying the donor as the common source for these infections.

full-text:
Next-Generation Sequencing of C. immitis | CDC EID


Suggested Citation for this Article
Engelthaler DM, Chiller T, Schupp JA, Colvin J, Beckstrom-Sternberg SM, Driebe EM, et al. Next-generation sequencing of Coccidioides immitis isolated during cluster investigation. Emerg Infect Dis [serial on the Internet]. 2011 Feb [date cited].
http://www.cdc.gov/EID/content/17/2/227.htm

DOI: 10.3201/eid1702.100620


Comments to the Authors
Please use the form below to submit correspondence to the authors or contact them at the following address:

S. Arunmozhi Balajee, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Mailstop G11, Atlanta, GA 30333, USA; email: fir3@cdc.gov