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Volume 25, Number 3—March 2019
Research

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

Hanna N. OlteanComments to Author , Kizee A. Etienne, Chandler C. Roe, Lalitha Gade, Orion Z. McCotter, David M. Engelthaler, and Anastasia P. Litvintseva
Author affiliations: Washington State Department of Health, Shoreline, Washington, USA (H.N. Oltean); Centers for Disease Control and Prevention, Atlanta, Georgia, USA (K.A. Etienne, L. Gade, O.Z. McCotter, A.P. Litvintseva); Translational Genomics Research Institute, Flagstaff, Arizona, USA (C.C. Roe, D.M. Engelthaler)

Main Article

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

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.

Main Article

References
  1. Brown  J, Benedict  K, Park  BJ, Thompson  GR III. Coccidioidomycosis: epidemiology. Clin Epidemiol. 2013;5:18597.PubMedGoogle Scholar
  2. Adams  D, Fullerton  K, Jajosky  R, Sharp  P, Onweh  D, Schley  A, et al. Summary of notifiable infectious diseases and conditions—United States, 2013. MMWR Morb Mortal Wkly Rep. 2015;62:1122.PubMedGoogle Scholar
  3. Cordeiro  RA, Brilhante  RS, Rocha  MF, Bandeira  SP, Fechine  MA, de Camargo  ZP, et al. Twelve years of coccidioidomycosis in Ceará State, Northeast Brazil: epidemiologic and diagnostic aspects. Diagn Microbiol Infect Dis. 2010;66:6572.PubMedGoogle Scholar
  4. Wilken  JA, Sondermeyer  G, Shusterman  D, McNary  J, Vugia  DJ, McDowell  A, et al. Coccidioidomycosis among workers constructing solar power farms, California, USA, 2011–2014. Emerg Infect Dis. 2015;21:19972005.PubMedGoogle Scholar
  5. Pappagianis  D; Coccidioidomycosis Serology Laboratory. Coccidioidomycosis in California state correctional institutions. Ann N Y Acad Sci. 2007;1111:10311.PubMedGoogle Scholar
  6. Colson  AJ, Vredenburgh  L, Guevara  RE, Rangel  NP, Kloock  CT, Lauer  A. Large-scale land development, fugitive dust, and increased coccidioidomycosis incidence in the antelope valley of California, 1999–2014. Mycopathologia. 2017;182:43958.PubMedGoogle Scholar
  7. Marsden-Haug  N, Goldoft  M, Ralston  C, Limaye  AP, Chua  J, Hill  H, et al. Coccidioidomycosis acquired in Washington State. Clin Infect Dis. 2013;56:84750.PubMedGoogle Scholar
  8. Galgiani  JN, Thompson  G III. Valley fever (coccidioidomycosis), tutorial for primary care professionals, 2016. Valley Fever Center for Excellence, The University of Arizona [cited 2018 Nov 30]. https://vfce.arizona.edu/sites/default/files/9-valley_fever_tutorial.pdf
  9. Arizona Department of Health Services (AZDoH). Valley fever 2016 annual report, 2017 [cited 2018 Nov 30]. https://www.azdhs.gov/documents/preparedness/epidemiology-disease-control/valley-fever/reports/valley-fever-2016.pdf
  10. Cooksey  GS, Nguyen  A, Knutson  K, Tabnak  F, Benedict  K, McCotter  O, et al. Notes from the field: increase in coccidioidomycosis—California, 2016. MMWR Morb Mortal Wkly Rep. 2017;66:8334.PubMedGoogle Scholar
  11. Gorris  M, Cat  L, Zender  C, Treseder  K, Randerson  J. Coccidioidomycosis dynamics in relation to climate in the southwestern United States. GeoHealth. 2018;2:624.
  12. Marsden-Haug  N, Hill  H, Litvintseva  AP, Engelthaler  DM, Driebe  EM, Roe  CC, et al.; Centers for Disease Control and Prevention (CDC). Coccidioides immitis identified in soil outside of its known range - Washington, 2013. MMWR Morb Mortal Wkly Rep. 2014;63:450.PubMedGoogle Scholar
  13. Litvintseva  AP, Marsden-Haug  N, Hurst  S, Hill  H, Gade  L, Driebe  EM, et al. Valley fever: finding new places for an old disease: Coccidioides immitis found in Washington State soil associated with recent human infection. Clin Infect Dis. 2015;60:e13.PubMedGoogle Scholar
  14. Washington State Department of Health (WADoH). Washington State annual report on fungal disease, 2014 [cited 2018 Nov 30]. https://www.doh.wa.gov/Portals/1/Documents/5100/420-146-FungalDiseaseAnnualReport.pdf
  15. Barker  BM, Jewell  KA, Kroken  S, Orbach  MJ. The population biology of coccidioides: epidemiologic implications for disease outbreaks. Ann N Y Acad Sci. 2007;1111:14763.PubMedGoogle Scholar
  16. Neafsey  DE, Barker  BM, Sharpton  TJ, Stajich  JE, Park  DJ, Whiston  E, et al. Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Res. 2010;20:93846.PubMedGoogle Scholar
  17. Fisher  MC, Rannala  B, Chaturvedi  V, Taylor  JW. Disease surveillance in recombining pathogens: multilocus genotypes identify sources of human Coccidioides infections. Proc Natl Acad Sci U S A. 2002;99:906771.PubMedGoogle Scholar
  18. Fisher  MC, Koenig  GL, White  TJ, Taylor  JW. Pathogenic clones versus environmentally driven population increase: analysis of an epidemic of the human fungal pathogen Coccidioides immitis. J Clin Microbiol. 2000;38:80713.PubMedGoogle Scholar
  19. Teixeira  MM, Barker  BM. Use of population genetics to assess the ecology, evolution, and population structure of Coccidioides. Emerg Infect Dis. 2016;22:102230.PubMedGoogle Scholar
  20. Engelthaler  DM, Roe  CC, Hepp  CM, Teixeira  M, Driebe  EM, Schupp  JM, et al. Local population structure and patterns of Western Hemisphere dispersal for Coccidioides spp., the fungal cause of Valley fever. MBio. 2016;7:e0055016.PubMedGoogle Scholar
  21. Salipante  SJ, SenGupta  DJ, Cummings  LA, Land  TA, Hoogestraat  DR, Cookson  BT. Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology. J Clin Microbiol. 2015;53:10729.PubMedGoogle Scholar
  22. Allard  MW, Bell  R, Ferreira  CM, Gonzalez-Escalona  N, Hoffmann  M, Muruvanda  T, et al. Genomics of foodborne pathogens for microbial food safety. Curr Opin Biotechnol. 2018;49:2249.PubMedGoogle Scholar
  23. Gardy  JL, Loman  NJ. Towards a genomics-informed, real-time, global pathogen surveillance system. Nat Rev Genet. 2018;19:920.PubMedGoogle Scholar
  24. Centers for Disease and Prevention. Coccidioidomycosis/Valley fever (Coccidioides spp.), 2011. Case definition. CSTE position statement. 10-ID-04 [cited 2018 Nov 30] https://wwwn.cdc.gov/nndss/conditions/coccidioidomycosi s/case-definition/2011
  25. Etienne  KA, Roe  CC, Smith  RM, Vallabhaneni  S, Duarte  C, Escadon  P, et al. Whole-genome sequencing to determine origin of multinational outbreak of Sarocladium kiliense bloodstream infections. Emerg Infect Dis. 2016;22:47681.PubMedGoogle Scholar
  26. Sahl  JW, Lemmer  D, Travis  J, Schupp  JM, Gillece  JD, Aziz  M, et al. NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats. Microb Genom. 2016;2:e000074.PubMedGoogle Scholar
  27. Li  H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011;27:298793.PubMedGoogle Scholar
  28. Vakatov  D. The NCBI C++ toolkit book, 2004. National Center for Biotechnology Information [cited 2018 Nov 30]. https://ncbi.github.io/cxx-toolkit
  29. Rice  P, Longden  I, Bleasby  A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000;16:2767.PubMedGoogle Scholar
  30. Untergasser  A, Cutcutache  I, Koressaar  T, Ye  J, Faircloth  BC, Remm  M, et al. Primer3—new capabilities and interfaces. Nucleic Acids Res. 2012;40:e115.PubMedGoogle Scholar
  31. Valdivia  L, Nix  D, Wright  M, Lindberg  E, Fagan  T, Lieberman  D, et al. Coccidioidomycosis as a common cause of community-acquired pneumonia. Emerg Infect Dis. 2006;12:95862.PubMedGoogle Scholar
  32. Chang  DC, Anderson  S, Wannemuehler  K, Engelthaler  DM, Erhart  L, Sunenshine  RH, et al. Testing for coccidioidomycosis among patients with community-acquired pneumonia. Emerg Infect Dis. 2008;14:10539.PubMedGoogle Scholar
  33. Tartof  SY, Benedict  K, Xie  F, Rieg  GK, Yu  KC, Contreras  R, et al. Testing for coccidioidomycosis among community-acquired pneumonia patients, southern California, USA. Emerg Infect Dis. 2018;24:77981.PubMedGoogle Scholar

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Page updated: February 19, 2019
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