Local Population Structure and Patterns of Western Hemisphere Dispersal for Coccidioides spp., the Fungal Cause of Valley Fever.
Coccidioidomycosis (or valley fever) is a fungal disease with high morbidity and mortality that affects tens of thousands of people each year. This infection is caused by two sibling species, Coccidioides immitis and C. posadasii, which are endemic to specific arid locales throughout the Western Hemisphere, particularly the desert southwest of the United States. Recent epidemiological and population genetic data suggest that the geographic range of coccidioidomycosis is expanding, as new endemic clusters have been identified in the state of Washington, well outside the established endemic range. The genetic mechanisms and epidemiological consequences of this expansion are unknown and require better understanding of the population structure and evolutionary history of these pathogens. Here we performed multiple phylogenetic inference and population genomics analyses of 68 new and 18 previously published genomes. The results provide evidence of substantial population structure in C. posadasii and demonstrate the presence of distinct geographic clades in central and southern Arizona as well as dispersed populations in Texas, Mexico, South America, and Central America. Although a smaller number of C. immitis strains were included in the analyses, some evidence of phylogeographic structure was also detected in this species, which has been historically limited to California and Baja, Mexico. Bayesian analyses indicated that C. posadasii is the more ancient of the two species and that Arizona contains the most diverse subpopulations. We propose a southern Arizona-northern Mexico origin for C. posadasii and describe a pathway for dispersal and distribution out of this region.


OBJECTIVE
Coccidioidomycosis, or valley fever, is caused by the pathogenic fungi Coccidioides posadasii and C. immitis The fungal species and disease are primarily found in the American desert southwest, with spotted distribution throughout the Western Hemisphere. Initial molecular studies suggested a likely anthropogenic movement of C. posadasii from North America to South America. Here we comparatively analyze eighty-six genomes of the two Coccidioides species and establish local and species-wide population structures to not only clarify the earlier dispersal hypothesis but also provide evidence of likely ancestral populations and patterns of dispersal for the known subpopulations of C. posadasii.
TGen North, Translational Genomics Research Institute, Flagstaff, Arizona, USA dengelthaler@tgen.org.
David M
DM
Engelthaler
TGen North, Translational Genomics Research Institute, Flagstaff, Arizona, USA.
Chandler C
CC
Roe
Informatics and Computing Center, Northern Arizona University, Flagstaff, Arizona, USA.
Crystal M
CM
Hepp
TGen North, Translational Genomics Research Institute, Flagstaff, Arizona, USA.
Marcus
M
Teixeira
TGen North, Translational Genomics Research Institute, Flagstaff, Arizona, USA.
Elizabeth M
EM
Driebe
TGen North, Translational Genomics Research Institute, Flagstaff, Arizona, USA.
James M
JM
Schupp
Mycotic Diseases Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Lalitha
L
Gade
Division of Public Health Services, Arizona Department of Health Services, Phoenix, Arizona, USA.
Victor
V
Waddell
Division of Public Health Services, Arizona Department of Health Services, Phoenix, Arizona, USA.
Kenneth
K
Komatsu
Asociación de Salud Integral, Guatemala City, Guatemala.
Eduardo
E
Arathoon
Universidad de San Carlos, Ciudad Universitaria, Guatemala City, Guatemala.
Heidi
H
Logemann
Division of Infectious Diseases, Department of Medicine, University of California, Davis, Davis, California, USA.
George R
GR
Thompson
Mycotic Diseases Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Tom
T
Chiller
TGen North, Translational Genomics Research Institute, Flagstaff, Arizona, USA.
Bridget
http://orcid.org/0000-0002-3439-4517
B
Barker
TGen North, Translational Genomics Research Institute, Flagstaff, Arizona, USA Microbial Genetics and Genomics Center, Northern Arizona University, Flagstaff, Arizona, USA.
Paul
P
Keim
Mycotic Diseases Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Anastasia P
AP
Litvintseva
D002489:Central America / Q000453:epidemiology; D003045:Coccidioides / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D003047:Coccidioidomycosis / Q000453:epidemiology / Q000382:microbiology*; D010802:Phylogeny; D013020:South America / Q000453:epidemiology; D015206:Southwestern United States / Q000453:epidemiology