Local Population Structure and Patterns of Western Hemisphere Dispersal for Coccidioides spp., the Fungal Cause of Valley Fever.

David M Engelthaler,Anastasia P Litvintseva,Tom Chiller,Bridget Barker,Marcus Teixeira,Victor Waddell,Lalitha Gade,Eduardo Arathoon,Kenneth Komatsu,Chandler C Roe,George R Thompson,Elizabeth M Driebe,Crystal M Hepp,Paul Keim,James M Schupp,Heidi Logemann,Joseph Heitman

doi:10.1128/mbio.00550-16

Abstract

ABSTRACTCoccidioidomycosis (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.

Highlights

IntroductionCoccidioidomycosis (or valley fever) is a fungal disease with high morbidity and mortality that affects tens of thousands of people each year
Coccidioidomycosis is a fungal disease with high morbidity and mortality that affects tens of thousands of people each year
We present results of a whole-genome SNP analysis of Coccidioides strains from geographically diverse locations that has further confirmed the presence of two species, C. immitis and C. posadasii, first established by Fisher et al [2] and further described in subsequent studies [4, 11]

Summary

Introduction

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, the desert southwest of the United States. Coccidioides immitis and C. posadasii are the etiological agents of coccidioidomycosis, or valley fever, a primarily pulmonary disease that causes tremendous morbidity (i.e., thousands of new infections per year) in the southwestern United States and other focal regions in the Americas [1]. Genomic epidemiology is needed to help establish the location of exposure of a nonclonal outbreak and robust phylogenomic analysis is needed for in-depth investigation of the local population structure to better understand pathogen emergence, dispersal, and expansion [15]. While that groundbreaking study was critical to understanding largescale phylogeographic features of Coccidioides epidemiology, and while evidence was identified for local population structure, additional microsatellite analysis of Arizona-only isolates was unable to identify a local structure within that state [18]

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Conclusion