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

Abstract

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.

Timing the Origin ofCryptococcus gattiisensu stricto, Southeastern United States

“…Although humans might have populated the southeastern United States by the time of the dispersal, most of the human movement was north to south rather than the reverse ( 12 ). This relatively recent emergence during the Pleistocene epoch is different from what has been hypothesized for other endemic mycoses, a much older fungal species dispersal resulting from mass migration of animal populations between continents ( 13 ). The idea of recent emergence also departs sharply from what has been hypothesized as a speciation attributable to prehistoric land movements, as has been proposed for larger Cryptococcus species separations ( 14 ).…”

Coccidioides immitis and posadasii; A review of their biology, genomics, pathogenesis, and host immunity

“…Some geographic overlap between the two species also occurs in Southern California and Baja California [7]. Both species contain subpopulations that cluster within smaller geographic areas [8].

10.1080/21505594.2018.1509667-F0001Figure 1.A phylogenetic tree of dimorphic fungi that are human pathogens.

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“…The DNA sequences of several of isolates of C. immitis and many C. posadasii isolates have been determined [8,34]. There is some hybridization between the two species [6,35].…”

“…There is some hybridization between the two species [6,35]. Sequencing of a large number of clinical isolates in Arizona established that almost all were genetically diverse strains of C. posadasii [8]. Groups of isolates from Tucson and Phoenix areas are genetically distinct.…”

Genetic differences between Coccidioides spp. and closely related nonpathogenic Onygenales

“…genome should be included. However, many more strains have been sequence but not annotated, so this may be an over-estimate of the total number of conserved genes [17]. The total number of genes in these isolates varies between 9,905 and 117,815 (mean = 9,768) so, on average, about 20% of the genes appear to be strain specific.…”