Factors Influencing Distribution of Coccidioides immitis in Soil, Washington State, 2016

Abstract

Coccidioides immitis and Coccidioides posadasii are causative agents of Valley fever, a serious fungal disease endemic to regions with hot, arid climate in the United States, Mexico, and Central and South America. The environmental niche of Coccidioides spp. is not well defined, and it remains unknown whether these fungi are primarily associated with rodents or grow as saprotrophs in soil. To better understand the environmental reservoir of these pathogens, we used a systematic soil sampling approach, quantitative PCR (qPCR), culture, whole-genome sequencing, and soil chemical analysis to identify factors associated with the presence of C. immitis at a known colonization site in Washington State linked to a human case in 2010. We found that the same strain colonized an area of over 46,000 m² and persisted in soil for over 6 years. No association with rodent burrows was observed, as C. immitis DNA was as likely to be detected inside rodent holes as it was in the surrounding soil. In addition, the presence of C. immitis DNA in soil was correlated with elevated levels of boron, calcium, magnesium, sodium, and silicon in soil leachates. We also observed differences in the microbial communities between C. immitis-positive and -negative soils. Our artificial soil inoculation experiments demonstrated that C. immitis can use soil as a sole source of nutrients. Taken together, these results suggest that soil parameters need to be considered when modeling the distribution of this fungus in the environment. IMPORTANCE Coccidioidomycosis is considered a highly endemic disease for which geographic range is likely to expand from climate change. A better understanding of the ecological niche of Coccidioides spp. is essential for generating accurate distribution maps and predicting future changes in response to the changing environment. Our study used a systematic sampling strategy, advanced molecular detection methods, and soil chemical analysis to identify environmental factors associated with the presence of C. immitis in soil. Our results demonstrate the fungus can colonize the same areas for years and is associated with chemical and microbiological soil characteristics. Our results suggest that in addition to climate parameters, soil characteristics need to be considered when building habitat distribution models for this pathogen.

Keywords: Coccidioides; Valley fever; coccidioidomycosis.

FIG 1

Distribution of C. immitis along the nine transects. Study site where a combination of a radial and an interrupted belt transect method was used. Nine 100-m transects were sampled in 10-m intervals; squares represent 1-m² plots (left and right), and circles represent rodent burrows within or near 1-m² plots. Transects are labeled T1 to T9. Plots and rodent burrows where samples were qPCR positive for Coccidioides species DNA are shown in red. Plots that were qPCR positive and from which C. immitis isolates were obtained are marked with blue marks. Examples of vegetation encountered in different areas of the transect are shown in Fig. S1 in the supplemental material.

FIG 2

Genetic relationships among C. immitis isolates recovered from 2010 to 2016 from the study site. Isolates in red are from samples collected during the survey. B10637 is from the clinical specimen of the patient infected in the ATV accident in 2010. B10992 and B10996 are environmental isolates recovered in 2013 from soils collected in 2010 at the site of the accident. B11001 is an environmental isolate recovered in 2014 from the same site. B11034 and B13956 are from other locally acquired cases in Washington (49). Isolates from this study are in red. Remaining isolates are from California coccidioidomycosis cases. The tree scale is in SNPs.

FIG 3

Fungal community for soils positive and negative for C. immitis. The fungal community of soils positive (A) and negative (B) for Coccidioides sp. DNA by qPCR was assessed by ITS1 amplicon sequencing.

FIG 4

Propagation of C. immitis B10992 strain in soil. Sterile (gray) and native (black) soil samples were inoculated with C. immitis arthroconidia and monitored for 6 weeks during incubation. DNA levels were measured by qPCR analysis.