The Epidemiology of Coccidioidomycosis (Valley fever) and the Disease Ecology of Coccidioides spp. in New Mexico (2006-2023)

Abstract

Coccidioidomycosis (Valley fever), caused by Coccidioides spp., is a fungal infection endemic to semi-arid regions of the Americas. Despite 80 years of disease recognition in New Mexico, there is limited disease awareness. We incorporated clinical, epidemiological, and ecological datasets to summarize the knowledge of Valley fever in New Mexico. We analyzed 1541 human cases from 2006 to 2023. On average, 86 cases were reported each year (4.1 cases per 100,000 population per year). The highest levels of incidence were in southwestern New Mexico. American Indian or Alaska Natives in New Mexico had a 1.9 times higher incidence rate of coccidioidomycosis than White people, and among age groups, older populations in New Mexico had the highest incidence rates. We analyzed 300 soil samples near Las Cruces, New Mexico, for the presence of Coccidioides and reported the first known positive soil samples collected from the state, the majority of which were from grassland-dominated sites and from animal burrows. Sequence analyses in clinical specimens, wild animals, and soil samples confirmed that Coccidioides posadasii is the main causative species of coccidioidomycosis in New Mexico. Environmental surveillance validated that locally acquired infections could occur in, but are not limited to, Catron, Doña Ana, Sierra, and Socorro Counties.

Keywords: Coccidioides; Valley fever; burrow; climate change; coccidioidomycosis; disease surveillance; mycoses; qPCR; soil.

Figure 1

Time series of (a) annual coccidioidomycosis cases and (b) monthly coccidioidomycosis cases in New Mexico from 2006 to 2023. Coccidioidomycosis case definitions changed in 2008, 2011, and 2023; these years are indicated by black arrow markers on the x-axis. (c) Mean annual seasonal cycle and the interquartile range of coccidioidomycosis cases in New Mexico from 2006 to 2023. The greatest case seasonal counts and variability occurred in the spring and summer seasons.

Figure 2

Age-stratified mean annual coccidioidomycosis incidence rates in New Mexico, averaged for 2006–2023, and 95% confidence intervals. Older populations had higher levels of coccidioidomycosis incidence, with the highest incidence among people aged 65–74 years.

Figure 3

(a) Mean annual coccidioidomycosis incidence (cases per 100,000 population per year) averaged from 2006 to 2023 by county. (b) Mean annual coccidioidomycosis incidence (cases per 100,000 population per year) averaged from 2006 to 2023 by New Mexico Health Jurisdiction (Supplementary Figure S1). In both maps, positive soil samples collected in 2023 and animal samples collected in 1998, 2014, and 2017 are indicated with grey markers, positive soil samples with squares, and positive animal samples with circles. The size of the marker corresponds to the number of positive samples within a given 12 km diameter surrounding a sampling location.

Figure 4

Maximum likelihood (ML) phylogenetic analysis of 33 Coccidioides ITS rRNA sequences from New Mexico. ML tree was inferred using best-fitting model, as determined by ModelFinder, with 10,000 ultrafast bootstrap replicates (denoted by branch thickness). The two described causative agents of coccidioidomycosis, C. immitis (dark blue) and C. posadasii (dark red), are included. Branch length of outgroup Uncinocarpus reesii (GenBank accession NR_111092) is 0.0782.