The epidemiology and clinical features of coccidioidomycosis (Valley fever) and disease ecology of Coccidioides spp. in New Mexico (2006-2023)

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 1,541 human cases from an 18-year period. 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 report 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 from clinical specimens, wild animals, and soil samples confirm Coccidioides posadasii is the main causative species of coccidioidomycosis in New Mexico. Environmental surveillance validates locally acquired infections could occur in, but are not limited to, Catron, Doña Ana, Sierra, and Socorro Counties.

Methods
Clinical specimens from 14 patients diagnosed with coccidioidomycosis in New Mexico were submitted to the NMDOH Scientific Laboratory Division (SLD) where they were extracted using the PrepMan® Ultra Reagent method (Applied Biosystems, Foster City, CA, USA). We amplified the internal transcribed spacer region (ITS) of ribosomal RNA (rRNA) with the ITS1-F and ITS4 primers, and crude PCR products were sent to Functional Biosciences (Madison, WI, USA) for Sanger sequencing using BigDye v.3.1 chemistry. Sequence quality was assessed with minimum phred20 cutoff. Forward and reverse sequences were visualized and assembled with Sequencher v.5.1 (Gene Codes, Ann Arbor, MI, USA).

ITS rRNA sequences collected from patients in New Mexico were subjected to phylogenetic analysis along with reference sequence Uncinocarpus reesii from GenBank (accession NR_111092). We aligned sequences with mafft v.7.481 using automatically determined settings and trimmed the resulting alignment with trimal v.1.4.1 in automated1 mode. A maximum liklihood phylogeny for within state comparisons was inferred using the TNe model from 33 Coccidioides sequences from New Mexico plus U. reesii as an outgroup from a final alignment of 583 nucleotides. The best fitting model for tree building was chosen by the ModelFinder algorithm. The tree was constructed in IQ-Tree v.1.6.12 with 10,000 ultrafast bootstraps replicates and visualized in ggtree.