DOI: 10.5061/dryad.sn02v6xgg
title: The epidemiology and clinical features of coccidioidomycosis (Valley fever) and disease ecology of Coccidioides spp. in New Mexico (2006-2023)

description: 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.
description: 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 <em>Uncinocarpus
 reesii </em>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 <em>automated1</em>
 mode. A maximum liklihood phylogeny for within state comparisons was
 inferred using the TNe model from 33 <em>Coccidioides</em>
 sequences from New Mexico plus <em>U. reesii</em> 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.
description: # The epidemiology and clinical features of coccidioidomycosis (Valley
 fever) and disease ecology of *Coccidioides* spp. in New Mexico
 (2006-2023)
 [https://doi.org/10.5061/dryad.sn02v6xgg](https://doi.org/10.5061/dryad.sn02v6xgg) ## Description of the data and file structure Molecular and phylogenetic analyses of clinical *Coccidioides* spp. isolated from patients in New Mexico from 2013-2023. ### Files and variables #### File: Cocci_33_NM_outgroup.trim.contree Description: Maximum likelihood phylogenetic analyses of *Coccidioides* ITS rRNA sequences from clinical patients diagnosed in New Mexico from 2013-2023. The tree was inferred using the TNe model, as chosen by the ModelFinder algorithm. #### File: Cocci_33_NM_outgroup.trim Description: The final trimmed alignment spanning 583 nucleotides of 33 *Coccidioides* ITS rRNA sequences from clinical patients diagnosed in New Mexico from 2013-2023. *Uncinocarpus reesii* was included as an outgroup. ## Code/software mafft v.7.481 trimal v.1.4.1 IQ-Tree v.1.6.12 ggtree v.3.10.1 ## Access information Data was derived from the following sources: * GenBank ## Human subjects data All samples and data were collected as part of routine New Mexico Department of Health surveillance for reportable conditions per New Mexico Administrative code 7.4.3.13 and were not collected as part of a study. Data were de-identified before provision to researchers. Because there were no human research subjects, there was no need to submit to an IRB for data collected as part of routine public health surveillance.