Coccidioidomycosis Dynamics in Relation to Climate in the Southwestern United States

Time series forecasting of Valley fever infection in Maricopa County, AZ using LSTM

Background

Coccidioidomycosis (CM), also known as Valley fever, is a respiratory infection. Recently, the number of confirmed cases of CM has been increasing. Precisely defining the influential factors and forecasting future infection can assist in public health messaging and treatment decisions.

Methods

We utilized Long Short-Term Memory (LSTM) networks to forecast CM cases, based on the daily pneumonia cases in Maricopa County, Arizona from 2020 to 2022. Besides weather and climate variables, we examined the impact of people's lifestyle change during COVID-19. Factors, including temperature, precipitation, wind speed, PM10 and PM2.5 concentration, drought, and stringency index, were included in LSTM networks, considering their association with CM prevalence, time-lag effect, and correlation with other factors.

Findings

LSTM can predict CM prevalence with accurate trend and low mean squared error (MSE). We also found a tradeoff between the length of the forecasting period and the performance of the forecasting model. The models with longer forecasting periods have less accurate trends over time and higher MSEs. Two models with different lengths of forecasting periods, 10 days and 30 days, are identified with good prediction.

Interpretation

LSTM algorithms, combined with traditional statistical methods, could help with the forecasting of CM cases. By predicting the CM prevalence, our results can inform researchers, epidemiologists, clinicians, and the public in order to assist public health.

Funding

"Getting to the Source of Arizona's Valley Fever Problem: A Tri-University Collaboration to Map and Characterize the Pathogen Where It Grows" funded by the Arizona Board of Regents.

Coccidioidomycosis Prophylaxis in Liver, Kidney, and Heart Transplant Recipients Residing in Endemic Areas Within the United States

BACKGROUND

Solid organ transplant (SOT) recipients residing in southwestern United States may be at an increased risk of symptomatic coccidioidomycosis (CM). Accordingly, clinical practice guidelines recommend the use of a universal oral azole antifungal prevention strategy for all SOT recipients residing in a CM endemic area. However, this recommendation is based on limited evidence. Our center does not routinely utilize CM azole antifungal prophylaxis for SOT recipients at low risk for de novo CM infection.

OBJECTIVE

To determine the incidence of CM with or without CM prophylaxis in Coccidioides seronegative liver, kidney, and heart transplant recipients residing in endemic areas with no documented history of CM at time of transplant.

STUDY DESIGN

A retrospective chart review was performed for SOT recipients who resided in CM endemic areas and received an organ transplant at Keck Hospital of USC between March 2017 and June 2023. Patients receiving CM prophylaxis with fluconazole were compared to patients not receiving CM prophylaxis. The primary end point was incidence of CM infection or asymptomatic seroconversion.

RESULTS

In our 85-patient cohort, 18 patients received CM prophylaxis compared to 67 patients who did not. Most patients who received prophylaxis were heart transplant recipients (66.6%). No cases of CM occurred within a median follow-up period of 2.2 years.

CONCLUSION

CM prophylaxis can be considered but may not be warranted for liver and kidney transplant recipients residing in Coccidioides endemic areas who are seronegative for Coccidioides and have no history of CM before transplant.

Prolonged coccidioidomycosis transmission seasons in a warming California: a Markov state transition model of shifting disease dynamics

Coccidioidomycosis, an emerging fungal disease in the southwestern United States, exhibits pronounced seasonal transmission, yet the influence of current and future climate on the timing and duration of transmission seasons remains poorly understood. We developed a distributed-lag Markov state transition model to estimate the effects of temperature and precipitation on the timing of transmission season onset and end, analysing reported coccidioidomycosis cases (n = 72 125) in California from 2000 to 2023. Using G-computation substitution estimators, we examined how hypothetical changes in seasonal meteorology impact transmission season timing. Transitions from cooler, wetter conditions to hotter, drier conditions were found to significantly accelerate season onset. Dry conditions (10th percentile of precipitation) in the spring shifted season onset an average of 2.8 weeks (95% CI: 0.43-3.58) earlier compared with wet conditions (90th percentile of precipitation). Conversely, transitions back to cooler, wetter conditions hastened season end, with dry autumn conditions extending the season by an average of 0.69 weeks (95% CI: 0.37-1.41) compared with wet conditions. When dry conditions occurred in the spring and autumn, the transmission season extended by 3.70 weeks (95% CI: 1.23-4.22). With prolonged dry seasons expected in California with climate change, our findings suggest this shift will extend the period of elevated coccidioidomycosis risk.

Valley-Forecast: Forecasting Coccidioidomycosis incidence via enhanced LSTM models trained on comprehensive meteorological data

Coccidioidomycosis (cocci), or more commonly known as Valley Fever, is a fungal infection caused by Coccidioides species that poses a significant public health challenge, particularly in the semi-arid regions of the Americas, with notable prevalence in California and Arizona. Previous epidemiological studies have established a correlation between cocci incidence and regional weather patterns, indicating that climatic factors influence the fungus's life cycle and subsequent disease transmission. This study hypothesizes that Long Short-Term Memory (LSTM) and extended Long Short-Term Memory (xLSTM) models, known for their ability to capture long-term dependencies in time-series data, can outperform traditional statistical methods in predicting cocci outbreak cases. Our research analyzed daily meteorological features from 2001 to 2022 across 48 counties in California, covering diverse microclimates and cocci incidence. The study evaluated 846 LSTM models and 176 xLSTM models with various fine-tuning metrics. To ensure the reliability of our results, these advanced neural network architectures are cross analyzed with Baseline Regression and Multi-Layer Perceptron (MLP) models, providing a comprehensive comparative framework. We found that LSTM-type architectures outperform traditional methods, with xLSTM achieving the lowest test RMSE of 282.98 (95% CI: 259.2-306.8) compared to the baseline's 468.51 (95% CI: 458.2-478.8), demonstrating a reduction of 39.60% in prediction error. While both LSTM (283.50, 95% CI: 259.7-307.3) and MLP (293.14, 95% CI: 268.3-318.0) also showed substantial improvements over the baseline, the overlapping confidence intervals suggest similar predictive capabilities among the advanced models. This improvement in predictive capability suggests a strong correlation between temporal microclimatic variations and regional cocci incidences. The increased predictive power of these models has significant public health implications, potentially informing strategies for cocci outbreak prevention and control. Moreover, this study represents the first application of the novel xLSTM architecture in epidemiological research and pioneers the evaluation of modern machine learning methods' accuracy in predicting cocci outbreaks. These findings contribute to the ongoing efforts to address cocci, offering a new approach to understanding and potentially mitigating the impact of the disease in affected regions.

Estimating coccidioidomycosis endemicity while accounting for imperfect detection using spatio-temporal occupancy modeling

Coccidioidomycosis, or Valley fever, is an infectious disease caused by inhaling Coccidioides fungal spores. Incidence has risen in recent years, and it is believed the endemic region for Coccidioides is expanding in response to climate change. While Valley fever case data can help us understand trends in disease risk, using case data as a proxy for Coccidioides endemicity is not ideal because case data suffer from imperfect detection, including false positives (eg, travel-related cases reported outside of endemic area) and false negatives (eg, misdiagnosis or underreporting). We proposed a Bayesian, spatio-temporal occupancy model to relate monthly, county-level presence/absence data on Valley fever cases to latent endemicity of Coccidioides, accounting for imperfect detection. We used our model to estimate endemicity in the western United States. We estimated high probability of endemicity in southern California, Arizona, and New Mexico, but also in regions without mandated reporting, including western Texas, eastern Colorado, and southeastern Washington. We also quantified spatio-temporal variability in detectability of Valley fever, given an area is endemic to Coccidioides. We estimated an inverse relationship between lagged 3- and 9-month precipitation and case detection, and a positive association with agriculture. This work can help inform public health surveillance needs and identify areas that would benefit from mandatory case reporting. This article is part of a Special Collection on Environmental Epidemiology.

Estimating the Exposure-Response Relationship between Fine Mineral Dust Concentration and Coccidioidomycosis Incidence Using Speciated Particulate Matter Data: A Longitudinal Surveillance Study

BACKGROUND

Coccidioidomycosis, caused by inhalation of Coccidioides spp. spores, is an emerging infectious disease that is increasing in incidence throughout the southwestern US. The pathogen is soil-dwelling, and spore dispersal and human exposure are thought to co-occur with airborne mineral dust exposures, yet fundamental exposure-response relationships have not been conclusively estimated.

OBJECTIVES

We estimated associations between fine mineral dust concentration and coccidioidomycosis incidence in California from 2000 to 2017 at the census tract level, spatiotemporal heterogeneity in exposure-response, and effect modification by antecedent climate conditions.

METHODS

We acquired monthly census tract-level coccidioidomycosis incidence data and modeled fine mineral dust concentrations from 2000 to 2017. We fitted zero-inflated distributed-lag nonlinear models to estimate overall exposure-lag-response relationships and identified factors contributing to heterogeneity in exposure-responses. Using a random-effects meta-analysis approach, we estimated county-specific and pooled exposure-responses for cumulative exposures.

RESULTS

We found a positive exposure-response relationship between cumulative fine mineral dust exposure in the 1-3 months before estimated disease onset and coccidioidomycosis incidence across the study region [incidence rate ratio (IRR) for an increase from 0.1 to 1.1   μ g / m 3 = 1.60 ; 95% CI: 1.46, 1.74]. Positive, supralinear associations were observed between incidence and modeled fine mineral dust exposures 1 [IRR = 1.13 (95% CI: 1.10, 1.17)], 2 [IRR = 1.15 (95% CI: 1.09, 1.20)] and 3 [IRR = 1.08 (95% CI: 1.04, 1.12)] months before estimated disease onset, with the highest exposures being particularly associated. The cumulative exposure-response relationship varied significantly by county [lowest IRR, western Tulare: 1.05 (95% CI: 0.54, 2.07); highest IRR, San Luis Obispo: 3.01 (95% CI: 2.05, 4.42)]. Season of exposure and prior wet winter were modest effect modifiers.

DISCUSSION

Lagged exposures to fine mineral dust were strongly associated with coccidioidomycosis incidence in the endemic regions of California from 2000 to 2017. https://doi.org/10.1289/EHP13875.

Valley fever under a changing climate in the United States

This review summarizes studies on the relationships between climate change and Valley Fever (VF), also termed Coccidioidomycosis, a potentially fatal upper-respiratory fungal infection caused by the pathogenic fungi, C. immitis or C. posadasii. The intensified onset of climate change has caused frequencies and possibly intensities of natural hazard events like dust storms and drought to increase, which has been correlated with greater prevalence of VF. These events, followed by changes in patterns of precipitation, not only pick up dust and spread it throughout the air, but also boost the growth and spread of Coccidioides. In California alone, cases of VF have increased fivefold from 2001 to 2021, and are expected to continue to increase. From 1999 to 2019, there was an average of 200 deaths per year caused by VF in the United States. The number of deaths caused by VF fluctuates year to year, but because more infections are predicted to occur due to a changing climate, deaths are expected to rise; thus, the rising prevalence of the disease is becoming a larger focus of the scientific community and poses an increased threat to public health. By reviewing recent and past studies on Coccidioidomycosis and its relationships with climate factors, we categorize future impacts of this disease on the United States, and highlight areas that need more study. Factors affecting the incidence of VF, such as modes of dispersal and the optimum environment for Coccidioides growth, that could potentially increase its prevalence as weather patterns change are discussed and how the endemic regions could be affected are assessed. In general, regions of the United States, including California and Arizona, where VF is endemic, are expanding and incidences of VF are increasing in those areas. The surrounding southern states, including Nevada, New Mexico, Utah, and Texas, are experiencing similar changes. In addition, the entire endemic region of the United States is predicted to spread northward as drought is prolonged and temperatures steadily increase. The findings from the keyword search from eight databases indicate that more studies on VF and its relation to dust and climate are needed especially for endemic states like Nevada that are currently not adequately studied. Overall, results of this survey summarize mechanisms and climate factors that might drive spread of VF and describes trends of incidence of VF in endemic states and predicted likely trends that might occur under a changing climate. Through reviewing recent and past studies of Coccidioidomycosis and its relationships with climate factors, future impacts of this disease have been categorized and speculated on effects it might have on the United States. Better understanding of how climate factors affect VF as well as identifying regions that require more research could inform both environmental managers and medical professionals with the resources needed to make more accurate predictions, design better mitigation strategies, send timely warnings, and protect public health. Shortened version This review explores how climate change affects Valley Fever (VF), a dangerous fungal infection caused by C. immitis or C. posadasii. Climate change has increased natural hazard events such as dust storms and droughts, which have caused the spread of VF. Cases of the disease have increased fivefold between 2001 and 2021 in California alone, and it poses an increasing threat to public health. The review summarizes mechanisms that drive the spread of VF and highlights trends in endemic states under a changing climate. It recommends more studies on VF and its relation to dust and climate, especially for states like Nevada. Identifying regions that require more research can help make more accurate predictions, design better mitigation strategies, send timely warnings, and protect public health.

Coccidioidomycosis seasonality in California: a longitudinal surveillance study of the climate determinants and spatiotemporal variability of seasonal dynamics, 2000-2021

Background

Coccidioidomycosis, an emerging fungal disease in the western USA, exhibits seasonal patterns that are poorly understood, including periods of strong cyclicity, aseasonal intervals, and variation in seasonal timing that have been minimally characterized, and unexplained as to their causal factors. Coccidioidomycosis incidence has increased markedly in recent years, and our limited understanding of intra- and inter-annual seasonality has hindered the identification of important drivers of disease transmission, including climate conditions. In this study, we aim to characterize coccidioidomycosis seasonality in endemic regions of California and to estimate the relationship between drought conditions and coccidioidomycosis seasonal periodicity and timing.

Methods

We analysed data on all reported incident cases of coccidioidomycosis in California from 2000 to 2021 to characterize seasonal patterns in incidence, and conducted wavelet analyses to assess the dominant periodicity, power, and timing of incidence for 17 counties with consistently high incidence rates. We assessed associations between seasonality parameters and measures of drought in California using a distributed lag nonlinear modelling framework.

Findings

All counties exhibited annual cyclicity in incidence (i.e., a dominant wavelet periodicity of 12 months), but there was considerable heterogeneity in seasonal strength and timing across regions and years. On average, 12-month periodicity was most pronounced in the Southern San Joaquin Valley and Central Coast. Further, the annual seasonal cycles in the Southern San Joaquin Valley and the Southern Inland regions occurred earlier than those in coastal and northern counties, yet the timing of annual cycles became more aligned among counties by the end of the study period. Drought conditions were associated with a strong attenuation of the annual seasonal cycle, and seasonal peaks became more pronounced in the 1-2 years after a drought ended.

Interpretation

We conclude that drought conditions do not increase the risk of coccidioidomycosis onset uniformly across the year, but instead promote increased risk concentrated within a specific calendar period (September to December). The findings have important implications for public health preparedness, and for how future shifts in seasonal climate patterns and extreme events may impact spatial and temporal coccidioidomycosis risk.

Funding

National Institutes of Health.

Clinical Characteristics and Mortality Risks Among Patients With Culture-Proven Coccidioidomycosis Who Are Critically Ill: A Multicenter Study in an Endemic Region

Background

Coccidioidomycosis is an endemic mycosis in the southwestern United States. While most infections are mild, severe cases can be devastating. We aimed to describe the clinical characteristics and mortality risks of patients in the intensive care unit (ICU) with culture-proven coccidioidomycosis.

Methods

We performed a retrospective chart review of patients in the ICU with positive Coccidioides spp culture in a large health care system in Arizona between 1 October 2017 and 1 July 2022. All data were entered into REDCap.

Results

An overall 145 patients were identified and included. The median age was 51 years, with the majority male (69%) and non-Hispanic White (39%). Most patients (n = 104, 72%) had pulmonary coccidioidomycosis, and 41 had extrapulmonary disease (17 meningitis, 13 fungemia, 10 musculoskeletal disease, and 4 pericardial or aortic involvement). Seventy patients (48%) died during hospitalization, and most (91%) received antifungal therapy during hospitalization. In the multivariate logistic regression model, age ≥60 years (odds ratio [OR], 7.0; 95% CI, 2.6-18.8), cirrhosis (OR, 13.1; 95% CI, 1.6-108.8), and mechanical ventilation or vasopressor support (OR, 15.4; 95% CI, 3.9-59.6) were independently associated with increased all-cause mortality, but pre-ICU antifungal use had a statistically insignificant mortality risk association (OR, 0.5; 95% CI, .2-1.2).

Conclusions

In our study of patients in the ICU with coccidioidomycosis and multiple comorbidities, the mortality rate was high. Older age, cirrhosis, and mechanical ventilation or vasopressor support were significantly associated with high mortality. Future studies are recommended to evaluate those risk factors and the efficacy of rapid diagnosis and early therapy in patients at high risk.

Diagnosis of Coccidioidomycosis with the Second-Generation Miravista IgG and IgM Enzyme Immunoassay and the Role of Adding Miravista Coccidioides Antigen Detection to Immunodiagnostic Assays

In the present study, we validate and compare the second-generation Miravista Coccidioides IgG and IgM enzyme immunoassays (EIA) (MiraVista Diagnostics [MVD] Ab EIA) to Meridian Diagnostics Coccidioides IgG and IgM EIA (Meridian Ab EIA), immunodiffusion (ID) and complement fixation (CF). We also evaluated whether the addition of Coccidioides antigen testing to anti-Coccidioides antibody testing increased the sensitivity for the diagnosis of currently active coccidioidomycosis. We retrospectively studied 555 patients evaluated at Valleywise Health Medical Center between January 2013 and May 2017 for whom coccidioidomycosis was suspected and samples were submitted to MVD for testing. Specimens were tested for antigen in the MVD antigen enzyme immunoassay (MVD Ag EIA) and for IgG and IgM antibodies with MVD and Meridian Diagnostics EIAs. ID and CF were obtained from medical records. Sensitivity and specificity were 83.0% and 91.1% or MVD Ab EIA, 69.3% and 99.7% for Meridian Ab EIA, 85.4% and 100% for ID and 65.5% and 100% for CF. Combined MVD antigen and antibody detection by EIA and ID resulted in increased sensitivity in disseminated and pulmonary disease (MVD Ag/MVD Ab: 100%, 88.3%; MVD Ag/Meridian Ab: 98.2%, 78.6%; and MVD Ag/ID: 100%, 91.7%). The detection of antibodies by MVD EIA was more sensitive than Meridian EIA or CF but similar to ID. This study supports the use of antigen testing in immunocompromised patients and those with suspected disseminated disease. Furthermore, the addition of antigen detection by EIA to antibody detection resulted in higher sensitivity of all serological tests.

Exploring Climate-Disease Connections in Geopolitical Versus Ecological Regions: The Case of West Nile Virus in the United States

Many infectious disease forecasting models in the United States (US) are built with data partitioned into geopolitical regions centered on human activity as opposed to regions defined by natural ecosystems; although useful for data collection and intervention, this has the potential to mask biological relationships between the environment and disease. We explored this concept by analyzing the correlations between climate and West Nile virus (WNV) case data aggregated to geopolitical and ecological regions. We compared correlations between minimum, maximum, and mean annual temperature; precipitation; and annual WNV neuroinvasive disease (WNND) case data from 2005 to 2019 when partitioned into (a) climate regions defined by the National Oceanic and Atmospheric Administration (NOAA) and (b) Level I ecoregions defined by the Environmental Protection Agency (EPA). We found that correlations between climate and WNND in NOAA climate regions and EPA ecoregions were often contradictory in both direction and magnitude, with EPA ecoregions more often supporting previously established biological hypotheses and environmental dynamics underlying vector-borne disease transmission. Using ecological regions to examine the relationships between climate and disease cases can enhance the predictive power of forecasts at various scales, motivating a conceptual shift in large-scale analyses from geopolitical frameworks to more ecologically meaningful regions.

Epidemiology of coccidioidomycosis in Argentina, an update

The National Reference Laboratory in Clinical Mycology of Argentina conducted a retrospective review of human coccidioidomycosis cases diagnosed by the National Mycology Laboratory Network of Argentina between 2010 and 2022 to determine the burden of the disease in the country. A total of 100 human coccidioidomycosis cases were documented, with a higher prevalence in male patients (male-to-female ratio of 1.9:1), with a median age of 41 years. Comparing the number of cases between two 10-year periods (2000-2009 and 2010-2019), the increase was 36.51% (from 63 to 86 cases). Among the 100 recorded cases, 79 tested positive using the double immunodiffusion test. Spherules were observed in 19 cases through histopathology or direct microscopic examination and the fungus was isolated in 39 cases. Thirty-six isolates were identified as Coccidioides posadasii through partial sequencing of the Ag2/PRA gene. Catamarca province had the highest number of cases, comprising 64% of the total, with an incidence rate above 1.0-2.5/100,000 inhabitants until 2018. However, there has been a recent downward trend in the region from 2018 to 2022. It is concerning that more than half of diagnosed cases were chronic pulmonary or disseminated forms, indicating a lack of early disease detection. To rectify this issue, it is imperative to conduct targeted training programs for healthcare personnel and enhance public awareness within the endemic area. This will contribute to a better understanding of the true burden of coccidioidomycosis and enable the implementation of appropriate sanitary control measures.

A microbial risk assessor's guide to Valley Fever (Coccidioides spp.): Case study and review of risk factors

Valley Fever is a respiratory disease caused by inhalation of arthroconidia, a type of spore produced by fungi within the genus Coccidioides spp. which are found in dry, hot ecosystems of the Western Hemisphere. A quantitative microbial risk assessment (QMRA) for the disease has not yet been performed due to a lack of dose-response models and a scarcity of quantitative occurrence data from environmental samples. A literature review was performed to gather data on experimental animal dosing studies, environmental occurrence, human disease outbreaks, and meteorological associations. As a result, a risk framework is presented with information for parameterizing QMRA models for Coccidioides spp., with eight new dose-response models proposed. A probabilistic QMRA was conducted for a Southwestern US agricultural case study, evaluating eight scenarios related to farming occupational exposures. Median daily workday risks for developing severe Valley Fever ranged from 2.53 × 10-7 (planting by hand while wearing an N95 facemask) to 1.33 × 10-3 (machine harvesting while not wearing a facemask). The literature review and QMRA synthesis confirmed that exposure to aerosolized arthroconidia has the potential to result in high attack rates but highlighted that the mechanistic relationships between environmental conditions and disease remain poorly understood. Recommendations for Valley Fever risk assessment research needs in order to reduce disease risks are discussed, including interventions for farmers.

The Ecology of Non-Candida Yeasts and Dimorphic Fungi in Cetaceans: From Pathogenicity to Environmental and Global Health Implications

Cetaceans, which are integral to marine ecosystems, face escalating anthropogenic threats, including climate change and pollution, positioning them as critical sentinel species for ocean and human health. This review explores the neglected realm of non-Candida yeasts in cetaceans, addressing the gaps in the understanding of their prevalence, pathogenicity, and environmental impacts. By examining identified species such as Cryptococcus spp., Paracoccidioides spp., and several dimorphic fungi, this review emphasizes global prevalence, epidemiology and ecology, pathogenicity, and potential zoonotic implications. It also discusses the fine line between yeast commensalism and pathogenicity by considering environmental influences such as pollution, climate shifts, and immune suppression. Environmental impact discussions delve into how rising ocean temperatures and pollution can modify yeast mycobiota, potentially affecting marine host health and broader ecosystem dynamics. The cetacean's unique physiology and ecological niches are considered, highlighting potential impacts on behaviors, reproductive success, and survival rates. Identifying crucial knowledge gaps, the review calls for intensified research efforts, employing advanced molecular techniques to unravel the cetacean mycobiome. Systematic studies on yeast diversity, antifungal susceptibility, and their influence on environmental and ecosystem health are proposed, and the balance between commensal and pathogenic species emphasizes the significance of the One Health approach. In conclusion, as marine mammals face unprecedented challenges, unveiling non-Candida yeasts in cetaceans emerges as a critical endeavor with far-reaching implications for the conservation of marine ecosystems and for both animal and human public health.

Understanding the exposure risk of aerosolized Coccidioides in a Valley fever endemic metropolis

Coccidioides is the fungal causative agent of Valley fever, a primarily pulmonary disease caused by inhalation of fungal arthroconidia, or spores. Although Coccidioides has been an established pathogen for 120 years and is responsible for hundreds of thousands of infections per year, little is known about when and where infectious Coccidioides arthroconidia are present within the ambient air in endemic regions. Long-term air sampling programs provide a means to investigate these characteristics across space and time. Here we present data from > 18 months of collections from 11 air sampling sites across the Phoenix, Arizona, metropolitan area. Overall, prevalence was highly variable across space and time with no obvious spatial or temporal correlations. Several high prevalence periods were identified at select sites, with no obvious spatial or temporal associations. Comparing these data with weather and environmental factor data, wind gusts and temperature were positively associated with Coccidioides detection, while soil moisture was negatively associated with Coccidioides detection. These results provide critical insights into the frequency and distribution of airborne arthroconidia and the associated risk of inhalation and potential disease that is present across space and time in a highly endemic locale.

Coccidioides spp. exposure among military working dogs in endemic regions of the United States

Coccidioidomycosis is a fungal disease in arid regions of the United States that is predicted to expand with climate change. Cases in military personnel and military working dogs (MWDs) impact personnel readiness and result in healthcare costs. To examine Coccidioides exposure among MWDs, 276 banked serum samples were retrieved from dogs housed in California, Texas, Arizona, New Mexico, Nevada, and Utah. Using gel immunodiffusion, six (2.1%) specimens were IgG-positive and three (1.1%) were equivocally IgM-positive. The IgG-positive samples were from Arizona (2 [prevalence 8.0%]) and California (4 [3.7%]). These data will guide future efforts to study MWDs as sentinels for human coccidioidomycosis.

Epidemiology of Coccidioidomycosis in the Veterans Health Administration, 2013-2022

We describe the epidemiology of coccidioidomycosis among a national cohort of Veterans. Using electronic health record data from adults tested for coccidioidomycosis between 1 January 2013 and 31 December 2022, we analyzed differences in baseline demographics (age, sex, race/ethnicity, birth country, comorbidities, residence, and Charlson Comorbidity Index score) between 4204 coccidioidomycosis-test-positive and 63,322 test-negative Veterans. Log-binomial regression models with adjusted risk ratios (aRRs) were used to evaluate risk factors associated with coccidioidomycosis including dissemination, hospitalization, and mortality. Case counts and incidence rates were highest in select counties in Arizona and California where Coccidioides is endemic. Coccidioidomycosis-positive Veterans were younger, more likely to be male, and Philippine-born. The risk factors most highly associated with being coccidioidomycosis-positive included Native Hawaiian/Pacific Islander (aRR 1.068 [95%CI: 1.039-1.098]), Asian (aRR 1.060 [95%CI: 1.037-1.083]), Black (aRR 1.029 [95%CI: 1.022-1.036]), American Indian/Alaska Native (aRR 1.026 [95%CI: 1.004-1.048]) race, and Hispanic/Latino ethnicity (aRR 1.021 [95%CI: 1.013-1.028]). Black race (aRR: 1.058 [95%CI: 1.037-1.081]) and Hispanic/Latino ethnicity (aRR 1.018 [95%CI: 1.0003-1.036]) were also associated with disseminated coccidioidomycosis, strengthening the evidence for the association of coccidioidomycosis, including severe infections, with specific racial and ethnic groups. There were no statistically significant differences in hospitalization within 45 days of testing or 30-day all-cause mortality. Improving our understanding of coccidioidomycosis risk factors is important for targeted prevention strategies and to reduce delays in diagnosis and ineffective treatment.

Love in the time of climate change: A review of sexual reproduction in the order Onygenales

Life-threatening infections caused by fungi in the order Onygenales have been rising over the last few decades. Increasing global temperature due to anthropogenic climate change is one potential abiotic selection pressure that may explain the increase in infections. The generation of genetically novel offspring with novel phenotypes through the process of sexual recombination could allow fungi to adapt to changing climate conditions. The basic structures associated with sexual reproduction have been identified in Histoplasma, Blastomyces, Malbranchea, and Brunneospora. However, for Coccidioides and Paracoccidioides, the actual structural identification of these processes has yet to be identified despite having genetic evidence that suggests sexual recombination is occurring in these organisms. This review highlights the importance of assessing sexual recombination in the order Onygenales as a means of understanding the mechanisms these organisms might employ to enhance fitness in the face of a changing climate and provides details regarding the known reproductive mechanisms in the Onygenales.

Combating the Dust Devil: Utilizing Naturally Occurring Soil Microbes in Arizona to Inhibit the Growth of Coccidioides spp., the Causative Agent of Valley Fever

The fungal disease Valley fever causes a significant medical and financial burden for affected people in the endemic region, and this burden is on the rise. Despite the medical importance of this disease, little is known about ecological factors that influence the geographic point sources of high abundance of the pathogens Coccidioides posadasii and C. immitis, such as competition with co-occurring soil microbes. These “hot spots”, for instance, those in southern Arizona, are areas in which humans are at greater risk of being infected with the fungus due to consistent exposure. The aim of this study was to isolate native microbes from soils collected from Tucson, Arizona (endemic area for C. posadasii) and characterize their relationship (antagonistic, synergistic, or neutral) to the fungal pathogen with in vitro challenge assays. Secreted metabolites from the microbes were extracted and described using analytical techniques including high-performance liquid chromatography (HPLC) and mass spectrometry. Bacteria belonging to the genus Bacillus and fungi in the Fennellomyces and Ovatospora genera were shown to significantly decrease the growth of Coccidioides spp. In vitro. In contrast, other bacteria in the Brevibacillus genus, as well as one species of Bacillus bacteria, were shown to promote growth of Coccidioides when directly challenged. The metabolites secreted from the antagonistic bacteria were described using HPLC and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The microbes identified in this study as antagonists to Coccidioides and/or the metabolites they secrete have the potential to be used as natural biocontrol agents to limit the amount of fungal burden at geographic point sources, and therefore limit the potential for human infection.

Was Coccidioides a Pre-Columbian Hitchhiker to Southcentral Washington?

Coccidioides immitis, a pathogenic environmental fungus that causes Valley fever (coccidioidomycosis) primarily in the American Southwest and parts of Central and South America, has emerged over the past 12 years in the Columbia River Basin region, near the confluence with the Yakima River, in southcentral Washington state, USA. An initial autochthonous Washington human case was found in 2010, stemming from a wound derived from soil contamination during an all-terrain vehicle crash. Subsequent analysis identified multiple positive soil samples from the park where the crash occurred (near the Columbia River in Kennewick, WA), and from another riverside location several kilometers upstream from the park location. Intensified disease surveillance identified several more cases of coccidioidomycosis in the region that lacked any relevant travel history to known endemic locales. Genomic analysis of both patient and soil isolates from the Washington cases determined that all samples from the region are phylogenetically closely related. Given the genomic and the epidemiological link between case and environment, C. immitis was declared to be a newly endemic fungus in the region, spawning many questions as to the scope of its presence, the causes of its recent emergence, and what it predicts about the changing landscape of this disease. Here, we review this discovery through a paleo-epidemiological lens in the context of what is known about C. immitis biology and pathogenesis and propose a novel hypothesis for the cause of the emergence in southcentral Washington. We also try to place it in the context of our evolving understanding of this regionally specific pathogenic fungus.

Microbiology and Climate Change: a Transdisciplinary Imperative

Climate change is a complex problem involving nonlinearities and feedback that operate across scales. No single discipline or way of thinking can effectively address the climate crisis. Teams of natural scientists, social scientists, engineers, economists, and policymakers must work together to understand, predict, and mitigate the rapidly accelerating impacts of climate change. Transdisciplinary approaches are urgently needed to address the role that microorganisms play in climate change. Here, we demonstrate with case studies how diverse teams and perspectives provide climate-change insight related to the range expansion of emerging fungal pathogens, technological solutions for harmful cyanobacterial blooms, and the prediction of disease-causing microorganisms and their vector populations using massive networks of monitoring stations. To serve as valuable members of a transdisciplinary climate research team, microbiologists must reach beyond the boundaries of their immediate areas of scientific expertise and engage in efforts to build open-minded teams aimed at scalable technologies and adoptable policies.

Risk of Exposure to Coccidioides spp. in the Temblor Special Recreation Management Area (SRMA), Kern County, CA

The Temblor Mountain Special Recreation Area (SRMA) on the western flank of the San Joaquin Valley, CA, is located in the endemic area of Coccidioides, a fungal pathogen responsible for the increasing incidence of coccidioidomycosis (Valley fever). Recreationists in the SRMA, such as off-highway vehicle (OHV) drivers and mountain bikers who disturb the soils, are at risk of being exposed to airborne arthroconidia (asexual spores) of the pathogen. To reduce the risk of pathogen exposure for visitors, the Bureau of Land Management (BLM) plans to limit recreational activities to areas with a reduced pathogen presence. They envision an official OHV park in the future, by also restricting access to areas with ongoing restoration efforts and by limiting soil erosion in sensitive areas. To investigate which soils in the Temblor SRMA are most likely to support the growth of Coccidioides spp., soil samples were collected over a 3-year period from dominant soil types in a northern and a southern sampling area and analyzed for the pathogen using a culture-independent PCR-based method. In addition, soil pH and electrical conductivity were determined. The results of this study revealed slight genetic variance in the Coccidioides sequences obtained from the soils of the Temblor SRMA. An analysis of variance (ANOVA) could not confirm differences in soil pH and electrical conductivity (EC) between the different soil types investigated and between sites where the pathogen was detected compared to sites where it could not be found. However, the year of sampling appeared to have an influence on observed soil pH and EC, and the presence of the pathogen. Of all dominant soil types investigated, those belonging to the Littlesignal-Cochora association were the least likely to contain the pathogen, whereas soils of the Beam-Panoza-Hillbrick association appeared more supportive. In addition to pointing out OHV areas with lower pathogen exposure risk in the Temblor SRMA, recommendations were made to educate visitors and BLM workers about the risk of contracting Valley fever.

Molecular Diagnosis of Endemic Mycoses

Diagnosis of endemic mycoses is still challenging. The moderated availability of reliable diagnostic methods, the lack of clinical suspicion out of endemic areas and the limitations of conventional techniques result in a late diagnosis that, in turn, delays the implementation of the correct antifungal therapy. In recent years, molecular methods have emerged as promising tools for the rapid diagnosis of endemic mycoses. However, the absence of a consensus among laboratories and the reduced availability of commercial tests compromises the diagnostic effectiveness of these methods. In this review, we summarize the advantages and limitations of molecular methods for the diagnosis of endemic mycoses.

Effects of precipitation, heat, and drought on incidence and expansion of coccidioidomycosis in western USA: a longitudinal surveillance study

BACKGROUND

Drought is an understudied driver of infectious disease dynamics. Amidst the ongoing southwestern North American megadrought, California (USA) is having the driest multi-decadal period since 800 CE, exacerbated by anthropogenic warming. In this study, we aimed to examine the influence of drought on coccidioidomycosis, an emerging infectious disease in southwestern USA.

METHODS

We analysed California census tract-level surveillance data from 2000 to 2020 using generalised additive models and distributed monthly lags on precipitation and temperature. We then developed an ensemble prediction algorithm of incident cases of coccidioidomycosis per census tract to estimate the counterfactual incidence that would have occurred in the absence of drought.

FINDINGS

Between April 1, 2000, and March 31, 2020, there were 81 448 reported cases of coccidioidomycosis throughout California. An estimated 1467 excess cases of coccidioidomycosis were observed in California in the 2 years following the drought that occurred between 2007 and 2009, and an excess 2649 drought-attributable cases of coccidioidomycosis were observed in the 2 years following the drought that occurred between 2012 and 2015. These increased numbers of cases more than offset the declines in cases that occurred during drought. An IQR increase in summer temperatures was associated with 2·02 (95% CI 1·84-2·22) times higher incidence in the following autumn (September to November), and an IQR increase in precipitation in the winter was associated with 1·45 (1·36-1·55) times higher incidence in the autumn. The effect of winter precipitation was 36% (25-48) stronger when preceded by two dry, rather than average, winters. Incidence in arid counties was most sensitive to precipitation fluctuations, while incidence in wetter counties was most sensitive to temperature.

INTERPRETATION

In California, multi-year cycles of dry conditions followed by a wet winter increases transmission of coccidioidomycosis, especially in historically wetter areas. With anticipated increasing frequency of drought in southwestern USA, continued expansion of coccidioidomycosis, along with more intense seasons, is expected. Our results motivate the need for heightened precautions against coccidioidomycosis in seasons that follow major droughts.

FUNDING

National Institutes of Health.

Breathing can be dangerous: Opportunistic fungal pathogens and the diverse community of the small mammal lung mycobiome

Human lung mycobiome studies typically sample bronchoalveolar lavage or sputum, potentially overlooking fungi embedded in tissues. Employing ultra-frozen lung tissues from biorepositories, we obtained fungal ribosomal RNA ITS2 sequences from 199 small mammals across 39 species. We documented diverse fungi, including common environmental fungi such as Penicillium and Aspergillus, associates of the human mycobiome such as Malassezia and Candida, and others specifically adapted for lungs (Coccidioides, Blastomyces, and Pneumocystis). Pneumocystis sequences were detected in 83% of the samples and generally exhibited phylogenetic congruence with hosts. Among sequences from diverse opportunistic pathogens in the Onygenales, species of Coccidioides occurred in 12% of samples and species of Blastomyces in 85% of samples. Coccidioides sequences occurred in 14 mammalian species. The presence of neither Coccidioides nor Aspergillus fumigatus correlated with substantial shifts in the overall mycobiome, although there was some indication that fungal communities might be influenced by high levels of A. fumigatus. Although members of the Onygenales were common in lung samples (92%), they are not common in environmental surveys. Our results indicate that Pneumocystis and certain Onygenales are common commensal members of the lung mycobiome. These results provide new insights into the biology of lung-inhabiting fungi and flag small mammals as potential reservoirs for emerging fungal pathogens.

Phylogenomic Placement of American Southwest-Associated Clinical and Veterinary Isolates Expands Evidence for Distinct Cryptococcus gattii VGVI

Whole-genome sequencing has advanced our understanding of the population structure of the pathogenic species complex Cryptococcus gattii, which has allowed for the phylogenomic specification of previously described major molecular type groupings and novel lineages. Recently, isolates collected in Mexico in the 1960s were determined to be genetically distant from other known molecular types and were classified as VGVI. We sequenced four clinical isolates and one veterinary isolate collected in the southwestern United States and Argentina from 2012 to 2021. Phylogenomic analysis groups these genomes with those of the Mexican VGVI isolates, expanding VGVI into a clade and establishing this molecular type as a clinically important population. These findings also potentially expand the known Cryptococcus ecological range with a previously unrecognized endemic area.

Coccidioidomycosis in Northern Arizona: an Investigation of the Host, Pathogen, and Environment Using a Disease Triangle Approach

Coccidioides immitis and Coccidioides posadasii are the etiological agents of coccidioidomycosis (Valley fever [VF]). Disease manifestation ranges from mild pneumonia to chronic or extrapulmonary infection. If diagnosis is delayed, the risk of severe disease increases. In this report, we investigated the intersection of pathogen, host, and environment for VF cases in Northern Arizona (NAZ), where the risk of acquiring the disease is much lower than in Southern Arizona. We investigated reported cases and assessed pathogen origin by comparing genomes of NAZ clinical isolates to isolates from other regions. Lastly, we surveyed regional soils for presence of Coccidioides. We found that cases of VF increased in NAZ in 2019, and Coccidioides NAZ isolates are assigned to Arizona populations using phylogenetic inference. Importantly, we detected Coccidioides DNA in NAZ soil. Given recent climate modeling of the disease that predicts that cases will continue to increase throughout the region, and the evidence presented in this report, we propose that disease awareness outreach to clinicians throughout the western United States is crucial for improving patient outcomes, and further environmental sampling across the western U.S. is warranted.

IMPORTANCE Our work is the first description of the Valley fever disease triangle in Northern Arizona, which addresses the host, the pathogen, and the environmental source in the region. Our data suggest that the prevalence of diagnosed cases rose in 2019 in this region, and some severe cases necessitate hospitalization. We present the first evidence of Coccidioides spp. in Northern Arizona soils, suggesting that the pathogen is maintained in the local environment. Until disease prevention is an achievable option via vaccination, we predict that incidence of Valley fever will rise in the area. Therefore, enhanced awareness of and surveillance for coccidioidomycosis is vital to community health in Northern Arizona.

Health and Clinical Impacts of Air Pollution and Linkages with Climate Change

Air Pollution Impacts and Climate Change LinksAs part of the NEJM Group series on climate change, Keswani and colleagues review the linkages between climate change and air pollution and suggest strategies that clinicians may use to mitigate the adverse health impacts of air pollution.

Landscape Topography and Regional Drought Alters Dust Microbiomes in the Sierra Nevada of California

Dust provides an ecologically significant input of nutrients, especially in slowly eroding ecosystems where chemical weathering intensity limits nutrient inputs from underlying bedrock. In addition to nutrient inputs, incoming dust is a vector for dispersing dust-associated microorganisms. While little is known about dust-microbial dispersal, dust deposits may have transformative effects on ecosystems far from where the dust was emitted. Using molecular analyses, we examined spatiotemporal variation in incoming dust microbiomes along an elevational gradient within the Sierra Nevada of California. We sampled throughout two dry seasons and found that dust microbiomes differed by elevation across two summer dry seasons (2014 and 2015), which corresponded to competing droughts in dust source areas. Dust microbial taxa richness decreased with elevation and was inversely proportional to dust heterogeneity. Likewise, dust phosphorus content increased with elevation. At lower elevations, early season dust microbiomes were more diverse than those found later in the year. The relative abundances of microbial groups shifted during the summer dry season. Furthermore, mutualistic fungal diversity increased with elevation, which may have corresponded with the biogeography of their plant hosts. Although dust fungal pathogen diversity was equivalent across elevations, elevation and sampling month interactions for the relative abundance, diversity, and richness of fungal pathogens suggest that these pathogens differed temporally across elevations, with potential implications for humans and wildlife. This study shows that landscape topography and droughts in source locations may alter the composition and diversity of ecologically relevant dust-associated microorganisms.

Update on the Epidemiology, Diagnosis, and Treatment of Coccidioidomycosis

Coccidioidomycosis is a fungal infection caused by Coccidioides immitis and Coccidioides posadasii. The dimorphic fungi live in the soils of arid and semi-arid regions of the western United States, as well as parts of Mexico, Central America, and South America. Incidence of disease has risen consistently in recent years, and the geographic distribution of Coccidioides spp. appears to be expanding beyond previously known areas of endemicity. Climate factors are predicted to further extend the range of environments suitable for the growth and dispersal of Coccidioides species. Most infections are asymptomatic, though a small proportion result in severe or life-threatening forms of disease. Primary pulmonary coccidioidomycosis is commonly mistaken for community-acquired pneumonia, often leading to inappropriate antibacterial treatment and unnecessary healthcare costs. Diagnosis of coccidioidomycosis is challenging and often relies on clinician suspicion to pursue laboratory testing. Advancements in diagnostic tools and antifungal therapy developments seek to improve the early detection and effective management of infection. This review will highlight recent updates and summarize the current understanding of the epidemiology, diagnosis, and treatment of coccidioidomycosis.

Coccidioidomycosis (Valley Fever), Soil Moisture, and El Nino Southern Oscillation in California and Arizona

The soil-borne fungal disease coccidioidomycosis (Valley fever) is prevalent across the southwestern United States (US). Previous studies have suggested that the occurrence of this infection is associated with anomalously wet or dry soil moisture states described by the "grow and blow" hypothesis. The growth of coccidioidomycosis is favored by moist conditions both at the surface and in the root zone. A statistical analysis identified two areas in Arizona and central California, with a moderate-to-high number of coccidioidomycosis cases. A Wavelet Transform Coherence (WTC) analysis between El Nino Southern Oscillation (ENSO), coccidioidomycosis cases, surface soil moisture (SSM; 0 to 5 cm) from European Space Agency-Climate Change Initiative (ESA-CCI), and shallow root zone soil moisture (RZSM; 0 to 40 cm depth) from Soil MERGE (SMERGE) was executed for twenty-four CA and AZ counties. In AZ, only SSM was modulated by ENSO. When case values were adjusted for overreporting between 2009 to 2012, a moderate but significant connection between ENSO and cases was observed at a short periodicity (2.1 years). In central CA, SSM, RZSM, and cases all had a significant link to ENSO at longer periodicities (5-to-7 years). This study provides an example of how oceanic-atmospheric teleconnections can impact human health.

Climate change and global health: A call to more research and more action

There is increasing understanding, globally, that climate change and increased pollution will have a profound and mostly harmful effect on human health. This review brings together international experts to describe both the direct (such as heat waves) and indirect (such as vector-borne disease incidence) health impacts of climate change. These impacts vary depending on vulnerability (i.e., existing diseases) and the international, economic, political, and environmental context. This unique review also expands on these issues to address a third category of potential longer-term impacts on global health: famine, population dislocation, and environmental justice and education. This scholarly resource explores these issues fully, linking them to global health in urban and rural settings in developed and developing countries. The review finishes with a practical discussion of action that health professionals around the world in our field can yet take.

PM10 and Other Climatic Variables Are Important Predictors of Seasonal Variability of Coccidioidomycosis in Arizona

Coccidioidomycosis (Valley fever) is a disease caused by the fungal pathogens Coccidioides immitis and Coccidioides posadasii that are endemic to the southwestern United States and parts of Mexico and South America. Throughout the range where the pathogens are endemic, there are seasonal patterns of infection rates that are associated with certain climatic variables. Previous studies that looked at annual and monthly relationships of coccidioidomycosis and climate suggest that infection numbers are linked with precipitation and temperature fluctuations; however, these analytic methods may miss important nonlinear, nonmonotonic seasonal relationships between the response (Valley fever cases) and explanatory variables (climate) influencing disease outbreaks. To improve our current knowledge and to retest relationships, we used case data from three counties of high endemicity in southern Arizona paired with climate data to construct a generalized additive statistical model that explores which meteorological parameters are most useful in predicting Valley fever incidence throughout the year. We then use our model to forecast the pattern of Valley fever cases by month. Our model shows that maximum monthly temperature, average PM10, and total precipitation 1 month prior to reported cases (lagged model) were all significant in predicting Valley fever cases. Our model fits Valley fever case data in the region of endemicity of southern Arizona and captures the seasonal relationships that predict when the public is at higher risk of being infected. This study builds on and retests relationships described by previous studies regarding climate variables that are important for predicting risk of infection and understanding this fungal pathogen. IMPORTANCE The inhalation of environmental infectious propagules from the fungal pathogens Coccidioides immitis and Coccidioides posadasii by susceptible mammals can result in coccidioidomycosis (Valley fever). Arizona is known to be a region where the pathogen is hyperendemic, and reported cases are increasing throughout the western United States. Coccidioides spp. are naturally occurring fungi in arid soils. Little is known about ecological factors that influence the growth of these fungi, and a higher environmental burden may result in increases in human exposure and therefore case rates. By examining case and climate data from Arizona and using generalized additive statistical models, we were able to examine the relationship between disease outbreaks and climatic variables and predict seasonal time points of increased infection risk.

No Consistent Link Between Dust Storms and Valley Fever (Coccidioidomycosis)

Dust storms, such as those associated with haboobs and strong regional winds, are frequently assumed to cause increases in cases of Valley fever (coccidioidomycosis). The disease is caused by inhaling arthroconidia of Coccidioides fungi that, after being disturbed from semi-desert subsoil, have become airborne. Fungal arthroconidia can be transported in low-wind conditions as well as in individual dust events, but there is no reliable evidence that all or most dust storms consistently lead to subsequent increases in coccidioidomycosis cases. Following a review of the relevant literature, this study examines the relationship between dust storms and coccidioidomycosis cases to determine if there is a consistent and general association between them. All recorded dust storms from 2006 to 2020 in and near the Phoenix area of Maricopa County, Arizona and the Bakersfield area of Kern County, California were used in a compositing analysis (superposed epoch analysis) of subsequent coccidioidomycosis cases in each area. Analyses of monthly and weekly disease case data showed no statistical differences in the patterns of coccidioidomycosis cases following dust storms versus non-dust storm conditions, for the entire data set as well as for seasonal subsets of the data. This study thoroughly analyzes post-dust storm coccidioidomycosis cases for a large set of dust storms, and it confirms and expands upon previous literature, including a recent study that measured airborne arthroconidia and found no consistent links connecting wind and dust conditions to increases in coccidioidomycosis.

Δcps1 vaccine protects dogs against experimentally induced coccidioidomycosis

Coccidioidomycosis is a significant health problem of dogs and humans in endemic regions, especially California and Arizona in the U.S. Both species would greatly benefit from a vaccine to prevent this disease. A live avirulent vaccine candidate, Δcps1, was tested for tolerability and efficacy to prevent pulmonary coccidioidomycosis in a canine challenge model. Vaccine injection-site reactions were transient and there were no systemic effects observed. Six of seven vaccine sites tested and all draining lymph nodes were sterile post-vaccination. Following infection with Coccidioides posadasii, strain Silveira, arthroconidia into the lungs, dogs given primary and booster vaccinations had significantly reduced lung fungal burdens (P = 0.0003) and composite disease scores (P = 0.0002) compared to unvaccinated dogs. Dogs vaccinated once had fungal burdens intermediate between those given two doses or none, but disease scores were not significantly different from unvaccinated (P = 0.675). Δcps1 was well-tolerated in the dogs and it afforded a high level of protection when given as prime and boost. These results drive the Δcps1 vaccine toward a licensed veterinary vaccine and support continued development of this vaccine to prevent coccidioidomycosis in humans.

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

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.

Epidemiology, Clinical Features, and Outcomes of Coccidioidomycosis, Utah, 2006-2015

On the basis of a 1957 geographic Coccidioides seropositivity survey, 3 counties in southwestern Utah, USA, were considered coccidioidomycosis-endemic, but there has been a paucity of information on the disease burden in Utah since. We report findings from a recent clinical and epidemiologic study of coccidioidomycosis in Utah. To describe clinical characteristics, we identified all coccidioidomycosis cases in an integrated health system in the state during 2006-2015. For epidemiologic analysis, we used cases reported to the Utah Department of Health during 2009-2015. Mean state incidence was 1.83 cases/100,000 population/year. Washington County, in southwestern Utah, had the highest incidence, 17.2 cases/100,000 population/year. In a generalized linear model with time as a fixed effect, mean annual temperature, population, and new construction were associated with regional variations in incidence. Using these variables in a spatiotemporal model, we estimated the adjusted regional variation by county to predict areas where Coccidioides infections might increase.

A Review of Coccidioides Research, Outstanding Questions in the Field, and Contributions by Women Scientists

Purpose of Review

Coccidioidomycosis is an infectious disease that gained clinical significance in the early 20th century. Many of the foundational contributions to coccidioidomycosis research, including the discovery of the fungal disease agent, Coccidioides spp., were made by women. We review recent progress in Coccidioides research and big questions remaining in the field, while highlighting some of the contributions from women.

Recent Findings

New molecular-based techniques provide a promising method for detecting Coccidioides, which can help determine the dominate reservoir host and ideal environmental conditions for growth. Genetic and genomic analyses have allowed an understanding of population structure, species level diversity, and evolutionary histories. We present a current, comprehensive genome list, where women contributed many of these entries. Several efforts to develop a coccidioidomycosis vaccine are underway.

Summary

Women continue to pioneer research on Coccidioides, including the relationships between the fungi and the environment, genetics, and clinical observations. Significant questions remain in the field of Coccidioides, including the main host reservoir, the relationships between genotypic and phenotypic variation, and the underlying cause for chronic clinical coccidioidomycosis cases.

Point Process Models for the Spread of Coccidioidomycosis in California

Coccidioidomycosis is an infectious disease of humans and other mammals that has seen a recent increase in occurrence in the southwestern United States, particularly in California. A rise in cases and risk to public health can serve as the impetus to apply newly developed methods that can quickly and accurately predict future caseloads. The recursive and Hawkes point process models with various triggering functions were fit to the data and their goodness of fit evaluated and compared. Although the point process models were largely similar in their fit to the data, the recursive point process model offered a slightly superior fit. We explored forecasting the spread of coccidioidomycosis in California from December 2002 to December 2017 using this recursive model, and we separated the training and testing portions of the data and achieved a root mean squared error of just 3.62 cases/week.

The Consequences of Our Changing Environment on Life Threatening and Debilitating Fungal Diseases in Humans

Human activities have significantly impacted the environment and are changing our climate in ways that will have major consequences for ourselves, and endanger animal, plant and microbial life on Earth. Rising global temperatures and pollution have been highlighted as potential drivers for increases in infectious diseases. Although infrequently highlighted, fungi are amongst the leading causes of infectious disease mortality, resulting in more than 1.5 million deaths every year. In this review we evaluate the evidence linking anthropomorphic impacts with changing epidemiology of fungal disease. We highlight how the geographic footprint of endemic mycosis has expanded, how populations susceptible to fungal infection and fungal allergy may increase and how climate change may select for pathogenic traits and indirectly contribute to the emergence of drug resistance.

Disseminated Coccidioidomycosis Presenting as Septic Shock with Multiorgan Failure

Coccidioidomycosis is a fungal infection caused by Coccidioides immitis and Coccidioides posadasii. While infections are usually mild, severe disease occurs in immunocompromised patients. Dissemination is associated with severe morbidity and mortality. Because of the tendency of this disease to imitate many diseases, diagnosis may be difficult on presentation. We present a case of disseminated coccidioidomycosis in a patient who was initially managed as miliary tuberculosis. In endemic areas, coccidioidomycosis is one of the two top differentials for miliary micronodular distribution on chest imaging. The patient was a recently diagnosed HIV positive patient and presented to the hospital with multiorgan failure, septic shock, and acute respiratory distress syndrome. He rapidly deteriorated and died within three days of presentation at the emergency department.

Coccidioidomycosis and COVID-19 Co-Infection, United States, 2020

We review the interaction between coronavirus disease (COVID-19) and coccidioidomycosis, a respiratory infection caused by inhalation of Coccidioides fungal spores in dust. We examine risk for co-infection among construction and agricultural workers, incarcerated persons, Black and Latino populations, and persons living in high dust areas. We further identify common risk factors for co-infection, including older age, diabetes, immunosuppression, racial or ethnic minority status, and smoking. Because these diseases cause similar symptoms, the COVID-19 pandemic might exacerbate delays in coccidioidomycosis diagnosis, potentially interfering with prompt administration of antifungal therapies. Finally, we examine the clinical implications of co-infection, including severe COVID-19 and reactivation of latent coccidioidomycosis. Physicians should consider coccidioidomycosis as a possible diagnosis when treating patients with respiratory symptoms. Preventive measures such as wearing face masks might mitigate exposure to dust and severe acute respiratory syndrome coronavirus 2, thereby protecting against both infections.

Using soil survey data to model potential Coccidioides soil habitat and inform Valley fever epidemiology

Coccidioidomycosis, also known as Valley fever, is a disease that can result in substantial illness and death. It is most common in the southwestern United States and areas of Latin America with arid climates, though reports increasingly suggest its range is wider than previously recognized. The natural habitat of the causative organisms, Coccidioides spp., have been associated with certain soil properties and climatic conditions. Current understanding of its geographic range is primarily defined by skin test studies and outbreak locations. We developed a fuzzy system model to predict suitable soil habitats for Coccidioides across the western United States based on parameters (electrical conductivity, organic matter content, pH, water holding capacity, temperature, and precipitation) from sites where soil sampling has confirmed the presence of Coccidioides. The model identified high coccidioidomycosis incidence areas as having high suitability and identified pockets of elevated suitability corresponding with outbreak locations outside the traditional range. By providing high-resolution estimates of Coccidioides suitability, including areas without public health surveillance for coccidioidomycosis, this model may be able to aid public health and clinical provider decision making. Awareness of possible Coccidioides soil habitats could help mitigate risk during soil-disturbing activities and help providers improve coccidioidomycosis diagnosis and treatment.

Endemic and Other Dimorphic Mycoses in The Americas

Endemic fungi are thermally dimorphic fungi that have a limited geographic range and can cause both primary disease and opportunistic infections. The Americas are home to more genera of endemic fungi than anywhere else on earth. These include Coccidioides, Histoplasma, Blastomyces, Paracoccidioides, and Sporothrix. Endemic fungi are found across the Americas and the Caribbean, from Blastomyces gilchristi, which extends into the northeast corners of North America, to Histoplasma capsulatum, which occurs all the way down in the southern regions of South America and into the Caribbean Islands. Symptoms of endemic fungal infection, when present, mimic those of many other diseases and are often diagnosed only after initial treatment for a bacterial or viral disease has failed. Endemic fungi place a significant medical burden on the populations they affect, especially in immunocompromised individuals and in resource-limited settings. This review summarizes the ecology, geographical range, epidemiology, and disease forms of the endemic fungi found in the Americas. An emphasis is placed on new and proposed taxonomic changes, including the assignment of new species names in Histoplasma, Blastomyces, and Paracoccidioides.

Economic Valuation of Coccidioidomycosis (Valley Fever) Projections in the United States in Response to Climate Change

Coccidioidomycosis, or valley fever, is an infectious fungal disease currently endemic to the southwestern United States. Symptoms of valley fever range in severity from flu-like illness to severe morbidity and mortality. Warming temperatures and changes in precipitation patterns may cause the area of endemicity to expand northward throughout the western United States, putting more people at risk for contracting valley fever. This may increase the health and economic burdens from this disease. We developed an approach to describe the relationship between climate conditions and valley fever incidence using historical data and generated projections of future incidence in response to both climate change and population trends using the Climate Change Impacts and Risk Analysis (CIRA) framework developed by the U.S. Environmental Protection Agency. We also developed a method to estimate economic impacts of valley fever that is based on case counts. For our 2000-15 baseline time period, we estimated annual medical costs, lost income, and economic welfare losses for valley fever in the United States were $400,000 per case, and the annual average total cost was $3.9 billion per year. For a high greenhouse gas emission scenario and accounting for population growth, we found that total annual costs for valley fever may increase up to 164% by year 2050 and up to 380% by 2090. By the end of the twenty-first century, valley fever may cost $620,000 per case and the annual average total cost may reach $18.5 billion per year. This work contributes to the broader effort to monetize climate change-attributable damages in the United States.

Differential Thermotolerance Adaptation between Species of Coccidioides

Coccidioidomycosis, or Valley fever, is caused by two species of dimorphic fungi. Based on molecular phylogenetic evidence, the genus Coccidioides contains two reciprocally monophyletic species: C. immitis and C. posadasii. However, phenotypic variation between species has not been deeply investigated. We therefore explored differences in growth rate under various conditions. A collection of 39 C. posadasii and 46 C. immitis isolates, representing the full geographical range of the two species, was screened for mycelial growth rate at 37 °C and 28 °C on solid media. The radial growth rate was measured for 16 days on yeast extract agar. A linear mixed effect model was used to compare the growth rate of C. posadasii and C. immitis at 37 °C and 28 °C, respectively. C. posadasii grew significantly faster at 37 °C, when compared to C. immitis; whereas both species had similar growth rates at 28 °C. These results indicate thermotolerance differs between these two species. As the ecological niche has not been well-described for Coccidioides spp., and disease variability between species has not been shown, the evolutionary pressure underlying the adaptation is unclear. However, this research reveals the first significant phenotypic difference between the two species that directly applies to ecological research.

Proper Care and Feeding of Coccidioides: A Laboratorian's Guide to Cultivating the Dimorphic Stages of C. immitis and C. posadasii

Coccidioidomycosis ("Valley fever") is caused by Coccidioides immitis and C. posadasii. These fungi are thermally dimorphic, cycling between mycelia and arthroconidia in the environment and converting into spherules and endospores within a host. Coccidioides can cause a broad spectrum of disease that can be difficult to treat. There has been a steady increase in disease, with an estimated 350,000 new infections per year in the United States. With the increase in disease and difficulty in treatment, there is an unmet need to increase research in basic biology and identify new treatments, diagnostics, and vaccine candidates. Here, we describe protocols required in any Coccidioides laboratory, such as growing, harvesting, and storing the different stages of this dimorphic fungal pathogen. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Growth and harvest of liquid mycelia cultures for extractions Alternate Protocol 1: Large-volume growth and harvest of liquid mycelia cultures Basic Protocol 2: Mycelial growth on solid medium Alternate Protocol 2: Maintaining mycelial growth on solid medium Basic Protocol 3: Harvesting and quantification of arthroconidia Alternate Protocol 3: Long-term storage of arthroconidia Basic Protocol 4: Parasitic spherule growth and harvest Alternate Protocol 4: Obtaining endospores from spherules Basic Protocol 5: Intranasal infection of murine models.