Update on the Epidemiology of coccidioidomycosis in the United States

Vaccines to Prevent Coccidioidomycosis: A Gene-Deletion Mutant of Coccidioides Posadasii as a Viable Candidate for Human Trials

Coccidioidomycosis is an endemic fungal infection that is reported in up to 20,000 persons per year and has an economic impact close to $1.5 billion. Natural infection virtually always confers protection from future exposure, and this suggests that a preventative vaccine strategy is likely to succeed. We here review progress toward that objective. There has been ongoing research to discover a coccidioidal vaccine over the past seven decades, including one phase III clinical trial, but for reasons of either efficacy or feasibility, a safe and effective vaccine has not yet been developed. This review first summarizes the past research to develop a coccidioidal vaccine. It then details the evidence that supports a live, gene-deletion vaccine candidate as suitable for further development as both a veterinary and a human clinical product. Finally, a plausible vaccine development plan is described which would be applicable to this vaccine candidate and also useful to other future candidates. The public health and economic impact of coccidioidomycosis fully justifies a public private partnership for vaccine development, and the development of a vaccine for this orphan disease will likely require some degree of public funding.

Comparison of Immunodiagnostic Assays for the Rapid Diagnosis of Coccidioidomycosis in Dogs

Coccidioidomycosis is a disease caused by the dimorphic fungi Coccidioides spp., which affects humans and a variety of animal species, including domestic dogs. In dogs, accurate diagnosis could provide a substantial improvement on the quality of canine life, as well as an advancement in the mapping of regions endemic for coccidioidomycosis. The purpose of this study was to compare immunodiagnostic assays for anti-Coccidioides antibody (Ab) detection in dogs’ serum. Three commercially available immunodiagnostic assays (IMMY^®; Norman, OK, USA) were evaluated, including the sōna Coccidioides Ab Lateral Flow Assay (LFA), Coccidioides IDCF immunodiffusion assay (IDCF), and the Clarus Coccidioides Ab Enzyme Immunoassay (EIA). Assays were evaluated using 98 dog serum samples: 29 from dogs with coccidioidomycosis, 15 from dogs diagnosed with histoplasmosis, 10 from dogs diagnosed with blastomycosis, and 44 from dogs without a fungal disease. Using specimens from dogs with coccidioidomycosis, the IDCF had an accuracy of 92% (95% confidence interval [95% CI] = 85–96%), the EIA had an accuracy of 91% (95% CI = 83–96%), and the LFA displayed an accuracy of 82% (95% CI = 73–89%). Using Kappa analysis, the agreement between LFA and EIA was 0.59 (95% CI = 0.42–0.75), that between LFA and IDCF was 0.64 (95% CI = 0.48–0.79), and that between EIA and IDCF was 0.79 (95% CI = 0.64–0.90). Most cross-reactions were observed in dogs with histoplasmosis. Compared with EIA and IDCF, the LFA requires substantially less laboratory equipment and infrastructure and rapidly produces results, offering a substantial improvement for the initial screening of coccidioidomycosis in dogs.

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.

Cross-Sectional Study of Clinical Predictors of Coccidioidomycosis, Arizona, USA

Demographic and clinical indicators have been described to support identification of coccidioidomycosis; however, the interplay of these conditions has not been explored in a clinical setting. In 2019, we enrolled 392 participants in a cross-sectional study for suspected coccidioidomycosis in emergency departments and inpatient units in Coccidioides-endemic regions. We aimed to develop a predictive model among participants with suspected coccidioidomycosis. We applied a least absolute shrinkage and selection operator to specific coccidioidomycosis predictors and developed univariable and multivariable logistic regression models. Univariable models identified elevated eosinophil count as a statistically significant predictive feature of coccidioidomycosis in both inpatient and outpatient settings. Our multivariable outpatient model also identified rash (adjusted odds ratio 9.74 [95% CI 1.03–92.24]; p = 0.047) as a predictor. Our results suggest preliminary support for developing a coccidioidomycosis prediction model for use in clinical settings.

Disseminated coccidioidomycosis in immunocompetent patients in non-endemic areas: a case series and literature review

Coccidioidomycosis is caused by the dimorphic fungi Coccidioides species which is endemic in the Western hemisphere. Reports on the characteristics of travel-related disseminated coccidioidomycosis in immunocompetent patients are rare, especially in non-endemic regions. The multifaceted symptoms of this condition present a diagnostic challenge to clinicians. This study aimed to review immunocompetent patients diagnosed with disseminated coccidioidomycosis in a tertiary hospital in Eastern China and other non-endemic areas, and to emphasize the importance of combining travel history with clinical manifestations and proper diagnostic examinations. This study retrospectively reviewed a case series of disseminated coccidioidomycosis diagnosed in an academic hospital in Eastern China. We conducted a global literature review of disseminated coccidioidomycosis in immunocompetent patients with travel history. We identified six patients in our case series and reviewed 42 cases in the literature. Travel history included Mexico, Arizona, California, and regions of low endemicity. Extrapulmonary sites of infection, which presented with diverse signs and symptoms, involved the skin and soft tissue, musculoskeletal system, lymph nodes, and central nervous system. Misdiagnoses and diagnostic delays were common. Next-generation sequencing substantially promoted precise diagnosis in our series. The overall prognosis for immunocompetent individuals was positive, mainly benefited from long-term azole therapies. The patients that succumbed had either central nervous system involvement or multiorgan dissemination. Progressive pneumonia with varied symptoms and travel history should alert healthcare professionals in non-endemic areas to consider the possibility of Coccidioides species infection. We recommend detailed history-taking and hypothesis-free detection of pathogens for cases with diagnostic delay.

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.

Current Landscape of Coccidioidomycosis

Coccidioidomycosis, also known as Valley fever, is an endemic fungal infection commonly found in the southwestern parts of the United States. However, the disease has seen an increase in both in its area of residency and its prevalence. This review compiles some of the latest information on the epidemiology, current and in-development pharmaceutical approaches to treat the disease, trends and projections, diagnostic concerns, and the overlapping dynamics of coccidioidomycosis and COVID-19, including in special populations. This review provides an overview of the current diagnostic and therapeutic strategies and identifies areas of future development.

Coccidioidomycosis Knowledge and Behaviors of California Hispanic Farm Workers

(1) Describe knowledge, attitudes, beliefs, and behaviors related to coccidioidomycosis (Valley fever, VF) reported by farm workers in a highly endemic area to design and evaluate prevention messages and (2) identify health information sources preferred by farm workers to disseminate VF prevention messages. There were 119 primarily Mexican-born residents of two migrant farm labor housing centers in Kern County, who completed an interviewer-administered survey on VF knowledge, attitudes, beliefs, and behaviors in 2017. The 73% of participants aware of VF demonstrated a knowledge score of 53%. Over 90% erroneously believed VF was associated with pesticide exposure; approximately two-thirds believed that wearing a bandana mask was protective. Over half of respondents believed that VF was contagious, could be contracted from contaminated food or water, and caused gastrointestinal symptoms. Of those aware of VF, 75% expressed concern about becoming infected because of where they lived and working outdoors. Working outdoors in dusty conditions was the most commonly reported risk-associated work practice. Among 67 participants reporting use of respiratory protection, 94% indicated they wear a bandana; most male participants did not wear face coverings in dusty conditions. The most frequent protective work practice was wetting soil. Preferred sources of health information included television; family, friend, or co-worker; healthcare provider; and radio. Farm workers reported multiple risk factors for VF. Results identified several areas of poor knowledge, risk behavior, and preferred channels of prevention messages. Important protective behaviors are not under the control of farm workers; engagement with employers is essential.

Coccidioidomycosis Cases at a Regional Referral Center, West Texas, USA, 2013–2019

We describe 73 patients with coccidioidomycosis diagnosed or treated at a regional referral center in West Texas, USA. Patients most at risk worked in oil production or agriculture; the most-associated health factors were smoking and diabetes. Patient demographics suggest that access to care may affect coccidioidomycosis diagnosis in this region.

Contribution of Biologic Response Modifiers to the Risk of Coccidioidomycosis Severity

BACKGROUND

The risk of coccidioidomycosis (CM) as a life-threatening respiratory illness or disseminated CM (DCM) increases as much as 150-fold in immunosuppressed patients. The safety of biologic response modifiers (BRMs) as treatment for patients with autoimmune disease (AI) in CM-endemic regions is not well defined. We sought to determine that risk in the Tucson and Phoenix areas.

METHODS

We conducted a retrospective study reviewing demographics, Arizona residency length, clinical presentations, specific AI diagnoses, CM test results, and BRM treatments in electronic medical records of patients ≥18 years old with International Classification of Diseases (ICD-10) codes for CM and AI from 1 October 2017 to 31 December 2019.

RESULTS

We reviewed 944 charts with overlapping ICD-10 codes for CM and AI, of which 138 were confirmed to have both diagnoses. Male sex was associated with more CM (P = .003), and patients with African ancestry were 3 times more likely than those with European ancestry to develop DCM (P < .001). Comparing CM+/AI+ (n = 138) with CM+/AI- (n = 449) patients, there were no significant differences in CM clinical presentations. Patients receiving BRMs had 2.4 times more DCM compared to pulmonary CM (PCM).

CONCLUSIONS

AI does not increase the risk of any specific CM clinical presentation, and BRM treatment of most AI patients does not lead to severe CM. However, BRMs significantly increase the risk of DCM, and prospective studies are needed to identify the immunogenetic subset that permits BRM-associated DCM.

Occupational and Environmental Hazards of Correctional Settings: A Scoping Literature Review From ACOEM's Presidential Task Force on Correctional Institutions

OBJECTIVE

Maintaining healthful, safe, and productive work environments for workers in correctional settings is a matter of deep consequence to the workers themselves, the institutions they serve, the incarcerated individuals with whom they share space, and inevitably, to our wider community. We hypothesized that an examination of the academic literature would reveal opportunities for an improved approach to research in these settings.

METHODS

We performed a scoping literature review using search terms related to the occupational and environmental health of workers in correctional environments, limited to studies performed in the United States.

RESULTS

A total of 942 studies underwent title and abstract screening, 342 underwent full-text review, and 147 underwent data extraction by a single reviewer. The results revealed a body of literature that tends strongly toward analyses of stress and burnout of correctional staff, largely based on self-reported data from cross-sectional surveys. Those studies related to physical health were predominantly represented by topics of infectious disease. There were few or no studies examining exposures or outcomes related to diagnosable mental health conditions, musculoskeletal injury, environmental hazards, medical or mental health staff, immigration detention settings, or regarding incarcerated workers. There were very few studies that were experimental, longitudinal, or based on objective data.

DISCUSSION

The National Institute for Occupational Safety and Health (NIOSH) has promulgated a research strategy for correctional officers that should guide future research for all workers in correctional settings, but realization of these goals will rely upon multidisciplinary collaboration, specific grants to engage researchers, and an improved understanding of the barriers inherent to correctional research, all while maintaining rigorous protection for incarcerated persons as an especially vulnerable population.

Pediatric coccidioidal orbital granuloma

Purpose

To report a case of orbital coccidiomycosis in an otherwise healthy 11-month-old male.

Observations

An 11-month-old male presented to his pediatrician with parental complaints of swelling, erythema, and pain of the right orbit that increased over ten days in the absence of constitutional symptoms. The child's parents reported an earlier fall onto a carpeted floor. After four weeks of conservative treatment and a course of oral cephalexin, he developed a fever, increased erythema, and palpable enlargement of a mass posterior to the lower eyelid. Ultrasound revealed an encysted mass in the inferior orbit, suggestive of an abscess. Urgent ophthalmic referral led to incision and drainage via orbitotomy. Culture, histopathology, and serological testing were positive for Coccidioides spp.. Blood studies revealed mild anemia and thrombocytosis. There was complete resolution of symptoms after surgical drainage and several weeks of oral fluconazole.

Conclusion and importance

We describe a patient with orbital coccidiomycosis without apparent systemic involvement, following what was most likely an unrelated minor trauma. Despite being rare, orbital coccidiomycosis should be considered as a primary manifestation of infection when ocular inflammation is encountered, especially in endemic regions.

Decoding Transcription Regulatory Mechanisms Associated with Coccidioides immitis Phase Transition Using Total RNA

New or emerging infectious diseases are commonly caused by pathogens that cannot be readily manipulated or studied under common laboratory conditions. These limitations hinder standard experimental approaches and our abilities to define the fundamental molecular mechanisms underlying pathogenesis. The advance of capped small RNA sequencing (csRNA-seq) now enables genome-wide mapping of actively initiated transcripts from genes and other regulatory transcribed start regions (TSRs) such as enhancers at a precise moment from total RNA. As RNA is nonpathogenic and can be readily isolated from inactivated infectious samples, csRNA-seq can detect acute changes in gene regulation within or in response to a pathogen with remarkable sensitivity under common laboratory conditions. Studying valley fever (coccidioidomycosis), an emerging endemic fungal infection that increasingly impacts livestock, pet, and human health, we show how csRNA-seq can unravel transcriptional programs driving pathogenesis. Performing csRNA-seq on RNA isolated from different stages of the valley fever pathogen Coccidioides immitis revealed alternative promoter usage, connected cis-regulatory domains, and a WOPR family transcription factor, which are known regulators of virulence in other fungi, as being critical for pathogenic growth. We further demonstrate that a C. immitis WOPR homologue, CIMG_02671, activates transcription in a WOPR motif-dependent manner. Collectively, these findings provide novel insights into valley fever pathogenesis and provide a proof of principle for csRNA-seq as a powerful means to determine the genes, regulatory mechanisms, and transcription factors that control the pathogenesis of highly infectious agents. IMPORTANCE Infectious pathogens like airborne viruses or fungal spores are difficult to study; they require high-containment facilities, special equipment, and expertise. As such, establishing approaches such as genome editing or other means to identify the factors and mechanisms underlying caused diseases, and, thus, promising drug targets, is costly and time-intensive. These obstacles particularly hinder the analysis of new, emerging, or rare infectious diseases. We recently developed a method termed capped small RNA sequencing (csRNA-seq) that enables capturing acute changes in active gene expression from total RNA. Prior to csRNA-seq, such an analysis was possible only by using living cells or nuclei, in which pathogens are highly infectious. The process of RNA purification, however, inactivates pathogens and thus enables the analysis of gene expression during disease progression under standard laboratory conditions. As a proof of principle, here, we use csRNA-seq to unravel the gene regulatory programs and factors likely critical for the pathogenesis of valley fever, an emerging endemic fungal infection that increasingly impacts livestock, pet, and human health.

Diagnosis of disseminated coccidioidomycosis in pregnancy through placental pathology: A case report

There are more than 150,000 new cases of coccidioidomycosis annually in the United States and the incidence is increasing. Although the majority of cases result in mild or no symptoms, pregnancy is a risk factor for complicated and disseminated disease. Overall, coccidioidomycosis is rare in pregnancy and there have been few reports in the literature of dissemination into the placenta. This report describes a 31-year-old primigravida with coccidioidomycosis diagnosed by placental examination. In retrospect, she had mild symptoms in the antepartum period but otherwise had no immediate complications due to the infection apart from the adhesive pelvic disease. The clinician should have a high index of suspicion for coccidioidomycosis in a pregnant woman presenting with a persistent respiratory illness who resides in, or who has recently recent travelled to, an endemic area. Additionally, a diagnosis of disseminated coccidioidomycosis should be considered for a woman with adhesive pelvic disease residing in an endemic region and one should consider microscopic placental examination if these findings are noted at cesarean delivery.

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Consider disseminated coccidioidomycosis when adhesive pelvic disease is found in a woman living in an endemic region.

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Consider coccidioidomycosis in women with respiratory symptoms living in or with recent travel to an endemic region.

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Pathological examination of the placenta may be helpful in cases of known coccidioidomycosis in pregnancy.

Genetic Vaccination as a Flexible Tool to Overcome the Immunological Complexity of Invasive Fungal Infections

The COVID-19 pandemic has highlighted genetic vaccination as a powerful and cost-effective tool to counteract infectious diseases. Invasive fungal infections (IFI) remain a major challenge among immune compromised patients, particularly those undergoing allogeneic hematopoietic bone marrow transplantation (HSCT) or solid organ transplant (SOT) both presenting high morbidity and mortality rates. Candidiasis and Aspergillosis are the major fungal infections among these patients and the failure of current antifungal therapies call for new therapeutic aids. Vaccination represents a valid alternative, and proof of concept of the efficacy of this approach has been provided at clinical level. This review will analyze current understanding of antifungal immunology, with a particular focus on genetic vaccination as a suitable strategy to counteract these diseases.

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.

An older male with an unusual presentation of disseminated coccidioidomycosis

Coccidioidomycosis is a fungal disease endemic to the southwestern United States and other areas in the Western Hemisphere. Infection is usually acquired through inhalation. While infection is most often asymptomatic, early respiratory illness and infrequently extrapulmonary dissemination may occur. Immunocompromised individuals, particularly those with impaired cell-mediated immunity, are at greatest risk for dissemination. We present an atypical case of disseminated coccidioidomycosis in an immunocompetent male manifesting as peritoneal disease diagnosed during elective inguinal herniorrhaphy.

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.

Mitochondrial genomes of the human pathogens Coccidioides immitis and Coccidioides posadasii

Fungal mitochondrial genomes encode genes involved in crucial cellular processes, such as oxidative phosphorylation and mitochondrial translation, and the molecule has been used as a molecular marker for population genetics studies. Coccidioides immitis and C. posadasii are endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents. To date, approximately 150 Coccidioides isolates have been sequenced to infer patterns of variation in nuclear genomes. However, less attention has been given to the mitochondrial genomes of Coccidioides. In this report, we describe the assembly and annotation of mitochondrial reference genomes for two representative strains of C. posadasii and C. immitis, as well as assess population variation among 77 selected genomes. The sizes of the circular-mapping molecules are 68.2 Kb in C. immitis and 75.1 Kb in C. posadasii. We identify 14 mitochondrial protein-coding genes common to most fungal mitochondria, which are largely syntenic across different populations and species of Coccidioides. Both Coccidioides species are characterized by a large number of group I and II introns, harboring twice the number of elements as compared to closely related Onygenales. The introns contain complete or truncated ORFs with high similarity to homing endonucleases of the LAGLIDADG and GIY-YIG families. Phylogenetic comparisons of mitochondrial and nuclear genomes show extensive phylogenetic discordance suggesting that the evolution of the two types of genetic material is not identical. This work represents the first assessment of mitochondrial genomes among isolates of both species of Coccidioides, and provides a foundation for future functional work.

Risk for Coccidioidomycosis among Hispanic Farm Workers, California, USA, 2018

To determine occupational risk factors for coccidioidomycosis among adult Hispanic outdoor agricultural workers in California, USA, we conducted a case-control study of workers seen at the Kern County medical facility and referred to the public health laboratory for coccidioidomycosis serologic testing. Participants completed an interviewer-administered health and work questionnaire. Among 203 participants (110 case-patients with positive and 93 controls with negative serologic results), approximately half were women, and more than three quarters were born in Mexico. Associated with coccidioidomycosis were self-reported dust exposure and work with root and bulb vegetable crops. A protective factor was leaf removal, an activity associated with grape cultivation. We conclude that subjective dust exposure and work with root and bulb vegetable crops are associated with increased risk for coccidioidomycosis among Hispanic farm workers. The agricultural industry should evaluate and promote dust-reduction measures, including wetting soil and freshly harvested products.

Recent Trends in the Epidemiology of Fungal Infections

The breadth of fungi causing human disease and the spectrum of clinical presentations associated with these infections has widened. Epidemiologic trends display dramatic shifts with expanding geographic ranges, identification of new at-risk groups, increasing prevalence of resistant infections, and emergence of novel multidrug-resistant pathogenic fungi. Certain fungi have been transmitted between patients in clinical settings. Major health events not typically associated with mycoses resulted in larger proportions of the population susceptible to secondary fungal infections. Many health care-related, environmental, and socioeconomic factors have influenced these epidemiologic shifts. This review summarizes updates to clinically significant fungal pathogens in North America.

The Known Unknowns of the Immune Response to Coccidioides

Coccidioidomycosis, otherwise known as Valley Fever, is caused by the dimorphic fungi Coccidioides immitis and C. posadasii. While most clinical cases present with self-limiting pulmonary infection, dissemination of Coccidioides spp. results in prolonged treatment and portends higher mortality rates. While the structure, genome, and niches for Coccidioides have provided some insight into the pathogenesis of disease, the underlying immunological mechanisms of clearance or inability to contain the infection in the lung are poorly understood. This review focuses on the known innate and adaptive immune responses to Coccidioides and highlights three important areas of uncertainty and potential approaches to address them. Closing these gaps in knowledge may enable new preventative and therapeutic strategies to be pursued.

Diagnosis of Pulmonary Infections Due to Endemic Fungi

Endemic mycoses including Histoplasma, Blastomyces, Coccidioides, Paracoccidioides, and Talaromyces are dimorphic fungi that can cause a variety of clinical manifestations, including respiratory infections. Their pulmonary presentations are variable, and diagnosis is often delayed as they can mimic other infectious and non-infectious causes of pulmonary disease. Delay in diagnosis can lead to unnecessary antibiotic use, repeat hospitalizations, and increased morbidity and mortality. The diagnosis of endemic fungal pulmonary infections often relies on multiple diagnostic tests including culture, tissue histopathology, antigen assays, and antibody assays. Due to the increased use of immunosuppressive agents and the widening geographic ranges where these infections are being found, the prevalence of endemic fungal infections is increasing. Physicians need to be aware of the clinical manifestations of pulmonary infections due to endemic fungal in order to ensure that the proper diagnostic work up is obtained promptly. A high index of suspicion is particularly important in patients with suspected pulmonary infections who have failed to improve despite antibiotics in the appropriate setting. We present a review diagnostic testing for pulmonary infections due to endemic mycoses.

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.

Advances in Diagnosis of Progressive Pulmonary and Disseminated Coccidioidomycosis

BACKGROUND

Antibody detection is the main method for diagnosis of coccidioidomycosis, but it has limitations. The Coccidioides antigen enzyme immunoassay is recommended for testing cerebrospinal fluid in suspected meningitis. Reports on urine and serum antigen detection evaluated small numbers of patients who were mostly immunocompromised. The purpose of this study was to assess the accuracy of combined antibody and antigen detection for diagnosis.

METHODS

A retrospective study, including all patients in whom Coccidioides antigen detection in serum was performed between January 2013 and May 2017, was conducted at Valleywise Health Medical Center (formerly Maricopa Integrated Health System). Sensitivity and specificity of antigen and antibody were evaluated in 158 cases and 487 controls.

RESULTS

The sensitivity of antibody detection by immunodiffusion (ID) was 84.2%. The sensitivity of antigen detection was 57.0% if both urine and serum were tested and 36.7% if urine alone was tested. The sensitivity of combining antigen and ID antibody detection was 93.0%. The sensitivity of urine and serum antigen detection was 55.4% in proven and 58.7% in probable cases, 79.1% in disseminated and 41.6% in pulmonary cases, and 74.7% in immunocompromised and 40.0% in immunocompetent patients. Specificity was 99.4% for antigen detection and 96.5% for ID antibody detection. Diagnostic accuracy was 95.4% for ID antibody and antigen detection, 93.6% for ID antibody alone, and 89.1% for pathology or culture.

CONCLUSIONS

These findings support combined antibody and antigen detection for diagnosis of progressive coccidioidomycosis. The diagnosis may have been missed if antigen detection was not performed.

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.

Clinical and Economic Burden of Valley Fever in Arizona: An Incidence-Based Cost-of-Illness Analysis

BACKGROUND

Coccidioidomycosis, ie, Valley fever, is an important fungal infection in the Southwest, with half to two thirds of all cases occurring in Arizona. This endemic respiratory disease can range from primary uncomplicated pneumonia to disseminated infection such as meningitis with chronic pulmonary complications. Valley fever diagnoses have risen over recent years and cause substantial morbidity and economic burden in Arizona.

METHODS

We estimated the lifetime cost-of-illness associated with all cases of Valley fever diagnosed in 2019 in Arizona. Natural history of the disease was determined from literature and expert opinion and assigned costs from national data sources to determine lifetime direct and indirect costs (work loss).

RESULTS

Total lifetime costs of $736 million were estimated for the 10 359 cases of Valley fever diagnosed in Arizona in 2019. Direct costs of $671 million accounted for over 90% of expenditures, with $65 million in indirect costs. Disseminated infection produces the highest economic burden at $1.26 million direct and $137 400 indirect costs per person. The lowest Valley fever lifetime costs were for cases of primary uncomplicated pneumonia with $23 200 in direct costs and $1300 in lost wages. The average lifetime direct costs across all Valley fever manifestations are $64 800 per person diagnosed in Arizona in 2019 and $6300 for indirect costs.

CONCLUSIONS

Valley fever is responsible for substantial economic burden in Arizona. Our estimates underscore the value of supporting research into developing more rapid diagnostic tests, better therapies, and ultimately a preventative vaccine to address this important public health problem in Arizona.

Activity and substrate specificity of Candida, Aspergillus, and Coccidioides Tpt1: essential tRNA splicing enzymes and potential anti-fungal targets

The enzyme Tpt1 is an essential agent of fungal tRNA splicing that removes an internal RNA 2'-PO4 generated by fungal tRNA ligase. Tpt1 performs a two-step reaction in which: (i) the 2'-PO4 attacks NAD+ to form an RNA-2'-phospho-(ADP-ribose) intermediate; and (ii) transesterification of the ADP-ribose O2'' to the RNA 2'-phosphodiester yields 2'-OH RNA and ADP-ribose-1'',2''-cyclic phosphate. Because Tpt1 does not participate in metazoan tRNA splicing, and Tpt1 knockout has no apparent impact on mammalian physiology, Tpt1 is considered a potential anti-fungal drug target. Here we characterize Tpt1 enzymes from four human fungal pathogens: Coccidioides immitis, the agent of Valley Fever; Aspergillus fumigatus and Candida albicans, which cause invasive, often fatal, infections in immunocompromised hosts; and Candida auris, an emerging pathogen that is resistant to current therapies. All four pathogen Tpt1s were active in vivo in complementing a lethal Saccharomyces cerevisiae tpt1∆ mutation and in vitro in NAD+-dependent conversion of a 2'-PO4 to a 2'-OH. The fungal Tpt1s utilized nicotinamide hypoxanthine dinucleotide as a substrate in lieu of NAD+, albeit with much lower affinity, whereas nicotinic acid adenine dinucleotide was ineffective. Fungal Tpt1s efficiently removed an internal ribonucleotide 2'-phosphate from an otherwise all-DNA substrate. Replacement of an RNA ribose-2'-PO4 nucleotide with arabinose-2'-PO4 diminished enzyme specific activity by ≥2000-fold and selectively slowed step 2 of the reaction pathway, resulting in transient accumulation of an ara-2'-phospho-ADP-ribosylated intermediate. Our results implicate the 2'-PO4 ribonucleotide as the principal determinant of fungal Tpt1 nucleic acid substrate specificity.

Coccidioidomycosis in Brazil: Historical Challenges of a Neglected Disease

Coccidioidomycosis is a deep-seated fungal infection that occurs exclusively in semiarid areas in the Americas. In Brazil, coccidioidomycosis occurs exclusively in rural areas in the northeast region and affects counties that are hit by recurrent droughts, poverty and economic stagnation. Since 1978, approximately 136 cases of the disease have been reported in Brazil, according to scientific publications. However, a lack of governmental epidemiological data as well as a similarity to tuberculosis have led scientists and experts to assume that a greater number of cases occur in the country, which are not diagnosed and/or reported. In this review, general characteristics of coccidioidomycosis are presented, followed by a description of the main clinical and epidemiological data of cases in Brazil. The purpose of this article is to discuss the inclusion of coccidioidomycosis in the list of neglected tropical diseases. We believe that the adoption of coccidioidomycosis as a neglected tropical disease will enable the creation of an effective epidemiological surveillance system and the development of feasible public health solutions for its control in vulnerable populations.

Coccidioidomycosis: Changing Concepts and Knowledge Gaps

Although first described more than 120 years ago, much remains unknown about coccidioidomycosis. In this review, new information that has led to changing concepts will be reviewed and remaining gaps in our knowledge will be discussed. In particular, new ideas regarding ecology and epidemiology, problems and promises of diagnosis, controversies over management, and the possibility of a vaccine will be covered.

Subcutaneous Mycoses in Travelers

Purpose of Review

The increase in international travel in recent decades has contributed to the risk of acquiring diseases considered endemic to a region or country and the change in the epidemiology of these diseases. Endemic mycoses that may be acquired by travelers in the short or long term are endemic subcutaneous mycoses such as sporotrichosis and lobomycosis, while endemic systemic mycoses are a group of serious diseases including histoplasmosis and coccidioidomycosis. Herein, we review the current knowledge and highlight the most important aspects of these fungal infections in travelers.

Recent Findings

The most relevant advances in the study of these mycoses involve the epidemiological distribution; human mycoses can be fatal and there are few antifungal drugs available, increasing drug resistance, and a risk of emerging fungal diseases associated with climate change, as well as the increasing virulence, and the diagnostic strategies that may be limited in many countries.

Summary

Although endemic mycoses are relatively rare, they should be considered as potentially travel-related illnesses. A recent or late trip to an endemic country may guide the clinical suspicion, an early diagnosis, and the institution of effective therapy.

Host Response to Coccidioides Infection: Fungal Immunity

Coccidioidomycosis is a fungal, respiratory disease caused by Coccidioides immitis and Coccidioides posadasii. This emerging infectious disease ranges from asymptomatic to pulmonary disease and disseminated infection. Most infections are cleared with little to no medical intervention whereas chronic disease often requires life-long medication with severe impairment in quality of life. It is unclear what differentiates hosts immunity resulting in disease resolution versus chronic infection. Current understanding in mycology-immunology suggests that chronic infection could be due to maladaptive immune responses. Immunosuppressed patients develop more severe disease and mouse studies show adaptive Th1 and Th17 responses are required for clearance. This is supported by heightened immunosuppressive regulatory responses and lowered anti-fungal T helper responses in chronic Coccidioides patients. Diagnosis and prognosis is difficult as symptoms are broad and overlapping with community acquired pneumonia, often resulting in misdiagnosis and delayed treatment. Furthermore, we lack clear biomarkers of disease severity which could aid prognosis for more effective healthcare. As the endemic region grows and population increases in endemic areas, the need to understand Coccidioides infection is becoming urgent. There is a growing effort to identify fungal virulence factors and host immune components that influence fungal immunity and relate these to patient disease outcome and treatment. This review compiles the known immune responses to Coccidioides spp. infection and various related fungal pathogens to provide speculation on Coccidioides immunity.

Occupational Respiratory Infections

Occupational respiratory infections can be caused by bacterial, viral, and fungal pathogens. Transmission in occupational settings can occur from other humans, animals, or the environment, and occur in various occupations and industries. In this article, we describe 4 occupationally acquired respiratory infections at the focus of NIOSH investigations over the last decade: tuberculosis (TB), influenza, psittacosis, and coccidioidomycosis. We highlight the epidemiology, clinical manifestations, occupational risk factors, and prevention measures.

Primary Cutaneous Coccidioidomycosis: An Update

Coccidioidomycosis is an endemic mycosis of the southern United States, Northern Mexico, and South America. Primary cutaneous coccidioidomycosis, despite being a very rare clinical presentation, has shown an increasing incidence. An extensive literature search for cutaneous coccidioidomycosis cases was performed using the OLDMEDLINE, PubMed, Cochrane, LILACS and Google Scholar databases for studies published from January 1927 through December 21, 2019. Forty-two observational studies were included totaling 82 cases of primary cutaneous coccidioidomycosis. Narrative reviews, systematic reviews, and meta-analyses were also included. Additionally, an original case was included. Patients with primary cutaneous coccidioidomycosis share the same geographical and epidemiological characteristics as those with pulmonary or disseminated coccidioidomycosis. Most of the imported cases came from endemic areas. A large portion of cases had prior local skin trauma. Tissue culture is still the leading diagnostic method; nevertheless, molecular techniques such as polymerase chain reaction (PCR) are currently relevant to differentiate between species. First-line treatment consists of azoles; however, it has an excellent prognosis even without treatment. Primary cutaneous coccidioidomycosis should be considered a differential diagnosis of unusual infections or neoformations in any part of the body in resident populations of endemic areas or in patients with a previous history of travel to these areas.

A quantitative enzyme-linked immunoassay (ELISA) to approximate complement-fixing antibody titers in serum from patients with coccidioidomycosis

Coccidioidomycosis is most frequently diagnosed serologically, and the quantitative test for complement-fixing antibodies is considered prognostically useful. Because complement-fixing antibody testing is complex, labor-intensive, and poorly standardized, an enzyme-linked immunoassay (ELISA) alternative would be attractive. In this report, we restrict the complement-fixing, antibody-binding domain to a 200-amino-acid recombinant peptide of the known antigen. Over-lapping truncations of this peptide do not bind complement-fixing antibodies, suggesting that the responsible epitope(s) are conformational. Further, anchoring the antigenic peptide to the ELISA plate by means of a C-terminal biotin-mimic peptide tag instead of allowing the peptide to randomly adhere to the plastic plate improves sensitivity of antibody detection by 1-2 logs in different sera. The newly developed ELISA shows a significant quantitative correlation with complement-fixing antibody titers. This ELISA shows potential as the basis for a new quantitative assay for coccidioidal antibodies.

Influenza challenging the diagnosis and management of pulmonary coccidioidomycosis

Lower respiratory infections are the most important cause of death due to a transmissible disease. We present a case of severe influenza and coccidioidomycosis lung coinfection in a 65-year-old Mexican migrant. This case highlights the challenges that respiratory viruses impose on the diagnosis of fungal infections and on the multidisciplinary management of these infections. In addition, this case shows how medical complications and superinfections could be potentially prevented if flu vaccination is provided.

Endemic mycoses: epidemiology and diagnostic strategies

INTRODUCTION

The global frequency of endemic mycoses has considerably increased, mainly due to environmental changes, population growth in endemic areas, and the increase in HIV-related immunosuppressed status. Among the most frequent endemic mycoses are coccidioidomycosis in semi-desert climates, and paracoccidioidomycosis, and histoplasmosis in tropical climates. The inoculum can enter the host through the airway or directly through the skin. Lymphatic and hematogenous spread may involve the skin.

AREAS COVERED

In this article, we provide up-to-date epidemiological and diagnostic data on major (histoplasmosis, paracoccidioidomycosis, coccidioidomycosis, blastomycosis) and minor (talaromycosis, adiaspiromycosis, emergomycosis) endemic mycoses.

EXPERT OPINION

Endemic mycoses include diseases with a localized endemic area, and a few of them converge. These mycoses all have in common the airway involvement and can cause pulmonary symptoms following initial asymptomatic infection. Among the risk groups to acquire these mycoses are travelers from endemic areas, archeologists, speleologists, and immigrants. Promising and useful diagnostic tools have been developed in endemic mycoses; however, most of them are not standardized or available in low-income countries.

Simultaneous coccidioidomycosis and phaeohyphomycosis in a kidney transplant recipient: A case report and literature review

Advances in solid organ transplantation have improved the survival of end-stage organ disease at the expense of an increased risk for opportunistic infections. Unusual clinical presentations and the possibility of concurrent infections make diagnosing invasive fungal infection (IFI) more difficult. Here, we present a case of simultaneous vertebral infection caused by Coccidioides immitis-posadasii and subcutaneous phaeohyphomycosis due to Nigrograna mackinnonii in a kidney transplant recipient. The diagnosis of both infections required invasive procedures to obtain tissue and a high index of suspicion that more than one IFI could be present. A multidisciplinary team approach for the management of immunocompromised patients with suspected or diagnosed IFI is warranted.

Clinician Practice Patterns That Result in the Diagnosis of Coccidioidomycosis Before or During Hospitalization

BACKGROUND

Coccidioidomycosis (CM) is common and important within endemic regions, requiring specific testing for diagnosis. Long delays in diagnosis have been ascribed to ambulatory clinicians. However, how their testing practices have impacted patient care has not been systematically unexplored.

METHODS

We analyzed practice patterns for CM diagnoses over 3 years within a large Arizona healthcare system, including diagnosis location, patient characteristics, and care-seeking patterns associated with missed diagnosis.

RESULTS

For 2043 CM diagnoses, 72.9% were made during hospital admission, 21.7% in ambulatory clinics, 3.2% in emergency units, and only 0.5% in urgent care units. A 40.6% subgroup of hospitalized patients required neither intensive care unit or hospital-requiring procedures, had a median length of stay of only 3 days, but still incurred both substantial costs ($27.0 million) and unnecessary antibiotic administrations. Prior to hospital diagnosis (median of 32 days), 45.1% of patients had 1 or more visits with symptoms consistent with CM. During those visits, 71.3% were not tested for CM. Diagnoses were delayed a median of 27 days.

CONCLUSIONS

Lack of testing for CM in ambulatory care settings within a region endemic for CM resulted in a large number of hospital admissions, attendant costs, and unneeded antibacterial drug use, much of which would otherwise be unnecessary. Improving this practice is challenging since many clinicians did not train where CM is common, resulting in significant inertia to change. Determining the best way to retrain clinicians to diagnose CM earlier is an opportunity to explore which strategies might be the most effective.

Risk factors and outcomes of culture-proven acute Coccidioides spp. infection in San Diego, California, United States

BACKGROUND

Coccidioides spp. are dimorphic fungi endemic to parts of the United States, Mexico, Central and South America. Infection can cause a range of disease from self-limited acute pneumonia to severe disseminated disease.

METHODS

We performed a retrospective chart review of medical records of cases of culture-proven acute coccidioidomycosis at the University of California San Diego between 1 April 2015 and 31 December 2019 and described the demographics, risk factors and outcomes of these cases.

RESULTS

Over the study period, fifteen evaluable cases of culture-proven acute coccidioidomycosis were identified. Of these, 87% (13/15) had traditional risk factors for coccidioidomycosis infection while two lacked known risk factors, including one patient with cirrhosis and one with chronic hepatitis C infection. Seven of fifteen (47%) had primary coccidioidomycosis of the lungs without dissemination and 7/15 (47%) disseminated disease. Of those with disseminated disease, 6/7 (86%) had either high-risk ethnicity or blood type as their only risk factor. At 90 days, 11/15 (73%) were alive, 3/15 (20%) deceased and 1/15 (7%) lost to follow-up. Of those not alive at 90 days, 1/3 (33%) had disseminated disease and 2/3 (67%) primary coccidioidomycosis, both on immunosuppressive therapy.

DISCUSSION

Coccidioides spp. infection occurs in a variety of hosts with varying underlying risk factors, with the majority in our cohort overall and 86% with disseminated disease lacking traditional risk factors for invasive fungal infection other than ethnicity and/or blood phenotype. Clinicians should be aware of these non-traditional risk factors in patients with coccidioidomycosis infection.

Re-drawing the Maps for Endemic Mycoses

Endemic mycoses such as histoplasmosis, coccidioidomycosis, blastomycosis, paracoccidioidomycosis, and talaromycosis are well-known causes of focal and systemic disease within specific geographic areas of known endemicity. However, over the past few decades, there have been increasingly frequent reports of infections due to endemic fungi in areas previously thought to be “non-endemic.” There are numerous potential reasons for this shift such as increased use of immune suppressive medications, improved diagnostic tests, increased disease recognition, and global factors such as migration, increased travel, and climate change. Regardless of the causes, it has become evident that our previous understanding of endemic regions for these fungal diseases needs to evolve. The epidemiology of the newly described Emergomyces is incomplete; our understanding of it continues to evolve. This review will focus on the evidence underlying the established areas of endemicity for these mycoses as well as new data and reports from medical literature that support the re-thinking these geographic boundaries. Updating the endemic fungi maps would inform clinical practice and global surveillance of these diseases.

Population Structure and Genetic Diversity among Isolates of Coccidioides posadasii in Venezuela and Surrounding Regions

Coccidioides posadasii is a pathogenic fungus that causes coccidioidomycosis in many arid regions of the Americas. One of these regions is bordered by the Caribbean Sea, and the surrounding landscape may play an important role in the dispersion of C. posadasii across South America through southeastern Mexico, Honduras, Guatemala, and Venezuela. Comparative phylogenomic analyses of C. posadasii reveal that clinical strains from Venezuela are genetically distinct from the North American populations found in (i) Arizona and (ii) Texas, Mexico, and the rest of South America (TX/MX/SA). We find evidence for admixture between the Venezuela and the North American populations of C. posadasii in Central America. Additionally, the proportion of Venezuelan alleles in the admixed population decreases as latitude (and distance from Venezuela) increases. Our results indicate that the population in Venezuela may have been subjected to a recent bottleneck and shows a strong population structure. This analysis provides insight into potential for Coccidioides spp. to invade new regions.IMPORTANCE Valley Fever is a fungal disease caused by two species of fungi: Coccidioides immitis and C. posadasii These fungi are found throughout the arid regions of North and South America; however, our understanding of genetic diversity and disease in South America is limited. In this report, we analyze 10 new genomes of Coccidioides posadasii from regions bordering the Caribbean Sea. We show that these populations are distinct and that isolates from Venezuela are likely a result of a recent bottleneck. These data point to patterns that might be observed when investigating recently established populations.

Host-Pathogen Interactions in Coccidioidomycosis: Prognostic Clues and Opportunities for Novel Therapies

PURPOSE

Coccidioidomycosis (CM) is a systemic fungal disease caused by the dimorphic fungi Coccidioides immitis and Coccidioides posadasii. In its endemic areas of the United States, CM is growing as a public health challenge with a marked increase in incidence in the last 15 years. Although Coccidioides infection is asymptomatic in most cases, symptomatic pulmonary disease occurs in ~40% and disseminated coccidioidomycosis (DCM) occurs in ~1% of previously healthy children and adults. DCM is markedly more common in immunocompromised people, who often experience life-threatening disease despite use of antifungal medications. Although options for antifungal therapy have improved, lifelong therapy is needed for those who develop coccidioidal meningitis. The purpose of this article was to review the state of antifungal therapy and recent studies of host-pathogen interactions in CM in light of advances in immunomodulatory therapy.

METHODS

The study included a review of PubMed and abstracts of the Coccidioidomycosis Study Group (years 2000-2019).

FINDINGS

Current therapy for CM relies upon azole and polyene antifungal agents. Murine models and studies of DCM in patients with monogenic primary immunodeficiency states and acquired immunodeficiency have revealed the importance of both innate and adaptive immune responses in the control of infections with Coccidioides species. In particular, defects in sensing of fungi and induction of cellular immune responses have been frequently reported. More recently, polymorphisms in key signaling pathways and in the generation of Th17 and Th1 immune responses have been linked with DCM.

IMPLICATIONS

Antifungal therapy is sufficient to control disease in most cases of CM, but treatment failure occurs in cases of severe pulmonary disease and nonmeningeal disseminated disease. Lifelong therapy is recommended for meningitis in view of the very high risk of recurrence. Corticosteroid therapy is advised by some experts for severe pulmonary disease and for some neurologic complications of DCM. DCM is only rarely the result of a severe monogenic immunodeficiency. Case studies suggest that reorienting cellular immune responses or augmenting effector immune responses may help resolve DCM. Systematic investigation of immunotherapy for coccidioidomycosis is advisable and may help to address the recent marked increase in reports of the disease in endemic areas.

Surveillance for Coccidioidomycosis - United States, 2011-2017

PROBLEM/CONDITION

Coccidioidomycosis (Valley fever) is an infection caused by the environmental fungus Coccidioides spp., which typically causes respiratory illness but also can lead to disseminated disease. This fungus typically lives in soils in warm, arid regions, including the southwestern United States.

REPORTING PERIOD

2011-2017.

DESCRIPTION OF SYSTEM

Coccidioidomycosis has been nationally notifiable since 1995 and is reportable in 26 states and the District of Columbia (DC), where laboratories and physicians notify local and state public health departments about possible coccidioidomycosis cases. Health department staff determine which cases qualify as confirmed cases according to the definition established by Council of State and Territorial Epidemiologists and voluntarily submit basic case information to CDC through the National Notifiable Diseases Surveillance System.

RESULTS

During 2011-2017, a total of 95,371 coccidioidomycosis cases from 26 states and DC were reported to CDC. The number of cases decreased from 2011 (22,634 cases) to 2014 (8,232 cases) and subsequently increased to 14,364 cases in 2017; >95% of cases were reported from Arizona and California. Reported incidence in Arizona decreased from 261 per 100,000 persons in 2011 to 101 in 2017, whereas California incidence increased from 15.7 to 18.2, and other state incidence rates stayed relatively constant. Patient demographic characteristics were largely consistent with previous years, with an overall predominance among males and among adults aged >60 years in Arizona and adults aged 40-59 years in California.

INTERPRETATION

Coccidioidomycosis remains an important national public health problem with a well-established geographic focus. The reasons for the changing trends in reported cases are unclear but might include environmental factors (e.g., temperature and precipitation), surveillance artifacts, land use changes, and changes in the population at risk for the infection.

PUBLIC HEALTH ACTION

Health care providers should consider a diagnosis of coccidioidomycosis in patients who live or work in or have traveled to areas with known geographic risk for Coccidioides and be aware that those areas might be broader than previously recognized. Coccidioidomycosis surveillance provides important information about the epidemiology of the disease but is incomplete both in terms of geographic coverage and data availability. Expanding surveillance to additional states could help identify emerging areas that pose a risk for locally acquired infections. In Arizona and California, where most cases occur, collecting systematic enhanced data, such as more detailed patient characteristics and disease severity, could help clarify the reasons behind the recent changes in incidence and identify additional opportunities for focused prevention and educational efforts.

Soil and climactic predictors of canine coccidioidomycosis seroprevalence in Washington State: An ecological cross-sectional study

Coccidioidomycosis is a predominantly respiratory infection of animals and humans caused by soil-dwelling fungi. Long known to be endemic to North American deserts, locally acquired human cases first emerged in Washington State in 2010. To inform development of an environmental niche map, we conducted an ecological cross-sectional study of the association between soil and climactic variables and canine seroprevalence in Washington State, at the zip code tabulation area level. Soil predictors included soil texture (per cent sand, silt and clay), pH, electrical conductivity and water storage capacity; climactic predictors included mean annual air temperature and liquid precipitation. Clustering was evaluated with Moran's I, and four modelling approaches were adopted a priori: two models without any smoothing (logistic regression and quasi-logistic regression) and two smoothing models (non-spatial and spatial smoothing). No evidence was found for clustering, and both smoothing models resulted in marked attenuation of all coefficients. Temperature was found to have a positive effect in the non-smoothing models (prevalence odds ratio, logistic model: 1.70, 95% confidence interval 1.02, 2.84). While no other significant associations were found, there was suggestive evidence of a positive effect for pH. Despite the limitations inherent to the ecological and cross-sectional nature of these data, these findings provide insight for the development of an environmental niche map in Washington State and demonstrate the utility of using data from an animal sentinel to predict human disease risk.

Characterization of an Uncinocarpus reesii-expressed recombinant tube precipitin antigen of Coccidioides posadasii for serodiagnosis

Early and accurate diagnosis of coccidioidomycosis, also known as Valley fever, is critical for appropriate disease treatment and management. Current serodiagnosis is based on the detection of patient serum antibodies that react with tube precipitin (TP) and complement fixation (CF) antigens of Coccidioides. IgM is the first class of antibodies produced by hosts in response to coccidioidal insults. The highly glycosylated β-glucosidase 2 (BGL2) is a major active component of the TP antigen that stimulates IgM antibody responses during early Coccidioides infection. The predominant IgM epitope on BGL2 is a unique 3-O-methyl-mannose moiety that is not produced by commonly used protein expression systems. We genetically engineered and expressed a recombinant BGL2 (rBGL2ur), derived from Coccidioides, in non-pathogenic Uncinocarpus reesii, a fungus phylogenetically related to the Coccidioides pathogen. The rBGL2ur protein was purified from the culture medium of transformed U. reesii by nickel affinity chromatography, and the presence of 3-O-methyl mannose was demonstrated by gas chromatography. Seroreactivity of the purified rBGL2ur protein was tested by enzyme-linked immunosorbent assays using sera from 90 patients with coccidioidomycosis and 134 control individuals. The sensitivity and specificity of the assay with rBGL2ur were 78.8% and 87.3%, respectively. These results were comparable to those obtained using a proprietary MiraVista Diagnostic (MVD) IgM (63.3% sensitivity; 96.3% specificity), but significantly better than the ID-TP assay using non-concentrated patient sera (33.3% sensitivity; 100% specificity). Expression of rBGL2ur in U. reesii retains its antigenicity for coccidioidomycosis serodiagnosis and greatly reduces biosafety concerns for antigen production, as Coccidioides spp. are biological safety level 3 agents.