Hiding in Plain Air: Recognizing Endemic Mycoses in Community-Acquired Pneumonia

The Epidemiologic Blind Spot

Community-acquired pneumonia (CAP) is among the most common infectious diagnoses in clinical practice, yet its true etiologic distribution remains poorly captured by routine workup. Bacterial pathogens and respiratory viruses dominate the clinical imagination, while endemic fungi occupy a diagnostic afterthought. This is not a benign oversight. Endemic mycoses collectively account for an estimated 3–10% of CAP in endemic regions, a proportion that is meaningful, likely underreported, and consistently underdiagnosed.^1-2

The practical consequence: delayed diagnosis, ineffective antibacterial therapy, and in vulnerable hosts, preventable clinical deterioration.

The geographic footprint of the three major North American endemic fungi—Histoplasma capsulatum in the Ohio and Mississippi River valleys, Blastomyces dermatitidis in the Great Lakes and upper Midwest, and Coccidioides species in the arid Southwest—is well-established in broad strokes but increasingly imprecise at the margins.³

A Medicare analysis of over 45 million beneficiaries found that 94% of US states had at least one county above the clinically relevant threshold for histoplasmosis, and national incidence rates for both histoplasmosis and blastomycosis roughly doubled between 2013 and 2023.^2,4

Clinicians should resist the instinct to rule out endemic fungi based solely on geography; patients increasingly acquire infection outside traditionally defined endemic zones.⁵

Presentation Clues

The clinical overlap with bacterial CAP is substantial—fever, cough, dyspnea, and infiltrates are common to all three organisms. However, several features should raise suspicion: subacute onset over days to weeks; failure to improve on antibacterial therapy; mediastinal lymphadenopathy disproportionate to pulmonary findings; skin or soft tissue lesions accompanying respiratory complaints; and a relevant exposure history involving soil disturbance, construction, farming, or spelunking.⁶

Histoplasmosis most commonly presents as a self-limited illness in immunocompetent hosts, but disseminated disease—characterized by fever, cytopenias, hepatosplenomegaly, and markedly elevated ferritin—occurs in advanced HIV, transplant recipients, and patients on TNF-α inhibitors or prolonged corticosteroids.^3,7

Blastomycosis is the most diagnostically treacherous: heterogeneous imaging, predilection for skin and bone dissemination, and a subset that progresses to ARDS with mortality approaching 40%.^8-9

Coccidioidomycosis accounts for 15–25% of CAP in hyperendemic areas yet remains underdiagnosed because most primary infections are mild; dissemination is the feared outcome in immunosuppressed hosts and individuals of Filipino or African descent.^3,10

Diagnostic Approach

Antigen detection is the primary diagnostic anchor. Urine Histoplasma antigen EIA exceeds 90% sensitivity in disseminated disease and 75–80% in acute pulmonary histoplasmosis, with known cross-reactivity with blastomycosis.¹¹

Urine Blastomyces antigen testing achieves 85–90% sensitivity in pulmonary disease.¹¹

For coccidioidomycosis, serology remains the mainstay—complement fixation titers ≥1:16 correlate with dissemination risk.^10-11

Beta-D-glucan is generally unhelpful; Coccidioides does not produce it, and Histoplasma results lack specificity.¹¹

Treatment Considerations

Treatment hinges on organism, severity, and immune status. Mild-to-moderate pulmonary histoplasmosis and coccidioidomycosis in immunocompetent patients frequently self-resolve; observation is legitimate when the diagnosis is secure and trajectory favorable.³

All confirmed blastomycosis warrants treatment.⁹

Itraconazole (200 mg TID loading, then BID with therapeutic drug monitoring) is standard for mild-to-moderate histoplasmosis and blastomycosis; lipid amphotericin B anchors severe and disseminated disease across all three pathogens.^9,12

Fluconazole is an acceptable alternative for non-meningeal coccidioidomycosis; meningeal disease demands lifelong azole suppression.¹⁰

The most impactful stewardship intervention is earlier diagnostic consideration. In a retrospective analysis of 3,825 blastomycosis patients, 41% experienced at least one missed diagnostic opportunity, with a mean diagnostic delay of 26.8 days.¹³

The Welker study demonstrated that compressing antibiotic timing metrics reduced diagnostic accuracy without improving actual time-to-treatment—a cautionary finding directly applicable to the endemic mycosis problem.¹⁴

The Steroid Question: A Preview

The CAPE COD trial showed hydrocortisone 200 mg/day reduced 28-day mortality in severe CAP (6.2% vs. 11.9%; NNT ~18), and the 2024 SCCM focused update issued a strong recommendation for corticosteroids in severe bacterial CAP.^15-16

However, these recommendations are predicated on bacterial etiology. CAPE COD excluded active fungal infection, and the SCCM guideline explicitly specifies "bacterial CAP." ^15-16

Endemic mycoses present as precisely the phenotype in which steroids are now increasingly considered—hypoxemia, systemic inflammation, radiographic progression. Glucocorticoids impair macrophage and T-cell function critical to host defense against dimorphic fungi.⁷

In a blastomycosis-ARDS cohort, corticosteroids were not associated with survival benefit.¹⁷

The modern severe CAP patient sits at the intersection of two competing pressures: treat early enough to reduce mortality, but pause long enough to avoid converting an unrecognized fungal pneumonia into a steroid-amplified diagnostic error.

This is a first in a series around CAP including testing, treatment, and severe CAP, steroids, and missed fungus.

References

1. Blastomycosis, Histoplasmosis, and Coccidioidomycosis in Outpatient Community-Acquired Pneumonia. Benedict K, Thompson GR, Ampel NM, et al. JAMA Network Open. 2026;9(1):e2553965. doi:10.1001/jamanetworkopen.2025.53965.

2. The Geographic Distribution of Dimorphic Mycoses in the United States for the Modern Era. Mazi PB, Sahrmann JM, Olsen MA, et al. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 2023;76(7):1295-1301. doi:10.1093/cid/ciac882.

3. Coccidioidomycosis and Histoplasmosis in Immunocompetent Persons. Galgiani JN, Kauffman CA. The New England Journal of Medicine. 2024;390(6):536-547. doi:10.1056/NEJMra2306821.

4. Updating the Epidemiology of Blastomycosis and Histoplasmosis in the United States, Using National Electronic Health Record Data, 2013-2023. Bartels JGE, Camponuri SK, Snow TT, et al. The Journal of Infectious Diseases. 2025;232(6):e1048-e1059. doi:10.1093/infdis/jiaf472.

5. Mapping the Geographic Distribution of Dimorphic Mycoses Using a US Commercial Insurance Database. Goodman R, Rauseo AM, Windham SL, et al. Open Forum Infectious Diseases. 2025;12(10):ofae755. doi:10.1093/ofid/ofae755.

6. Diagnosing Fungal Causes of Community-Acquired Pneumonia: Guidance From the CDC and MSGERC. Hamrick Y, Hamrick A. American Family Physician. 2026;113:509-510.

7. Glucocorticoids and Invasive Fungal Infections. Lionakis MS, Kontoyiannis DP. Lancet (London, England). 2003;362(9398):1828-38. doi:10.1016/S0140-6736(03)14904-5.

8. Outcomes With Severe Blastomycosis and Respiratory Failure in the United States. Rush B, Lother S, Paunovic B, Mooney O, Kumar A. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 2021;72(9):1603-1607. doi:10.1093/cid/ciaa294.

9. Clinical Practice Guidelines for the Management of Blastomycosis: 2008 Update by the Infectious Diseases Society of America. Chapman SW, Dismukes WE, Proia LA, et al. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 2008;46(12):1801-12. doi:10.1086/588300.

10. 2016 Infectious Diseases Society of America (IDSA) Clinical Practice Guideline for the Treatment of Coccidioidomycosis. Galgiani JN, Ampel NM, Blair JE, et al. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 2016;63(6):e112-46. doi:10.1093/cid/ciw360.

11. Microbiological Laboratory Testing in the Diagnosis of Fungal Infections in Pulmonary and Critical Care Practice. An Official American Thoracic Society Clinical Practice Guideline. Hage CA, Carmona EM, Epelbaum O, et al. American Journal of Respiratory and Critical Care Medicine. 2019;200(5):535-550. doi:10.1164/rccm.201906-1185ST.

12. Global Guideline for the Diagnosis and Management of the Endemic Mycoses: An Initiative of the European Confederation of Medical Mycology in Cooperation With the International Society for Human and Animal Mycology. Thompson GR, Le T, Chindamporn A, et al. The Lancet. Infectious Diseases. 2021;21(12):e364-e374. doi:10.1016/S1473-3099(21)00191-2.

13. The Incidence, Duration and Risk Factors for Diagnostic Delays Associated With Blastomycosis. Barber DD, Struble RD, Arakkal AT, et al. Medical Mycology. 2026;:myag009. doi:10.1093/mmy/myag009.

14. Antibiotic Timing and Errors in Diagnosing Pneumonia. Welker JA, Huston M, McCue JD. Archives of Internal Medicine. 2008;168(4):351-6. doi:10.1001/archinternmed.2007.84.

15. Hydrocortisone in Severe Community-Acquired Pneumonia. Dequin PF, Meziani F, Quenot JP, et al. The New England Journal of Medicine. 2023;388(21):1931-1941. doi:10.1056/NEJMoa2215145.

16. 2024 Focused Update: Guidelines on Use of Corticosteroids in Sepsis, Acute Respiratory Distress Syndrome, and Community-Acquired Pneumonia. Chaudhuri D, Nei AM, Rochwerg B, et al. Critical Care Medicine. 2024;52(5):e219-e233. doi:10.1097/CCM.0000000000006172.

17. Management and Outcomes of Acute Respiratory Distress Syndrome Caused by Blastomycosis: A Retrospective Case Series. Schwartz IS, Embil JM, Sharma A, Goulet S, Light RB. Medicine. 2016;95(18):e3538. doi:10.1097/MD.0000000000003538.