Theodore C. White

Background: International Classification of Diseases (ICD) codes are used in healthcare for documenting disease and billing, but also for research in epidemiological and translational studies for cohort identification and specimen selection. Periodic code revisions, while necessary, significantly differ in structure and descriptive content, preventing direct cross–version mapping while also complicating use in longitudinal research and coding accuracy during the transition to newer versions. Methods: Mycoses codes within ICD–9, ICD–10, and ICD–11 were manually identified within fungal and non–fungal disease sections using systematic searches for fungal–associated text and eponymous diseases with confirmed fungal etiology. Code descriptions were analyzed to classify etiologic and clinical characteristics for harmonized match scoring. Code similarity was assessed using a heuristically weighted match–score algorithm incorporating classification variables with description–based text mining for clinically relevant semantic harmonization. Codes were categorized into twelve fungal groups (Aspergillus, Blastomyces, Candida, Coccidioides, Cryptococcus, Histoplasma, Mucorales, Paracoccidioides, Sporothrix, Other Fungus–specific Mycoses, Dermatomycoses, and General Mycoses). Bidirectional best–match mapping was performed within each fungal group and manually verified. Results: Fungal codes were organized within and outside the mycoses section in all ICD versions, with several requiring expertise for identification. ICD–9, ICD–10, and ICD–11 contained 94, 117, and 148 mycoses codes accounting for 0.7%, 0.2%, and 0.4% of all codes, respectively. Most codes were taxon-specific (56%, 69%, 61%), but code proportion varied by fungal group and was version-specific. Cross–version bidirectional mapping revealed distinct patterns of code continuity, expansion, and consolidation. Conclusions: A description–based matching approach integrating disease classification and text mining enabled reliable cross–version best–match mapping and produced a resource to improve coding accuracy, support ICD–11 adoption in the United States, and simplify code use in ICD–based studies. Findings emphasize the importance of nomenclature consistency in science and medicine as molecular studies reclassify fungal pathogens.

The gain or loss of chromosomes in eukaryotes often drives aberrant phenotypes by altering the expression levels of hundreds or thousands of genes. In the case of beneficial aneuploidies, the genetic basis of fitness improvement has rarely been pinpointed, and identifying the causal genes remains a major challenge in engineering biology. The leading cause of human fungal infections, Candida albicans, frequently acquires extra copies of chromosome R (ChrR) following exposure to azole antifungal drugs, resulting in heightened antifungal tolerance. Despite this, why this aneuploidy frequently emerges following azole exposure and how it promotes antifungal tolerance remain unknown. Here, we combine RNA-seq with parallel chromosome-wide CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) screens to systematically profile the ChrR genes contributing to azole tolerance. Using multiplexed CRISPR-dCas12a tools, we further characterize the combinatorial effects of candidate genes and uncover a central role for post-Golgi secretory trafficking in antifungal tolerance. Specifically, we demonstrate that the secretory pathway regulators SEC4 and YPT31 are both necessary and sufficient for ChrR-mediated azole tolerance, and drive increased ergosterol content in the cell membrane. By leveraging a large-scale CRISPRa screen in a fungal pathogen, our work functionally dissects one of the most common aneuploidies observed in C. albicans, provides mechanistic insight into the molecular basis of antifungal tolerance, and establishes a generalizable framework for studying aneuploidy-mediated phenotypes across eukaryotic organisms.

Fluconazole (FLC)-resistant Candidozyma auris isolates have reduced drug accumulation compared to azole-susceptible isolates. Of 119 C. auris isolates, 83 out of 87 resistant isolates (~95%) had extremely low fluconazole uptake, whereas 30 out of 32 susceptible isolates (~93%) had high fluconazole uptake. In search of a genetic explanation for this phenomenon, we compared metadata for TAC1B and CDR1 single-nucleotide polymorphisms (SNPs) and found overlap with many but not all isolates that are FLC resistant. We found that CDR1 mutations are common in resistant isolates from Clade 1, and TAC1B mutations are commonly found in resistant isolates from clades 1 and 3. There is clearly an association between FLC resistance and certain CDR1 and TAC1B polymorphisms, but mutations in these genes do not account for all mechanisms of resistance in this species and do not account for the difference in FLC accumulation. However, when ERG11 SNPs were included in the analysis, there is a clear correlation between low FLC accumulation and isolates that have one of five ERG11 variants and also high FLC accumulation and isolates that have non-variant ERG11 sequences. The ERG11 mutations F126L, K143R, V125/F126L, Y132F, or Y501H are correlated to fluconazole resistance and reduced fluconazole accumulation. This is a unique characteristic of C. auris, suggesting mutations in ERG11 can cause changes in the ergosterol biosynthesis pathway and membrane composition, organization, and permeability. IMPORTANCE: Candidozyma auris is a global human health threat because of its near-universal resistance to the antifungal fluconazole as well as a predisposition to multidrug resistance among clinical isolates. The underlying mechanisms of antifungal drug resistance in this species are still largely under investigation, and these efforts are significantly supported by research that increase our understanding of unique aspects of C. auris biology. We have identified a correlation between C. auris isolates’ susceptibility to fluconazole and intracellular drug accumulation in which drug-resistant isolates have significantly reduced intracellular fluconazole compared to isolates that are susceptible to fluconazole. We have proposed a mechanism for this phenomenon and demonstrated important roles for mutations in ERG11, TAC1B, and CDR1 gene sequences for drug resistance.

Background: Aspergillosis is a fungal infection associated with rising hospitalizations and substantial morbidity and mortality. In the United States, data remain fragmented due to the absence of centralized surveillance. This study aimed to evaluate demographic, geographic, and temporal trends in aspergillosis diagnoses across the United States and evaluate changes in those patterns following the emergence of COVID-19. Methods: We conducted a retrospective cohort study using electronic health record data from 142 US healthcare systems (Oracle Health), including adults aged ≥18 years who received care between 2013 and 2023. The cohort included over 76 million patients and 127 million person-years. Aspergillosis prevalence was calculated using post-stratification weights. Adjusted prevalence ratios (aPRs) were estimated via quasi-Poisson and Bayesian spatiotemporal regression. COVID-19-related shifts were evaluated using estimated marginal means. Results: From 2013 to 2023, aspergillosis prevalence increased by 5% annually, peaking in 2022. Rhode Island had the highest state-level aPR; Utah the lowest. Diagnosis was higher among males (aPR 1.37), older adults (≥65 years vs 18–24 years: aPR 4.95), and urban residents (rural aPR 0.86). Following the emergence of COVID-19, prevalence increased disproportionately among Hispanic or Latino patients and several racial minority groups. A nonsignificant upward trend was also observed among rural residents. Conclusions: This study provides a comprehensive national assessment of aspergillosis diagnosis patterns in the United States, revealing rising prevalence and shifts in affected populations following the emergence of COVID-19. These findings may aid earlier clinical recognition, especially among groups not traditionally considered high-risk, and support efforts to expand diagnostic access and improve fungal disease surveillance.

In Candida species, including Candidozyma auris (formerly Candida auris), overexpression of efflux pumps is a well-established mechanism of antifungal resistance. However, accumulating evidence indicates that impaired drug import may also significantly contribute to reduced antifungal susceptibility. Sugar importers, historically viewed solely as hexose transporters (HGTs), are now emerging as potential indirect modulators of antifungal uptake. Here, we performed a comprehensive inventory and functional analysis of the HGT family in C. auris to assess its contribution to antifungal import. Phylogenetic analyses revealed that C. auris HGTs are more closely related to those of Candida albicans (C. albicans) than Saccharomyces cerevisiae (S. cerevisiae). All HGT genes showed basal expression, with several significantly downregulated upon fluconazole (FLC) exposure. To establish functional relevance, we generated a mini-library of HGT deletion mutants. Notably, the Δhgt13 strain exhibited markedly increased FLC resistance, concomitant with reduced intracellular FLC accumulation and decreased membrane permeability. Consistently, molecular docking and molecular dynamics simulations demonstrated strong and stable interactions between FLC and Hgt13p. Together, these findings implicate Hgt13p as a key determinant of FLC import and membrane permeability, revealing reduced FLC import could also contribute to antifungal resistance in C. auris.

In Candida species, including Candidozyma auris (formerly Candida auris), overexpression of efflux pumps is a well-established mechanism of antifungal resistance. However, accumulating evidence indicates that impaired drug import may also significantly contribute to reduced antifungal susceptibility. Sugar importers, historically viewed solely as hexose transporters (HGTs), are now emerging as potential indirect modulators of antifungal uptake. Here, we performed a comprehensive inventory and functional analysis of the HGT family in C. auris to assess its contribution to antifungal import. Phylogenetic analyses revealed that C. auris HGTs are more closely related to those of Candida albicans (C. albicans) than Saccharomyces cerevisiae (S. cerevisiae). All HGT genes showed basal expression, with several significantly downregulated upon fluconazole (FLC) exposure. To establish functional relevance, we generated a mini-library of HGT deletion mutants. Notably, the Δhgt13 strain exhibited markedly increased FLC resistance, concomitant with reduced intracellular FLC accumulation and decreased membrane permeability. Consistently, molecular docking and molecular dynamics simulations demonstrated strong and stable interactions between FLC and Hgt13p. Together, these findings implicate Hgt13p as a key determinant of FLC import and membrane permeability, revealing reduced FLC import could also contribute to antifungal resistance in C. auris.

Background: Where surveillance data are limited, nationally representative electronic health records allow for geographic, temporal, and demographic characterization of the fungal diseases blastomycosis and histoplasmosis. Methods: We identified incident blastomycosis and histoplasmosis cases from 2013 to 2023 within Oracle EHR Real-World Data, which comprises 1.6 billion healthcare encounters nationally. To characterize spatiotemporal incidence trends, we used generalized estimating equations weighted for nonrepresentativeness of electronic health record–reporting facilities. We computed standardized incidence rate ratios (sIRRs), which relay relative differences in standardized incidence rates between regions, race/ethnicity, gender, and age subgroups and the national population. Results: National incidence rates in 2023 were 2.4 (95% confidence interval [CI]: 1.6–3.5) and 1.9 times (95% CI: 1.6–2.2) rates in 2013, for blastomycosis and histoplasmosis, respectively. Blastomycosis incidence rates among Hispanic or Latino and non-Hispanic Black individuals were 60% (sIRR: 1.6 [95% CI: 1.0–2.4]) and 30% (sIRR: 1.3 [95% CI: 1.0–1.6]) higher than the standardized national incidence rate. Histoplasmosis incidence rates were elevated among non-Hispanic White patients (sIRR: 1.05 [95% CI: 1.02–1.08]). Standardized incidence rates of both diseases were higher among older and male patients, were consistently elevated in the Upper Midwest and Ohio Valley regions, and increased greatly in the Northern Rockies and Plains from 2013 to 2023. We estimated high incidence in states (blastomycosis: Illinois, Kentucky, and West Virginia; histoplasmosis: Missouri, Iowa, and Oklahoma) that do not report to surveillance. Conclusions: This analysis revealed increasing incidence rates of blastomycosis and histoplasmosis, with increasing diagnoses outside of historically endemic regions, and notable differences in incidence by race/ethnicity, gender, and age.

Importance Aspergillosis is an under-recognized fungal infection associated with rising hospitalizations, concerns about antifungal resistance, and substantial morbidity and mortality in the U.S. Yet, national data on aspergillosis remain fragmented due to absence of centralized surveillance. Objective To examine demographic and geographic variation and temporal trends in aspergillosis prevalence in the U.S. from 2013 to 2023; to assess how the COVID-19 pandemic influenced prevalence across population subgroups. Design Retrospective cohort study using a large, national electronic health record (EHR) database. Setting 142 healthcare systems in the U.S. using Oracle Health EHR systems, encompassing disparate care settings. Participants Adults aged 18 years and older who received care between January 1, 2013, and December 31, 2023. The cohort included over 76 million patients, and over 127 million person-years, with 20,764 aspergillosis diagnoses. Exposures Calendar year, patient characteristics (age, sex, race, ethnicity, residence type), and state of residence. COVID-19 was treated as a time-varying exposure. Main Outcomes and Measures Annual and overall prevalence of aspergillosis per 100,000 person-years; adjusted prevalence ratios (aPRs) by demographic group and state, estimated using quasi-Poisson and Bayesian spatiotemporal regression. COVID-19-related shifts in prevalence were assessed using estimated marginal means. Results Between 2013 and 2023, aspergillosis prevalence increased 5% annually, peaking in 2022. Rhode Island had the highest aPR across all years; Utah the lowest. Prevalence was higher in males (aPR: 1.37), older adults (aPR for ≥65 vs. 18 to 34: 4.95), and urban residents (rural aPR: 0.86). Post-COVID-19, prevalence increased disproportionately among Hispanic or Latino patients and several racial minority groups. Suggestive trends of increasing prevalence were also observed among rural residents. Conclusions and Relevance This study provides the most comprehensive national assessment to date of aspergillosis patterns in the U.S., revealing evidence of rising prevalence and emerging disparities shaped by the COVID-19 pandemic. Clinicians should consider regional and demographic risk patterns to support earlier diagnosis, guide antifungal treatment, and improve outcomes—especially among older adults and populations disproportionately affected by COVID-19. Clinicians practicing in rural or underserved areas should be particularly mindful of shifting risk profiles and advocate for improved diagnostic resources to reduce delays in care. Question How has aspergillosis prevalence changed in the U.S. over time, and how did the COVID-19 pandemic influence prevalence among demographic and geographic subgroups? Findings In a nationally representative EHR cohort of over 76 million adults, aspergillosis prevalence increased by 5% annually from 2013 to 2023. After the emergence of COVID-19, prevalence increased disproportionately among Hispanic or Latino patients and racial minority groups. Meaning Findings suggest increasing aspergillosis prevalence in the U.S., with indications of widening disparities. While subject to data limitations, these trends underscore the importance of considering regional and demographic factors in clinical decision-making, particularly for populations disproportionately affected by COVID-19.

Candida auris is an emerging fungal infection of humans and is particularly problematic because it is multi-drug resistant and difficult to treat. It is also known to be spread from person to person by contact and can remain on surfaces for long periods of time. In this report, a dog in a shelter in Kansas is found to be colonized with Candida auris . This is the first study to document the presence of Candida auris on a pet, the first to document C. auris presence on a non-human mammal in the United States, and the first to report an isolate of C. auris within the state of Kansas. The presence of C. auris in a pet dog raises the possibility of zoonotic transmission from pets to human or vice versa.

The purpose of this study was to characterize the variety and diversity of the oral mycobiome of domestic dogs and to identify the commensal and potentially pathogenic fungi present. Two hundred fifty-one buccal swabs from domestic dogs were obtained and struck onto a chromogenic fungal growth medium that distinguishes between fungal species based on colony color and morphology. After isolating and harvesting single colonies, genomic DNA was extracted from pure cultures. PCR was used to amplify a fungal-specific variable rDNA region of the genome, which was then sent for sequencing. Sequencing results were input into the NCBI BLAST database to identify individual components of the oral mycobiome of tested dogs. Of the 251 dogs swabbed, 73 had cultivable fungi present and 10 dogs had multiple fungal species isolated. Although the dogs did not show signs of oral infections at the time, we did find fungal species that cause pathogenicity in animals and humans. Among fungal isolates, Malassezia pachydermatis and species from the genus Candida were predominant. Following fungal isolate identification, antifungal drug susceptibility tests were performed on each isolate toward the medically important antifungal drugs including fluconazole, ketoconazole, and terbinafine. Drug susceptibility test results indicated that a large number of isolates had high MIC values for all three drugs. Exploring the oral mycobiome of dogs, as well as the corresponding drug susceptibility profiles, can have important implications for canine dental hygiene, health, and medical treatment. Identifying the microorganisms within the canine mouth can illustrate a common pathway for fungal pathogens of One Health concern to spread from our canine companions to humans.