Avian-associated Aspergillus fumigatus displays broad phylogenetic distribution, no evidence for host specificity, and multiple genotypes within epizootic events

Mass spectrometric methods for evaluation of voriconazole avian pharmacokinetics and the inhibition of its cytochrome P450-induced metabolism

Invasive fungal aspergillosis is a leading cause of morbidity and mortality in many species including avian species such as common ravens (Corvus corax). Methods were developed for mass spectral determination of voriconazole in raven plasma as a means of determining pharmacokinetics of this antifungal agent. Without further development, GC/MS/MS (gas chromatography-tandem quadrupole mass spectrometry) proved to be inferior to LC/MS/MS (liquid chromatography-tandem quadrupole mass spectrometry) for measurement of voriconazole levels in treated raven plasma owing to numerous heat-induced breakdown products despite protection of voriconazole functional groups with trimethylsilyl moieties. LC/MS/MS measurement revealed in multi-dosing experiments that the ravens were capable of rapid or ultrarapid metabolism of voriconazole. This accounted for the animals' inability to raise the drug into the therapeutic range regardless of dosing regimen unless cytochrome P450 (CYP) inhibitors were included. Strategic selection of CYP inhibitors showed that of four selected compounds including cimetidine, enrofloxacin and omeprazole, only ciprofloxacin (Cipro) was able to maintain voriconazole levels in the therapeutic range until the end of the dosing period. The optimal method of administration involved maintenance doses of voriconazole at 6 mg/kg and ciprofloxacin at 20 mg/kg. Higher doses of voriconazole such as 18 mg/kg were also tenable without apparent induction of toxicity. Although most species employ CYP2C19 to metabolize voriconazole, it was necessary to speculate that voriconazole might be subject to metabolism by CYP1A2 in the ravens to explain the utility of ciprofloxacin, a previously unknown enzymatic route. Finally, despite its widespread catalog of CYP inhibitions including CYP1A2 and CYP2C19, cimetidine may be inadequate at enhancing voriconazole levels owing to its known effects on raising gastric pH, a result that may limit voriconazole solubility.

A single fungal strain was the unexpected cause of a mass aspergillosis outbreak in the world’s largest and only flightless parrot

Kākāpō are a critically endangered species of parrots restricted to a few islands off the coast of New Zealand. Kākāpō are very closely monitored, especially during nesting seasons. In 2019, during a highly successful nesting season, an outbreak of aspergillosis affected 21 individuals and led to the deaths of 9, leaving a population of only 211 kākāpō. In monitoring this outbreak, cultures of aspergillus were grown, and genome sequenced. These sequences demonstrate that, very unusually for an aspergillus outbreak, a single strain of aspergillus caused the outbreak. This strain was found on two islands, but only one had an outbreak of aspergillosis; indicating that the strain was necessary, but not sufficient, to cause disease. Our analysis provides an understanding of the 2019 outbreak and provides potential ways to manage such events in the future.

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In 2019, the kākāpō, an endangered parrot species, was threatened by aspergillosis

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The outbreak was associated with a single strain of Aspergillus fumigatus

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The first reported case of a single strain of Aspergillus causing a disease outbreak

The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high levels of lineage-specific diversity driven by recombination

Aspergillus fumigatus is a deadly agent of human fungal disease where virulence heterogeneity is thought to be at least partially structured by genetic variation between strains. While population genomic analyses based on reference genome alignments offer valuable insights into how gene variants are distributed across populations, these approaches fail to capture intraspecific variation in genes absent from the reference genome. Pan-genomic analyses based on de novo assemblies offer a promising alternative to reference-based genomics with the potential to address the full genetic repertoire of a species. Here, we evaluate 260 genome sequences of A. fumigatus including 62 newly sequenced strains, using a combination of population genomics, phylogenomics, and pan-genomics. Our results offer a high-resolution assessment of population structure and recombination frequency, phylogenetically structured gene presence-absence variation, evidence for metabolic specificity, and the distribution of putative antifungal resistance genes. Although A. fumigatus disperses primarily via asexual conidia, we identified extraordinarily high levels of recombination with the lowest linkage disequilibrium decay value reported for any fungal species to date. We provide evidence for 3 primary populations of A. fumigatus, with recombination occurring only rarely between populations and often within them. These 3 populations are structured by both gene variation and distinct patterns of gene presence-absence with unique suites of accessory genes present exclusively in each clade. Accessory genes displayed functional enrichment for nitrogen and carbohydrate metabolism suggesting that populations may be stratified by environmental niche specialization. Similarly, the distribution of antifungal resistance genes and resistance alleles were often structured by phylogeny. Altogether, the pan-genome of A. fumigatus represents one of the largest fungal pan-genomes reported to date including many genes unrepresented in the Af293 reference genome. These results highlight the inadequacy of relying on a single-reference genome-based approach for evaluating intraspecific variation and the power of combined genomic approaches to elucidate population structure, genetic diversity, and putative ecological drivers of clinically relevant fungi.

Important Mycoses of Wildlife: Emphasis on Etiology, Epidemiology, Diagnosis, and Pathology—A Review: PART 1

Simple Summary

The number of wild animals is steadily declining globally, so the early diagnosis and proper treatment of emerging diseases are vital. Fungal diseases are commonly encountered in practice and have a high zoonotic potential. This article describes aspergillosis, candidiasis, histoplasmosis, cryptococcosis, and penicilliosis, and is only the first part of a detailed review. The laboratory methods (fungal isolation, gross pathology, histopathology, histochemistry, cytology, immunohistochemistry, radiography, CT, PCR, or ELISA) used in the diagnosis and the clinical details that provide a complete view of the mycoses are presented.

Abstract

In the past few years, there has been a spurred tripling in the figures of fungal diseases leading to one of the most alarming rates of extinction ever reported in wild species. Some of these fungal diseases are capable of virulent infections and are now considered emerging diseases due to the extremely high number of cases diagnosed with fungal infections in the last few decades. Most of these mycotic diseases in wildlife are zoonotic, and with the emergence and re-emergence of viral and bacterial zoonotic diseases originating from wildlife, which are causing devastating effects on the human population, it is important to pay attention to these wildlife-borne mycotic diseases with zoonotic capabilities. Several diagnostic techniques such as fungal isolation, gross pathology, histopathology, histochemistry, cytology, immunohistochemistry, radiography, CT, and molecular methods such as PCR or ELISA have been invaluable in the diagnosis of wildlife mycoses. The most important data used in the diagnosis of these wildlife mycoses with a zoonotic potential have been re-emphasized. This will have implications for forestalling future epidemics of these potential zoonotic mycotic diseases originating from wildlife. In conclusion, this review will highlight the etiology, epidemiology, diagnosis, pathogenesis, pathogenicity, pathology, and hematological/serum biochemical findings of five important mycoses found in wild animals.