Publications by authors named "Christina A Cuomo"

The gut mycobiota is crucial for intestinal homeostasis and immune function. Yet its variability and inconsistent fungal colonization of laboratory mice hinders the study of the evolutionary and immune processes that underpin commensalism. Here, we show that Kazachstania pintolopesii is a fungal commensal in wild urban and rural mice, with an exceptional ability to colonize the mouse gastrointestinal tract and dominate the gut mycobiome.

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Candida auris is a growing concern due to its resistance to antifungal drugs, particularly amphotericin B (AMB), detected in 30 to 60% of clinical isolates. However, the mechanisms of AMB resistance remain poorly understood. Here we investigated 441 in vitro- and in vivo-evolved C.

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Copper has been widely used as a main component in fungicides due to its versatility and effectivity. However, copper contamination from the environment creates selective pressure for the emergence of copper-tolerant pathogenic fungal strains that may proliferate and further cause damage to important agricultural crops. Although some studies focused on specific cellular mechanisms of copper tolerance, comprehensive genomic data is lacking.

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Article Synopsis
  • Understanding pathogen diversity is essential for controlling emerging infectious diseases, as different variants interact uniquely with hosts and the environment.
  • This study focuses on Batrachochytrium salamandrivorans (Bsal), a fungal pathogen harming European amphibians, by analyzing 13 isolates to examine their reproductive rates and thermal tolerances.
  • The research suggests that the combination of host body temperature and the thermal range of Bsal can significantly affect pathogen growth, highlighting the importance of identifying pathogen variants to assess risk to host populations.
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Unlabelled: Cryptococcal meningitis causes an estimated 112,000 global deaths per annum. Genomic and phenotypic features of the infecting strain of spp. have been associated with outcomes from cryptococcal meningitis.

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is a fungal pathogen of significant worldwide concern, typically resistant to one or more antifungal drugs. We report a completed genome for clade Ia isolate B8441 and gene annotations of clade Ic isolate B11205. These resources will support public health investigations and population genomic studies of this pathogen.

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In exploring the evolutionary trajectories of both pathogenesis and karyotype dynamics in fungi, we conducted a large-scale comparative genomic analysis spanning the Cryptococcus genus, encompassing both global human fungal pathogens and nonpathogenic species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species, covering virtually all known diversity within these genera. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.

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We used whole-genome sequencing to analyze a collection of 35 fluconazole-resistant and 7 susceptible isolates together with coverage analysis and GWAS techniques to identify new mechanisms of fluconazole resistance. Phylogenetic analysis shows that although the collection is diverse, two persistent clinical lineages were identified. We identified copy number variation (CNV) of two genes, and , in resistant isolates.

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Triazole antifungals function as ergosterol biosynthesis inhibitors and are frontline therapy for invasive fungal infections, such as invasive aspergillosis. The primary mechanism of action of triazoles is through the specific inhibition of a cytochrome P450 14-α-sterol demethylase enzyme, Cyp51A/B, resulting in depletion of cellular ergosterol. Here, we uncover a clinically relevant secondary mechanism of action for triazoles within the ergosterol biosynthesis pathway.

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A large-scale comparative genomic analysis was conducted for the global human fungal pathogens within the genus, compared to non-pathogenic species, and related species from the sister genus . Chromosome-level genome assemblies were generated for multiple species of both genera, resulting in a dataset encompassing virtually all of their known diversity. Although and have comparable genome sizes (about 19.

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We used whole-genome sequencing to analyse a collection of 35 fluconazole resistant and 7 susceptible isolates together with coverage analysis and GWAS techniques to identify new mechanisms of fluconazole resistance. Phylogenetic analysis shows that although the collection is diverse, two probable outbreak groups were identified. We identified copy number variation of two genes, and , in resistant isolates.

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Article Synopsis
  • Cryptococcal meningitis is a major cause of death in people with HIV/AIDS, but there's still a limited understanding of how the fungus changes during infection.
  • A study analyzed the whole genomes of 372 clinical isolates from patients in Malawi and Cameroon, revealing that Cameroonian isolates are more genetically uniform compared to their Malawian counterparts, and show different rates of mutations in key genes.
  • Longitudinal samples taken from patients in Cameroon highlighted genetic changes during infection and revealed mixed infections in 13% of patients, showcasing the evolutionary dynamics of the fungus in this context.
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Lichtheimia ornata is an emerging opportunistic Mucorales pathogen that is associated with fatal infections in immunocompromised individuals. While these environmentally acquired infections have rarely been reported to date, cases were noted in a recent analysis of coronavirus disease 2019 (COVID-19)-associated mucormycosis in India. Here, we report the annotated genome sequence of the environmental isolate CBS 291.

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Talaromycosis, a severe and invasive fungal infection caused by Talaromyces marneffei, is difficult to treat and impacts those living in endemic regions of Southeast Asia, India, and China. While 30% of infections result in mortality, our understanding of the genetic basis of pathogenesis for this fungus is limited. To address this, we apply population genomics and genome-wide association study approaches to a cohort of 336 T.

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Genomic analyses are widely applied to epidemiological, population genetic and experimental studies of pathogenic fungi. A wide range of methods are employed to carry out these analyses, typically without including controls that gauge the accuracy of variant prediction. The importance of tracking outbreaks at a global scale has raised the urgency of establishing high-accuracy pipelines that generate consistent results between research groups.

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Article Synopsis
  • * Researchers analyzed 336 fungal isolates from a clinical trial in Vietnam, discovering distinct genetic clades linked to disease severity and instances of relapse due to multi-strain infections.
  • * The study highlights specific genetic variants associated with patient outcomes, showing how pathogen genetics affects disease progression and identifying rapid evolutionary responses to external pressures.
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Genomic approaches are widely applied to study the genetic basis of antifungal drug resistance in clinical isolates and experimental studies. Whole-genome sequencing of clinical isolates can comprehensively identify mutations associated with drug resistance and their frequency across fungal populations. In addition, genome comparison of serially collected isolates, such as from patient samples or in vitro drug selection experiments, will identify a small number of changes that can be evaluated for association with drug resistance.

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Recent technological and computational advances have made metagenomic assembly a viable approach to achieving high-resolution views of complex microbial communities. In previous benchmarking, short-read (SR) metagenomic assemblers had the highest accuracy, long-read (LR) assemblers generated the most contiguous sequences and hybrid (HY) assemblers balanced length and accuracy. However, no assessments have specifically compared the performance of these assemblers on low-abundance species, which include clinically relevant organisms in the gut.

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Background: The aetiology of the major outbreak of COVID-19-associated mucormycosis (CAM) in India in spring 2021 remains incompletely understood. Herein, we provide a multifaceted and multi-institutional analysis of clinical, pathogen-related, environmental and healthcare-related factors during CAM outbreak in the metropolitan New Delhi area.

Methods: We reviewed medical records of all patients diagnosed with biopsy-proven CAM (n = 50) at 7 hospitals in the New Delhi, and NCR area in April-June 2021.

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A pet cockatoo was the suspected source of recovered from an immunocompromised patient with cryptococcosis based on molecular analyses available in 2000. Here, we report whole genome sequence analysis of the clinical and cockatoo strains. Both are closely related MATα strains belonging to the VNII lineage, confirming that the human infection likely originated from pet bird exposure.

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Article Synopsis
  • Cryptococcus neoformans causes cryptococcosis, which leads to around 180,000 deaths annually, particularly affecting patients with HIV, highlighting a need to understand the link between genetic diversity of the fungus and clinical outcomes.
  • A genome-wide association study (GWAS) of 284 C. neoformans isolates from Malawi reveals variants associated with fungal growth rates and burdens, with significant variations in genes related to metabolism and growth.
  • The findings demonstrate that glycolysis is crucial for the fungus's survival in the central nervous system and may influence patient mortality, suggesting that understanding these genetic factors can improve treatment outcomes for cryptococcosis.
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