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Identification of Pathogen Genomic Differences That Impact Human Immune Response and Disease during Cryptococcus neoformans Infection

https://doi.org/10.1128/mbio.01440-19
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Molecular typing of global isolates ofCryptococcus neoformans var.neoformans by polymerase chain reaction fingerprinting and randomly amplified polymorphic DNA — a pilot study to standardize techniques on which to base a detailed epidemiological survey
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It's not all about us: evolution and maintenance ofCryptococcusvirulence requires selection outside the human host
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Systematic Genetic Analysis of Virulence in the Human Fungal Pathogen Cryptococcus neoformans
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Aimless mutants of Cryptococcus neoformans: Failure to disseminate
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Cryptococcus neoformans mutant screening: a genome-scale's worth of function discovery
inferredcites →https://doi.org/10.1016/j.fgb.2015.02.009openalex-snapshot
Recognition of seven species in the Cryptococcus gattii/Cryptococcus neoformans species complex
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Virulence factors in fungal pathogens of man
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Deletion of the CAP10 gene of Cryptococcus neoformans results in a pleiotropic phenotype with changes in expression of virulence factors
inferredcites →https://doi.org/10.1016/s0076-6879(10)70033-1openalex-snapshot
Applying Genetics and Molecular Biology to the Study of the Human Pathogen Cryptococcus neoformans
inferredcites →https://doi.org/10.1016/s1473-3099(17)30243-8openalex-snapshot
Global burden of disease of HIV-associated cryptococcal meningitis: an updated analysis
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A framework for variation discovery and genotyping using next-generation DNA sequencing data
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Loss-of-function genetic tools for animal models: cross-species and cross-platform differences
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Genome-wide association studies for common diseases and complex traits
inferredcites →https://doi.org/10.1038/nrm1583openalex-snapshot
Friendly rivalry
inferredcites →https://doi.org/10.1038/s41467-019-10092-5openalex-snapshot
Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans
inferredcites →https://doi.org/10.1056/nejmoa1312884openalex-snapshot
Timing of Antiretroviral Therapy after Diagnosis of Cryptococcal Meningitis
inferredcites →https://doi.org/10.1056/nejmsr1203730openalex-snapshot
The Prevention and Treatment of Missing Data in Clinical Trials
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp698openalex-snapshot
Fast and accurate long-read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/biomet/69.3.553openalex-snapshot
A Class of Rank Test Procedures for Censored Survival Data
inferredcites →https://doi.org/10.1093/infdis/jiu441openalex-snapshot
A Multi-Host Approach for the Systematic Analysis of Virulence Factors inCryptococcus neoformans
inferredcites →https://doi.org/10.1093/infdis/jiv067openalex-snapshot
Early ART After Cryptococcal Meningitis Is Associated With Cerebrospinal Fluid Pleocytosis and Macrophage Activation in a Multisite Randomized Trial
inferredcites →https://doi.org/10.1093/mmy/myw089openalex-snapshot
Activity of VT-1129 againstCryptococcus neoformansclinical isolates with high fluconazole MICs
inferredcites →https://doi.org/10.1101/356816openalex-snapshot
Genomics of Cryptococcus neoformans
inferredcites →https://doi.org/10.1101/cshperspect.a019752openalex-snapshot
Mechanisms of Antifungal Drug Resistance
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.218727.116openalex-snapshot
Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans
inferredcites →https://doi.org/10.1128/aac.01299-15openalex-snapshot
Increased Antifungal Drug Resistance in Clinical Isolates of Cryptococcus neoformans in Uganda
inferredcites →https://doi.org/10.1128/ec.00073-13openalex-snapshot
The Transcriptional Response of Cryptococcus neoformans to Ingestion by Acanthamoeba castellanii and Macrophages Provides Insights into the Evolutionary Adaptation to the Mammalian Host
inferredcites →https://doi.org/10.1128/ec.00327-10openalex-snapshot
Two Major Inositol Transporters and Their Role in Cryptococcal Virulence
inferredcites →https://doi.org/10.1128/iai.00046-19openalex-snapshot
The Mouse Inhalation Model of Cryptococcus neoformans Infection Recapitulates Strain Virulence in Humans and Shows that Closely Related Strains Can Possess Differential Virulence
inferredcites →https://doi.org/10.1128/iai.00768-06openalex-snapshot
The Cryptococcal Enzyme Inositol Phosphosphingolipid-Phospholipase C Confers Resistance to the Antifungal Effects of Macrophages and Promotes Fungal Dissemination to the Central Nervous System
inferredcites →https://doi.org/10.1128/iai.55.3.742-748.1987openalex-snapshot
Production, characterization, and antibody specificity of a mouse monoclonal antibody reactive with Cryptococcus neoformans capsular polysaccharide
inferredcites →https://doi.org/10.1128/iai.71.9.4831-4841.2003openalex-snapshot
Sexual Cycle of Cryptococcus neoformans var. grubii and Virulence of Congenic a and α Isolates
inferredcites →https://doi.org/10.1128/jb.01982-07openalex-snapshot
Determination of Antibiotic Hypersensitivity among 4,000 Single-Gene-Knockout Mutants of Escherichia coli
inferredcites →https://doi.org/10.1128/jcm.01277-10openalex-snapshot
Analyses of Pediatric Isolates of Cryptococcus neoformans from South Africa
inferredcites →https://doi.org/10.1128/mbio.00084-10openalex-snapshot
Role of an Expanded Inositol Transporter Repertoire in Cryptococcus neoformans Sexual Reproduction and Virulence
inferredcites →https://doi.org/10.1128/mbio.00196-12openalex-snapshot
Cryptococcal Genotype Influences Immunologic Response and Human Clinical Outcome after Meningitis
inferredcites →https://doi.org/10.1128/mbio.00311-15openalex-snapshot
Cryptococcosis Serotypes Impact Outcome and Provide Evidence of Cryptococcus neoformans Speciation
inferredcites →https://doi.org/10.1128/mbio.01087-13openalex-snapshot
The Cryptococcus neoformans Transcriptome at the Site of Human Meningitis
inferredcites →https://doi.org/10.1128/mbio.01340-15openalex-snapshot
Polyploid Titan Cells Produce Haploid and Aneuploid Progeny To Promote Stress Adaptation
inferredcites →https://doi.org/10.1128/mbio.02016-18openalex-snapshot
Phenotypic Variability Correlates with Clinical Outcome in Cryptococcus Isolates Obtained from Botswanan HIV/AIDS Patients
inferredcites →https://doi.org/10.1128/msphere.00238-17openalex-snapshot
Importance of Resolving Fungal Nomenclature: the Case of Multiple Pathogenic Species in the Cryptococcus Genus
inferredcites →https://doi.org/10.1128/msphere.00357-16openalex-snapshot
The Case for Adopting the “Species Complex” Nomenclature for the Etiologic Agents of Cryptococcosis
inferredcites →https://doi.org/10.1155/2009/840452openalex-snapshot
Cryptococcus gattii: An Emerging Cause of Fungal Disease in North America
inferredcites →https://doi.org/10.1172/jci18309openalex-snapshot
Identification of App1 as a regulator of phagocytosis and virulence of Cryptococcus neoformans
inferredcites →https://doi.org/10.1172/jci72950openalex-snapshot
Efficient phagocytosis and laccase activity affect the outcome of HIV-associated cryptococcosis
inferredcites →https://doi.org/10.1186/1471-2164-15-162openalex-snapshot
SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data
inferredcites →https://doi.org/10.1371/journal.pgen.1004261openalex-snapshot
Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation
inferredcites →https://doi.org/10.1371/journal.pmed.1000384openalex-snapshot
Clinical Features and Serum Biomarkers in HIV Immune Reconstitution Inflammatory Syndrome after Cryptococcal Meningitis: A Prospective Cohort Study
inferredcites →https://doi.org/10.1371/journal.pntd.0003847openalex-snapshot
Genotypic Diversity Is Associated with Clinical Outcome and Phenotype in Cryptococcal Meningitis across Southern Africa
inferredcites →https://doi.org/10.1371/journal.pntd.0005223openalex-snapshot
MLST-Based Population Genetic Analysis in a Global Context Reveals Clonality amongst Cryptococcus neoformans var. grubii VNI Isolates from HIV Patients in Southeastern Brazil
inferredcites →https://doi.org/10.1371/journal.pntd.0005628openalex-snapshot
Comparative genomics of Cryptococcus neoformans var. grubii associated with meningitis in HIV infected and uninfected patients in Vietnam
inferredcites →https://doi.org/10.1371/journal.pone.0072222openalex-snapshot
Geographically Structured Populations of Cryptococcus neoformans Variety grubii in Asia Correlate with HIV Status and Show a Clonal Population Structure
inferredcites →https://doi.org/10.1371/journal.pone.0141974openalex-snapshot
Direct Comparison of a Natural Loss-Of-Function Single Nucleotide Polymorphism with a Targeted Deletion in the Ncf1 Gene Reveals Different Phenotypes
inferredcites →https://doi.org/10.1371/journal.pone.0193237openalex-snapshot
Genotypic analysis of clinical and environmental Cryptococcus neoformans isolates from Brazil reveals the presence of VNB isolates and a correlation with biological factors
inferredcites →https://doi.org/10.1371/journal.ppat.1002870openalex-snapshot
Antifungal Drug Discovery: Something Old and Something New
inferredcites →https://doi.org/10.15252/msb.20198831openalex-snapshot
The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae
inferredcites →https://doi.org/10.2307/1555045openalex-snapshot
(1557) Proposal to conserve the name Cryptococcus gattii against C. hondurianus and C. bacillisporus ( Basidiomycota, Hymenomycetes, Tremellomycetidae )
inferredcites →https://doi.org/10.3390/jof2040029openalex-snapshot
Virulence Factors as Targets for Anticryptococcal Therapy
inferredcites →https://doi.org/10.4161/fly.19695openalex-snapshot
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Multi-locus Sequence Typing and Whole Genome Sequence Analysis of Cryptococcus neoformans Isolated from Clinical Specimens in Vajira Hospital, Bangkok, Thailand
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Distinct pathways of adaptive evolution in Cryptococcus neoformans reveal a mutation in adenylyl cyclase with trade-offs for pathogenicity
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Investigation of human leukocyte antigen alleles as risk factors for cryptococcal disease in Ugandan individuals with HIV
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Whole Blood Proteome Dynamics Defines Predictive Diagnostic and Prognostic Signatures of Cryptococcal Infection
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Genome-wide association study analysis of single nucleotide variants in L. infantum associated with IL-6 inflammatory response in visceral leishmaniasis
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Docusate-Based Ionic Liquids of Anthelmintic Benzimidazoles Show Improved Pharmaceutical Processability, Lipid Solubility, and in Vitro Activity against Cryptococcus neoformans
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Cryptococcus neoformans adapts to the host environment through TOR-mediated remodeling of phospholipid asymmetry
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Single nucleotide polymorphisms are associated with strain-specific virulence differences among clinical isolates of Cryptococcus neoformans
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Paths to pathogenicity: exploring the diversity and evolution of Cryptococcus neoformans
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The interplay of phenotype and genotype inCryptococcus neoformansdisease
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Similar evolutionary trajectories in an environmental Cryptococcus neoformans isolate after human and murine infection
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Cryptococcus neoformans releases proteins during intracellular residence that affect the outcome of the fungal–macrophage interaction
inferred← citeshttps://doi.org/10.1093/genetics/iyad100openalex-snapshot
Impact of pathogen genetics on clinical phenotypes in a population of Talaromyces marneffei from Vietnam
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Genetic diversity and microevolution in clinical Cryptococcus isolates from Cameroon
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Cryptococcus neoformans responds to presence of Mycobacterium by diversifying its morphologies and remodelling its capsular material
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Host environmental conditions induce small fungal cell size and alter population heterogeneity in Cryptococcus neoformans
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Human commensal Candida albicans strains demonstrate substantial within-host diversity and retained pathogenic potential
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Distinct pathways of adaptive evolution in Cryptococcus neoformans reveal a point mutation in adenylate cyclase with drastic tradeoffs for pathogenicity
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Impact of pathogen genetics on clinical phenotypes in a population of Talaromyces marneffei from Vietnam
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Reconstruction and exploitation of a dedicated Genome-Scale Metabolic Model of the human pathogen C. neoformans
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Deciphering the global genomic landscape of C. neoformans : Population dynamics, molecular epidemiology and genomic signatures of pathogenicity
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Human immune polymorphisms associated with the risk of cryptococcal disease
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Landmark clinical observations and immunopathogenesis pathways linked to HIV and Cryptococcus fatal central nervous system co‐infection
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The hypervirulent Type-1/Type-17 phenotype of Cryptococcus neoformans clinical isolates is specific to A/J mice
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Phenotypic Variability Correlates with Clinical Outcome in Cryptococcus Isolates Obtained from Botswanan HIV/AIDS Patients
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Genomic Variation across a Clinical Cryptococcus Population Linked to Disease Outcome
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Is It Time To Kill the Survival Curve? A Case for Disease Progression Factors in Microbial Pathogenesis and Host Defense Research
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Cryptococcal nutrient acquisition and pathogenesis: dining on the host
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Global proteomic analysis of Cryptococcus neoformans clinical strains reveals significant differences between latent and lethal infection
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Virulence-associated variants in Cryptococcus neoformans sequence type 93 are less likely to be associated with population structure compared to independent rare mutations
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A Novel Cryptococcal Meningitis Therapy: The Combination of Amphotericin B and Posaconazole Promotes the Distribution of Amphotericin B in the Brain Tissue
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Candida albicans selection for human commensalism results in substantial within-host diversity without decreasing fitness for invasive disease
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An inositol receptor Itr4 coordinates carbon catabolite regulation and virulence in Cryptococcus neoformans
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Environmental sources of Cryptococcus neoformans species complex in Kampala, Uganda: A preliminary study
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Genome-wide association study of Pseudomonas aeruginosa adaptations to the cystic fibrosis lung
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Divergent neuroimmune signatures in the cerebrospinal fluid predict differential gender-specific survival among patients with HIV-associated cryptococcal meningitis
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Molecular Diagnostics of Cryptococcus spp. and Immunomics of Cryptococcosis-Associated Immune Reconstitution Inflammatory Syndrome
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Computational Approaches for Discovering Virulence Factors in Coccidioides
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Associations between Cryptococcus Genotypes, Phenotypes, and Clinical Parameters of Human Disease: A Review
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Deciphering the Association among Pathogenicity, Production and Polymorphisms of Capsule/Melanin in Clinical Isolates of Cryptococcus neoformans var. grubii VNI
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Cryptococcus neoformans Genotypic Diversity and Disease Outcome among HIV Patients in Africa
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Sterile Cerebrospinal Fluid Culture at Cryptococcal Meningitis Diagnosis Is Associated with High Mortality
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Importance of Clinical Isolates in Cryptococcus neoformans Research
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Outbreaks of Fungal Infections in Hospitals: Epidemiology, Detection, and Management
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Recent Advances in Cryptococcus and Cryptococcosis
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Assessing Differences between Clinical Isolates of Aspergillus fumigatus from Cases of Proven Invasive Aspergillosis and Colonizing Isolates with Respect to Phenotype (Virulence in Tenebrio molitor Larvae) and Genotype
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An Inositol Receptor Orchestrates Carbon Utilization and Fungal Virulence
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Ex Vivo Cytokine Profiling of Cryptococcus neoformans Strains Suggests Strain-Specific Immune Modulation: A Cross-Sectional Study
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