Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris

Chatterjee, Sharanya; Alampalli, Shuba Varshini; Nageshan, Rishi Kumar; Chettiar, Sivarajan T.; Joshi, Sangeeta; Tatu, Utpal S.

doi:10.1186/s12864-015-1863-z

Cited by 247Antifungal resistance and susceptibilityYeasts and Rust Fungi StudiesFungal and yeast genetics research

Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris

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Chatterjee, Sharanya, Alampalli, Shuba Varshini, Nageshan, Rishi Kumar, Chettiar, Sivarajan T., Joshi, Sangeeta, Tatu, Utpal S.·2015·BMC Genomics

DOI 10.1186/s12864-015-1863-zPMC PMC4562351

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Abstract

BACKGROUND: Candida auris is a multidrug resistant, emerging agent of fungemia in humans. Its actual global distribution remains obscure as the current commercial methods of clinical diagnosis misidentify it as C. haemulonii. Here we report the first draft genome of C. auris to explore the genomic basis of virulence and unique differences that could be employed for differential diagnosis. RESULTS: More than 99.5 % of the C. auris genomic reads did not align to the current whole (or draft) genome sequences of Candida albicans, Candida lusitaniae, Candida glabrata and Saccharomyces cerevisiae; thereby indicating its divergence from the active Candida clade. The genome spans around 12.49 Mb with 8527 predicted genes. Functional annotation revealed that among the sequenced Candida species, it is closest to the hemiascomycete species Clavispora lusitaniae. Comparison with the well-studied species Candida albicans showed that it shares significant virulence attributes with other pathogenic Candida species such as oligopeptide transporters, mannosyl transfersases, secreted proteases and genes involved in biofilm formation. We also identified a plethora of transporters belonging to the ABC and major facilitator superfamily along with known MDR transcription factors which explained its high tolerance to antifungal drugs. CONCLUSIONS: Our study emphasizes an urgent need for accurate fungal screening methods such as PCR and electrophoretic karyotyping to ensure proper management of fungemia. Our work highlights the potential genetic mechanisms involved in virulence and pathogenicity of an important emerging human pathogen namely C. auris. Owing to its diversity at the genomic scale; we expect the genome sequence to be a useful resource to map species specific differences that will help develop accurate diagnostic markers and better drug targets.

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Many putative transporter genes in the C. auris genome suggest that drug efflux may be an important determinant of azole resistance.
“Further, the identification of many putative transporter genes in the C. auris genome suggests that drug efflux may also be an important determinant of azole resistance (16–18).”
From Genetic Analysis of Candida auris Implicates Hsp90 in Morphogenesis and Azole Tolerance and Cdr1 in Azole Resistance (2019) · cites this paper as [16]

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Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?
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Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species
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Candida auris : The recent emergence of a multidrug-resistant fungal pathogen
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Biofilm-Forming Capability of Highly Virulent, Multidrug-Resistant Candida auris
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Candida auris: an Emerging Fungal Pathogen
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Epidemiology, clinical characteristics, resistance, and treatment of infections by Candida auris
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Multidrug-Resistant Candida haemulonii and C. auris , Tel Aviv, Israel
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Candida auris : A systematic review and meta‐analysis of current updates on an emerging multidrug‐resistant pathogen
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Comparison of EUCAST and CLSI Reference Microdilution MICs of Eight Antifungal Compounds for Candida auris and Associated Tentative Epidemiological Cutoff Values
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Candida auris: epidemiology, diagnosis, pathogenesis, antifungal susceptibility, and infection control measures to combat the spread of infections in healthcare facilities
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Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris
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Review on Antifungal Resistance Mechanisms in the Emerging Pathogen Candida auris
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Transcriptome Assembly and Profiling of Candida auris Reveals Novel Insights into Biofilm-Mediated Resistance
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Multidrug-resistant Candida auris: ‘New kid on the block’ in hospital-associated infections?
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Candida auris—the growing menace to global health
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Candida auris Pan-Drug-Resistant to Four Classes of Antifungal Agents
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Candida auris : An Overview of the Emerging Drug-Resistant Fungal Infection
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Biofilm formation in medically important Candida species
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On the Origins of a Species: What Might Explain the Rise of Candida auris?
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A CRISPR–Cas9-based gene drive platform for genetic interaction analysis in Candida albicans
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The NDV-3A vaccine protects mice from multidrug resistant Candida auris infection
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New pathogens, new tricks: emerging, drug‐resistant fungal pathogens and future prospects for antifungal therapeutics
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Nosocomial fungemia by Candida auris: First four reported cases in continental Europe
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Diversity of cytosine methylation across the fungal tree of life
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First Candida auris Outbreak during a COVID-19 Pandemic in a Tertiary-Care Center in Lebanon
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Candida Auris, An Agent of Hospital-Associated Outbreaks: Which Challenging Issues Do We Need to Have in Mind?
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Genetic Analysis of Candida auris Implicates Hsp90 in Morphogenesis and Azole Tolerance and Cdr1 in Azole Resistance
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Candida auris: Epidemiology, risk factors, virulence, resistance, and therapeutic options
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Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina)
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Emergence ofCandida auris: An International Call to Arms
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Genomics and the making of yeast biodiversity
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Identification of Drug Resistant Candida auris
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Candida auris: What Have We Learned About Its Mechanisms of Pathogenicity?
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Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts
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Inhibition of Candida auris Biofilm Formation on Medical and Environmental Surfaces by Silver Nanoparticles
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Hog1 regulates stress tolerance and virulence in the emerging fungal pathogen Candida auris
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Pathogenesis and Clinical Relevance of Candida Biofilms in Vulvovaginal Candidiasis
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Review on Current Status of Echinocandins Use
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Pseudohyphal growth of the emerging pathogen Candida auris is triggered by genotoxic stress through the S phase checkpoint
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Resistance to Antifungal Drugs
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Attack, Defend and Persist: How the Fungal Pathogen Candida auris was Able to Emerge Globally in Healthcare Environments
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Nine Things Genomics Can Tell Us About Candida auris
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The Candida auris Alert: Facts and Perspectives
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Candida auris: An emerging drug resistant yeast – A mini-review
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Detection and treatment of Candida auris in an outbreak situation: risk factors for developing colonization and candidemia by this new species in critically ill patients
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Antifungal Resistance in Candida auris: Molecular Determinants
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Candida auris for the Clinical Microbiology Laboratory: Not Your Grandfather's Candida Species
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Identification of Candida auris by Use of the Updated Vitek 2 Yeast Identification System, Version 8.01: a Multilaboratory Evaluation Study
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Synergistic interactions of sulfamethoxazole and azole antifungal drugs against emerging multidrug-resistant Candida auris
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ABC Transporter Genes Show Upregulated Expression in Drug-Resistant Clinical Isolates of Candida auris: A Genome-Wide Characterization of ATP-Binding Cassette (ABC) Transporter Genes
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Screening a Repurposing Library for Inhibitors of Multidrug-Resistant Candida auris Identifies Ebselen as a Repositionable Candidate for Antifungal Drug Development
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Candida auris: A Decade of Understanding of an Enigmatic Pathogenic Yeast
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What do we know about the biology of the emerging fungal pathogen of humans Candida auris?
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Candida auris: A Quick Review on Identification, Current Treatments, and Challenges
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First report of sporadic cases of Candida auris in Colombia
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Candida auris : a worrisome, globally emerging pathogen
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Candida auris: An Overview of How to Screen, Detect, Test and Control This Emerging Pathogen
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Multiple roles of ABC transporters in yeast
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Fluconazole-Resistant Candida auris Is Susceptible to Salivary Histatin 5 Killing and to Intrinsic Host Defenses
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Identification of Off-Patent Compounds That Present Antifungal Activity Against the Emerging Fungal Pathogen Candida auris
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Candida auris: An emerging pathogen “incognito”?
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Update on the Pathogenesis, Virulence, and Treatment of Candida auris
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Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases
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Candida auris: a comparison between planktonic and biofilm susceptibility to antifungal drugs
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Mechanisms of pathogenicity for the emerging fungus Candida auris
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Characterization of the differential pathogenicity of Candida auris in a Galleria mellonella infection model
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From environmental adaptation to host survival: Attributes that mediate pathogenicity of Candida auris
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Multidrug-resistant Candida auris : an epidemiological review
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Linking Cellular Morphogenesis with Antifungal Treatment and Susceptibility in Candida Pathogens
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The environmental stress sensitivities of pathogenic Candida species, including Candida auris, and implications for their spread in the hospital setting
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Candida haemulonii Complex and Candida auris: Biology, Virulence Factors, Immune Response, and Multidrug Resistance
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Rapid and extensive karyotype diversification in haploid clinical Candida auris isolates
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Virulence of Candida auris from different clinical origins in Caenorhabditis elegans and Galleria mellonella host models
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Diagnosis, management and prevention of Candida auris in hospitals: position statement of the Australasian Society for Infectious Diseases
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Clade II Candida auris possess genomic structural variations related to an ancestral strain
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Multidrug transporters of Candida species in clinical azole resistance
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Repositionable compounds with antifungal activity against multidrug resistant Candida auris identified in the medicines for malaria venture's pathogen box
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Heat shock protein 90 localizes to the surface and augments virulence factors of Cryptococcus neoformans
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Self-citation
Copper-only superoxide dismutase enzymes and iron starvation stress in Candida fungal pathogens
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Candida auris: A Continuing Threat
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The emerging pathogen Candida auris: A focus on the Middle-Eastern countries
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Promising Drug Candidates and New Strategies for Fighting against the Emerging Superbug Candida auris
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The laboratory investigation, management, and infection prevention and control of Candida auris: a narrative review to inform the 2024 national guidance update in England
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Antifungal Resistance: Specific Focus on Multidrug Resistance in Candida auris and Secondary Azole Resistance in Aspergillus fumigatus
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RESEARCH ARTICLE Open Access Draft genome of a commonly misdiagnosed
Chatterjee, S., Alampalli, S. V., Nageshan, R. K., Chettiar, S. T., Joshi, S., & Tatu, U. S. (2016)
Self-citation
Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species
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Genomic basis of multidrug-resistance, mating, and virulence in Candida auris and related emerging speciesPreprint
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Multi-omics Signature of Candida auris , an Emerging and Multidrug-Resistant Pathogen
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Nine Things Genomics Can Tell Us About Candida auris
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Authors: Chatterjee, S., Alampalli, S. V., Nageshan, R. K., Chettiar, S. T., Joshi, S., & Tatu, U. S.
Affiliations: Indian Institute of Science Bangalore (IN)
Manipal Hospital (IN)
Corresponding author: Tatu, Utpal S.
ORCID: Chatterjee, Sharanya
Alampalli, Shuba Varshini
Nageshan, Rishi Kumar
Chettiar, Sivarajan T.
Tatu, Utpal S.
Venue: BMC Genomics
Publisher: Springer Science and Business Media LLC
Published: 2015-09-07
Volume: 16
Issue: 1
Pages: 686-686
ISSN: 1471-2164 (ISSN-L)
DOI: 10.1186/s12864-015-1863-z
PMC: PMC4562351
OpenAlex: W1817471568
Cited by: 247
References: 70
Citations by year: 2026: 12 · 2025: 16 · 2024: 17 · 2023: 21 · 2022: 26 · 2021: 22 · 2020: 41 · 2019: 32 · 2018: 27 · 2017: 28 · 2016: 4 · 2015: 1
FWCI: 15.54
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
Locations: BMC Genomics (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
NOT FOUND REPOSITORY (Indian Institute of Science Bangalore) (acceptedVersion)
Funders: Indian Institute of Science
Department of Biotechnology, Ministry of Science and Technology, India
Department of Science and Technology, Ministry of Science and Technology, India
Topics: Health Sciences › Medicine › Infectious Diseases › Antifungal resistance and susceptibility
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Yeasts and Rust Fungi Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
Keywords: Candida auris, draft genome sequence, multidrug resistance, fungemia, misdiagnosis, Candida haemulonii, Candida lusitaniae, virulence factors, biofilm formation, ABC transporters, major facilitator superfamily, antifungal drug tolerance, differential diagnosis, emerging fungal pathogens
MeSH terms: Mating Factor, Amino Acid Sequence, Antifungal Agents, Candida, Candidiasis, Codon, Humans, Microbial Sensitivity Tests, Molecular Sequence Data, Peptides, Phylogeny, Virulence, Genome, Fungal, Drug Resistance, Multiple, Evolution, Molecular, Computational Biology, DNA, Intergenic, Drug Resistance, Fungal, Genetic Loci, Molecular Sequence Annotation, High-Throughput Nucleotide Sequencing

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Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris

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