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Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris.

Chatterjee S, Alampalli SV, Nageshan RK, Chettiar ST, Joshi S, Tatu US - BMC Genomics (2015)

Bottom Line: 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.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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India, 560012. sharanya@biochem.iisc.ernet.in.

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.

No MeSH data available.


Related in: MedlinePlus

Functional annotation of C. auris genome. a, b, c Represents Level 2 GO terms for the three main domains. The most abundant terms in Biological process (a) is cellular process, metabolic process and single-organism process and in Molecular functions (b), binding, catalytic activity and transporter activity. The common cellular component (c) termed are the cell, organelle and membrane. d Distribution of various enzymes into the six enzyme classes according to E.C numbers. e, f represents gene families predicted in C. auris that are orthologous to C. albicans
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Fig6: Functional annotation of C. auris genome. a, b, c Represents Level 2 GO terms for the three main domains. The most abundant terms in Biological process (a) is cellular process, metabolic process and single-organism process and in Molecular functions (b), binding, catalytic activity and transporter activity. The common cellular component (c) termed are the cell, organelle and membrane. d Distribution of various enzymes into the six enzyme classes according to E.C numbers. e, f represents gene families predicted in C. auris that are orthologous to C. albicans

Mentions: Functional annotation was done in Blast2GO that combined the blastp annotation results (against NR database) with the predicted InterProScan results. The assigned GO descriptions to each protein were considered at an E-value greater than e−10. Out of 8358 predicted proteins 10958 GO terms were annotated to 3560 sequences. The GO terms were placed in three domains, Biological process (39.45 %), Molecular Function (43.25 %) and Cellular Components (16.52 %). Figure 6a-c represents the level 2 GO terms for all the three domains. As evident from Fig. 6a, a major proportion of the genome is devoted to cellular and metabolic processes. A significant number of proteins were annotated to have transporter activity apart from binding and catalytic activity.Fig. 6


Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris.

Chatterjee S, Alampalli SV, Nageshan RK, Chettiar ST, Joshi S, Tatu US - BMC Genomics (2015)

Functional annotation of C. auris genome. a, b, c Represents Level 2 GO terms for the three main domains. The most abundant terms in Biological process (a) is cellular process, metabolic process and single-organism process and in Molecular functions (b), binding, catalytic activity and transporter activity. The common cellular component (c) termed are the cell, organelle and membrane. d Distribution of various enzymes into the six enzyme classes according to E.C numbers. e, f represents gene families predicted in C. auris that are orthologous to C. albicans
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4562351&req=5

Fig6: Functional annotation of C. auris genome. a, b, c Represents Level 2 GO terms for the three main domains. The most abundant terms in Biological process (a) is cellular process, metabolic process and single-organism process and in Molecular functions (b), binding, catalytic activity and transporter activity. The common cellular component (c) termed are the cell, organelle and membrane. d Distribution of various enzymes into the six enzyme classes according to E.C numbers. e, f represents gene families predicted in C. auris that are orthologous to C. albicans
Mentions: Functional annotation was done in Blast2GO that combined the blastp annotation results (against NR database) with the predicted InterProScan results. The assigned GO descriptions to each protein were considered at an E-value greater than e−10. Out of 8358 predicted proteins 10958 GO terms were annotated to 3560 sequences. The GO terms were placed in three domains, Biological process (39.45 %), Molecular Function (43.25 %) and Cellular Components (16.52 %). Figure 6a-c represents the level 2 GO terms for all the three domains. As evident from Fig. 6a, a major proportion of the genome is devoted to cellular and metabolic processes. A significant number of proteins were annotated to have transporter activity apart from binding and catalytic activity.Fig. 6

Bottom Line: 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.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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India, 560012. sharanya@biochem.iisc.ernet.in.

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.

No MeSH data available.


Related in: MedlinePlus