Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistant Candida albicans isolate causing cerebral abscess

Monika Kumaraswamy; Alison Coady; Richard Szubin; Thomas CS Martin; Bernhard Palsson; Victor Nizet; Jonathan M. Monk

doi:10.1016/j.crmicr.2023.100180

Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistant Candida albicans isolate causing cerebral abscess

Monika Kumaraswamy, Alison Coady, Richard Szubin, Thomas CS Martin, Bernhard Palsson, Victor Nizet, Jonathan M. Monk

Research output: Contribution to journal › Article › peer-review

Abstract

Comprehensive whole genome sequencing (WGS) with hybrid assembly of a multi-drug resistant (MDR) Candida albicans (CA) isolate causing cerebral abscess was performed using Illumina paired end and Oxford Nanopore long read technologies. The innovative technologies utilized here enabled us to resolve fragmented assemblies, and implement comprehensive and detailed genomic analyses involved in antifungal resistance of Candida spp. Functionally important genes (MDR1, CDR2 and SQN2) involved in antifungal resistance were identified and a phylogenetic analysis of the clinical isolate was performed. Additionally, our clinical isolate was found to share 4 single nucleotide polymorphisms with two other sequenced strains of MDR C. auris (381 and 386) including translation elongation factor EF1α and EF3, ATPase activity associated proteins, and the lysine tRNA ligase.

Original language	English (US)
Article number	100180
Journal	Current Research in Microbial Sciences
Volume	4
DOIs	https://doi.org/10.1016/j.crmicr.2023.100180
State	Published - Jan 2023
Externally published	Yes

Keywords

Brain abscess
Candida albicans
Hybrid assembly
Multi-drug resistance
Whole genome sequencing

ASJC Scopus subject areas

Microbiology
Immunology and Microbiology (miscellaneous)
Microbiology (medical)
Infectious Diseases

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10.1016/j.crmicr.2023.100180

Cite this

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title = "Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistant Candida albicans isolate causing cerebral abscess",

abstract = "Comprehensive whole genome sequencing (WGS) with hybrid assembly of a multi-drug resistant (MDR) Candida albicans (CA) isolate causing cerebral abscess was performed using Illumina paired end and Oxford Nanopore long read technologies. The innovative technologies utilized here enabled us to resolve fragmented assemblies, and implement comprehensive and detailed genomic analyses involved in antifungal resistance of Candida spp. Functionally important genes (MDR1, CDR2 and SQN2) involved in antifungal resistance were identified and a phylogenetic analysis of the clinical isolate was performed. Additionally, our clinical isolate was found to share 4 single nucleotide polymorphisms with two other sequenced strains of MDR C. auris (381 and 386) including translation elongation factor EF1α and EF3, ATPase activity associated proteins, and the lysine tRNA ligase.",

keywords = "Brain abscess, Candida albicans, Hybrid assembly, Multi-drug resistance, Whole genome sequencing",

author = "Monika Kumaraswamy and Alison Coady and Richard Szubin and Martin, {Thomas CS} and Bernhard Palsson and Victor Nizet and Monk, {Jonathan M.}",

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doi = "10.1016/j.crmicr.2023.100180",

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AU - Kumaraswamy, Monika

AU - Coady, Alison

AU - Szubin, Richard

AU - Martin, Thomas CS

AU - Palsson, Bernhard

AU - Nizet, Victor

AU - Monk, Jonathan M.

PY - 2023/1

Y1 - 2023/1

N2 - Comprehensive whole genome sequencing (WGS) with hybrid assembly of a multi-drug resistant (MDR) Candida albicans (CA) isolate causing cerebral abscess was performed using Illumina paired end and Oxford Nanopore long read technologies. The innovative technologies utilized here enabled us to resolve fragmented assemblies, and implement comprehensive and detailed genomic analyses involved in antifungal resistance of Candida spp. Functionally important genes (MDR1, CDR2 and SQN2) involved in antifungal resistance were identified and a phylogenetic analysis of the clinical isolate was performed. Additionally, our clinical isolate was found to share 4 single nucleotide polymorphisms with two other sequenced strains of MDR C. auris (381 and 386) including translation elongation factor EF1α and EF3, ATPase activity associated proteins, and the lysine tRNA ligase.

AB - Comprehensive whole genome sequencing (WGS) with hybrid assembly of a multi-drug resistant (MDR) Candida albicans (CA) isolate causing cerebral abscess was performed using Illumina paired end and Oxford Nanopore long read technologies. The innovative technologies utilized here enabled us to resolve fragmented assemblies, and implement comprehensive and detailed genomic analyses involved in antifungal resistance of Candida spp. Functionally important genes (MDR1, CDR2 and SQN2) involved in antifungal resistance were identified and a phylogenetic analysis of the clinical isolate was performed. Additionally, our clinical isolate was found to share 4 single nucleotide polymorphisms with two other sequenced strains of MDR C. auris (381 and 386) including translation elongation factor EF1α and EF3, ATPase activity associated proteins, and the lysine tRNA ligase.

KW - Brain abscess

KW - Candida albicans

KW - Hybrid assembly

KW - Multi-drug resistance

KW - Whole genome sequencing

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Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistant Candida albicans isolate causing cerebral abscess

Abstract

Keywords

ASJC Scopus subject areas

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