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

Current Research in Microbial Sciences (Jan 2023)

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

Affiliations

Monika Kumaraswamy: Collaborative to Halt Antibiotic-Resistant Microbes (CHARM), University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Infectious Diseases Section, VA San Diego Healthcare System, San Diego, CA 92161, USA; Corresponding author at: Division of Infectious Diseases, Department of Medicine, University of California San Diego, 9500 Gilman Drive, Mail Code 0711, La Jolla, CA 92093-0711, USA.
Alison Coady: Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
Richard Szubin: Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
Thomas CS Martin: Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
Bernhard Palsson: Collaborative to Halt Antibiotic-Resistant Microbes (CHARM), University of California San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
Victor Nizet: Collaborative to Halt Antibiotic-Resistant Microbes (CHARM), University of California San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
Jonathan M. Monk: Collaborative to Halt Antibiotic-Resistant Microbes (CHARM), University of California San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA; Corresponding author at: Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.

Journal volume & issue: Vol. 4
p. 100180

Abstract

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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.

Published in Current Research in Microbial Sciences

ISSN: 2666-5174 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Science: Microbiology; Science: Biology (General): Genetics
Website: https://www.journals.elsevier.com/current-research-in-microbial-sciences

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