Nanopore Genome Sequencing and Variant Analysis of the Susceptible Candida auris Strain L1537/2020, Salvador, Brazil

Auke W De Jong,Felicidade M Pereira,Ferry Hagen,Pedro H Presta Dias,João Nóbrega De Almeida,Duong Vu,Magda M De Miranda Costa,Arnaldo L Colombo,Igor B Brandão,Elaine C Francisco,Regiane T De Souza Jordão

doi:10.1007/s11046-021-00593-7

Abstract

Candida auris has been reported worldwide, but only in December 2020, the first strain from a COVID-19 patient in Brazil was isolated. Here, we describe the genome sequence of this susceptible C. auris strain and performed variant analysis of the genetic relatedness with strains from other geographic localities.

Highlights

Candida auris is an emerging multidrug-resistant pathogen able to cause invasive infection outbreaks in tertiary care hospitals worldwide
The sample was sequenced on the MK1B MinION (MIN-101B) device with a FLO-MIN106 (SpotON R9.4) flowcell using MinKNOWN release 20.10.3
Variant calling was performed using a subset of 47 published genomes representing the five C. auris clades, including a benchmark set for clades: South East Asia (clade I), (Fig. 1; [3, 8,9,10,11,12])

Summary

Introduction

Candida auris is an emerging multidrug-resistant pathogen able to cause invasive infection outbreaks in tertiary care hospitals worldwide. Genome assembly was performed using Flye v2.8.2b1689 (https://github.com/fenderglass/Flye; [7]) with the parameters --nano-raw \ fastq [ --out-dir \ directory [ --genome-size 12.5 m. Variant calling was performed using a subset of 47 published genomes representing the five C. auris clades, including a benchmark set for clade I, (Fig. 1; [3, 8,9,10,11,12]).

Results

Conclusion