Draft Genome Sequence of Candida auris Strain LOM, a Human Clinical Isolate from Greater Metropolitan Houston, Texas

Candida auris is an emerging pathogen of considerable public health importance. We present the draft genome sequence of a strain recently cultured from the urine of a patient hospitalized in the greater Houston metropolitan region. Two combined Oxford Nanopore sequencing runs provided sufficient data to rapidly generate a draft genome.

C andida auris recently has emerged worldwide and caused outbreaks in health care facilities (1,2). An isolate of C. auris was cultured from the urine of a patient from the Houston metropolitan region on 5% sheep blood tryptic soy agar and identified by Brucker matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analysis using the research use only (RUO) v4.1.80 database. The patient had not recently traveled outside the United States and had transferred from a long-term-care facility. This work was approved by our institutional review board (IRB1010-0199).
The organism was classified as present on admission. Given the potential infection control and public health importance of this isolate, we rapidly characterized its genome using two Oxford Nanopore GridION runs using FLO-MIN106 flow cells and the Guppy v2.0.10 base caller. DNA was extracted from overnight growth on solid agar using ballistic lysis with FastPrep matrix B (first run) or Y (second run) and the Qiagen DNA blood and tissue kit. The first GridION run used the rapid barcoding kit (catalog number SQK-RBK004), yielding 1.29 million reads and 3.48 gigabases (Gb) of sequence with an average read length of 2.7 kb. The second run used the ligation sequencing kit (catalog number SQK-LSK109) with a long-read wash, yielding 2.98 million reads and 13.72 Gb of sequence with an average read length of 4.6 kb. The reads from both runs were combined and filtered using Filtlong v0.1.1 with a 5-kb-read cutoff and 100-fold coverage (https://github.com/rrwick/Filtlong). Unicycler v0.4.3 was used to assemble the genome with miniasm and pilon polishing (3). The assembly had 9 contigs (total length, 12,293,266 bp). The largest contig was 4,297,164 bp, and the N 50 value was 2,304,466 bp. The average GC content was 45.19%.
This work further demonstrates the usefulness of real-time long-read whole-genome sequencing to rapidly provide relevant information concerning emerging pathogens of significant concern (8,9). The availability of this high-quality draft genome sequence will serve as a useful resource if additional isolates are recovered in the greater Houston metropolitan area. The sequence data also will assist translational research efforts designed to more fully understand the molecular mechanisms underlying host interactions in an emerging pathogen that has substantial detrimental public health potential.

ACKNOWLEDGMENTS
We thank the technical staff in the Houston Methodist Hospital Clinical Microbiology Laboratory for assistance. We thank Andrew Pann for his development and continued support of the prephix and phrecon tools.
This work was supported by funds from the L. E. Simmons Family Foundation and