Clade II Candida auris possess genomic structural variations related to an ancestral strain

Abstract

Candida auris is an invasive and multidrug-resistant ascomycetous yeast that is under global surveillance. All clinical cases of C. auris infection diagnosed from 1997 to 2019 in Japan were non-invasive and sporadic otitis media cases. In the present study, we performed whole-genome sequencing of seven C. auris strains isolated from patients with otitis media in Japan, all of which belonged to clade II. Comparative genome analysis using the high-quality draft genome sequences JCM 15448T revealed that single nucleotide variations (SNVs), clade-specific accessory genes, and copy number variations (CNVs) were identified in each C. auris clade. A total of 61 genes involved in cell wall and stress response-related functions was absent in clade II, and the pattern of conserved CNVs in each clade was more stable in clade II than in other clades. Our data suggest that the genomic structural diversity is stable in C. auris isolated from each biogeographic location, and Japanese strains isolated from patients with otitis media might belong to an ancestral type of C. auris. One Japanese strain, TWCC 58362, with reduced susceptibility to fluconazole, exhibited no mutation in ergosterol biosynthesis-related genes (ERG). However, TWCC 58362-specific variations, including SNVs, indels, and CNVs were detected, suggesting that gene duplication events in C. auris might contribute to antifungal drug resistance. Taken together, we demonstrated that genomic structural variations in C. auris could correlate to geographical dissemination, epidemiology, lesions in the host, and antifungal resistance.

Mitochondrial Genome Sequences of the Emerging Fungal Pathogen Candida auris

“…For 67 isolates of C. auris we obtained mitochondrial genome reference assemblies, mapping the Illumina reads to the reference sequence, the mitochondrial genome assembly of isolate C. auris B8441 (28,212 bp) we had obtained. This additional analysis gave us the opportunity to include the sequences of seven isolates of Japan that were published more recently by Sekizuka et al (2019). We again found the four clades described above ( Supplementary Figure S4A).…”

“…A stand-alone de novo assembly has the advantage, over read alignment to an existing assembly of a conspecific strain or congeneric species, that it does not make structural assumptions and is thus less likely to miss insertions, rearrangements or breaks in synteny. Indeed, we found an intron of the cox1 gene in our clade I mtDNA that is present in clade I but not present in the clade II mtDNA genome assembly of Sekizuka et al (2019).…”

“…Recently, the first annotated assembly of a mitochondrial genome of C. auris was released and published, for an isolate from Japan belonging to the East Asian clade II (isolate JCM 15448, or B11220 in the numbering we have used here, with sequence accession number AP018713; 2019-10-11) (Sekizuka et al, 2019). This recent sequence gave us an opportunity to double check our finished sequence of the clade I isolate B8441 for base-level accuracy, after discounting the 11 singlenucleotide differences and the COX1 intron's presence/absence difference, compared to B8441, that we had observed when aligning the reads of the JCM 15448 isolate to our B8441 assembly ( Supplementary Table S3).…”

“…that is present in our clade I sequence was absent not only in the Japanese isolate assembled from clade II (Sekizuka et al, 2019), but also in seven other Japanese strains from clade II for which reads were available (Supplementary Figure S4B). Although it may be too early to conclude that this feature is characteristic of all of clade II until more of this clade's isolates are sequenced, it is clear that the missing COX1 intron feature distinguishes at least a part of clade II from the other isolates worldwide that have been sequenced so far ( Supplementary Figure S4).…”

“…Isolate B8441 was chosen as a representative of clade I and because its nuclear genome has previously been sequenced and characterized (Lockhart et al, 2017b). The novel assembly of this isolate complements the recently published first de novo genome assembly, including the mtDNA chromosome (Sekizuka et al, 2019), of the original clade II isolate from Tokyo (Satoh et al, 2009), which was obtained independently and in parallel with our clade I mtDNA assembly. We reasoned that the de novo assembly, annotation and characterization of the mitochondrial sequence of a clade I isolate together with a comparative analysis would contribute a needed resource and might ultimately provide also a basis for improving our understanding of the fundamental roles played by the mitochondria of Candida spp.…”