Clade-specific chromosomal rearrangements and loss of subtelomeric adhesins in Candida auris

Abstract

Candida auris is an emerging fungal pathogen of rising concern due to global spread, the ability to cause healthcare-associated outbreaks, and antifungal resistance. Genomic analyses revealed that early contemporaneously detected cases of C. auris were geographically stratified into four major clades. While Clades I, III, and IV are responsible for ongoing outbreaks of invasive and multidrug-resistant infections, Clade II, also termed the East Asian clade, consists primarily of cases of ear infection, is often susceptible to all antifungal drugs, and has not been associated with outbreaks. Here, we generate chromosome-level assemblies of twelve isolates representing the phylogenetic breadth of these four clades and the only isolate described to date from Clade V. This Clade V genome is highly syntenic with those of Clades I, III, and IV, although the sequence is highly divergent from the other clades. Clade II genomes appear highly rearranged, with translocations occurring near GC-poor regions, and large subtelomeric deletions in most chromosomes, resulting in a substantially different karyotype. Rearrangements and deletion lengths vary across Clade II isolates, including two from a single patient, supporting ongoing genome instability. Deleted subtelomeric regions are enriched in Hyr/Iff-like cell-surface proteins, novel candidate cell wall proteins, and an ALS-like adhesin. Cell wall proteins from these families and other drug-related genes show clade-specific signatures of selection in Clades I, III, and IV. Subtelomeric dynamics and the conservation of cell surface proteins in the clades responsible for global outbreaks causing invasive infections suggest an explanation for the different phenotypes observed between clades.

Keywords: Candida auris; cell wall proteins; chromosome rearrangement; fungal genome; karyotype variation; selection; subtelomeric variation.

Figure 1

Phylogenetic breadth and karyotypic variation in C. auris . (A) Phylogenetic tree of 87 C. auris whole-genome sequences clustering into four major clades and the basal isolate B18474; potential fifth clade. Maximum likelihood phylogeny using 63,674 SNPs based on 1,000 bootstrap replicates. Isolate labels are color-coded by clade and gray circles indicated those isolates selected for chromosomal-level sequencing and assembly. (B) Chromosome sizes of fourteen isolates based on chromosome scale contigs.

Figure 2

Genome dynamics in C. auris . Guanine-Cytosine (GC) content 0.38 to 0.50. GC content is color-coded <0.42 blue or >0.42 gray. Ribosomal DNA array are depicted as green lines and telomeres as red lines.

Figure 3

Chromosomal rearrangements in C. auris . Circos plots showing syntenic chromosomes by color and links for inversions (twisted filled links) and translocations (flat transparent links) using B8441 (Clade I) as reference compared to B11221 (Clade III), B11245 (Clade IV), and B18474 (Clade V) in the top row. The lower row of Circos plots depicts B8441 compared to four Clade II isolates (B11220, B11809, B12043, and B13463). Scaffolds/contigs to chromosome mapping for these genome assemblies is included in Supplementary Table S1.

Figure 4

Subtelomeric decay in C. auris Clade II. (A) Length of the deleted sequences in subtelomeric regions in thirteen C. auris genomes. (B) Length of the deleted sequences in subtelomeric regions in seventeen isolates from Clade II. (C) Chromosome wide synteny between B11245 (Clade IV) and B11220 (Clade II). Chromosome 6 includes telomeres at both ends in both isolates (dark red square). Shared synteny regions based on genome alignment (blastn) are depicted in gray vertical blocks connecting the chromosome regions. Depicted genes in blue and light gray arrows showing the direction of transcription are color-coded according to the location in conserved (gray) or nonconserved (blue) regions. (D) Comparison corresponds to a zoom in of the subtelomeric region depleted in Clade II (B11220), which encompasses auris-clade specific adhesins in tandem (red line).

Figure 5

Differences in the repertoire GPI-anchor proteins in C. auris . (A) Conserved domains in two clusters of GPI-anchor found in C. auris B8441. (Top) Hyr/Iff GPI-anchor family and (bottom) C. auris clade-specific GPI-anchor protein. Conservation across C. auris isolates representing Clades I, II, III, and IV is color-coded indicating whether the gene is present (dark blue) or absent (white). (B) Phylogenetic analysis of the Hyr/Iff GPI-anchor family (left), the C. auris clade-specific GPI-anchor family (middle) and Als GPI-anchor family (right) using one representative isolate for C. auris Clades I and II, C. haemulonii and C albicans. Gene IDs are color-coded by species/isolate.

Figure 6

Conservation of GPI-anchor proteins across C. auris clades. Phylogenetic tree of 64 C. auris isolates from Clades I, II, III, IV, and V. Right panel depicts the conservation (present: blue; absent: white) of three families of adhesins. *B18474 a.k.a. NG19339.