First Genome Sequences of Two Multidrug-Resistant Candida haemulonii var. vulnera Isolates From Pediatric Patients With Candidemia

Abstract

Candida haemulonii is a complex formed by C. haemulonii sensu stricto , C. haemulonii var. vulnera , and C. duobushaemulonii . Members of this complex are opportunistic pathogens closely related to C. pseudohaemulonii , C. lusitaniae , and C. auris , all members of a multidrug-resistant clade. Complete genome sequences for all members of this group are available in the GenBank database, except for C. haemulonii var. vulnera . Here, we report the first draft genomes of two C. haemulonii var. vulnera (isolates K1 and K2) and comparative genome analysis of closely related fungal species. The isolates were biofilm producers and non-susceptible to amphotericin B and fluconazole. The draft genomes comprised 350 and 387 contigs and total genome sizes of 13.21 and 13.26 Mb, with 5,479 and 5,507 protein-coding genes, respectively, allowing the identification of virulence and resistance genes. Comparative analyses of orthologous genes within the multidrug-resistant clade showed a total of 4,015 core clusters, supporting the conservation of 24,654 proteins and 3,849 single-copy gene clusters. Candida haemulonii var. vulnera shared a larger number of clusters with C. haemulonii and C. auris ; however, more singletons were identified in C. lusitaniae and C. auris . Additionally, a multiple sequence alignment of Erg11p proteins revealed variants likely involved in reduced susceptibility to azole and polyene antifungal agents. The data presented in this work will, therefore, be of utmost importance for researchers studying the biology of the C. haemulonii complex and related species.

Insights into the Multi-Azole Resistance Profile in Candida haemulonii Species Complex

“…However, Erg11p substitutions F126L, Y132F, and K143R, which were implicated in reduced susceptibilities to azoles upon heterologous expression in S. cerevisiae [ 45 , 46 ], were not identified in our isolates. Corroborating our data, a recent study by Rodrigues et al [ 13 ] again found that Brazilian resistant isolates of C. haemulonii var . vulnera also lacked these common mutations.…”

“…Although the role of ERG11 gene point mutations in azole resistance is a well-recognized phenomenon in Candida spp. [ 38 ], only recently a few studies have characterized the polymorphisms of the ERG11 gene in azole-resistant isolates of the C. hameulonii complex [ 2 , 13 ]. In the study of Gade et al [ 2 ], an increasing azole resistance in isolates of C. haemulonii and C. duobushaemulonii was evidenced in Colombia, Panama, and Venezuela, associated with substitutions in the ERG11 gene, suggesting the existence of an evolutionary pressure for the development of azoles resistance in Latin America.…”

“…This fungal complex is often associated with bloodstream infections, onychomycosis, vaginal infections, catheter-related fungemia, and outbreaks in neonatal intensive care units [ 3 , 4 , 5 , 6 , 7 , 8 , 9 ]. In Brazil, most of the studies reported candidemia by the C. haemulonii species complex, associated with high antifungal resistance profiles [ 10 , 11 , 12 , 13 ]. Since phenotypic identification methods cannot accurately distinguish among these species, the prevalence of C. haemulonii species complex in hospital settings may be underestimated.…”

Susceptibility of the Candida haemulonii Complex to Echinocandins: Focus on Both Planktonic and Biofilm Life Styles and a Literature Review

“… * Antifungal susceptibility testing was interpreted according to the document M27-S3 published by CLSI; n , number of fungal isolates; the references used to construct this table were [ 5 , 7 , 25 , 29 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 ]. …”

“… a CAS, caspofungin; MCF, micafungin; ANF, anidulafungin; b MIC 50 , MIC at which 50% of isolates were inhibited; c MIC 90 , MIC at which 90% of isolates were inhibited; Modal MICs are indicated with underlined numbers; MIC values of <0.03 were allocated as ≤0.015; Clinical and Laboratory Standards Institute (CLSI) document M27S3 suggests the following breakpoints for echinocandins against Candida spp. : susceptible ≤ 2 mg/L and non-susceptible > 2 mg/L; the references used to construct this table were [ 5 , 29 , 31 , 34 , 35 , 38 , 39 , 40 , 41 , 42 , 44 , 46 , 47 ]. …”