Directed Evolution Detects Supernumerary Centric Chromosomes Conferring Resistance to Azoles in Candida auris

Narayanan, Aswathy; Kumar, Praveen; Chauhan, Anshu; Kumar, Mohit; Yadav, Kusum; Banerjee, Atanu; Sharma, Ravi Datta; Rudramurthy, Shivaprakash M; Chakrabarti, Arunaloke; Sanyal, Kaustuv; Prasad, Rajendra

doi:10.1128/mbio.03052-22

Cited by 14 publications

(12 citation statements)

References 55 publications

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“…S6). This is in contrast to our previous findings on fluconazole-resistant isolates (32). Additionally, copy number variation analysis of DNA sequencing raw reads did not reveal any alterations in comparison to the parental genome.…”

Section: Evolved Amb Resistant a And P-lines Show No Change In Ploidycontrasting

confidence: 99%

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Microevolution of clade II isolates ofCandida aurishighlights multifaceted intra-clade heterogeneity in acquiring resistance towards amphotericin B

Chauhan,

Kumar,

Kumar

et al. 2023

Preprint

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Candida aurisexhibits high-level resistance to amphotericin B (AmB). Mechanisms such as ergosterol biosynthesis malfunction, oxidative damage mismanagement, and increased drug efflux contribute to AmB resistance inC. auris. In this study, we experimentally evolved two East Asian drug-susceptible clade II isolates ofC. auris(P2428 and CBS10913T) isolated from different geographical locations to develop resistance against AmB. We analysed alterations in karyotype, genome sequence, and gene expression profiles to uncover the mechanisms driving AmB resistance. The independently evolved clade II adaptors displayed up to 4-16-fold higher MIC50, as compared to the parental cells.AOX2(alternative oxidase) and the cell wall integrity pathway have been identified as critical in the development of AmB resistance. However, we noted certain intra-clade heterogeneity in the associated mechanisms. While in P2428 adaptors (P-lines), the ergosterol and sphingolipid pathways appear to play a crucial role, this was not the case for CBS10913Tadaptors (A-lines), which acquired resistance independent of lipid-associated changes. The transcriptomic, WGS, and phenotypic analyses also confirm that the evolved AmB-resistant isolates follow distinct trajectories for adaptation, Furthermore, unlike the fluconazole-resistant isolates, as reported previously, changes in ploidy do not seem to contribute to the differential mechanisms of AmB resistance. Overall, this study not only provides insights into the mechanisms and pathways involved in AmB resistance but also highlights intra-clade-heterogeneity that exists within clade II ofC. auris.ImportanceCandida aurisdemonstrates significant resistance to amphotericin B (AmB) that stems from factors like alteration of ergosterol biosynthesis, perturbation of the oxidative damage response, etc. A comprehensive understanding of underlying mechanisms can be studied in a holistic manner by subjecting resistant as well as susceptible clinical isolates to a comparative genome-level analysis. An alternate and more dynamic approach is to expose susceptible isolates to a certain concentration of drug which is not lethal but can trigger the resistance mechanisms. In the present study, we evolvedC. auristowards AmB and observed novel and differential mechanisms of resistance development, in two different isolates despite belonging to the same clade. This study provides insights into the intra-clade heterogeneous behavior ofC. auristowards AmB.

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Section: Evolved Amb Resistant a And P-lines Show No Change In Ploidycontrasting

confidence: 99%

“…For in vitro evolution, C. auris strains CBS10913 T and P2428 (MIC 50 -AmB-0.5 µgmL - 1 , and 1 µgmL -1 ) was used. The protocol of in vitro evolution described earlier by (40) and our group (32), was followed with some modifications. The strains were revived from a frozen stock on a YEPD plate and incubated for 24 hours at 30°C.…”

Section: Methodsmentioning

confidence: 99%

Microevolution of clade II isolates ofCandida aurishighlights multifaceted intra-clade heterogeneity in acquiring resistance towards amphotericin B

Chauhan,

Kumar,

Kumar

et al. 2023

Preprint

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“…A similar in vitro acquisition of azole resistance in an evolving population derived from a single C. auris parent strain was explained by aneuploidy occurring in the form of segmental duplications, coexisting alongside aneuploidy-independent mechanisms [37]. In addition, Narayanan and colleagues recently demonstrated a novel mechanism of antifungal resistance involving generation of a mitotically stable supernumerary chromosome, which leads to an increase in the copy number of a set of genes in C. auris [46]. Echinocandins inhibit the activity of 1,3-β-D-glucan synthase, an enzyme encoded by the FKS1 and FKS2 genes, which is important for synthesis of a primary fungal cell wall polymer.…”

Section: What Are the Molecular And Genetic Determinants Of Antifunga...mentioning

confidence: 88%

“…In addition, Narayanan and colleagues recently demonstrated a novel mechanism of antifungal resistance involving generation of a mitotically stable supernumerary chromosome, which leads to an increase in the copy number of a set of genes in C . auris [ 46 ].…”

Section: What Are the Molecular And Genetic Determinants Of Antifunga...mentioning

confidence: 99%

Perspective on the origin, resistance, and spread of the emerging human fungal pathogen Candida auris

Sharma

Kadosh

2023

PLoS Pathog

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“…auris and C . glabrata [ 43 , 44 ]. An isochromosome formed due to a break at the centromere flanked by inverted repeats followed by a fusion of left arms of the same chromosome was detected in C .…”

Section: Centromeres and Antifungal Drug Resistancementioning

confidence: 99%

Behind the scenes: Centromere-driven genomic innovations in fungal pathogens

Narayanan,

Reza,

Sanyal

2024

PLoS Pathog

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Directed Evolution Detects Supernumerary Centric Chromosomes Conferring Resistance to Azoles in Candida auris

Abstract: Fungal pathogens develop drug resistance through multiple pathways by acquiring gene mutations, increasing the copy number of genes, or altering gene expression. In this study, we attempt to understand the mechanisms of drug resistance in the recently emerged superbug, C. auris .

Cited by 14 publications

References 55 publications

Microevolution of clade II isolates ofCandida aurishighlights multifaceted intra-clade heterogeneity in acquiring resistance towards amphotericin B

Microevolution of clade II isolates ofCandida aurishighlights multifaceted intra-clade heterogeneity in acquiring resistance towards amphotericin B

Perspective on the origin, resistance, and spread of the emerging human fungal pathogen Candida auris

Behind the scenes: Centromere-driven genomic innovations in fungal pathogens

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