Candida auris

Candida auris: Comparison

Please note this is a comparison between Version 1 by Célia Fortuna Rodrigues and Version 2 by Camila Xu.

Candida auris is a multidrug-resistant species associated with high morbidity and mortality in immunocompromised individuals worldwide.

Candida auris
resistance
antifungal
biofilm
infection
novel therapy

1. Candida auris

and Treatment Failure of Common Commercial Antifungal Drugs

C andida auris is a multidrug-resistant species associated with high morbidity and mortality in immunocompromised individuals worldwide ^[1]. As mentioned, the key characteristics of

is a multidrug-resistant species associated with high morbidity and mortality in immunocompromised individuals worldwide [12]. As mentioned, the key characteristics of

C. auris comprise spreading easily in the environment, transiting quickly among hospitalization patients ^[2][3], as well as being resilient to common disinfectants in the healthcare setting ^[4]. The lack of availability of microbiological diagnostic methods and subsequent misidentification ^[5][6] and high levels of antifungal resistance ^[7][8] makes

comprise spreading easily in the environment, transiting quickly among hospitalization patients [62,63], as well as being resilient to common disinfectants in the healthcare setting [64]. The lack of availability of microbiological diagnostic methods and subsequent misidentification [65,66] and high levels of antifungal resistance [36,67] makes

C. auris

as a potential virulent species, and globally emerging pathogen, causing challenges to control policies against infection.

The number of antifungal drugs targeting the treatment of

C. auris infection have been limited. Generally, three main classes of available antifungal including azoles, polyenes, and echinocandins have been used for treatment of infected patients in the clinics ^[9]. Different countries have reported various levels of resistance to common antifungals used against

infection have been limited. Generally, three main classes of available antifungal including azoles, polyenes, and echinocandins have been used for treatment of infected patients in the clinics [27]. Different countries have reported various levels of resistance to common antifungals used against

C. auris infections worldwide, as described by Sekyere ^[10]. In this study, a systematic review and meta-analysis were carried out on 267

infections worldwide, as described by Sekyere [68]. In this study, a systematic review and meta-analysis were carried out on 267

C. auris clinical isolates in 16 countries in 2019, and the analysis of data displayed that resistance to Flu, AmB, voriconazole (Vcz), and caspofungin was 44.29%, 15.46%, 12.67%, and 3.48%, respectively. Two novel drugs, SCY-078 and VT-1598, are currently in the pipeline ^[10].

clinical isolates in 16 countries in 2019, and the analysis of data displayed that resistance to Flu, AmB, voriconazole (Vcz), and caspofungin was 44.29%, 15.46%, 12.67%, and 3.48%, respectively. Two novel drugs, SCY-078 and VT-1598, are currently in the pipeline [68].

In contrast, the first case report in China investigated that the

C. auris

isolated from bronchoalveolar lavage fluid (BALF) of a hospitalized woman interestingly was sensitive to Flu, AmB, and echinocandins. Additionally, the copper sulfate (CuSO4) also had a potent antifungal effect on

C. auris ^[11]. Likewise,

[69]. Likewise,

C. auris isolate as a causative agent of urinary tract infection (UTI) showed sensitivity to AmB and echinocandins, and in the case of refractory and persistence of infections and different combination therapy, flucytosine are recommended as an appropriate alternatives therapy ^[12].

isolate as a causative agent of urinary tract infection (UTI) showed sensitivity to AmB and echinocandins, and in the case of refractory and persistence of infections and different combination therapy, flucytosine are recommended as an appropriate alternatives therapy [70].

C. auris isolates of patients with candidemia in Russia were susceptible to echinocandins, whereas the high-level of resistance against Flu and AmB was seen in the majority of isolates. More investigation regarding surveillance might be helpful to achieve proper guidelines for the management of candidemia ^[13].

isolates of patients with candidemia in Russia were susceptible to echinocandins, whereas the high-level of resistance against Flu and AmB was seen in the majority of isolates. More investigation regarding surveillance might be helpful to achieve proper guidelines for the management of candidemia [71].

Response to antifungal agents have also indicated a significant difference between the planktonic and sessile state of

C. auris

growth.

C. auris enable biofilm structures to form on both medical implementation surfaces in immunocompromised patients and bio-surfaces ^[14][15] that are strongly associated with the type and phenotypic behavior of the isolates ^[16]. Additionally, biofilms are capable of triggering the antifungal resistance in this species and developing the persistent infection ^[17]. Romea et al. found that the minimum biofilm eradication concentration (MBEC) was higher than the minimum inhibitory concentration (MIC) against antifungal drugs. In addition, biofilm was resistant to all classes of antifungals drugs; whereas, it was sensitive to echinocandins and polyenes. Therefore, the biofilm feature seems a fundamental factor to antifungal resistance in

enable biofilm structures to form on both medical implementation surfaces in immunocompromised patients and bio-surfaces [50,72] that are strongly associated with the type and phenotypic behavior of the isolates [73]. Additionally, biofilms are capable of triggering the antifungal resistance in this species and developing the persistent infection [74]. Romea et al. found that the minimum biofilm eradication concentration (MBEC) was higher than the minimum inhibitory concentration (MIC) against antifungal drugs. In addition, biofilm was resistant to all classes of antifungals drugs; whereas, it was sensitive to echinocandins and polyenes. Therefore, the biofilm feature seems a fundamental factor to antifungal resistance in

C. auris ^[18]. It has been reported that

[75]. It has been reported that

C. auris

clinical isolates with a mutation in

FKS1

gene were echinocandin resistant, whereas

FKS1

wild-type (WT) isolates were sensitive. The findings suggested micafungin represented the most potent echinocandin against

C. auris. In addition, all WT isolates showed the Eagle effect (paradoxical growth effect) against the caspofungin susceptibility test performed according to the CLSI microdilution method ^[19]. However, echinocandins are only available intravenously and are related to increasingly higher rates of resistance by

. In addition, all WT isolates showed the Eagle effect (paradoxical growth effect) against the caspofungin susceptibility test performed according to the CLSI microdilution method [76]. However, echinocandins are only available intravenously and are related to increasingly higher rates of resistance by

C. auris.

Thus, a need exists for novel treatments that reveal potent activity against

C. auris

. Recently, therapies focused on echinocandins’ synergism with other antifungal drugs were widely explored, representing a novel possibility for the treatment of

C. auris infections ^[20].

infections [77].

2. Facing the Challenges to Fight against

: Molecular Resistance Mechanisms

The majority of clinical

C. auris isolates display resistance to main classes of antifungals (azoles, polyenes, or echinocandins), and there is multi (MDR)- or pan-drug resistance to more than two antifungal classes ^[21]. Many research groups have studied the molecular mechanisms implicated in resistance development, resulting in limited therapeutic options ^[21][22]. As previously noted, in order to not fail in treatment of

isolates display resistance to main classes of antifungals (azoles, polyenes, or echinocandins), and there is multi (MDR)- or pan-drug resistance to more than two antifungal classes [13]. Many research groups have studied the molecular mechanisms implicated in resistance development, resulting in limited therapeutic options [13,78]. As previously noted, in order to not fail in treatment of

C. auris infections, accurate detection and identification of this pathogen is necessary ^[23][22]. Setting the MICs of antifungals against

infections, accurate detection and identification of this pathogen is necessary [35,78]. Setting the MICs of antifungals against

C. auris strains has also been requested, since elevated MICs are severe problem ^[24]. Importantly, it is equally critical to monitor the antifungal resistance in different geographical areas and implement efficient guidelines for treatment ^[25].

strains has also been requested, since elevated MICs are severe problem [79]. Importantly, it is equally critical to monitor the antifungal resistance in different geographical areas and implement efficient guidelines for treatment [45].

The antifungal resistance in

C. auris has been shown to be acquired rather than intrinsic ^[26]. Currently, the worldwide findings conclude that susceptibility to Flu is the most decreased from

has been shown to be acquired rather than intrinsic [80]. Currently, the worldwide findings conclude that susceptibility to Flu is the most decreased from

C. auris isolates, followed by AmB, and 5-fluorocytosine and echinocandins are also not 100% effective ^[7][27]. WGS studies revealed that

isolates, followed by AmB, and 5-fluorocytosine and echinocandins are also not 100% effective [36,81]. WGS studies revealed that

ERG3

ERG11

FKS1

FKS2

, and

FKS3

homologs were found in the

C. auris

genome and these loci share around 80% similarity with

C. albicans

and

C. glabrata genes ^[24][28][29]. In general, preliminary genomic studies showed that the targets of several classes of antifungal drugs are conserved in

genes [79,82,83]. In general, preliminary genomic studies showed that the targets of several classes of antifungal drugs are conserved in

C. auris

, including the azole target lanosterol 14-α-demethylase (

ERG11

), the echinocandin target 1,3-β-(D)-glucan synthase (

FKS1

), and the flucytosine target uracil phosphoribosyl-transferase (

FUR1) ^[7][30].

) [36,84].

2.1. Mechanisms of Resistance to Azoles

Mechanistically, resistance to azole is acquired through different mechanisms; a number of genes encoding efflux pumps, including ATP-binding cassette (ABC) and overexpressed major facilitator superfamily (MFS) transporters are well known for deliberate major multidrug resistance in

C. auris ^[28][31]. The

[82,85]. The

C. auris

genome contains three genes encoding Mrr1 homologs and two genes encoding Tac1 homologs. Mutations in the zinc cluster transcription factors Mrr1 and Tac1 cause intrinsic Flu resistance of

C. auris ^[32]. Deletion of

[86]. Deletion of

TAC1b

decreased the resistance to Flu and Vcz in both mutant Flu-resistant strains from clade III and clade IV. It has been shown that the encoded transcription factor is associated with azole resistance in

C. auris strains from different clades ^[32].

strains from different clades [86].

CDR1

expression was not or only minimally affected in the mutants, representing that

TAC1b

can confer increased azole resistance by a

CDR1-independent mechanism. A recent study from Rybak et al. suggested that the Δcdr1 mutation in a resistant isolate was able to increase susceptibility to Flu and itraconazole by 64- and 128-fold, respectively, with notable reductions in MIC also demonstrated in other azoles ^[33][34]. The function of efflux pumps in azole resistance appears to be predominantly associated with

-independent mechanism. A recent study from Rybak et al. suggested that the Δcdr1 mutation in a resistant isolate was able to increase susceptibility to Flu and itraconazole by 64- and 128-fold, respectively, with notable reductions in MIC also demonstrated in other azoles [87,88]. The function of efflux pumps in azole resistance appears to be predominantly associated with

CDR1, as analysis of the Δmdr1 mutant showed minimal effects on increasing azole sensitivity ^[34].

, as analysis of the Δmdr1 mutant showed minimal effects on increasing azole sensitivity [88].

ERG11 gene mutations are mostly considered to be involved in Flu resistance or higher expression of genes participating in efflux ^[27][35]. Like other

gene mutations are mostly considered to be involved in Flu resistance or higher expression of genes participating in efflux [81,89]. Like other

Candida

species, specific

C. auris ERG11 mutations resulted directly in reduced azole susceptibility ^[36]. Furthermore, genes encoding efflux pumps may play a role too ^{[37][24][28][29]}. Analysis confirmed increased expression of the

mutations resulted directly in reduced azole susceptibility [90]. Furthermore, genes encoding efflux pumps may play a role too [33,79,82,83]. Analysis confirmed increased expression of the

CDR1

orthologous gene belonging to ABC superfamily transporters and supposed involvement in multidrug resistance in

C. auris

together with other transporter genes such as

CDR4

CDR6

, and

SNQ2 ^[38]. Study of

[91]. Study of

C. auris

and

C. haemulonii

clinical isolates from 2 hospitals in central Israel revealed that

C. auris

exhibited higher thermotolerance, virulence in a mouse infection model, and ATP-dependent drug efflux activity than

C. haemulonii ^[37]. Chawdary et al. found 15 missense mutations when aligned to the

[33]. Chawdary et al. found 15 missense mutations when aligned to the

C. albicans

wild-type

ERG11

sequence in

C. auris

azole-resistant in India, and two variants were found in every resistant strain called Y132F or K143R along 5 mutations that were already identified in azole-resistant

C. albicans ^[39][7][36]. Isolates with the K143R mutation were resistant to Vcz ^[39]. Research of AlJindan and colleagues showed that all selected

[32,36,90]. Isolates with the K143R mutation were resistant to Vcz [32]. Research of AlJindan and colleagues showed that all selected

C. auris

isolates were resistant to Flu and sequencing of

ERG11

revealed the same mutation (F132Y and K143R) in

ERG11 ^[25]. Similarly, another only two-hour-lasting assay identified mutations Y132F and K143R in

[45]. Similarly, another only two-hour-lasting assay identified mutations Y132F and K143R in

ERG11

, and S639F in

FKS1 HS1, and results were 100% concordant with DNA sequencing results ^[22]. From the 350 isolates collected in a hospital in India, 90% of

HS1, and results were 100% concordant with DNA sequencing results [78]. From the 350 isolates collected in a hospital in India, 90% of

C. auris were Flu resistant, and 2% and 8% were resistant to echinocandins and AmB, respectively ^[7]. Interestingly, mutations in

were Flu resistant, and 2% and 8% were resistant to echinocandins and AmB, respectively [36]. Interestingly, mutations in

ERG11 were markedly related with geographic clades (i.e., F126T in South Africa, Y132F in Venezuela, and Y132F or K143R in India/Pakistan) ^[40][24]. These variants have similarly been reported in the

were markedly related with geographic clades (i.e., F126T in South Africa, Y132F in Venezuela, and Y132F or K143R in India/Pakistan) [9,79]. These variants have similarly been reported in the

ERG11

gene of

C. auris in Columbia ^[36]. Later, overexpression of

in Columbia [90]. Later, overexpression of

ERG11

in resistant isolates of

Candida

spp. overcame the activity of azole drugs to inhibit the synthesis of lanosterol 14α-demethylase. Molecular experiments have shown that resistant

C. auris

expressed the increased level of

ERG11 genes compared to susceptible species; however, until now, this was not examined on susceptible isolates ^[7].

genes compared to susceptible species; however, until now, this was not examined on susceptible isolates [36].

Furthermore, multidrug resistance in

C. auris is driven by prior antifungal prescription in hospitals and subsequent antifungal treatment failures ^[41][42]. However, the resistance/sensitivity profile depends on the specific clades. This is the case of

is driven by prior antifungal prescription in hospitals and subsequent antifungal treatment failures [92,93]. However, the resistance/sensitivity profile depends on the specific clades. This is the case of

C. auris isolates in India, which are almost Flu sensitive, whereas a significant level of Flu resistance has been reported in other geographic areas worldwide ^[26].

isolates in India, which are almost Flu sensitive, whereas a significant level of Flu resistance has been reported in other geographic areas worldwide [80].

2.2. Mechanisms of Resistance to Polyenes

The mechanisms responsible for polyene resistance are poorly understood in

C. auris. Generally, whole-genome sequencing of resistant isolates has identified four novel nonsynonymous mutations, emphasizing a probable correlation with AmB resistance. The reduction in ergosterol content in the cellular membrane ^[21][43] is due to overexpression of several mutated

. Generally, whole-genome sequencing of resistant isolates has identified four novel nonsynonymous mutations, emphasizing a probable correlation with AmB resistance. The reduction in ergosterol content in the cellular membrane [13,25] is due to overexpression of several mutated

ERG genes ^[27]. These mutations included those in genes with homology to the transcription factor

genes [81]. These mutations included those in genes with homology to the transcription factor

FLO8

gene of

C. albicans and a membrane transporter ^[44]. Munoz and colleagues carried out a comparative transcriptional analysis on a resistant isolate and a sensitive isolate after exposure to AmB ^[30]. Using RNA sequencing (RNA-seq), it was revealed that 106 genes were induced in response to AmB in the resistant isolate. Most notably, genes involved in the ergosterol biosynthesis pathway were highly induced (

and a membrane transporter [94]. Munoz and colleagues carried out a comparative transcriptional analysis on a resistant isolate and a sensitive isolate after exposure to AmB [84]. Using RNA sequencing (RNA-seq), it was revealed that 106 genes were induced in response to AmB in the resistant isolate. Most notably, genes involved in the ergosterol biosynthesis pathway were highly induced (

ERG1, ERG2, ERG6,

and

ERG13), which logically showed an association with the maintenance of cell membrane stability ^[30]. Rhodes et al. screened 27

), which logically showed an association with the maintenance of cell membrane stability [84]. Rhodes et al. screened 27

C. auris

isolates from the UK for SNPs in

ERG genes in strains representing reduced sensitivity to AmB. However, variants lighting these differences in drug susceptibility were not found ^[45].

genes in strains representing reduced sensitivity to AmB. However, variants lighting these differences in drug susceptibility were not found [95].

2.3. Mechanisms of Resistance to Echinocandins

The development of resistance to echinocandins is rare, and they are the first-line therapy drugs against

C. auris infections ^[21][43]. This resistance is typically associated with hot spot mutations in the

infections [13,25]. This resistance is typically associated with hot spot mutations in the

FKS1 gene, which encodes the (1,3)-β-D-glucan synthase enzyme, the target of echinocandins, resulting in lower affinity of the enzyme to the drug ^[19]. Sequencing of the corresponding hot-spot regions of 38

gene, which encodes the (1,3)-β-D-glucan synthase enzyme, the target of echinocandins, resulting in lower affinity of the enzyme to the drug [76]. Sequencing of the corresponding hot-spot regions of 38

C. auris strains resulted in the discovery that an S639F amino acid substitution was related to pan-echinocandin resistance ^[7]. Remarkably, this mutation is in the region aligning to the HS1 of

strains resulted in the discovery that an S639F amino acid substitution was related to pan-echinocandin resistance [36]. Remarkably, this mutation is in the region aligning to the HS1 of

C. albicans FKS1 ^[45]. Indeed, different mutations have also been revealed in the same location in

[95]. Indeed, different mutations have also been revealed in the same location in

C. auris-resistant isolates including S639Y and S639P, which led to echinocandin resistance in a mouse model in vivo ^[19]. Identical to other cases of

-resistant isolates including S639Y and S639P, which led to echinocandin resistance in a mouse model in vivo [76]. Identical to other cases of

Candida

spp., changes in the

FKS1 gene leads to caspofungin resistance ^[27]. On the other side, micafungin-resistant isolates

gene leads to caspofungin resistance [81]. On the other side, micafungin-resistant isolates

C. auris

from patients in Kuwait contained the S639F mutation in hot-spot 1 of

FKS1 ^[39]. Multiple studies have reported the isolation of resistant echinocandins across various geographical regions, with the highest levels of resistance reported in India ^[19][46].

[32]. Multiple studies have reported the isolation of resistant echinocandins across various geographical regions, with the highest levels of resistance reported in India [76,96].

2.4. Mechanisms of Resistance to Flucytosine (5-Fluorocytosine)

Flucytosine, a nucleoside analog, inhibits nucleic acid synthesis. Since this antifungal compound is less used compared to other drugs, the mechanism of resistance is also less understood because fewer studies have been implemented to discover the resistance of

C. auris

to this drug. However, a mutation of

FUR1

was shown to be associated with flucytosine resistance in non-

Candida auris Candida ^[47], and mutations in the

[97], and mutations in the

FCY2

and

FCY1 genes also seem to be involved in resistance to 5-fluorocytosine ^[27]. A specific missense mutation of

genes also seem to be involved in resistance to 5-fluorocytosine [81]. A specific missense mutation of

FUR1

causing F211I amino acid substituted in the

FUR1

gene was demonstrated in resistant

C. auris

that had not previously been reported; therefore, more studies are required to confirm the probable mechanisms responsible for the resistance to flucytosine in the tested

C. auris strain ^[45]. Antifungal drugs used for treatment of

strain [95]. Antifungal drugs used for treatment of

C. auris

infection and mechanism of resistance are summarized in

Table 1

Table 1.

Antifungal drugs commonly used against

C. auris

infection and mechanisms of resistance already reported.

	Antifungal Drug Class			Mode of Action	Mechanism of Resistance

Azoles

Inhibit the activity of lanosterol 14-α-demethylase enzyme; prevent converting lanosterol to ergosterol, leading to damaging integrity of cell membrane.

Overexpression of ATP-binding cassette (ABC) and major facilitator superfamily (MFS) transporters.

ERG11	point mutation: Y132F and K143R.

Mutation in zinc cluster transcription factors Mrr1 and Tac1.		^[40]^[39]^[7]^[25]^[24]^[28]^[31]^[32]^[33]^[34]^[35]^[38]^[41]^[42]
		[9,32,36,45,79,82,85,86,87,88,89,91,92,93]

Polyenes

Bind ergosterol molecules in the cytoplasmic membrane; disturb the permeability of cell membrane by formation of pores, causing oxidative damage.

Induction of genes associated with sterol biosynthetic process including	ERG1	, ERG2, ERG6, and ERG13.

SNPs in different genomic loci related to increased resistance.		^[27]^[30]^[44]^[45]
		[81,84,94,95]

Echinocandins

Inhibit β-(1,3)-D-glucan synthase enzyme, leading to defective cell wall formation.

Hot-spot mutation in	FKS1	gene associated with S639Y, S639P, and S639Y regions and FKS2.	^[39]^[7]^[19]^[27]^[46]
		[32,36,76,81,96]
	Flucytosine			Inhibit the nucleic acid synthesis (DNA and RNA) of fungi.	Mutation of FUR1 gene, specifically missense mutation of FUR1 causing F211I amino acid substituted in the FUR1 gene in one flucytosine-resistant isolate.	Mutations in the FCY2, FCY1 genes.	^[27]^[45]^[47]	[81,95,97]