Detection of ERG11 point mutations in iranian fluconazole-resistant Candida albicans isolates

Authors

1 Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran

2 Department of Parasitology and Mycology, Ghaem Hospital, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran

Abstract

Background and Purpose: Candidiasis is referred to a group of superficial and deep-tissue fungal infections often caused by Candida albicans. The superficial infections affect the oral, oropharynx, esophagus, and vaginal mucosa. The treatment of choice for these infections is the use of azoles, such as fluconazole. However, the increased use of these antifungal agents has led to the emergence of azole-resistant isolates of C. albicans. Different mechanisms have been suggested for the development of drug resistance, such as mutations in the encoding gene ERG11. Mutations in ERG11 result in changes in the ERG11p spatial construction and reduce the affinity between the protein and azole. This study aimed to determine the susceptibility profile of C. albicans clinical isolates to fluconazole using microdilution method. The present research was also targeted toward the detection of mutations that might be related to fluconazole resistance by the amplification and sequencing of ERG11 gene.

Materials and Methods: This study was conducted on a total of 216 clinical isolates obtained from Mashhad, Isfahan, and Tehran cities in Iran, during 2016-2018. The clinical isolates were identified using molecular techniques. Furthermore, minimum inhibitory concentration (MICs) was determined according to the clinical and laboratory standards institute M27-A3 and M27-S4 documents. The concentration range for fluconazole was obtained as 0.063-64 μg/ml. In the resistant strains, ERG11 genes were amplified by specific primers. Subsequently, cycle sequencing reactions were performed on purified polymerase chain reaction (PCR) products in forward and reverse directions. Finally, the results were analyzed by MEGA (version 7) and Gene Runner software (version 6.5.30).

Results: Out of 216 strains, 100 (46.3%) species were identified as C. albicans. The MIC values for fluconazole had a range of 0.125-16 μg/ml with the MIC50 and MIC90 values of 0.5 and 1 μg/ml, respectively. Totally, 41 nucleotide changes were detected among 4 resistant isolates. In this regard, 4 out of 41 mutations in codons caused changes in ERG11p; however, these mutations did not lead to fluconazole resistance.

Conclusion: Fluconazole resistance among clinical isolates is not merely due to the changes in ERG11p. This resistance may be also related to some other mechanisms, such as the prevention of the intracellular accumulation of the antifungal agent and alteration of the target enzyme to diminish drug binding.

Keywords


Introduction

Candida albicans is an important opportunistic yeast that can cause mucosal infections, such as thrush and oropharyngeal candidiasis (OPC) in AIDS patients, as well as systemic life-threatening infections in immunocompromised patients [1]. The use of potent antifungal agents is crucial for the management of these potentially fatal infections. Azole antifungal agents, such as fluconazole, are the treatment of choice for these infections [2].

However, the increased use of these antifungal agents, especially in HIV/AIDS patients receiving long-term therapy, has resulted in the emergence of azole-resistant isolates of C. albicans. Azole resistance mechanisms are different and may contribute to mutations in encoding gene ERG11. It is based on the spatial configuration alterations of the target enzyme 14a-demethylase (ERG11p) [3, 4]. Erg11p is a significant protein of the cytochrome P450 superfamily enzyme and has an important role in the ergosterol synthesis pathway of C. albicans. Ergosterol (ergosta-5,7,22-trien-3β-ol) is a kind of sterol found in the fungal cell membranes and play a major role in maintaining the integrity and function of C. albicans membrane [5].

Mutations in ERG11 result in changes in the ERG11p spatial construction and reduce the affinity between the protein and azole [6]. The aim of the present study was to determine the susceptibility pattern of C. albicans clinical isolates to fluconazole using microdilution method. This study was also targeted toward the detection of mutations that might be responsible for fluconazole resistance by the amplification and sequencing of ERG11 gene.

Materials and Methods

Clinical Isolates

This study was conducted on a total of 216 clinical isolates obtained from Tehran (n=67), Isfahan (n=37), and Mashhad (n=112) cities in Iran, from July 2016 to February 2018. All strains were sub-cultured on Sabouraud glucose agar (SGA; Difco, Detroit, MI, USA) and incubated at 37°C for 24-48 h.

Molecular Identification

DNA Extraction

Genomic DNA was extracted using the boiling method. Briefly, a bit of fresh colonies were suspended in 80 µL of distilled water and boiled for 20 min. They were then centrifuged for 5 min at 6,000 rpm. The resultant supernatant was used for polymerase chain reaction (PCR). Clinical isolates of Tehran and Isfahan were identified using the PCR-restriction fragment length polymorphism (PCR-RFLP) of the ITS1-5.8S-ITS2 regions as described previously [7, 8]. Furthermore, the identification of the clinical samples of Mashhad was performed through matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF or MT-MS) mass spectrometry (Bruker Daltonics, Bremen, Germany), which is a new method.

In vitro antifungal susceptibility testing

Minimum inhibitory concentration (MICs) was determined according to the clinical and laboratory standards institute M27-A3 and M27-S4 documents [9, 10]. Antifungal effect of fluconazole (Pfizer Central Research, Sandwich, United Kingdom) was evaluated on the clinical isolates of C. albicans. To this end, fluconazole was diluted in the RPMI-1640 medium (Sigma Chemical Co.), buffered to pH 7.0 with 0.165 M morpholinepropanesulfonic acid (MOPS; Sigma) with L-glutamine without bicarbonate.

A final concentration of 0.063-64 μg/ml was considered for fluconazole. The MIC results were read after 24 h of incubation at 35°C. These values were determined visually as the lowest concentration of drug that caused a significant (>50%) reduction in the microorganism growth. According to the M27-S4 document, a fluconazole concentration of > 8 was considered for the resistant isolates [10].

Amplification of ERG11 gene and sequencing

Three pairs of primers were used for the amplification of ERG11 gene [6]. ERGSec1A (50-TTAGTGTTTTATTGGATTCCTTGGTT-30) and ERGSec1B (50-TCTCATTTCATCACCAAATAAAGATC-30) yielded an amplicon expanding from 295 to 777 bp of the ERG11 gene. Furthermore, ERGSec2A (50-ACCAGAAATTACTATTTTCACTGCTTCA-30) and ERGSec2B (50-AAGTCAAATCATTCAAATCACCA CCT-30) yielded a product extending from 723-1204 bp of the ERG11 gene. Finally, ERGSec3A (50-AGGTGGTGATTTGAATGATTTGACTT-30) and ERGSec3B (50-GAACTATAATCAGGGTCAGGCACTTT-30) provided an expected PCR product extending from 1179-1667 bp of the ERG11 gene.

One susceptible isolate (No. 27) was used as the control strain. The PCR mixture included 2.5 μl of 10X reaction buffer, 0.5 ml of 30 pmol/ml of each primer, 0.5 ml of 10 mM dNTP, 0.25 ml of Taq polymerase (5U/ml), and 2 μl of extracted DNA in a final volume of 25 μl. The PCR products were purified by means of the ethanol purification method. The cycle sequencing reactions were performed in forward and reverse directions (Bioneer, Korea).

The sequencing products were aligned and analyzed in comparison with the nucleotide sequence of cytochrome P450 L1A1 (lanosterol 14 alpha-demethylase) from C. albican [11] and published ERG11 sequence in GenBank by Lai and Kirsch (accession number: X13296) using MEGA (version 7) and Gene Runner software.

Results

Out of 216 strains, 100 (46.3%) species were identified as C. albicans. The majority of the patients (23%) were in the age group of 31-40 years. Most of the specimens were collected from vaginitis (30%), onychomycosis (26%), and bronchoalveolar lavage (BAL; 21%) cases. The study population had a male to female ratio of 31:69. The most frequent predisposing factors among the patients included pregnancy (29%), cancer (9%), and diabetes mellitus (9%). An MIC range of 0.125-16 μg/ml was obtained for fluconazole having the MIC50 and MIC90 values of 0.5 and 1 μg/ml, respectively.

Table 1 summarizes the demographic and clinical data of the patients enrolled in the present study. Isolates number 3, 11, 15, 23, and 45 were resistant to fluconazole (MIC=16); therefore, they were applied for sequencing. However, isolate number 3 was contaminated with Aspergillus species and did not recover on SGA. Totally, 41 nucleotides changes were detected among the isolates. Out of 41 mutations, 4 mutations in codons caused changes in ERG11p (Table 1) [6, 12-17].

No City Age Gender Source of specimen Risk factor MIC (µg/ml) Site of nucleotide (bp) mutation Nucleic acid mutation Amino acid substitution Change in ERG11p
1 Mashhad 80 F BAL - 0.125 - - - -
2 Mashhad 39 F Vaginitis Pregnancy 0.25 - - - -
3 Mashhad 55 M BAL Hepatitis 16 - - - -
4 Mashhad 39 F Bladder Biopsy - 0.25 - - - -
5 Mashhad 65 M BAL Lung Cancer 0.25 - - - -
6 Mashhad 52 M BAL - 0.125 - - - -
7 Mashhad 42 F Vaginitis Pregnancy 0.125 - - - -
8 Mashhad 39 F Vaginitis Pregnancy 0.25 - - - -
9 Mashhad 28 F Vaginitis Pregnancy 0.25 - - - -
10 Mashhad 48 M BAL - 0.125 - - - -
11 Mashhad 28 F Vaginitis Pregnancy 16 4625586968051143 TTT→TTCTCC→TCTCAT→CACCTA→TTAGTT→GTC Phe→PheSer→SerHis→HisLeu→LeuVal→Val N/CN/CN/CN/CN/C
12 Mashhad 55 F BAL Lung cancer 0.125 - - - -
13 Mashhad 63 M BAL Leukemia 0.25 - - - -
14 Mashhad 44 M BAL Lung cancer 4 - - - -
15 Mashhad 45 M Joint Rheumatic diseases 16 462504558805945114311671257135014431449158716091617 TTT→TTCAAA→AAGTCC→TCTCTA→TTAGAA→GACGTT→GTCTTA→TTGCTC→CTTTAT→TACGCC→GCTGCT→GCCTTA→TTGGTT→ATTAAT→AAC Phe→PheLys→LysSer→SerLeu→LeuGlu→AspVal→ValLeu→LeuLeu→LeuTyr→TyrAla→AlaAla→AlaLeu→LeuVal→IleAsn→Asn N/CN/CN/CN/CE266D12N/CN/CN/CN/CN/CN/CN/CV488I12N/C
16 Mashhad 65 M BAL Lung cancer 0.25 - - - -
17 Mashhad 79 F BAL - 0.25 - - - -
18 Mashhad 45 F BAL Lung cancer 0.25 - - - -
19 Mashhad 29 F Vaginitis Pregnancy 0.25 - - - -
20 Mashhad 39 M BAL Kidney transplantation 0.25 - - - -
21 Mashhad 53 F Urine Kidney transplantation 0.25 - - - -
22 Mashhad 53 M BAL - 0.125 - - - -
23 Mashhad 74 F BAL Lung Cancer 16 69680511431287135014431449 CAT→CACCTA→TTAGTT→GTCTTT→TTCTAT→TACGCC→GCTGCT→GCC His→HisLeu→LeuVal→ValPhe→PheTyr→TyrAla→AlaAla→Ala N/CN/CN/CN/CN/CN/CN/C
24 Mashhad 70 F Biopsy Diabetes mellitus 0.25 - - - -
25 Mashhad 35 F Vaginitis Pregnancy 0.5 - - - -
26 Mashhad 45 F Vaginitis Pregnancy 0.25 - - - -
27 Mashhad 29 F Vaginitis Pregnancy 0.125 - - - -
28 Mashhad 44 F Vaginitis Pregnancy 0.5 - - - -
29 Mashhad 29 F Vaginitis Pregnancy 0.5 - - - -
30 Mashhad 35 F Thrush Lupus 0.25 - - - -
31 Mashhad 40 M BAL Rheumatic diseases 0.25 - - - -
32 Mashhad 28 F Vaginitis Pregnancy 0.125 - - - -
33 Mashhad 33 F Vaginitis Pregnancy 0.125 - - - -
34 Mashhad 26 F Vaginitis Pregnancy 0.5 - - - -
35 Mashhad 21 F Vaginitis Pregnancy 0.125 - - - -
36 Mashhad 32 F Vaginitis Pregnancy 0.25 - - - -
37 Mashhad 22 F Vaginitis Pregnancy 0.25 - - - -
38 Mashhad 31 F Vaginitis Pregnancy 0.5 - - - -
39 Mashhad 43 F Vaginitis Pregnancy 0.25 - - - -
40 Mashhad 22 F Vaginitis Pregnancy 0.25 - - - -
41 Mashhad 24 F Vaginitis Pregnancy 0.125 - - - -
Table 1. Continued
42 Mashhad 29 F Vaginitis Pregnancy 0.125 - - - -
43 Mashhad 28 F Vaginitis Pregnancy 0.125 - - - -
44 Mashhad 36 F Vaginitis Pregnancy 0.5 - - - -
45 Mashhad 28 F Vaginitis Pregnancy 16 462504558696805945114311671257135014431449158716091617 TTT→TTCAAA→AAGTCC→TCTCAT→CACCTA→TTAGAA→GACGTT→GTCTTA→TTGCTC→CTTTAT→TACGCC→GCTGCT→GCCTTA→TTGGTT→ATTAAT→AAC Phe→PheLys→LysSer→SerHis→HisLeu→LeuGlu→AspVal→ValLeu→LeuLeu→LeuTyr→TyrAla→AlaAla→AlaLeu→LeuVal→IleAsn→Asn N/CN/CN/CN/CN/CE266D12N/CN/CN/CN/CN/CN/CN/CV488I12N/C
46 Mashhad 44 F Vaginitis Pregnancy 0.5 - - - -
47 Mashhad 73 M BAL Lung cancer 0.25 - - - -
48 Mashhad 34 F Vaginitis Pregnancy 0.5 - - - -
49 Mashhad 26 F Vaginitis Pregnancy 0.5 - - - -
50 Mashhad 32 F Vaginitis Pregnancy 0.25 - - - -
51 Mashhad 64 M Urine Kidney transplantation 0.5 - - - -
52 Isfahan 24 M Groin - 0.5 - - - -
53 Isfahan 28 F Fingernail - 0.5 - - - -
54 Isfahan 37 F Toenail - 0.25 - - - -
55 Isfahan 16 F Fingernail Diabetes mellitus 0.25 - - - -
56 Isfahan 35 M Fingernail - 0.5 - - - -
57 Isfahan 39 M Skin - 2 - - - -
58 Isfahan 48 F Fingernail - 0.5 - - - -
59 Isfahan 69 F Fingernail - 0.5 - - - -
60 Isfahan 41 M BAL - 0.5 - - - -
61 Isfahan 39 F Fingernail - 0.5 - - - -
62 Isfahan 3 M Thrush - 0.5 - - - -
63 Isfahan 40 F Vaginitis - 0.5 - - - -
64 Isfahan 29 F Fingernail Diabetes mellitus 1 - - - -
65 Isfahan 14 F Groin - 2 - - - -
66 Isfahan 45 F Fingernail - 2 - - - -
67 Isfahan 56 F Fingernail - 0.5 - - - -
68 Isfahan 39 M Blood Leukemia 1 - - - -
69 Isfahan 19 M Toenail - 0.5 - - - -
70 Tehran 74 F Groin Diabetes mellitus 0.25 - - - -
71 Tehran 65 F BAL - 0.5 - - - -
72 Tehran 71 F Groin - 0.5 - - - -
73 Tehran 78 M Sputum - 2 - - - -
74 Tehran 48 M Lung Biopsy - 0.5 - - - -
75 Tehran 68 F Toenail - 0.5 - - - -
76 Tehran 52 F BAL - 0.5 - - - -
77 Tehran 39 F Fingernail Diabetes mellitus 0.5 - - - -
78 Tehran 61 F Fingernail - 0.25 - - - -
79 Tehran 40 F Toenail - 0.5 - - - -
80 Tehran 65 M Toenail Diabetes mellitus 0.5 - - - -
81 Tehran 70 M Interdigitale - 0.5 - - - -
82 Tehran 28 F Fingernail - 0.25 - - - -
83 Tehran 34 M Toenail Diabetes mellitus 0.5 - - - -
84 Tehran 19 F Fingernail - 1 - - - -
85 Tehran 48 F Fingernail - 0.5 - - - -
86 Tehran 18 M Cornea - 0.5 - - - -
87 Tehran 77 F BAL - 0.25 - - - -
88 Tehran 61 M Sputum - 0.5 - - - -
89 Tehran 59 F Fingernail - 1 - - - -
90 Tehran 47 F Fingernail Diabetes mellitus 0.5 - - - -
91 Tehran 62 F Fingernail - 0.25 - - - -
92 Tehran 34 F Groin Hyperhidrosis 0.25 - - - -
Table 1. Continued
93 Tehran 46 F Toenail - 0.25 - - - -
94 Tehran 58 M Fingernail - 0.25 - - - -
95 Tehran 70 F Toenail - 0.5 - - - -
96 Tehran 86 F Groin - 0.25 - - - -
97 Tehran 27 M Esophagitis - 0.25 - - - -
98 Tehran 10 M Thrush Diabetes mellitus 0.5 - - - -
99 Tehran 65 F BAL - 0.5 - - - -
100 Tehran 58 M Skin Hyperhidrosis 0.5 - - - -
*BAL: Bronchoalveolar lavage, MIC: minimum inhibitory concentration, M: male, F: female, N/C: no change, aa: amino acid, Phe: phenylalanine, Ser: serine, His: histidine, Leu: leucine, Val: valine, Lys: lysine, Glu: glutamine, Asp: aspartic acid, Tyr: tyrosine, Ala: alanine, Ile: isoleucine, Asn: asparagine
Table 1.Characteristics of patients with candidiasis and nucleotide changes and mutations of Candida albicans ERG11 gene and correlated changes in ERG11p among resistant isolates in the present study

Discussion

Candidiasis is referred to both superficial and deep-tissue fungal infections often caused by C. albicans. Based on the epidemiological surveys performed in the Europe [18], United States [19], and the Middle East [20], the superficial types can affect the oral, oropharynx, esophagus, and vaginal mucosa. Candida albicans is the main cause of invasive Candida infections in the majority of obtained clinical specimens, accounting for 50-70% of the cases [21]. The treatments of Candida infections differ considerably and are based on the patients' underlying disease and immune status, anatomic location of the infection, Candida species responsible for infection, predisposing factors, and, in some cases, the susceptibility of Candida species to antifungal agents [22, 23].

Nystatin, itraconazole, miconazole, voriconazole, echinocandins, flucytosine, and amphotericin B are the anti-Candida agents applied for the management of this infection. However, the most prevalently recommended antifungal used for the majority of C. albicans isolates is fluconazole, which is a member of the azole class [24]. Azoles inhibit 14-α-sterol demethylase encoded by ERG11 gene, which is a significant enzyme involved in the biosynthesis of ergosterol (i.e., fungal-specific membrane sterol).

Some investigations have shown the ability of Candida species to expand high resistance to azole agents [25, 26]. Prior fluconazole exposure has been shown to increase the risk of fluconazole resistance in Candida species [26]. Increased resistance to fluconazole is caused by different factors, such as the change of the target enzyme to diminish drug binding, reduction of the toxic effects of the antifungal, enhancement of the amount of the target enzyme, prevention from the intracellular accumulation of the antifungal agent [27], raised expression of ERG11 as a result of activating mutations in the gene encoding the zinc-cluster transcriptional regulator Upc2p [28], overexpression of drug efflux pumps [29], and inactivation of ERG3 gene [30].

Candida albicans strains isolated from patients with candidemia have the lowest incidence of azole resistance (0-5%) [31, 32]. However, the incidence of fluconazole resistance among the C. albicans clinical isolates of OPC is higher and is associated with prior OPC infections and previous fluconazole treatment [33]. Out of the 100 C. albicans clinical isolates, 5 isolates were resistant to fluconazole (MIC=16 μg/ml). Interestingly, all resistant strains belonged to Mashhad.

Resistant isolates were obtained from BAL (n=2), vaginitis (n=2), and joint (n=1). One isolate (from BAL) did not grow after re-passaging on SGA; therefore, it was excluded from the study. Amino acid substitutions have been delineated in 61 parts of the ERG11p due to mutations in ERG11 gene [6]. Erg11p mutations, such as D153E, E266D, D116E, K128T, K147R, E266Q, K287R, G129A, and G303D, do not cause fluconazole resistance [12-14, 34, 35]. However, ERG11p mutations, such as G464S, Y132H, S405F, R467K, T315A, and I471T, have been shown to cause resistance to azoles [34, 36-40].

The C-terminal and N-terminal of ERG11p are on the protein surface rather than on the active site; therefore, the 295-1667 bp part of ERG11 gene was amplified to look for possible mutations. Biofilms, multidrug transporters in Candida species, multiple drug resistance gene MDR1, drug segregation within intracellular vacuoles, and also overexpression of CDR1 and CDR2 as Candida drug-resistant genes can significantly reduce the intracellular drug concentration [4, 41, 42].

Susceptibility to fluconazole in C. albicans isolates may reach to 95.8% [43, 44]. However, as indicated in a number of investigations, the fluconazole resistance of such clinical isolates might be as high as 35% [45, 46]. In the present study, the incidence rate of fluconazole resistance in C. albicans was 5%. This low rate may be related to the administration of an appropriate dosage of antifungal agents or completion of the therapeutic course.

In this study, two types of mutations, including E266D and V488I, were detected among the resistant isolates. E266D mutation was also reported previously; nonetheless, this mutation does not result in fluconazole resistance [12]. V488I (G1609A) mutation may not also lead to fluconazole resistance because V488 is located far from the active center of ERG11p [47]. Khademi et al. found four resistant C. albicans strains among patients in Guilan, Iran. Missense mutations, such as C470G, K291N, and Q474R, were detected in all resistant isolates.

Similar to our results, Teymori et al. [48] detected 5 (5.1%) resistant C. albicans isolates (MIC≥64 μg/ml) out of 97 clinical samples. They revealed that ERG11 gene in the five fluconazole-resistant C. albicans isolates was up-regulated 4.15-5.84 folds, compared to the control strain. Eftekhari et al. [49] isolated 4 resistant C. albicans out of 40 strains and screened ERG11 gene mutations by PCR sequencing. Their isolated strains had D116E and V456G polymorphisms.

In another study carried out during April 2015-April 2016, Alizadeh et al. [50] isolated 28 strains of C. albicans from muco-cutaneous candidiasis among immunocompromised patients in Omidiyeh, Khuzestan, Iran. In the mentioned study, all isolates were resistant to fluconazole. They evaluated ERG gene expression by semi-quantitative reverse transcriptase-(RT) PCR. In line with the results of the present study, they showed no significant changes in fluconazole-resistant isolates in comparison with untreated controls and ERG11 reference sequence.

In 2017, Balabandi et al. [51] detected two missense mutations (i.e., D116E and E266D) in ERG11 gene among 20 resistant C. albicans in Rasht, Iran. Furthermore, Peron et al. [52] found two fluconazole-resistant C. albicans isolates from oral cavity (MIC=8 μg/ml) and esophageal cavity (MIC=64 μg/ml). They found six mutations encoding distinct amino acid substitutions (i.e., E116D, T128K, E266D, A298V, G448V, and G464S) that were previously reported to be associated with fluconazole resistance.

Moron and Cabrera [53] isolated 26 clinical strains from two tertiary hospitals in Metro Manila, Philippines, during November 2016 to January 2017. Out of 26 C. albicans, a high percentage of the isolates (73.08%) showed resistance to fluconazole. They detected the presence of point mutations T462C, A369C, and C558T. Mutations A369C and T462C have been also identified as possible factors associated with resistance to azole agents [54].

Conclusion

In accordance with many investigations in this field, our results demonstrated that the majority of C. albicans isolates were susceptible to fluconazole. Since the main mechanism of azole resistance is the mutation occurring through the ERG11 gene in C. albicans, this gene was selected for analysis in the present study. Our analysis resulted in the detection of 41 mutations in codons, only 4 of which caused changes in ERG11p. Nonetheless, these mutations (i.e., E266D and V488I) cannot lead to fluconazole resistance. Resistance among these isolates could be due to other mechanisms, such as the prevention of the intracellular accumulation of the antifungal agent and alteration of the target enzyme to diminish drug binding.

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