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Revista do Instituto de Medicina Tropical de São Paulo

On-line version ISSN 1678-9946

Rev. Inst. Med. trop. S. Paulo vol.48 no.1 São Paulo Jan./Feb. 2006 



Molecular identification of Candida dubliniensis isolated from oral lesions of HIV-positive and HIV-negative patients in São Paulo, Brazil


Identificação molecular de amostras de Candida dubliniensis isoladas de lesões orais de pacientes HIV positivos e negativos em São Paulo, Brasil



Jorge Kleber ChavascoI; Claudete Rodrigues PaulaII; Mario Hiroyuki HirataIII; Natanael Atilas AlevaIV; Carlos Eduardo de MeloV; Walderez GambaleII; Luciana da Silva RuizII; Marília Caixeta FrancoVI

IUniversidade Federal de Alfenas, UNIFAL, UNIFENAS and UNINCOR (postdoctorate ICB/USP), MG, Brazil
IIDepartamento de Microbiologia do Instituto de Ciências Biomédicas da Universidade de São Paulo, SP, Brazil
IIIDepartamento de Análises Clínicas da Universidade de São Paulo, SP, Brazil
IVUNINCOR, Três Corações, MG, Brazil
VDepartamento de Análises Clínicas da Universidade de São Paulo, SP, Brazil
VIUniversidade Federal de Alfenas, UNIFAL, Alfenas, MG, Brazil

Correspondence to




Candida dubliniensis is a new, recently described species of yeast. This emerging oral pathogen shares many phenotypic and biochemical characteristics with C. albicans, making it hard to differentiate between them, although they are genotypically distinct. In this study, PCR (Polymerase Chain Reaction) was used to investigate the presence of C. dubliniensis in samples in a culture collection, which had been isolated from HIV-positive and HIV-negative patients with oral erythematous candidiasis. From a total of 37 samples previously identified as C. albicans by the classical method, two samples of C. dubliniensis (5.4%) were found through the use of PCR. This study underscores the presence of C. dubliniensis, whose geographical and epidemiological distribution should be more fully investigated.

Keywords: HIV-positive; HIV-negative; Candida dubliniensis; PCR.


Candida dubliniensis é uma nova espécie recentemente descrita. Este patógeno oral emergente compartilha muitas características fenotípicas e bioquímicas com C. albicans dificultando assim a diferenciação entre elas. As mesmas, porém, mostram-se genotipicamente distintas. Este trabalho tem como objetivo identificar, pela técnica de PCR (Polymerase Chain Reaction), a possível presença de C. dubliniensis dentre amostras isoladas de candidose oral eritematosa, provenientes de pacientes HIV positivos e HIV negativos. Em um total de 37 amostras identificadas anteriormente, por método clássico, como C. albicans encontramos duas amostras de C. dubliniensis (5,4%) utilizando a técnica do PCR. Esta técnica mostrou-se útil, prática e com identificação taxonômica mais acurada.




An increased incidence of fungal infections has been well documented throughout the last decade. The most important factor contributing to this phenomenon has been the increased number of immunocompromised individuals. As a result, many species previously unassociated with human diseases have become important pathogens, some examples being Penicillium marneffei, Emmonsia pasteurina and Candida dubliniensis6,30.

Candida dubliniensis was first identified as a new species in 1995 in Dublin, Ireland39. Since then, infections by this yeast have been widely reported in a large number of HIV-positive and AIDS patients23, being isolated mainly from the oral cavity9. Moreover, C. dubliniensis has been implicated as a causative agent for oral candidoses and HIV-negative individuals, both in healthy individuals and diabetics42,43.

This species shares many phenotypic and biochemical characteristics with C. albicans39, making it difficult to differentiate between the two species, since C. dubliniensis expresses the serotype A of C. albicans, and is able to form germ tubes and abundant numbers of chlamydoconidia3,4,39,41. Moreover, C. dubliniensis is characterized by a high resistance to fluconazole, and the susceptible isolates are able to develop resistance to this drug in vitro26,40. This high degree of similarity between the two species has contributed to the identification of some isolates of C. dubliniensis as C. albicans31. This species has most likely been present in the community for long time, although identified as C. albicans36.

Therefore, various phenotypic methods for the identification of C. dubliniensis and its differentiation from C. albicans have been reported. These tests include: the formation of chlamydospores39; the pattern of carbohydrate assimilation33, b-D-glucosidase activity35; the color of colonies after seeding in different mediums such as CHROMagar Candida, Staib agar37, Niger agar17, Tobacco agar13 and others; as well as growth in Sabouraud agar at temperatures between 42 and 45 °C31.

However, individual variations among the strains have been reported for these phenotypic characteristics3,39, raising the necessity to study its genotypic characteristics. Analyses of the DNA of different samples of C. dubliniensis have demonstrated that this species presents conserved sequences of DNA elements, these being important in the identification of isolates for a differential diagnosis of candidiasis between C. dubliniensis and C. albicans11.

Currently, there exists a wide variety of molecular techniques able to identify C. dubliniensis, which include: DNA tests using analyses with restriction endonucleases, methods based in pulsed field electrophoresis, DNA tests using probes, as well as PCR-based methods16,19,28,42.

The definitive identification of C. dubliniensis is still a problem in routine laboratories; it is therefore necessary to know the phenotypic and genotypic characteristics of the isolates to obtain a final characterization. Studies on the incidence of this yeast, carried out by reference laboratories, are necessary for a better understanding of the epidemiology of this new species, especially in South America, where its frequency is not well known5.

In this study, PCR (polymerase chain reaction) was used to identify the presence of C. dubliniensis in samples isolated from HIV-positive and HIV-negative patients with oral erythematous candidiasis, in the city of São Paulo, Brazil.



Yeast isolates: This study involved 39 isolates of yeasts from HIV-positive and HIV-negative patients with erythematous oral candidiasis, which had originally been identified by the classical method15. All the patients released the HIV tests by the ELISA method. These samples were kept, for nine months, at the culture collection of the Laboratory of Pathogenic Yeasts, Department of Microbiology, Biomedical Science Institute, University of São Paulo (ICB II/USP). Parallel to this, analyses were made of standard samples of C. albicans (LSHT 330) and C. dubliniensis (ATCC 777).

DNA analysis: The DNA analyses were carried out on the isolated samples using PCR, according to MAGEE et al.18, PFALLER et al.29 and SMITH et al.38.

DNA extraction: Each sample was inoculated into 5 mL of YPD medium and incubated for 18 hours at 37 °C. After incubation, 1.5 mL of the culture was transferred to an Eppendorf tube and centrifuged at 10,000 rpm for five minutes, under refrigeration. The supernatant was discarded, the pellet was resuspended by vortexing after addition of 1 mL sorbitol (Merck), and the resulting suspension was centrifuged at 10,000 rpm for two minutes. The pellet was resuspended in 1 mL of lyticase buffer (50,000 U - Sigma) with 350 µg/mL of that enzyme. The Eppendorf tube was then incubated at 30 °C in a humidified incubator for 30 minutes and subsequently centrifuged at 10,000 rpm for one minute. The supernatant was discarded and 0.5 mL of the digestion solution was added to the tube containing the pellet. The tube was then incubated at 70 °C for 30 minutes in a humidified incubator. The Eppendorf tube was then left at room temperature for 10 minutes, followed by the addition of 50 µL of 5M potassium acetate solution. After 60 minutes at 0 °C, the Eppendorf tube was centrifuged at 10,000 rpm for 15 minutes. The supernatant was transferred to another Eppendorf tube containing 1 mL of 95% ethanol (Merck) for the precipitation of DNA. Then the tube was centrifuged at 10,000 rpm for five minutes and the sediment was washed twice with 0.5 mL of 70% ethanol (Merck). The precipitated and washed DNA was centrifuged at 10,000 rpm for five minutes. Then, the sediment was resuspended in 100 µL of TE (Tris + EDTA).

Estimation of the quantity of DNA: The agarose gel (Sigma) was prepared at 1% in TBE buffer and placed on an acrylic plate for an 8-toothed comb, and covered by TBE run buffer on a horizontal electrophoresis plate. Each well was loaded with 10 µL of a mixture of the extracted DNA with bromophenol blue stain (V/V). The run was carried out at 90 V for 30 minutes, until the material reached the opposite end of the gel. The gel was stained with ethidium bromide in a concentration of 1 µL of a 20 mg/mL stock solution in 100 µL of distilled water, for 15 minutes. The total-DNA band was observed in a UV transilluminator.

PCR reaction: According to MANNARELLI & KURTZMAN, 199819. The primers were obtained from Life Technologies do Brasil. Two pairs of the primers were used: one for C. dubliniensis (sense: CDU2 – 5'AGT TAC TCT TTC GGG GGT GGC CT 3'; anti-sense: NL4CAL – 5' AAG ATC ATT ATG CCA ACA TCC TAG GTA AA 3') and another for C. albicans (sense: CAL5 – 5' TGT TGC TCT CTC GGG GGC GGC CG 3'; anti-sense: NL4CAL – 5' AAG ATC ATT ATG CCA ACA TCC TAG GTA AA 3'). The mix was prepared in an Eppendorf tube with 10x MgCl2 (2 mM), 0.2 mM of dNTP, 0.4 µM of each primer, 1 U of Taq and 2 µL of the sample, resulting in a final volume of 50.0 µL. Amplification was carried out in a PTC-200 thermal cycler (Peltier Thermal Cycler, MJ Research) as follows: 98 °C for three minutes, 95 °C for one minute, 52 °C for 1.5 minutes, 72 °C for 10 minutes, for total of 35 cycles. After the DNA of the sample was amplified, it was submitted to electrophoresis on a horizontal plate (Horizon 58-Life Technologies) in 1% agarose gel in TBE buffer at 100V for 35 minutes. The gel was then stained with ethidium bromide (Sigma) and the DNA bands were observed in a UV transilluminator fitted with a video camera linked to a computer (Multiimage Light Cabinet by Alpha Innotech Corporation) and photographed.



The results obtained in the amplification of the fragments using the primers CAL5 and NL4CAL (C. albicans), and CDU2 and NL4CAL (C. dubliniensis) are shown in Table 1.

The samples numbered from 3 to 24 are from HIV-negative patients, and those numbered from 25 to 39 are from HIV-positive patients. The samples numbered 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38 and 39 produced fragments with the primers CAL5 and NL4CAL and were identified as C. albicans. In relation to the primers CDU2 and NL4CAL, only the samples 20 (25 P) and 31 (15 H) produced fragments, being therefore identified as C. dubliniensis (Fig. 1).



The size of the fragment amplified by primers CAL5 and NL4CAL, and by primers CDU2 and NA4CAL, being 175 bp, corresponds to those observed by MANNARELLI & KURTZMAN (1998), thus allowing for the identification of the two respective species.



C. dubliniensis is a yeast species recently described as an opportunistic pathogen associated with oral candidiasis, particularly in HIV-positive individuals and AIDS patients41.

This species is phenotypically similar to C. albicans, which has resulted in problems in the identification of clinical samples8, as well as in the reidentification of isolates kept in culture collections and initially identified as C. albicans.

In a retrospective study carried out on a collection of yeast, COLEMAN et al.3 demonstrated that 2% of the isolates originally identified as C. albicans were actually C. dubliniensis. ODDS et al.27 reidentified 2589 cultures in a culture collection initially identified as C. albicans, finding that 2.1% were actually C. dubliniensis. JABRA-RIZK et al.10 found that 1.2% of 1251 isolates originally identified as C. albicans were actually C. dubliniensis. COLOMBO et al.5 investigated the presence of C. dubliniensis among 548 isolates kept in a collection and previously identified as C. albicans, finding that 11 of the isolates were actually C. dubliniensis.

In the present study, it was found that two of 37 samples previously identified as C. albicans were actually C. dubliniensis, for percentage of 5.4%.

In Brazil, C. dubliniensis was isolated for the first time in two AIDS patients in the state of São Paulo. One patient was a 3-year-old child with oropharyngeal candidiasis34 and the other was an adult24. ALVES et al.1 reported the first three cases of C. dubliniensis isolation from AIDS patients in the state of Rio Grande do Sul.

According to MARIANO et al.20 in South America the prevalence of C. dubliniensis isolates appears to be less than that encountered in North America.

The incidence of C. dubliniensis in HIV-positive and AIDS patients observed in Brazil is less than that encountered in Europe and the United States. MILAN et al.25 carried out the first multicenter prospective study of the oral incidence of C. dubliniensis in Brazilian HIV-positive and AIDS patients. Their study was conducted over a period of two years, at six medical centers around Brazil that provided treatment for HIV-positive patients. Of a total of 155 samples isolated, 2.8% were identified as C. dubliniensis. In a study done in Ireland, it was found that the incidence of C. dubliniensis ranged from 18 to 32% in HIV-infected individuals3,42, while studies conducted in the United States have reported rates ranging from 11.1 to 17.5%14,21.

The isolation of C. dubliniensis in HIV-negative patients has also been reported2,7,12,22,32,43. Recent studies have shown that this species is more prevalent in HIV-positive individuals, and it is encountered as a commensal organism that can cause various forms of candidiasis12. We point out, that in the present study, of the two samples identified as C. dubliniensis, one was isolated from an HIV-negative patient who only suffered from erythematous candidiasis.

In this study, the genotypic differentiation between C. albicans and C. dubliniensis was carried out by means of PCR, which proved to be a useful and practical method yielding an accurate identification, thereby showing that PCR can be an effective tool for elucidating the epidemiology of C. dubliniensis, and for establishing its clinical significance.



Our thanks go to FAPESP, UNIFAL-MG, USP for financial support, and to Dr. John Norman for his revision of the English manuscript.



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Correspondence to:
Dr. Jorge Kleber Chavasco
Departamento de Microbiologia, Instituto de Ciências Biomédicas II, Universidade de São Paulo
Av. Prof. Lineu Prestes 1374
05508-900 São Paulo, SP, Brazil
Tel: 55.11.3091-7294; Fax: 55.11.3091-7354

Received: 29 March 2005
Accepted: 25 August 2005

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