Improvements of PCR-based identification targeting the DNA topoisomerase II gene to determine major species of the opportunistic fungi Candida and Aspergillus fumigatus

Detection of Candida species by nested PCR method in one-humped camels (Camelus dromedarius)

Systemic fungal diseases are the infections caused by false treatment protocols and generally are not taken into consideration especially in the veterinary field. One-humped camels are found in the western side of the Aegean region of our country and bred for wrestling. The aim of this study is the application of diagnosing systemic fungi infection from camel blood samples by the PCR method. In this study, specific primers for DNA topoisomerase II gene sequences were used. As a result, a systemic fungal infection was detected by the nested PCR method from 10 (20%) out of 50 DNA samples taken from camels located on the western side of the Aegean region. In this study, 3 (30%) samples were identified as Candida albicans, 3 (30%) samples were identified as C. glabrata, and 4 (40%) samples were identified as C. parapsilosis. In conclusion, the 20% positive systemic fungal infection rate in one-humped camels observed in the present study showed that the systemic fungal infections are not taken into considerations in veterinary medicine. Further studies are suggested in order to obtain and to maintain extensive data for systemic fungal diseases in our country for one-humped camels.

Antiseptic effect of slightly acidic electrolyzed water on dental unit water systems

Biofilm formation in dental unit water systems (DUWSs) can contaminate water from three-in-one syringes, air rotors, and low-speed handpieces. This may serve as a potential source of infection for dentists, dental staff, and patients, so these systems must be sterilized. Because slightly acidic electrolyzed water (SAEW) is often used as a disinfectant for food, the aim of this study was to investigate the possibility of using SAEW as a DUWS disinfectant. Slightly acidic electrolyzed water was injected into a dental unit and its effects evaluated. Chemical properties such as chlorine ion and potential hydrogen in the SAEW were measured. Detection of both ordinary and heterotrophic bacteria from the DUWS was performed by culture, and biofilm formation of the bacteria in the DUWS evaluated. Polymerase chain reaction (PCR) was used to detected contamination by nosocomial pathogens. Almost all the chlorine ions in the SAEW were exhausted during the two-day trials, and the pH value of the SAEW fell from 5 to 4. No viable cells were detected in the SAEW collected. Biofilm formation in the water from the DUWS with SAEW was almost at a baseline level, whereas that without SAEW was 4 times higher. The PCR analysis showed that no nosocomial infecting pathogens were detected in the SAEW. The present study demonstrated the antiseptic effect of SAEW in DUWS.

Genotypes of Candida albicans involved in development of candidiasis and their distribution in oral cavity of non-candidiasis individuals

Genotype characteristics and distribution of commensal Candida albicans should be studied to predict the development of candidiasis, however, extensive genotype analysis of commensal C. albicans has not been made. In this study, 508 C. albicans isolates were collected from patients with/without candidiasis and divided into 4 isolate groups (SG-1, oral cavity of non-candidiasis patients; SG-2, patients with cutaneous candidiasis; SG-3, patients with vaginal candidiasis; SG-4, patients with candidemia). These isolates were characterized to study the relationship between genotypes and pathogenicity using microsatellite analysis. Using CDC3 and CAI, 5 genotypes (I, 111: 115/33: 41; II, 115: 119/23: 23; III, 115: 123/18: 27; IV, 115: 123/33: 40; and V, 123: 127/32: 41) were found in 4.2%, 8.9%, 7.1%, 2.2% and 3.1% of the isolates, respectively. Genotypes II and III were commonly found in all isolate groups. These genotypes were further divided into 28 types by additional HIS3 and CAIII microsatellite markers. In this analysis, C. albicans with type 6 and type 23 was widely distributed as a commensal species in the oral cavity of non-candidiasis patients and found to be related with candidiasis development. Additionally, genotypes I and IV were found in SG-2 and/or SG-4, suggesting that the fungus with those genotypes is also involved in this development. In contrast, genotype V was not identified in any infective isolates.

Microsatellite-based genotyping of Candida albicans isolated from patients with superficial candidiasis

This study aimed to examine the genotype distribution of Candida albicans and the major genotypes involved in superficial candidiasis. The genotypes of C. albicans isolated from the infection sites of patients with superficial candidiasis (referred to as infection isolates) were analyzed by fragment analysis using 4 microsatellite markers (HIS3, CDC3, CAI and CAIII). Genotypes of the infection isolates were compared with those of C. albicans isolated from oral mucosa of non-candidiasis patients (referred to as oral isolates). Isolates of C. albicans showed 4 major genotypes for HIS3/CAI (" a " for 148 : 148 / 23 : 23," b " for 148 : 160 / 33 : 41," c " for 148 : 164 / 32 : 41 and " d " for 152 : 152 / 18 : 27). The genotypes " a "," b " and " d " were commonly found in oral (4.7, 8.8 and 7.6%, respectively) and infection (6.6, 9.2 and 15.4%, respectively) isolates. No isolates of genotype " c " were isolated from infection sites. The genotype " a " was found in the isolates from patients with genitalia candidiasis. Genotyping of multiple isolates from an individual patient showed that C. albicans from infection sites was genetically homogenous as compared with that of oral isolates, even in the same patient with candidiasis.

Application of an oligonucleotide microarray-based nano-amplification technique for the detection of fungal pathogens

BACKGROUND

The traditional techniques for diagnosis of invasive fungal infections in the clinical microbiology laboratory need improvement. These techniques are prone to delay results due to their time-consuming process, or result in misidentification of the fungus due to low sensitivity or low specificity. The aim of this study was to develop a method for the rapid detection and identification of fungal pathogens.

METHODS

The internal transcribed spacer two fragments of fungal ribosomal DNA were amplified using a polymerase chain reaction for all samples. Next, the products were hybridized with the probes immobilized on the surface of a microarray. These species-specific probes were designed to detect nine different clinical pathogenic fungi including Candida albicans, Candida tropocalis, Candida glabrata, Candida parapsilosis, Candida krusei, Candida lusitaniae, Candida guilliermondii, Candida keyfr, and Cryptococcus neoformans. The hybridizing signals were enhanced with gold nanoparticles and silver deposition, and detected using a flatbed scanner or visually.

RESULTS

Fifty-nine strains of fungal pathogens, including standard and clinically isolated strains, were correctly identified by this method. The sensitivity of the assay for Candida albicans was 10 cells/mL. Ten cultures from clinical specimens and 12 clinical samples spiked with fungi were also identified correctly.

CONCLUSIONS

This technique offers a reliable alternative to conventional methods for the detection and identification of fungal pathogens. It has higher efficiency, specificity and sensitivity compared with other methods commonly used in the clinical laboratory.

Phospholipase and proteinase activities of Candida isolates from denture wearers

The aim of the present study was to characterise phospholipase and proteinase activities of oral Candida isolates from 100 denture wearers and to study the relationship of these activities with denture stomatitis. Of 100 patients studied, 44 suffered from denture stomatitis. Specimens were collected by swabbing the denture and underlying mucosa. Isolates were previously identified by conventional mycological and genotypic methods. The phospholipase and proteinase activities were evaluated by agar plate methods. A total of 152 isolates were recovered from denture and underlying mucosa, including 101 Candida albicans, 18 Candida tropicalis, 14 Candida glabrata, 11 Candida guilliermondii, four Candida parapsilosis, two Saccharomyces cerevisiae and one isolate each of Candida dubliniensis and Candida krusei. Most C. albicans (97%) showed phospholipase activity; furthermore, the unique C. dubliniensis isolate showed a moderate phospholipase activity. The isolation of C. albicans (chi-square test, P = 0.0016) and phospholipase production by Candida spp. (chi-square test, P = 0.0213) was found to be significantly associated with denture stomatitis. Proteinase production was observed in <30% of isolates, and it was not related to the presence of denture stomatitis (P = 0.7675). Candida albicans isolates may produce both virulence factors, although the proteinase production was only observed in <30% of the isolates. Phospholipase production was exclusive of C. albicans and C. dubliniensis.

Genotyping of Candida albicans by fragment analysis of microsatellites combined with 25S rDNA and RPS-based strategies

Because of its high discriminatory potential, fragment analysis of microsatellites has been frequently used for genotyping of Candida albicans at the strain level. In order to evaluate a genotyping system based on the fragment analysis of microsatellites combined with PCRs targeting 25S rDNA and RPS, 456 independent strains of C. albicans were subjected to genotype analysis using 4 microsatellite markers (CDC3, HIS3, CA I and CA III), followed by 25S rDNA and RPS-based genotyping. The fragment analysis using CA I showed the highest discriminatory potential (DP=0.9782), followed by HIS3 (DP=0.8780). Using combined microsatellite markers, 456 C. albicans strains were divided into 384 genotypes (DP=0.9984). PCRs targeting 25S rDNA and RPS were performed to differentiate the strains that showed identical genotypes in the fragment analysis, resulting in 434 genotypes (DP=0.9996). The combined genotyping system showed high discriminatory power at the strain level, and therefore is useful for rapid genotyping in molecular epidemiological studies of candidiasis.

Evaluation of the new chromogenic medium Candida ID 2 for isolation and identification of Candida albicans and other medically important Candida species

The usefulness of Candida ID 2 (CAID2) reformulated medium (bioMérieux, France) has been compared with that of the former Candida ID (CAID; bioMérieux), Albicans ID 2 (ALB2; bioMérieux), and CHROMagar Candida (CAC; Chromagar, France) chromogenic media for the isolation and presumptive identification of clinically relevant yeasts. Three hundred forty-five stock strains from culture collections, and 103 fresh isolates from different clinical specimens were evaluated. CAID2 permitted differentiation based on colony color between Candida albicans (cobalt blue; sensitivity, 91.7%; specificity, 97.2%) and Candida dubliniensis (turquoise blue; sensitivity, 97.9%; specificity, 96.6%). Candida tropicalis gave distinguishable pink-bluish colonies in 97.4% of the strains in CAID2 (sensitivity, 97.4%; specificity, 100%); the same proportion was reached in CAC, where colonies were blue-gray (sensitivity, 97.4%; specificity, 98.7%). CAC and CAID2 showed 100% sensitivity values for the identification of Candida krusei. However, with CAID2, experience is required to differentiate the downy aspect of the white colonies of C. krusei from other white-colony-forming species. The new CAID2 medium is a good candidate to replace CAID and ALB2, and it compares well to CAC for culture and presumptive identification of clinically relevant Candida species. CAID2 showed better results than CAC in some aspects, such as quicker growth and color development of colonies from clinical specimens, detection of mixed cultures, and presumptive differentiation between C. albicans and C. dubliniensis.

Biology of the pathogenic yeast Candida glabrata

The yeasts, being favorite eukaryotic microorganisms used in food industry and biotechnologies for production of biomass and various substances, are also used as model organisms in genetic manipulation, molecular and biological research. In this respect, Saccharomyces cerevisiae is the best-known species but current situation in medicine and industry requires the use of other species. Here we summarize the basic taxonomic, morphological, physiological, genetic, etc. information about the pathogenic yeast Candida glabrata that is evolutionarily very closely related to baker's yeast.

Genotype analysis of Candida albicans isolates obtained from different body locations of patients with superficial candidiasis using PCRs targeting 25S rDNA and ALT repeat sequences of the RPS

BACKGROUND

Several molecular biology-based genotyping techniques have been adapted for studying the molecular characteristics of Candida albicans strains, which constitute the majority of the etiologic agents in candidiasis. Recently, we reported a PCR system targeting 25S rDNA and ALT repeat sequences in the repetitive sequence (RPS) for genotyping of C. albicans.

OBJECTIVE

To assess the potential of 25S rDNA and RPS-based genotyping for studying the molecular epidemiology of C. albicans, and define the genotypic relationship of C. albicans between invasive and non-invasive lesions in the same individual.

METHODS

C. albicans strains were isolated from infected lesions and commensal sites, such as oral mucosa and/or feces, of patients with superficial candidiasis. The genomic DNAs were amplified by PCRs using P-I and P-II to determine the 25S rDNA- and RPS-based genotypes of the isolates.

RESULTS

Genotype A:3 C. albicans constituted the majority of the isolates, followed by A:3/4 and B:3 C. albicans. There was usually one genotype of C. albicans per person. The genotypes of infected lesion isolates and non-infected oral mucosa and/or feces isolates were identical in the same individual, even in serially isolated C. albicans.

CONCLUSION

The results indicate that our combined PCR technique using P-I and P-II is a potential tool for molecular typing of C. albicans, and reveal that the genotypes of isolates are identical in the same individual, independent of the infective and non-infective phases or the body location.

Use of PCR Based Diagnosis for Common Invasive Fungal Infections in the Intensive Care Unit

Deep-seated Candida infections and invasive aspergilloma are becoming a serious problem for individuals who need intensive care. The laboratory diagnosis of such infections is sometimes delayed due to relatively slow growth of these yeasts from clinical specimens. Several studies seem to indicate that early detection of deep-seated and invasive fungal infections is possible using genomic amplification methods. In the present study, we used a novel PCR assay that can assay five clinically common species (C. albicans, C. parapsilosis, C. tropicalis, C. glablata, and A. fumigatus) simultaneously. We evaluated the utility of this PCR based diagnosis with seven patients with candidiases. This assay is more sensitive than the culture result in 26 clinical samples (chi(2)=5.16, p < 0.05). In the clinical course of each patient, the number of detected fungal species gradually increased. More than two species were detected from single or several clinical specimens, and these patients would die within 14 days compared with the 61 day period individuals with zero or one species would live (p < 0.005). Before super infections of fungus, an antifungal drug could be applied to a suspected patient in the ICU. To improve sensitivity of this diagnosis from blood samples, we evaluated them after one day incubation at 34 degree. We found a PCR product in 10 of 20 blood samples taken from five children after bone marrow transplantation. One of four negative samples became positive after more than 48 hours of incubation.

Genotyping of Candida albicans on the basis of polymorphisms of ALT repeats in the repetitive sequence (RPS)

BACKGROUND

Candida albicans is one of the most important etiologic agents causing superficial and deep fungal infections. For prevention of candidiasis, it is important to develop a rapid system that discriminates C. albicans at the strain level.

OBJECTIVE

To develop a system that can identify C. albicans at the strain level.

METHODS

Genomic DNAs were purified from 179 clinical isolates of C. albicans, and were used as templates for PCR amplification of 25S rDNA and ALT repeats in repetitive sequences (RPSs). PCR products generated from ALT repeats were digested with EcoRI and/or ClaI in order to study the relationships between restriction profiles and amplification profiles.

RESULTS

One hundred and seventy nine clinical isolates were grouped into genotypes A (92 isolates), B (38 isolates) and C (49 isolates) on the basis of their 25S rDNA, and each was further classified into five types (types 3, 4, 3/4, 2/3/4 and 3/4/5) by PCR amplification targeting ALT repeats. Type 3 C. albicans constituted the majority of isolates in any genotypes (66.3% for genotype A, 76.3% for genotype B and 73.4% for genotype C). Each C. albicans type showed several amplification patterns, indicating the existence of subtypes. RFLP analysis revealed that restriction profiles of PCR products corresponded to amplification patterns from PCR.

CONCLUSION

The present results indicate that PCR amplifications targeting 25S rDNA and ALT repeats are useful for rapid genotyping and distinction of C. albicans involved in superficial candidiasis.

Rapid identification of Candida albicans and its related species Candida stellatoidea and Candida dubliniensis by a single PCR amplification using primers specific for the repetitive sequence (RPS) of Candida albicans

BACKGROUND

Candidiasis is caused by several Candida species, of which Candida stellatoidea and C. dubliniensis are phenotypically close to C. albicans. Although current molecular biology-based techniques can distinguish between C. albicans and C. dubliniensis, a convenient tool that can distinguish C. stellatoidea from C. albicans has not yet been developed.

OBJECTIVE

To develop a system that can simply, rapidly and specifically distinguish C. albicans from the related Candida species C. stellatoidea and C. dubliniensis.

MATERIALS

Genomic DNAs were purified from various yeast species and amplified by primers specific for the repetitive sequence (RPS) of C. albicans. The PCR products were purified and sequenced in order to test the specificity of the PCR amplification.

RESULTS

The PCR primers only amplified several products from C. albicans, C. stellatoidea and C. dubliniensis. Sequence analysis of the products revealed that C. stellatoidea and C. dubliniensis both had RPSs including alt repeats, similar to C. albicans. After the PCR amplification, each of the three Candida species showed a unique amplification profile. Furthermore, RFLP analysis of the PCR products using EcoRI and ClaI produced species-specific restriction profiles.

CONCLUSIONS

This PCR-based technique targeting the alt repeats in the RPS is useful as a tool for the rapid identification and distinction of C. albicans, C. stellatoidea and C. dubliniensis.

Monochrome LightCycler PCR assay for detection and quantification of five common species of Candida and Aspergillus

Invasive fungal pathogens, especially in immunocompromised hosts, can result in life-threatening infections. Current laboratory/radiological methods for fungal identification are time-consuming and lack sensitivity and specificity. A monochrome, multiplex, real-time PCR assay for the identification and quantification of Candida albicans, Candida krusei, Candida tropicalis, Aspergillus flavus and Aspergillus fumigatus is described here. Detection of each of these fungi was specific and demonstrated 100 % concordance with biochemical/culture identification in all 60 isolates tested. Samples from 16 febrile neutropenic patients with haematological malignancies were also analysed and the utility of the assay in clinical samples was reconfirmed without false-negative results. The sensitivity of this assay was 0.1 pg fungal genomic DNA, corresponding to three cells, for C. albicans, C. krusei, C. tropicalis and A. flavus, and 0.01 pg fungal genomic DNA, i.e. less than one cell, for A. fumigatus. The analysis allows a low-cost, simple, rapid and sensitive alternative for clinical identification and quantification of these five common fungal species.

Epidemiological study of Candida species in cutaneous candidiasis based on PCR using a primer mix specific for the DNA topoisomerase II gene

BACKGROUND

We have previously reported a PCR-based identification system for pathogenic fungi by targeting the DNA topoisomerase II gene, in which primer mixes specific for this gene were used for the PCR amplifications.

OBJECTIVE

To test the potential of the PCR using primer mix that is specific for the DNA topoisomerase II gene and are designated as PsVIc, for rapid identification of Candida species involved in cutaneous candidiasis, and to define the relation between Candida species and the infection lesion.

METHODS

Scales from 48 patients with cutaneous candidiasis were cultured on GYEP agar plates, and the genomic DNAs were purified from the colonies and used as DNA templates for PCR amplifications. Candida was identified as individual species based on the sizes of the PCR products generated in the PCR amplifications using PsVlc.

RESULTS

Four Candida species (five genotypes; Candida albicans, Candida glabrata, Candida parapsilosis I, Candida parapsilosis II and Candida tropicalis II) were identified in the patients' scales. In 19 of the patients (39.6%), multiple PCR products (two or three bands) were amplified in a DNA sample, especially derived from scales at the groin of bed-ridden older patients using napkins.

CONCLUSION

The PCR-based identification using the primer mix was useful for an epidemiological study of Candida species in cutaneous candidiasis.

PCR and PCR–RFLP techniques targeting the DNA topoisomerase II gene for rapid clinical diagnosis of the etiologic agent of dermatophytosis

BACKGROUND

We have focused on the DNA topoisomerase II genes of several pathogenic fungi, and developed polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (RFLP) methods targeting this gene for identification of dermatophytes.

OBJECTIVE

To assess the availability of the PCR-based identification for an etiologic study of dermatophytosis, by testing these PCR and PCR-RFLP methods for stability and reproducibility.

METHODS

Three hundred and fifty-six dermatophyte strains were isolated from 305 patients with tinea, and their genomic DNAs were used as templates for the PCR using primer mixes (PsT, PsME, dPsD1 or dPsD2) composed of gene-specific primers for identification of dermatophytes to the species level. The genomic DNAs of Trichophyton rubrum were further subjected to subrepeat element analysis of the nontranscribed spacer (NTS) of ribosomal DNA (rDNA).

RESULTS

In this study, six dermatophyte species (T. rubrum, Trichophyton mentagrophytes, Trichophyton tonsurans, Microsporum canis, Microsporum gypseum, and Epidermophyton floccosum) were obtained. In all cases, the identifications obtained from the PCR and PCR-RFLP targeting the DNA topoisomerase II gene coincided with those from the conventional morphological features-based identification technique. The sensitivity of the PCR-based identification was found to be a colony of approximately 3mm in diameter. Furthermore, T. rubrum was divided into three groups (17 types) on the basis of the sizes and numbers of the products generated from the TRS-1 region, and three types from the TRS-2 region.

CONCLUSION

The PCR and PCR-RFLP targeting the DNA topoisomerase II gene were rapid, stable, and reproducible for species identification of dermatophytes, and thus are convenient tools for an etiologic study of dermatophytosis.