Rapid and unequivocal differentiation of Candida dubliniensis from other Candida species using species-specific DNA probes: comparison with phenotypic identification methods

Genotyping of Candida albicans and Comparison of its Antifungal Resistance Pattern in the South Indian Region

Recent studies have documented an increase in the incidence of antifungal resistance in newly emerging species closely related to C. albicans, and the coexistence of genotypic variants. Hence, an application of PCR-based molecular typing is crucial in identifying these fungi. Our study used molecular methods to characterize the latest genotypic subgroups of C. albicans and analysed if there was a relationship between the genotypes and the antifungal resistance pattern. The study was conducted in JSS Hospital, Mysuru, Karnataka between July 2018 and December 2020. A total of 1427 Candida species were isolated from clinical samples. Candida albicans were isolated and confirmed using Germ tube test, ID VITEK 2 and PCR (ITS primer). DNA extraction was done using the Hi-Media Yeast DNA Extraction Kit. The amplified products were analysed using Agarose gel electrophoresis (2%). Among 1427 Candida species, 282 were Candida albicans. The following resistance was exhibited to major antifungals – Caspofungin (3.5%), Amphotericin B (1.4%), flucytosine (2.8%) Fluconazole (6%) Micafungin (2.8%) Voriconazole (3.1%) and all were sensitive to miconazole. ABC genotyping showed Genotype A (450 bp) predominant (87.58%) followed by genotype B (840bp) (9.92 %) and genotype C (450bp and 840 bp) (0.2%). Genotype D and E were not observed. Our study showed the growing antifungal resistance in clinical isolates. Genotype A was predominant in South Karnataka region followed by Genotype B and C. There was no correlation between genotyping and antifungal resistance. However, a study with greater number of samples from diverse geographical locations may give more insight.

Comparison of duplex PCR and phenotypic analysis in differentiating Candida dubliniensis from Candida albicans from oral samples

Candida dubliniensis shares a wide range of phenotypic characteristics with Candida albicans including a common trait called germ tube positivity. Hence, laboratory differentiation of these two species is cumbersome. Duplex PCR analyses for C. albicans and C. dubliniensis was performed directly on DNA extracted from a total of 122 germ tube positive isolates derived from 100 concentrated oral rinse samples from a random cohort of diabetics attending a clinic in Sri Lanka. These results were confirmed by DNA sequencing of internal transcribed spacer (ITS) region of rDNA of the yeasts. Performance efficacy of duplex PCR was then compared with phenotypic identification using a standard battery of phenotypic tests. Of the 122 germ tube positive isolates three were identified by duplex PCR as C. dubliniensis and the remainder as C. albicans. On the contrary, when the standard phenotypic tests, sugar assimilation and chlamydospore formation, were used to differentiate the two species 13 germ tube positive isolates were erroneously identified as C. dubliniensis. Duplex PCR was found to be rapid, sensitive and more specific than phenotypic identification methods in discriminating C. dubliniensis from C. albicans. This is also the first report on the oral carriage of C. dubliniensis in a Sri Lankan population.

Candida dubliniensis Pneumonia: A Case Report and Review of Literature

Candida dubliniensis is an uncommon species of Candida which has been implicated in fungal pneumonia only very rarely. We present the case of a 75-year-old man with laryngeal cancer undergoing chemotherapy on broad-spectrum antibiotics and tuberculosis therapy with blood and endotracheal cultures positive for C. dubliniensis. Subsequent autopsy was performed with postmortem lung cultures positive for C. dubliniensis and lung histopathology demonstrating an invasive fungal infection. Molecular analysis of the lung tissue confirmed the identity of the fungi as C. dubliniensis. Since its discovery as a pathogen in the oral cavities of HIV-positive patients, C. dubliniensis has been identified in a wide spectrum of clinical scenarios and anatomic locations but manifests only rarely as pneumonia. This report represents a novel case of C. dubliniensis pneumonia confirmed by culture, histopathology, and molecular identification.

Rapid identification of medically important Candida isolates using high resolution melting analysis

An increasing trend in non albicans infections and various susceptibility patterns to antifungal agents implies a requirement for the quick and reliable identification of a number of medically important Candida species. Real-time PCR followed by high resolution melting analysis (HRMA) was developed, tested on 25 reference Candida collection strains and validated on an additional 143 clinical isolates in this study. All reference strains and clinical isolates inconclusive when using phenotypic methods and/or HRMA were analysed using ITS2 sequencing. Considering reference and clinical strains together, 23 out of 27 Candida species could be clearly distinguished by HRMA, while the remaining 4 species were grouped in 2 pairs, when applying the mean Tm ± 3 SD values, the shape of the derivative melting curve (dMelt curve) and, in some cases, the normalized and temperature—shifted difference plot against C. krusei. HRMA as a simple, rapid and inexpensive tool was shown to be useful in identifying a wide spectrum of clinically important Candida species. It may complement the current clinical diagnostic approach based on commercially available biochemical kits.

Identification and characterization of nine atypical Candida dubliniensis clinical isolates

Candida dubliniensis is a pathogenic yeast of the genus Candida closely related to Candida albicans. The phenotypic similarity of these two species often leads to misidentification of C. dubliniensis isolates in clinical samples. DNA-based methods continue to be the most effective means of discriminating accurately between the two species. Here, we report on the identification of nine unusual Candida isolates that showed ambiguous identification patterns on the basis of their phenotypic and immunological traits. The isolates were categorized into two groups. Group I isolates were unable to produce germ tubes and chlamydospores, and to agglutinate commercial latex particles coated with a mAb highly specific for C. dubliniensis. Group II isolates grew as pink and white colonies on CHROMagar Candida and ChromID Candida, respectively. Carbohydrate assimilation profiles obtained with API/ID32C together with PCR amplification with specific primers and DNA sequencing allowed reliable identification of the nine unusual clinical isolates as C. dubliniensis.

Rare case of exogenous Candida dubliniensis endophthalmitis: a case report and brief review of the literature

Background

Candida dubliniensis is a recently described opportunistic fungal pathogen that rarely infects the eye. Reported cases of C. dubliniensis endophthalmitis have been of endogenous etiology and demonstrated recovery of visual acuity with timely treatment. We herein report an unusual case of severe C. dubliniensis endophthalmitis requiring enucleation.

Findings

This is a retrospective, descriptive case report with a brief literature review. A 41-year-old Caucasian man, with a history of blunt trauma 8 months prior, presented to the emergency department with left eye pain and loss of vision 2 days after complicated cataract surgery. He was first evaluated by an outside ophthalmologist 3 months after trauma for left eye pain and progressive vision loss. He was found to have light perception vision with non-granulomatous anterior uveitis but no sign of ruptured globe. A dense cataract developed while he was treated with topical and subtenon's corticosteroids for which he underwent cataract surgery. Our examination revealed no light perception vision with a relative afferent pupillary defect, elevated intraocular pressure, moderate anterior chamber reaction, pupillary membrane, vitritis, and choroidal thickening on B-scan ultrasonography. Diagnostic vitrectomy revealed purulent vitreal debris, retinal detachment with severe retinal necrosis, and choroidal infiltrates. Operative fungal cultures grew C. dubliniensis. Despite intravitreal and systemic anti-fungal treatment, vision and pain did not improve, resulting in subsequent enucleation.

Conclusion

C. dubliniensis endophthalmitis is uncommonly encountered and typically has reasonable visual outcomes. This is the first reported case of C. dubliniensis, likely exogenous endophthalmitis, resulting in enucleation, illustrating the potential virulence of this newly described organism.

The usefulness of DNA sequencing after extraction by Whatman FTA filter matrix technology and phenotypic tests for differentiation of Candida albicans and Candida dubliniensis

Since C. dubliniensis is similar to C. albicans phenotypically, it can be misidentified as C. albicans. We aimed to investigate the prevalence of C. dubliniensis among isolates previously identified as C. albicans in our stocks and to compare the phenotypic methods and DNA sequencing of D1/D2 region on the ribosomal large subunit (rLSU) gene. A total of 850 isolates included in this study. Phenotypic identification was performed based on germ tube formation, chlamydospore production, colony colors on chromogenic agar, inability of growth at 45 °C and growth on hypertonic Sabouraud dextrose agar. Eighty isolates compatible with C. dubliniensis by at least one phenotypic test were included in the sequence analysis. Nested PCR amplification of D1/D2 region of the rLSU gene was performed after the fungal DNA extraction by Whatman FTA filter paper technology. The sequencing analysis of PCR products carried out by an automated capillary gel electrophoresis device. The rate of C. dubliniensis was 2.35 % (n = 20) among isolates previously described as C. albicans. Consequently, none of the phenotypic tests provided satisfactory performance alone in our study, and molecular methods required special equipment and high cost. Thus, at least two phenotypic methods can be used for identification of C. dubliniensis, and molecular methods can be used for confirmation.

Issues in identifying germ tube positive yeasts by conventional methods

Candida speciation is vital for epidemiology and management of candidiasis. Nonmolecular conventional methods often fail to identify closely related germ tube positive yeasts from clinical specimens. The present study was conducted to identify these yeasts and to highlight issues in conventional versus molecular methods of identification. A total of 98 germ tube positive yeasts from high vaginal swabs were studied over a 12-month period. Isolates were examined with various methods including growth at 42 °C and 45 °C on Sabouraud dextrose agar (SDA), color development on CHROMagar Candida medium, chlamydospore production on corn meal agar at 25 °C, carbohydrate assimilation using ID 32C system, and polymerase chain reaction using a single pair of primers targeting the hyphal wall protein 1 (Hwp1) gene. Of all the isolates studied, 97 were molecularly confirmed as C. albicans and one isolate was identified as C. dubliniensis. No C. africana was detected in this study. The molecular method used in our study was an accurate and useful tool for discriminating C. albicans, C. dubliniensis, and C. africana. The conventional methods, however, were less accurate and riddled with many issues that will be discussed in further details.

Distribution of Candida in the oral cavity and its differentiation based on the internally transcribed spacer (ITS) regions of rDNA

This study aimed to determine the distribution of Candida species in the oral cavity and differentiate the species based on PCR amplification, including HinfI and MspI digestion, in order to assess the effectiveness of using the rDNA region for species identification. Samples from saliva as well as palate, tongue and cheek mucosa surfaces were collected from 45 individuals, consisting of three groups: periodontal disease patients; denture-wearers; and the control group. The samples were serially diluted, spread on BHI and YPD agar plates and scored for colony-forming units (CFUs). Fifteen random candidal colonies were isolated and subjected to genomic DNA extraction, based on glass beads disruption. Four primers were used to amplify regions in the rDNA, and the ITSI-5.8S-ITSII PCR product was digested by HinfI and MspI restriction enzymes. The microbial loads on all sites of the denture-wearers were found to be significantly higher than control, while in the periodontal disease group only the microbial loads on the tongue were significantly higher than control. Meanwhile, there was no significant difference at other sites. The restriction fragment lengths of the clinical samples were compared to those of seven control species, allowing the differentiation of all seven species and the identification of 14 species from the clinical samples. The MspI restriction digest was not able to distinguish between C. albicans and C. dubliniensis, whereas the HinfI digest could not distinguish between C. tropicalis and C. parapsilosis. It was concluded that PCR-RFLP of the candidal rDNA region has potential for species identification. This study demonstrates the potential use of candidal rDNA as a means for identifying Candida species, based on genotype. The results also indicate the possibility of constructing genetic probes that target specific restriction fragments in the ITSI-5.8S-ITSII region, enabling swift and precise identification of Candida species.

Use of denaturing gradient gel electrophoresis for the identification of mixed oral yeasts in human saliva

A PCR-denaturing gradient gel electrophoresis (DGGE) method was established for the simultaneous presumptive identification of multiple yeast species commonly present in the oral cavity. Published primer sets targeting different regions of the Saccharomyces cerevisiae 26-28S rRNA gene (denoted primer sets N and U) and the 18S rRNA gene (primer set E) were evaluated with ten Candida and four non-Candida yeast species, and twenty Candida albicans isolates. Optimized PCR-DGGE conditions using primer set N were applied to presumptively identify, by band matching, yeasts in the saliva of 25 individuals. Identities were confirmed by DNA sequencing and compared with those using CHROMagar Candida culture. All primer sets yielded detectable DGGE bands for all species tested. Primer set N yielded mainly single bands and could distinguish all species examined, including differentiating Candida dubliniensis from C. albicans. Primer set U was less discriminatory among species but yielded multiple bands that distinguished subspecies groups within C. albicans. Primer set E gave poor yeast discrimination. DGGE analysis identified yeasts in 17 of the 25 saliva samples. Six saliva samples contained two yeast species: three contained C. albicans and three C. dubliniensis. C. dubliniensis was present alone in one saliva sample (total prevalence 16 %). CHROMagar culture detected yeasts in 16 of the yeast-containing saliva samples and did not enable identification of 7 yeast species identified by DGGE. In conclusion, DGGE identification of oral yeast species with primer set N is a relatively fast and reliable method for the simultaneous presumptive identification of mixed yeasts in oral saliva samples.

Rapid differentiation of Candida dubliniensis from Candida albicans by early D-xylose assimilation

OBJECTIVE

To determine if D-xylose (XYL) and/or α-methyl-D-glucoside (MDG) assimilation can be used reliably as a rapid test to differentiate Candida dubliniensis from Candida albicans at an earlier time point such as 2 h after inoculation.

MATERIALS AND METHODS

Thirty isolates of C. albicans and C. dubliniensis recovered from anatomical sites and clinical specimens were used. Isolates were inoculated into the API 20C AUX yeast identification system, and incubated at 30°C. XYL and MDG assimilations were read at 2-hour intervals beginning 2 h after the initial inoculation and up to 24 h of incubation; thereafter, results were read after 48 and 72 h.

RESULTS

Twenty-nine (97%) C. albicans isolates had assimilated XYL at 16 h and, by 24 h, all isolates were positive for XYL assimilation. None of the C. dubliniensis isolates assimilated XYL. The MDG assimilation revealed that 24, 40, 92 and 100% of C. albicans isolates became positive after 16, 24, 48 and 72 h of incubation, respectively, whereas only 3% of C. dubliniensis isolates assimilated MDG after 72 h.

CONCLUSIONS

The findings showed that it is possible to rapidly differentiate C. albicans from C. dubliniensis isolates using the API 20C AUX carbohydrate assimilation kits after 16 h of incubation at 30°C based on the XYL assimilation.

Research on Candida dubliniensis in a Brazilian yeast collection obtained from cardiac transplant, tuberculosis, and HIV-positive patients, and evaluation of phenotypic tests using agar screening methods

The aim of this study was to research Candida dubliniensis among isolates present in a Brazilian yeast collection and to evaluate the main phenotypic methods for discrimination between C. albicans and C. dubliniensis from oral cavity. A total of 200 isolates, presumptively identified as C. albicans or C. dubliniensis obtained from heart transplant patients under immunosuppressive therapy, tuberculosis patients under antibiotic therapy, HIV-positive patients under antiretroviral therapy, and healthy subjects, were analyzed using the following phenotypic tests: formation and structural arrangement of chlamydospores on corn meal agar, casein agar, tobacco agar, and sunflower seed agar; growth at 45 °C; and germ tube formation. All strains were analyzed by polymerase chain reaction (PCR). In a preliminary screen for C. dubliniensis, 48 of the 200 isolates on corn meal agar, 30 of the 200 on casein agar, 16 of the 200 on tobacco agar, and 15 of the 200 on sunflower seed agar produced chlamydoconidia; 27 of the 200 isolates showed no or poor growth at 45 °C. All isolates were positive for germ tube formation. These isolates were considered suggestive of C. dubliniensis. All of them were subjected to PCR analysis using C. dubliniensis-specific primers. C. dubliniensis isolates were not found. C. dubliniensis isolates were not recovered in this study done with immunocompromised patients. Sunflower seed agar was the medium with the smallest number of isolates of C. albicans suggestive of C. dubliniensis. None of the phenotypic methods was 100% effective for discrimination between C. albicans and C. dubliniensis.

Candida albicans or Candida dubliniensis?

Candida albicans is increasing as an opportunistic pathogen causing candidemia and candidiasis worldwide. In addition, other non-albicans Candida species are now also associated with pertinent infections. These include the closely related C. dubliniensis, which shares many phenotypic similarities with C. albicans. These similarities pose problems in the identification of isolates and have previously led to misidentification of these species. As a result, several identification techniques based on phenotypic and genotypic characteristics have been developed to differentiate between these Candida species. This review will focus on the similarities and differences between these two Candida species highlighting different identification methods and their advantages and disadvantages.

High-throughput identification and quantification of Candida species using high resolution derivative melt analysis of panfungal amplicons

Fungal infections pose unique challenges to molecular diagnostics; fungal molecular diagnostics consequently lags behind bacterial and viral counterparts. Nevertheless, fungal infections are often life-threatening, and early detection and identification of species is crucial to successful intervention. A high throughput PCR-based method is needed that is independent of culture, is sensitive to the level of one fungal cell per milliliter of blood or other tissue types, and is capable of detecting species and resistance mutations. We introduce the use of high resolution melt analysis, in combination with more sensitive, inclusive, and appropriately positioned panfungal primers, to address these needs. PCR-based amplification of the variable internal transcribed regions of the rDNA genes generates an amplicon whose sequence melts with a shape that is characteristic and therefore diagnostic of the species. Simple analysis of the differences between test and reference melt curves generates a single number that calls the species. Early indications suggest that high resolution melt analysis can distinguish all eight major species of Candida of clinical significance without interference from excess human DNA. Candida species, including mixed and novel species, can be identified directly in vaginal samples. This tool can potentially detect, count, and identify fungi in hundreds of samples per day without further manipulation, costs, or delays, offering a major step forward in fungal molecular diagnostics.

Current status and future perspectives on molecular and serological methods in diagnostic mycology

Invasive fungal infections are an important cause of infectious morbidity. Nonculture-based methods are increasingly used for rapid, accurate diagnosis to improve patient outcomes. New and existing DNA amplification platforms have high sensitivity and specificity for direct detection and identification of fungi in clinical specimens. Since laboratories are increasingly reliant on DNA sequencing for fungal identification, measures to improve sequence interpretation should support validation of reference isolates and quality control in public gene repositories. Novel technologies (e.g., isothermal and PNA FISH methods), platforms enabling high-throughput analyses (e.g., DNA microarrays and Luminex® xMAP™) and/or commercial PCR assays warrant further evaluation for routine diagnostic use. Notwithstanding the advantages of molecular tests, serological assays remain clinically useful for patient management. The serum Aspergillus galactomannan test has been incorporated into diagnostic algorithms of invasive aspergillosis. Both the galactomannan and the serum β-D-glucan test have value for diagnosing infection and monitoring therapeutic response.

[Candida dubliniensis: Identification methods and epidemiologic implication]

Candida dubliniensis was recently described (1995) associated with oral candidiasis in HIV-positive patients. This organism is very closely related to the pathogenic human yeast, Candida albicans, and share a great number of phenotypic and genotypic characters. This great similarity limits the discrimination between these two species. Several phenotypic and molecular methods were developed. The phenotypic methods are simply used in routine discrimination between these two species and depend on the growth at high temperature, sugar assimilation, growth on special mediums and chlamydospore production…; but these methods are insensitive in discrimination between these two species. The molecular biology methods are highly reliable and able to confirm rapidly the identification of this species. In this article, we will review the various studies run out concerning the methods deployed for the identification of C. dubliniensis as well as the epidemiological implication of this new pathogen.

DNA pyrosequencing-based identification of pathogenic Candida species by using the internal transcribed spacer 2 region

CONTEXT

The incidence of infections due to diverse Candida species is increasing, with correspondingly different antifungal susceptibility patterns. Routine yeast identification methods cause significant delays in appropriate patient management.

OBJECTIVE

A DNA pyrosequencing strategy was evaluated for identification of pathogenic Candida species associated with human infections.

DESIGN

Clinical (n = 51) and commercial (n = 9) Candida isolates were identified in a blinded, parallel study consisting of routine fungal cultures and biochemical analyses in comparison with DNA pyrosequencing.

RESULTS

DNA pyrosequencing yielded species-level identification of all 60 Candida isolates, and sequencing interpretations agreed in all cases with results of biochemical and morphologic testing. Different Candida species were identified, such as C. albicans, C. dubliniensis, C. glabrata, C. guilliermondii, C. krusei, C. lusitaniae, C. parapsilosis, and C. tropicalis. Automated and manual approaches to DNA sequence interpretation, each coupled with the Identifire identification software, demonstrated 100% agreement with respect to Candida species identification. Twenty-one isolates yielded intraspecies DNA sequence differences (90%-98% nucleic acid sequence identity) by automated interpretation. Sequence differences resulted from single-nucleotide polymorphisms or single-base additions/deletions, in addition to interpretative challenges in homopolymeric tracts.

CONCLUSION

DNA pyrosequencing coupled with automated DNA sequence alignment provides a practical approach for accurate and timely identification of Candida pathogens. Relatively rapid and facile genotypic studies by DNA pyrosequencing matched the effectiveness of extensive biochemical/morphologic studies for yeast identification.

Paradoxical growth effects of the echinocandins caspofungin and micafungin, but not of anidulafungin, on clinical isolates of Candida albicans and C. dubliniensis

OBJECTIVES

To analyze the effects of a high concentration of three antifungal substances, the echinocandins anidulafungin, caspofungin, and micafungin, on the growth of Candida spp.

METHODS

The growth of 127 C. dubliniensis isolates and 103 C. albicans isolates cultured in medium containing anidulafungin, caspofungin, or micafungin was analyzed using a broth microdilution test according to the guidelines of the CLSI M27-A2 [NCCLS (1997), Wayne, PA]. The final concentrations of all three echinocandins ranged from 0.125 to 64 microg/L.

RESULTS

The different effects of these three antifungal substances on C. albicans cells in comparison to C. dubliniensis cells were quite distinct. When both Candida species were grown in the presence of anidulafungin only a trailing effect was observed. Micafungin induced an Eagle effect in C. dubliniensis only (63%), while caspofungin induced this effect in the majority of C. dubliniensis isolates (90%) and in only a few C. albicans isolates (14%).

CONCLUSIONS

Based on our observations, anidulafungin has effects that are different from the ones produced by micafungin and caspofungin. Whether this different response to high concentrations of echinocandins is based on genetic or phenotypic differences between C. albicans and C. dubliniensis has to be determined in future experiments.

Yeast identification--past, present, and future methods

The focus of this review is the evolution of biochemical phenotypic yeast identification methods with emphasis on conventional approaches, rapid screening tests, chromogenic agars, comprehensive commercial methods, and the eventual migration to genotypic methods. As systemic yeast infections can be devastating and resistance is common in certain species, accurate identification to the species level is paramount for successful therapy and appropriate patient care.

Diagnostic biologique des candidoses systémiques : difficultés et perspectives

The diagnosis of systemic Candidiasis is difficult to establish and biologic diagnosis raises problems. Blood culture which is the gold standard for the diagnosis of systemic Candidiasis lacks sensitivity and usually takes several days to become positive. Early diagnostic approach is imperative to avoid delays in the initiation for treatment. Therefore, nonculture methods like test for Candida antigen detection, metabolite detection or Candida DNA detection by PCR are being developed for the laboratory diagnosis. Candida derived metabolites and antigens detection lacks sensitivity. A new strategy consisting of the combined detection of mannanemia and an antibody response was developed. The combined detection has a high specificity and sensitivity in the diagnosis of invasive candidiasis. The results of tests for the detection of yeast DNA by PCR obtained recently are promising in terms of sensitivity, specificity and identification of species of Candida.

Bacterial genotyping by 16S rRNA mass cataloging

Background

It has recently been demonstrated that organism identifications can be recovered from mass spectra using various methods including base-specific fragmentation of nucleic acids. Because mass spectrometry is extremely rapid and widely available such techniques offer significant advantages in some applications. A key element in favor of mass spectrometric analysis of RNA fragmentation patterns is that a reference database for analysis of the results can be generated from sequence information. In contrast to hybridization approaches, the genetic affinity of any unknown isolate can in principle be determined within the context of all previously sequenced 16S rRNAs without prior knowledge of what the organism is. In contrast to the original RNase T₁ cataloging method, when digestion products are analyzed by mass spectrometry, products with the same base composition cannot be distinguished. Hence, it is possible that organisms that are not closely related (having different underlying sequences) might be falsely identified by mass spectral coincidence. We present a convenient spectral coincidence function for expressing the degree of similarity (or distance) between any two mass-spectra. Trees constructed using this function are consistent with those produced by direct comparison of primary sequences, demonstrating that the inherent degeneracy in mass spectrometric analysis of RNA fragments does not preclude correct organism identification.

Results

Neighbor-joining trees for important bacterial pathogens were generated using distances based on mass spectrometric observables and the spectral coincidence function. These trees demonstrate that most pathogens will be readily distinguished using mass spectrometric analyses of RNA digestion products. A more detailed, genus-level analysis of pathogens and near relatives was also performed, and it was found that assignments of genetic affinity were consistent with those obtained by direct sequence comparisons. Finally, typical values of the coincidence between organisms were also examined with regard to phylogenetic level and sequence variability.

Conclusion

Cluster analysis based on comparison of mass spectrometric observables using the spectral coincidence function is an extremely useful tool for determining the genetic affinity of an unknown bacterium. Additionally, fragmentation patterns can determine within hours if an unknown isolate is potentially a known pathogen among thousands of possible organisms, and if so, which one.

Molecular fingerprinting methods for the discrimination between C. albicans and C. dubliniensis

Opportunistic fungal pathogens are becoming increasingly important causes of both community-acquired and nosocomial infections. The most important fungal pathogens are yeast species belonging to the genus Candida. These species show differences in levels of resistance to antifungal agents and mortality. Consequently, it is important to correctly identify the causative organism to the species level. Identification of Candida dubliniensis in particular remains problematic because of the high degree of phenotypic similarity between this species and Candida albicans. However, as the differences between both are most pronounced at the genetic level, several studies have been conducted in order to provide a specific and rapid identification fingerprinting molecular test. In most candidal infectious, no single DNA fingerprinting technique has evolved as a dominant method, and each method has its advantages, disadvantages and limitations. Moreover, the current challenge of these techniques is to compile standardized patterns in a database for interlaboratory use and future reference. This review provides an overview of most common molecular fingerprinting techniques currently available for discrimination of C. albicans and C. dubliniensis.

Development and evaluation of a rapid latex agglutination test using a monoclonal antibody to identify Candida dubliniensis colonies

Cell components of the dimorphic pathogenic fungus Candida dubliniensis were used to prepare monoclonal antibodies (MAbs). One MAb, designated 12F7-F2, was shown by indirect immunofluorescence to be specific for a surface antigen of Candida dubliniensis yeast cells. No reactivity was observed with other fungal genera or with other Candida species, including Candida albicans, that share many phenotypic features with C. dubliniensis. The use of different chemical and physical treatments for cell component extraction suggested that the specific epitope probably resides on a protein moiety absent from C. albicans. However, we failed to identify the target protein by Western blotting, owing to its sensitivity to heat and sodium dodecyl sulfate. MAb 12F7-F2 was further used to develop a commercial latex agglutination test to identify C. dubliniensis colonies (Bichro-dubli Fumouze test; Fumouze Diagnostics). The test was validated on yeast strains previously identified by PCR and on fresh clinical isolates; these included 46 C. dubliniensis isolates, 45 C. albicans isolates, and other yeast species. The test had 100% sensitivity and specificity for C. dubliniensis isolated on Sabouraud dextrose, CHROMagar Candida, and CandiSelect media and 97.8% sensitivity for C. dubliniensis grown on Candida ID medium. The test is rapid (5 min) and easy to use and may be recommended for routine use in clinical microbiology laboratories and for epidemiological investigations.

Microbial identification by mass cataloging

Background

The public availability of over 180,000 bacterial 16S ribosomal RNA (rRNA) sequences has facilitated microbial identification and classification using hybridization and other molecular approaches. In their usual format, such assays are based on the presence of unique subsequences in the target RNA and require a prior knowledge of what organisms are likely to be in a sample. They are thus limited in generality when analyzing an unknown sample.

Herein, we demonstrate the utility of catalogs of masses to characterize the bacterial 16S rRNA(s) in any sample. Sample nucleic acids are digested with a nuclease of known specificity and the products characterized using mass spectrometry. The resulting catalogs of masses can subsequently be compared to the masses known to occur in previously-sequenced 16S rRNAs allowing organism identification. Alternatively, if the organism is not in the existing database, it will still be possible to determine its genetic affinity relative to the known organisms.

Results

Ribonuclease T₁ and ribonuclease A digestion patterns were calculated for 1,921 complete 16S rRNAs. Oligoribonucleotides generated by RNase T₁ of length 9 and longer produce sufficient diversity of masses to be informative. In addition, individual fragments or combinations thereof can be used to recognize the presence of specific organisms in a complex sample. In this regard, 140 strains out of 1,921 organisms (7.3%) could be identified by the presence of a unique RNase T₁-generated oligoribonucleotide mass. Combinations of just two and three oligoribonucleotide masses allowed 54% and 72% of the specific strains to be identified, respectively. An initial algorithm for recovering likely organisms present in complex samples is also described.

Conclusion

The use of catalogs of compositions (masses) of characteristic oligoribonucleotides for microbial identification appears extremely promising. RNase T₁ is more useful than ribonuclease A in generating characteristic masses, though RNase A produces oligomers which are more readily distinguished due to the large mass difference between A and G. Identification of multiple species in mixtures is also feasible. Practical applicability of the method depends on high performance mass spectrometric determination, and/or use of methods that increase the one dalton (Da) mass difference between uracil and cytosine.

Phenotypic methods and commercial systems for the discrimination between C. albicans and C. dubliniensis

Candida dubliniensis is a recently described Candida species associated with oral candidosis that exhibits a high degree of phenotypic similarity to Candida albicans. However, these species show differences in levels of resistance to antimycotic agents and ability to cause infections. Therefore, accurate clinical identification of C. dubliniensis and C. albicans species is important in order to treat oral candidal infections. Phenotypic identification methods are easy-to-use procedures for routine discrimination of oral isolates in the clinical microbiology laboratory. However, C. dubliniensis may be so far underreported in clinical samples because most currently used identification methods fail to recognize this yeast. Phenotypic methods depend on growth temperature, carbon source assimilation, chlamydospore and hyphal growth production, positive or negative growth on special media and intracellular enzyme production, among others. In this review, some phenotypic methods are presented with a special emphasis on the discrimination of C. dubliniensis and C. albicans.

Candida dubliniensis bloodstream infection: a fatal case in a lung transplant recipient

Candida dubliniensis is an emerging opportunistic yeast initially identified as a cause of oropharyngeal candidiasis in human immunodeficiency virus-infected individuals, and recently associated with invasive disease in other immunocompromised hosts. Certain diagnostic characteristics are shared with C. albicans, but differences in epidemiology, microbiology, and potentially clinical management are notable. We report a case of fatal C. dubliniensis bloodstream infection in a solid-organ transplant recipient and review the literature.

Candida orthopsilosis and Candida metapsilosis spp. nov. to replace Candida parapsilosis groups II and III

Two new species, Candida orthopsilosis and C. metapsilosis, are proposed to replace the existing designations of C. parapsilosis groups II and III, respectively. The species C. parapsilosis is retained for group I isolates. Attempts to construct a multilocus sequence typing scheme to differentiate individual strains of C. parapsilosis instead revealed fixed DNA sequence differences between pairs of subgroups in four genes: COX3, L1A1, SADH, and SYA1. PCR amplicons for sequencing were obtained for these four plus a further seven genes from 21 group I isolates. For nine group II isolates, PCR products were obtained from only 5 of the 11 genes, and for two group III isolates PCR products were obtained from a different set of 5 genes. Three of the PCR products from group II and III isolates differed in size from the group I products. Cluster analysis of sequence polymorphisms from COX3, SADH, and SYA1, which were common to the three groups, consistently separated the isolates into three distinct sets. All of these differences, together with DNA sequence similarities <90% in the ITS1 sequence, suggest the subgroups should be afforded species status. The near absence of DNA sequence variability among isolates of C. parapsilosis and relatively high levels of sequence variability among isolates of C. orthopsilosis suggest that the former species may have evolved very recently from the latter.

Evaluation of API ID 32C and VITEK-2 to identify Candida dubliniensis

We have compared two diagnostic systems, API-ID32C (bioMerieux) and VITEK-2ID-YST (bioMerieux), in their ability to diagnose 50 clinical isolates of Candida dubliniensis. API identified 48 isolates and VITEK-2 identified 33 of the 50 isolates. Lactic acid assimilation showed highly dispersed results with API, being of special importance, since this test is one of the four that makes it possible to differentiate C. dubliniensis from C. albicans. The detection of one enzyme, Phosphate-4MU, was always positive with VITEK-2 when it should have been negative. Overall, API ID 32C obtained better results than VITEK-2. However, the latter is simpler to use and has a greater database.

Tobacco agar, a new medium for differentiating Candida dubliniensis from Candida albicans

Isolates of Candida dubliniensis may be misidentified as Candida albicans in microbiological laboratories if only the germ tube and/or the chlamydospore test is used for identification to the species level. In this study, we have evaluated the efficacy of tobacco agar for the differentiation of C. dubliniensis from C. albicans. On this medium at 28 degrees C, all 30 C. dubliniensis isolates produced yellowish-brown colonies with hyphal fringes and abundant chlamydospores, whereas 54 C. albicans isolates formed smooth, white-to-cream-colored colonies with no chlamydospore production. This medium provides a simple tool for presumptive differentiation of C. dubliniensis from C. albicans.

Rapid differentiation of Aspergillus species from other medically important opportunistic molds and yeasts by PCR-enzyme immunoassay

We developed a PCR-based assay to differentiate medically important species of Aspergillus from one another and from other opportunistic molds and yeasts by employing universal, fungus-specific primers and DNA probes in an enzyme immunoassay format (PCR-EIA). Oligonucleotide probes, directed to the internal transcribed spacer 2 region of ribosomal DNA from Aspergillus flavus, Aspergillus fumigatus, Aspergillus nidulans, Aspergillus niger, Aspergillus terreus, Aspergillus ustus, and Aspergillus versicolor, differentiated 41 isolates (3 to 9 each of the respective species; P < 0.001) in a PCR-EIA detection matrix and gave no false-positive reactions with 33 species of Acremonium, Exophiala, Candida, Fusarium, Mucor, Paecilomyces, Penicillium, Rhizopus, Scedosporium, Sporothrix, or other aspergilli tested. A single DNA probe to detect all seven of the most medically important Aspergillus species (A. flavus, A. fumigatus, A. nidulans, A. niger, A. terreus, A. ustus, and A. versicolor) was also designed. Identification of Aspergillus species was accomplished within a single day by the PCR-EIA, and as little as 0.5 pg of fungal DNA could be detected by this system. In addition, fungal DNA extracted from tissues of experimentally infected rabbits was successfully amplified and identified using the PCR-EIA system. This method is simple, rapid, and sensitive for the identification of medically important Aspergillus species and for their differentiation from other opportunistic fungi.

Resolution of discrepant results for Candida species identification by using DNA probes

Candida species bloodstream isolates were collected from institutions participating in an active, population-based surveillance for candidemia. Species identifications were performed locally and then confirmed at the Centers for Disease Control and Prevention (CDC) by phenotype-based methods. Discrepancies in species identification between the referring institution and the CDC were noted for 43 of 935 isolates (4.6%). A DNA probe-based species identification system (PCR-enzyme immunoassay [EIA]) was then used to resolve these discrepancies. The PCR-EIA result was identical to the CDC phenotypic identification method for 98% of the isolates tested. The most frequently misidentified species was Candida glabrata (37% of all discrepant identifications). Such misidentifications could lead to the administration of inappropriate therapy given the propensity of C. glabrata to develop resistance to azole antifungal drugs.