Identification of medically important yeast species by sequence analysis of the internal transcribed spacer regions

Comparison of integrated sustainable biodiesel and antibacterial nano silver production by microalgal and yeast isolates

Microalgal isolates (Chlorella sp. and Spirulina sp.) and yeast isolates (Candida albicans and Saccharomyces sp.) were employed as the resources of biodiesel production and silver nanoparticle synthesis. The prominent peaks of the FTIR spectrum accustomed the efficient lipid property. The developed profile containing fatty acid methyl ester (FAME) displayed the elevated amount of both saturated (C15:0, C17:0, C21:0) and unsaturated (C17:1, C18:2, C20:4) fatty acids. The physicochemical properties analyzed by using Biodiesel analyzer V1.1.software, confirmed the competency of the isolates for sustainable biodiesel production. Biosynthesis of silvernanoparticles (AgNPs) were accomplished extracellularly by using supernatant of microalgal and yeast culture. The maximum absorbance at 420 and 421 nm under UV-visible spectra showed the presence of nanoparticles. The purity of the synthesized AgNPs were analyzed by XRD analysis. The elemental silver presence was affirmed by EDAX, SEM and AFM, the results revealed spherical crystalline shaped nanoparticles of size ranging from 2.0 to 7.3 nm. The antimicrobial efficacy of the silver nanoparticles (AgNPs) against various clinical pathogens which includes Bacillus sp., E. coli, Klebsiella sp., Proteus sp. and Staphylococcus aureus were observed. However, enhanced antimicrobial activity was displayed by the AgNPs, produced by Candida albicans (12 mm) against Bacillus sp., and E.coli, the nanoparticle produced by Chlorella sp. showed the least antagonistic activity (07 mm).

Clinical and Microbiological Characteristics of Candida guilliermondii and Candida fermentati

A total of 46 clinical isolates of Candida guilliermondii and Candida famata were reidentified genetically, resulting in 27 C. guilliermondii and 12 Candida fermentati strains. The majority of C. guilliermondii strains, but not C. fermentati strains, were isolated from blood cultures. C. fermentati was more sensitive to antifungals, hydrogen peroxide, and killing by murine macrophages than was C. guilliermondii The C. guilliermondii isolates were echinocandin susceptible in vitro but resistant to micafungin in a murine model of invasive candidiasis.

Multilocus Sequence Typing Reveals a New Cluster of Closely Related Candida tropicalis Genotypes in Italian Patients With Neurological Disorders

Candida tropicalis is a pathogenic yeast that has emerged as an important cause of candidemia especially in elderly patients with hematological malignancies. Infections caused by this species are mainly reported from Latin America and Asian-Pacific countries although recent epidemiological data revealed that C. tropicalis accounts for 6-16.4% of the Candida bloodstream infections (BSIs) in Italy by representing a relevant issue especially for patients receiving long-term hospital care. The aim of this study was to describe the genetic diversity of C. tropicalis isolates contaminating the hands of healthcare workers (HCWs) and hospital environments and/or associated with BSIs occurring in patients with different neurological disorders and without hematological disease. A total of 28 C. tropicalis isolates were genotyped using multilocus sequence typing analysis of six housekeeping (ICL1, MDR1, SAPT2, SAPT4, XYR1, and ZWF1) genes and data revealed the presence of only eight diploid sequence types (DSTs) of which 6 (75%) were completely new. Four eBURST clonal complexes (CC2, CC10, CC11, and CC33) contained all DSTs found in this study and the CC33 resulted in an exclusive, well-defined, clonal cluster from Italy. In conclusion, C. tropicalis could represent an important cause of BSIs in long-term hospitalized patients with no underlying hematological disease. The findings of this study also suggest a potential horizontal transmission of a specific C. tropicalis clone through hands of HCWs and expand our understanding of the molecular epidemiology of this pathogen whose population structure is still far from being fully elucidated as its complexity increases as different categories of patients and geographic areas are examined.

Oropharyngeal candidiasis in head and neck cancer patients in Iran: Species identification, antifungal susceptibility and pathogenic characterization

OBJECTIVE

Oropharyngeal candidiasis (OPC) is the most frequent opportunistic fungal infection in head and neck cancer patients. This study was done to identify the Candida species, which cause OPC, and to evaluate their antifungal susceptibility pattern and pathogenic characteristics in Iranian head and neck cancer patients treated by radiotherapy.

MATERIAL AND METHODS

The oral clinical samples were determined by culturing on CHROMagar, carbohydrate assimilation and ITS sequencing methods. Biofilm formation, phospholipase and proteinase activity and antifungal susceptibility were examined too.

RESULTS

Among 54 patients with confirmed OPC, 39 (72.22%) patients were male and 15 (27.77%) were female. The most frequently Candida species from a total of 60 isolates was C. albicans (53.3%), followed by C. tropicalis (21.66%), C. glabrata (15%), C. kefyr (5%) and C. dubliniensis (1.66%). All the isolates were high-producers of biofilm. All of Candida isolates were proteinase positive and 47 isolates (81.04%) represented phospholipase activity. The maximum and minimum rates of antifungal resistance belonged to ketoconazole (93.75% of C. albicans and 89.28% of Candida non-albicans) and fluconazole (62.50% and 42.85% of C. albicans and Candida non-albicans), respectively. The most effective antifungal against all candida isolates was fluconazole.

CONCLUSION

Our data can estimate abundance of OPC in male and female head and neck cancer patients and is helpful to use effective strategies for antifungal treatment, prophylaxis, and preventive therapies in these patients.

Clinically relevant yeast species identified by sequencing the internal transcribed spacer region of r-RNA gene and Vitek 2 compact (YST card) commercial identification system: Experience in a Tertiary Care Hospital in Assam, Northeast India

In this retrospective study from 2012 to 2015, 333 clinical isolates of yeasts were identified using Vitek 2 Compact System YST ID card (Biomerieux, France) and internal transcribed spacer (ITS) sequencing. Eighteen species were identified by ITS sequencing. Candida albicans was the most common species (46.5%), followed by Candida tropicalis (27%). The total species supported by Vitek System was 11 (61.11%). The sensitivity of the system in identifying these 11 species was 66.66%-100%; specificity 98.37%-100%; positive predictive value 70%-100%, negative predictive value 96.05%-100%, and diagnostic accuracy 96.99%-100%. Diagnostic accuracy of ITS1 and ITS2 sequences individually was 98.49% and 100% using NCBI Genbank database.

Candida infanticola and Candida spencermartinsiae yeasts: Possible emerging species in cancer patients

Opportunistic infections due to Candida species occur frequently in intensive care settings. We investigated the prevalence of Candida species among 65 clinical specimens obtained from 200 cancer patients by phenotypic and molecular (ITS sequencing and AFLP) methods. Among the 65 yeast isolates, Candida albicans was the most commonly isolated species (n = 34, 52.3%), whereas other Candida species comprised 47.7% (n = 31) and consisted of Candida glabrata (n = 14, 21.5%), Candida tropicalis (n = 5, 7.7%) and uncommon Candida species (n = 12, 18.5%) such as Candida pelliculosa (n = 3, 4.6%), Pichia kudriavzevii (= Candida krusei, n = 2, 3.1%), Candida orthopsilosis (n = 2, 3.1%), Candida parapsilosis (n = 1, 1.5%), Candida infanticola (n = 2, 3.1%), Candida spencermartinsiae (n = 1, 1.5%), and Kluyveromyces marxianus (=Candida kefyr, n = 1, 1.5%). Candida infanticola and Candida spencermartinsiae were recovered from oral lesions of cancer patients. Matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) easily confirmed these isolates as less common Candida isolates (4.6%). The in vitro antifungal susceptibilities of C. spencermartinsiae and the two strains of C. infanticola were determined according to CLSI guidelines (M27-A3). MIC results among these isolates showed they were susceptible to isavuconazole, posaconazole and voriconazole, however, fluconazole and caspofungin had high MIC values. These Candida species that may occur more commonly in infections remain unnoticed using commonly used phenotypical methods in routine microbiology laboratories. MALDI-TOF MS proved to be a more fast and robust diagnostic technique for identification of the yeasts isolated from different clinical specimens of cancer patients.

Matrix-assisted laser desorption/ionization–time of flight mass spectrometry: protocol standardization and database expansion for rapid identification of clinically important molds

Aim: To standardize the matrix-assisted laser desorption ionization–time of flight mass spectrometry protocols and expansion of existing Bruker Biotyper database for mold identification. Materials & methods: Four different sample preparation methods (protocol A, B, C and D) were evaluated. Results: On analyzing each protein extraction method, reliable identification and best log scores were achieved through protocol D. The same protocol was used to identify 153 clinical isolates. Of these 153, 123 (80.3%) were accurately identified by using existing database and remaining 30 (19.7%) were not identified due to unavailability in database. On inclusion of missing main spectrum profile in existing database, all 153 isolates were identified. Conclusion: Matrix-assisted laser desorption ionization–time of flight mass spectrometry can be used for routine identification of clinically important molds.

Identification of Candida species isolated from vulvovaginitis using matrix assisted laser desorption ionization-time of flight mass spectrometry

Background and Purpose:

Vulvovaginal candidiasis (VVC) is a common problem in women. The purpose of this study was to identify Candida isolates by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) from women with vulvovaginitis that were referred to Ghaem Hospital, Mashhad, Iran.

Materials and Methods:

This study was conducted on 65 clinical samples isolated from women that were referred to Ghaem Hospital. All specimens were identified using phenotyping techniques, such as microscopy and culture on Sabouraud dextrose agar and corn meal agar. In addition, all isolates were processed for MALDI-TOF MS identification.

Results:

Out of the 65 analyzed isolates, 61 (94%) samples were recognized by MALDI-TOF MS. However, the remaining four isolates (6%) had no reliable identification. According to the results, C. albicans (58.5%) was the most frequently isolated species, followed by C. tropicalis (16.9%), C. glabrata (7.7%), C. parapsilosis (7.7%), and guilliermondii (3.1%).

Conclusion:

As the findings indicated, MALDI TOF MS was successful in the identification of clinical Candida species. C. albicans was identified as the most common Candida species isolated from the women with VVC. Moreover, C. tropicalis was the most common species among the non-albicans Candida species.

Detection of bacterial pathogens from clinical specimens using conventional microbial culture and 16S metagenomics: a comparative study

Background

Infectious disease is the leading cause of death worldwide, and diagnosis of polymicrobial and fungal infections is increasingly challenging in the clinical setting. Conventionally, molecular detection is still the best method of species identification in clinical samples. However, the limitations of Sanger sequencing make diagnosis of polymicrobial infections one of the biggest hurdles in treatment. The development of massively parallel sequencing or next generation sequencing (NGS) has revolutionized the field of metagenomics, with wide application of the technology in identification of microbial communities in environmental sources, human gut and others. However, to date there has been no commercial application of this technology in infectious disease diagnostic settings.

Methods

Credence Genomics Rapid Infection Detection™ test, is a molecular based diagnostic test that uses next generation sequencing of bacterial 16S rRNA gene and fungal ITS1 gene region to provide accurate identification of species within a clinical sample. Here we present a study comparing 16S and ITS1 metagenomic identification against conventional culture for clinical samples. Using culture results as gold standard, a comparison was conducted using patient specimens from a clinical microbiology lab.

Results

Metagenomics based results show a 91.8% concordance rate for culture positive specimens and 52.8% concordance rate with culture negative samples. 10.3% of specimens were also positive for fungal species which was not investigated by culture. Specificity and sensitivity for metagenomics analysis is 91.8 and 52.7% respectively.

Conclusion

16S based metagenomic identification of bacterial species within a clinical specimen is on par with conventional culture based techniques and when coupled with clinical information can lead to an accurate diagnostic tool for infectious disease diagnosis.

Electronic supplementary material

The online version of this article (10.1186/s12879-017-2727-8) contains supplementary material, which is available to authorized users.

The identification of Meyerozyma guilliermondii from blood cultures and surveillance samples in a university hospital in Northeast Turkey: A ten-year survey

Meyerozyma (Pichia) guilliermondii exists in human skin and mucosal surface microflora. It can cause severe fungal infections like candidemia, which is an opportunistic pathogen. One hundred and forty-one M. guilliermondii isolates, consisting of 122 blood culture isolates, belonging to 126 patients; 13 total parenteral nutrition solution isolates; and two rectal swab isolates were identified according to carbohydrate assimilation reactions in a university hospital in Turkey between January 2006 and December 2015. Following Candida albicans (34.0%) and C. parapsilosis (21.2%), the third yeast species most commonly isolated from blood cultures in the Farabi Hospital was M. guilliermondii (20.6%). The patients were hospitalised in 27 different departments. A total of 50% of the patients were in pediatric departments, 49.2% were in intensive care units, and 17.2% were in haematology-oncology departments. Molecular identification of the isolates was performed using DNA sequence analysis of ribosomal ITS gene regions and IGS amplification-AluI fingerprinting (IGSAF). With molecular identification, 140 isolates were identified as M. guilliermondii and one isolate was identified as Candida membranifaciens. It was observed that the ITS1 region specifically helps in identifying these species. It was demonstrated that biochemical and molecular methods were 99.3% consistent in identifying M. guilliermondii. The Wild-Type (WT) Minimum Inhibitory Concentrations (MICs) distribution of fluconazole, voriconazole, itraconazole, and flucytosine were determined using the Sensititre YeastOne YO2V system after 24h of incubation. One M. guilliermondii strain was determined to be non-WT for fluconazole, voriconazole, itraconazole and flucytosine. In total, three M. guilliermondii strains, for fluconazole, were determined to be non-WT in this study.

Comparison of sequencing the D2 region of the large subunit ribosomal RNA gene (MicroSEQ®) versus the internal transcribed spacer (ITS) regions using two public databases for identification of common and uncommon clinically relevant fungal species

CONTEXT

Fungal infections cause considerable morbidity and mortality in immunocompromised patients. Rapid and accurate identification of fungi is essential to guide accurately targeted antifungal therapy. With the advent of molecular methods, clinical laboratories can use new technologies to supplement traditional phenotypic identification of fungi.

OBJECTIVE

The aims of the study were to evaluate the sole commercially available MicroSEQ® D2 LSU rDNA Fungal Identification Kit compared to the in-house developed internal transcribed spacer (ITS) regions assay in identifying moulds, using two well-known online public databases to analyze sequenced data.

DESIGN

85 common and uncommon clinically relevant fungi isolated from clinical specimens were sequenced for the D2 region of the large subunit (LSU) of ribosomal RNA (rRNA) gene with the MicroSEQ® Kit and the ITS regions with the in house developed assay. The generated sequenced data were analyzed with the online GenBank and MycoBank public databases.

RESULTS

The D2 region of the LSU rRNA gene identified 89.4% or 92.9% of the 85 isolates to the genus level and the full ITS region (f-ITS) 96.5% or 100%, using GenBank or MycoBank, respectively, when compared to the consensus ID. When comparing species-level designations to the consensus ID, D2 region of the LSU rRNA gene aligned with 44.7% (38/85) or 52.9% (45/85) of these isolates in GenBank or MycoBank, respectively. By comparison, f-ITS possessed greater specificity, followed by ITS1, then ITS2 regions using GenBank or MycoBank. Using GenBank or MycoBank, D2 region of the LSU rRNA gene outperformed phenotypic based ID at the genus level. Comparing rates of ID between D2 region of the LSU rRNA gene and the ITS regions in GenBank or MycoBank at the species level against the consensus ID, f-ITS and ITS2 exceeded performance of the D2 region of the LSU rRNA gene, but ITS1 had similar performance to the D2 region of the LSU rRNA gene using MycoBank.

CONCLUSION

Our results indicated that the MicroSEQ® D2 LSU rDNA Fungal Identification Kit was equivalent to the in-house developed ITS regions assay to identify fungi at the genus level. The MycoBank database gave a better curated database and thus allowed a better genus and species identification for both D2 region of the LSU rRNA gene and ITS regions.

Utilization of size polymorphism in ITS1 and ITS2 regions for identification of pathogenic yeast species

PURPOSE

Despite the existence of a variety of available yeast-identification strategies, easier and more cost-effective methods are required for routine use in clinical laboratories. The internal transcribed spacer (ITS) regions of fungal rRNA genes exhibit variable sizes depending on the yeast species. In the present study, fragment size polymorphism (FSP) analysis of the ITS1 and ITS2 regions for identification of the clinically most important yeast species was assessed.

METHODOLOGY

The ITS1 and ITS2 regions of 190 strains, including isolates of 31 standard strains and 159 clinical isolates, were separately PCR amplified with two primer sets: ITS1-ITS2 and ITS3-ITS4. PCR products were mixed and the two-band electrophoretic pattern of each sample was analysed according to the size of the ITS regions as predicted from the GenBank database.

RESULTS

Using this method and avoiding expensive tools such as sequencing or capillary electrophoresis, we were able to differentiate nearly all pathogenic yeast species, including Candida albicans, Candida tropicalis, Candida glabrata, Candida parapsilosis, Candida krusei, Candida guilliermondii, Candida kefyr, Candida lusitaniae, Candida rugosa, Cryptococcus neoformans and Saccharomyces cerevisiae. The method showed limited discriminatory power to differentiate species of the Candida parapsilosis complex. Differentiation of Candida albicans and Candida tropicalis needs already identified controls.

CONCLUSION

FSP method benefits from advantages such as lower cost, higher speed and wider range of species than some commercial yeast-identification methods. We consider this method as one of the easiest molecular approaches for identifying a wide range of human pathogenic yeast species, applicable to both diagnostic and epidemiological purposes.

Oleaginous yeasts from Ethiopia

Oleaginous microorganisms can produce high amounts of oil (>20 % of their biomass) under suitable cultivation conditions. In this research work 200 samples were collected from soil, plant surfaces (leaves, flowers and fruits), waste oils from traditional oil milling houses and dairy products (cheese, milk and yoghurt) in Ethiopia. Three hundred and forty yeast colonies were isolated from these samples. By applying Sudan III staining tests, 18 strains were selected as possible oleaginous yeasts. The 18 strains were identified and characterized for their lipid production as a feedstock for biodiesel production in the future. They were identified using morphological and physiological methods as well as sequencing the 3'end of the small-subunit rRNA gene, the internal transcribed spacer regions (ITS; ITS 1, ITS 2 and the intervening 5.8S rRNA gene), and the D1/D2 domain of the 26S rRNA gene. The 18 yeasts were identified as Cutaneotrichosporon curvatus (syn, Cryptococcus curvatus) (PY39), Rhodotorula kratochvilovae (syn, Rhodosporidium kratochvilovae) (SY89), Rhodotorula dairenensis (SY94) and Rhodotourula mucilaginosa (SY09, SY18, SY20, PY21, PY23, PY25, SY30, PY32, SY43, PY44, SY52, PY55, PY61, SY75 and PY86). Under nitrogen-limited cultivation conditions, R. mucilaginosa PY44 produced the highest biomass (15.10 ± 0.54 g/L), while R. mucilaginosa PY32 produced the lowest biomass (10.32 ± 0.18 g/L). The highest lipid yield of 6.87 ± 0.62 g/L and lipid content of 46.51 ± 0.70 % were attained by C. curvatus (syn, C. curvatus) PY39. On the other hand, R. mucilaginosa PY61 gave the lowest lipid yield (2.06 ± 0.52 g/L) and R. mucilaginosa SY52 gave the lowest lipid content of 16.99 ± 0.85 %. The results in this research work suggest that much more oleaginous yeasts can be isolated from Ethiopian environment. On the basis of their substantial lipid production abilities, the three oleaginous yeast strains PY39, SY89 and SY18 were selected and recommended for further optimization processes.

Analysis of Metagenomics Next Generation Sequence Data for Fungal ITS Barcoding: Do You Need Advance Bioinformatics Experience?

During the last few decades, most of microbiology laboratories have become familiar in analyzing Sanger sequence data for ITS barcoding. However, with the availability of next-generation sequencing platforms in many centers, it has become important for medical mycologists to know how to make sense of the massive sequence data generated by these new sequencing technologies. In many reference laboratories, the analysis of such data is not a big deal, since suitable IT infrastructure and well-trained bioinformatics scientists are always available. However, in small research laboratories and clinical microbiology laboratories the availability of such resources are always lacking. In this report, simple and user-friendly bioinformatics work-flow is suggested for fast and reproducible ITS barcoding of fungi.

First isolation of Candida wangnamkhiaoensis from the blood of immunocompromised paediatric patient

Candida wangnamkhiaoensis is a species clustered under the Hyphopichia clade has not ever been isolated from any clinical specimens. To the best of our knowledge, this is the first report of C. wangnamkhiaoensis associated with fungaemia in immunocompromised paediatric patient. The isolate was assigned a strain name as UZ1679/14, in which the identification was confirmed by a polymerase chain reaction-sequencing of the internal transcribed spacer (ITS) and large subunit (LSU) regions of the rRNA gene. Antifungal susceptibility pattern showed that the isolate was sensitive to anidulafungin, caspofungin, fluconazole and voriconazole. The patient clinically improved after the antifungal treatment with caspofungin.

Performance assessment of two lysis methods for direct identification of yeasts from clinical blood cultures using MALDI-TOF mass spectrometry

In cases of fungal infection of the bloodstream, rapid species identification is crucial to provide adapted therapy and thereby ameliorate patient outcome. Currently, the commercial Sepsityper kit and the sodium-dodecyl sulfate (SDS) method coupled with MALDI-TOF mass spectrometry are the most commonly reported lysis protocols for direct identification of fungi from positive blood culture vials. However, the performance of these two protocols has never been compared on clinical samples. Accordingly, we performed a two-step survey on two distinct panels of clinical positive blood culture vials to identify the most efficient protocol, establish an appropriate log score (LS) cut-off, and validate the best method. We first compared the performance of the Sepsityper and the SDS protocols on 71 clinical samples. For 69 monomicrobial samples, mass spectrometry LS values were significantly higher with the SDS protocol than with the Sepsityper method (P < .0001), especially when the best score of four deposited spots was considered. Next, we established the LS cut-off for accurate identification at 1.7, based on specimen DNA sequence data. Using this LS cut-off, 66 (95.6%) and 46 (66.6%) isolates were correctly identified at the species level with the SDS and the Sepsityper protocols, respectively. In the second arm of the survey, we validated the SDS protocol on an additional panel of 94 clinical samples. Ninety-two (98.9%) of 93 monomicrobial samples were correctly identified at the species level (median LS = 2.061). Overall, our data suggest that the SDS method yields more accurate species identification of yeasts, than the Sepsityper protocol.

Malassezia arunalokei sp. nov., a Novel Yeast Species Isolated from Seborrheic Dermatitis Patients and Healthy Individuals from India

The majority of species within the genus Malassezia are lipophilic yeasts that colonize the skin of warm-blooded animals. Two species, Malassezia globosa and Malassezia restricta, are implicated in the causation of seborrheic dermatitis/dandruff (SD/D). During our survey of SD/D cases, we isolated several species of Malassezia and noticed vast variations within a few lipid-dependent species. Variations observed in the phenotypic characteristics (colony morphology, absence of catalase activity, growth at 37°C, and precipitation surrounding wells containing Tween 20 or Cremophor EL) suggested the possible presence of a novel species. Sequence divergence observed in the internal transcribed spacer (ITS) region, the D1/D2 domain, and the intergenic spacer 1 (IGS1) region of rDNA and the TEF1 gene, PCR-restriction fragment length polymorphism (RFLP) analysis of the ITS2 region, and fluorescent amplified fragment length polymorphism analysis support the existence of a novel species. Based on phenotypic and molecular characterization of these strains, we propose a new species, namely, M. arunalokei sp. nov., and we designate NCCPF 127130 (= MTCC 12054 = CBS 13387) as the type strain.

Fungal peritonitis in patients undergoing peritoneal dialysis (PD) in Brazil: molecular identification, biofilm production and antifungal susceptibility of the agents

This paper presents data on fungal peritonitis (FP) in patients undergoing peritoneal dialysis (PD) at the University Hospital of Botucatu Medical School, São Paulo, Brazil. In a total of 422 patients, 30 developed FP, from which the medical records and the fungal isolates of 23 patient cases were studied. All patients presented abdominal pain, cloudy peritoneal effluent, needed hospitalization, had the catheter removed and were treated with fluconazole or fluconazole plus 5-flucitosine; six of them died due to FP. Concerning the agents, it was observed that Candida parapsilosis was the leading species (9/23), followed by Candida albicans (5/23), Candida orthopsilosis (4/23), Candida tropicalis (3/23), Candida guilliermondii (1/23), and Kodamaea ohmeri (1/23). All the isolates were susceptible to amphotericin B, voriconazole and caspofungin whereas C. albicans isolates were susceptible to all antifungals tested. Resistance to fluconazole was observed in three isolates of C. orthopsilosis, and dose-dependent susceptibility to this antifungal was observed in two isolates of C. parapsilosis and in the K. ohmeri isolate. Biofilm production estimates were high or moderate in most isolates, especially in C. albicans species, and low in C. parapsilosis species, with a marked variation among the isolates. This Brazilian study reinforces that FP in PD is caused by a diverse group of yeasts, most prevalently C. parapsilosis sensu stricto species. In addition, they present significant variation in susceptibility to antifungals and biofilm production, thus contributing to the complexity and severity of the clinical features.

Evaluation of Fluorescent Capillary Electrophoresis for Rapid Identification of Candida Fungal Infections

Early diagnosis of fungal infection is critical for initiating antifungal therapy and reducing the high mortality rate in immunocompromised patients. In this study, we focused on rapid and sensitive identification of clinically important Candida species, utilizing the variability in the length of the ITS2 rRNA gene and fluorescent capillary electrophoresis (f-ITS2-PCR-CE). The method was developed and optimized on 29 various Candida reference strains from which 26 Candida species were clearly identified, while Candida guilliermondii, C. fermentati, and C. carpophila, which are closely related, could not be distinguished. The method was subsequently validated on 143 blinded monofungal clinical isolates (comprising 26 species) and was able to identify 88% of species unambiguously. This indicated a higher resolution power than the classical phenotypic approach which correctly identified 73%. Finally, the culture-independent potential of this technique was addressed by the analysis of 55 retrospective DNA samples extracted directly from clinical material. The method showed 100% sensitivity and specificity compared to those of the combined results of cultivation and panfungal PCR followed by sequencing used as a gold standard. In conclusion, this newly developed f-ITS2-PCR-CE analytical approach was shown to be a fast, sensitive, and highly reproducible tool for both culture-dependent and culture-independent identification of clinically important Candida strains, including species of the "psilosis" complex.

Antifungal susceptibility of invasive Candida bloodstream isolates from the Asia-Pacific region

Bloodstream infections caused by Candida species are of increasing importance and associated with significant mortality. We performed a multi-centre prospective observational study to identify the species and antifungal susceptibilities of invasive bloodstream isolates of Candida species in the Asia-Pacific region. The study was carried out over a two year period, involving 13 centers from Brunei, Philippines, Singapore, South Korea, Taiwan, Thailand, and Vietnam. Identification of Candida species was performed at each study center, and reconfirmed at a central laboratory. Susceptibility testing was performed using a commercial broth dilution panel (Sensititre YeastOne YST-010, Thermofisher, United Kingdom) with susceptibility categorisation (S = susceptible, S-DD = susceptible dose-dependent) applied using breakpoints from the Clinical Laboratory Standards Institute. Eight hundred and sixty-one Candida isolates were included in the study. The most common species were C. albicans (35.9%), C. tropicalis (30.7%), C. parapsilosis (15.7%), and C. glabrata (13.6%). Non-albicans species exceeded C. albicans species in centers from all countries except Taiwan. Fluconazole susceptibility was almost universal for C. albicans (S = 99.7%) but lower for C. tropicalis (S = 75.8%, S-DD = 6.1%), C. glabrata (S-DD = 94.9%), and C. parapsilosis (S = 94.8%). Echinocandins demonstrated high rates of in vitro susceptibility (S>99%) against C. albicans, C. tropicalis, and C. parapsilosis This study demonstrates that non-albicans species are the most common isolates from bloodstream infections in most countries in the Asia-Pacific region, with C. tropicalis as the predominant species. Because of the prevalence of reduced susceptibility to fluconazole in non-albicans species, the study indicates that echinocandins should be the antifungal of choice in clinically unstable or high-risk patients with documented candidemia.

Stress tolerance and biocontrol performance of the yeast antagonist, Candida diversa, change with morphology transition

As an eco-friendly management method, biological control of postharvest diseases, utilizing antagonistic yeasts, is a research topic receiving considerable attention. Detailed knowledge on the biology of yeast antagonists is crucial when considering their potential application and development as biocontrol products. Changes in the growth form, such as single-cell to pseudohyphae, have been associated with the mode of action in postharvest biocontrol yeasts. In this study, the antagonistic yeast, Candida diversa, reversibly shifted from a single-cell morphology on yeast peptone dextrose (YPD) medium with 2 % agar to a pseudohyphal morphology on YPD with 0.3 % agar. The tolerance of the pseudohyphal form to heat and oxidative stresses, as well as the biocontrol efficacy against Botrytis cinerea on apple and kiwifruit stored at 25 and 4 °C, was significantly higher as compared to the single-cell form. This study provides new information on the ability of C. diversa to change its morphology and the impact of the morphology shift on stress tolerance and biocontrol performance.

Identification of Taxol-producing endophytic fungi isolated from Salacia oblonga through genomic mining approach

The most promising anti-tumor agent developed in the past three decades is Taxol. It is proven to be effective against many cancers. It is necessary to isolate pharmacologically potent endophytic microbial strains from medicinal plants with special reference to Taxol production. In the current study, endophytic fungi were isolated from the bark of the medicinal plant, Salacia oblonga. The isolated endophytes were identified morphologically, and further characterized by ITS-PCR using genomic DNA samples, later the products were sequenced for identification and phylogenetic linkage mapping. The samples were screened for the potential to produce Taxol or taxanes, employing PCR. The resulted data have been sequenced to confirm the presence of the two genes implicated in Taxol biosynthesis, 10-deacetylbaccatin III-10-O-acetyl transferase (DBAT) and C-13 phenylpropanoid side chain-CoA acyltransferase (BAPT). Seven samples showed the amplicons of DBAT gene and one showed the amplicons of BAPT gene. Sequencing of these products was carried out, of which one sample has revealed sequence homology to the original DBAT gene from Taxus. The present work confirms and substantiates the potential of genomic mining approach to discover novel Taxol-producing endophytic fungi.

Molecular Characterization of Candida africana in Genital Specimens in Shanghai, China

Candida africana, an emerging yeast pathogen, is closely related to Candida albicans and most commonly involved in vulvovaginal candidiasis (VVC). However, its prevalence in candidal balanoposthitis is still unclear. In this study, the prevalence of C. africana in both candidal balanoposthitis and VVC in a sexually transmitted diseases (STD) clinic in Shanghai, China, was analyzed, and the molecular characterization and susceptible profiles of C. africana isolates were investigated. As results, C. africana was only isolated in 5 out of 79 (6.3%) cases of candidal balanoposthitis rather than cases with vulvovaginal candidiasis. Among them, 4 out of 5 isolates share the same genotype of DST 782 with an isolate from vaginal swab in Japan published previously. All C. africana isolates were susceptible to amphotericin B, flucytosine, fluconazole, itraconazole, voriconazole, posaconazole, caspofungin, and micafungin.

Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and Bayesian phylogenetic analysis to characterize Candida clinical isolates

Clinical Candida isolates from two different hospitals in Rome were identified and clustered by MALDI-TOF MS system and their origin and evolution estimated by Bayesian phylogenetic analysis. The different species of Candida were correctly identified and clustered separately, confirming the ability of these techniques to discriminate between different Candida species. Focusing MALDI-TOF analysis on a single Candida species, Candida albicans and Candida parapsilosis strains clustered differently for hospital setting as well as for period of isolation than Candida glabrata and Candida tropicalis isolates. The evolutionary rates of C. albicans and C. parapsilosis (1.93×10(-2) and 1.17×10(-2)substitutions/site/year, respectively) were in agreement with a higher rate of mutation of these species, even in a narrow period, than what was observed in C. glabrata and C. tropicalis strains (6.99×10(-4) and 7.52×10(-3)substitutions/site/year, respectively). C. albicans resulted as the species with the highest between and within clades genetic distance values in agreement with the temporal-related clustering found by MALDI-TOF and the high evolutionary rate 1.93×10(-2)substitutions/site/year.

First Report of Ventriculoperitoneal Shunt Infection due to Cyberlindnera fabianii

Fungal infections in the central nervous system (CNS) are associated with significant morbidity and death. Transient fungemia in immunocompetent patients without any other risk factors for fungemia has been suggested as a possible mechanism that may lead to serious fungal ventriculoperitoneal (VP) shunt infections, but evidence is lacking. The clinical spectrum, diagnosis, and optimal therapy of Cyberlindnera fabianii infections remain to be determined. We describe the first case of CNS infection due to C. fabianii that occurred in an immunocompetent adult with a VP shunt. Spontaneous translocation with yeast that is not part of the normal gastrointestinal flora in the setting of ingestion of multiple servings of a fermentation product was the likely source from which Cyberlindnera fabianii gained entrance into the VP shunt system, causing meningitis in this patient. The authors conclude that, in view of the high morbidity associated with yeast infection of the CNS, long-term antifungal therapy should be strongly considered in cases where the VP shunt cannot be completely removed. Transient fungemia may lead to invasive disease in an immunocompetent host with VP shunt, even in the absence of any other risk factors for fungemia and even after remote placement of the VP shunt.

Mediated amperometry reveals different modes of yeast responses to sugars

Menadione-mediated amperometry at carbon paste electrodes modified with various yeasts (Saccharomyces cerevisiae, Candida pulcherrima, Pichia guilliermondii and Debaryomyces hansenii) was employed to monitor redox activity inside the yeast cells induced by glucose, fructose, sucrose, maltose or galactose. Continuous measurements revealed distinct modes (transient or gradually increasing) of the current development during the first 2 to 3 min after subjection to glucose, fructose and sucrose at electrodes containing S. cerevisiae and non-Saccharomyces strains. Different modes (increasing or decreasing) of the current development after yeast subjection to galactose at electrodes with S. cerevisiae or D. hansenii and at electrodes with C. pulcherrima and P. guilliermondii suggested different mechanisms of galactose assimilation.

Comparison of Vitek Matrix-assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Versus Conventional Methods in Candida Identification

Candida species are generally identified by conventional methods such as germ tube or morphological appearance on corn meal agar, biochemical methods using API kits and molecular biological methods. Alternative to these methods, rapid and accurate identification methods of microorganisms called matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDİ-TOF MS) has recently been described. In this study, Candida identification results by API Candida kit, API 20C AUX kit and identifications on corn meal agar (CMA) are compared with the results obtained on Vitek-MS. All results were confirmed by sequencing internal transcribed spacer (ITS) regions of rDNA. Totally, 97 Candida strains were identified by germ tube test, CMA, API and Vitek-MS. Vitek-MS results were compatible with 74.2 % of API 20C AUX and 81.4 % of CMA results. The difference between the results of API Candida and API 20C AUX was detected. The ratio of discrepancy between Vitek-MS and API 20C AUX was 25.8 %. Candida species mostly identified as C. famata or C. tropicalis by and not compatible with API kits were identified as C. albicans by Vitek-MS. Sixteen Candida species having discrepant results with Vitek-MS, API or CMA were randomly chosen, and ITS sequence analysis was performed. The results of sequencing were compatible 56.2 % with API 20C AUX, 50 % with CMA and 93.7 % with Vitek-MS. When compared with conventional identification methods, MS results are more reliable and rapid for Candida identification. MS system may be used as routine identification method in clinical microbiology laboratories.

Combining UV-C treatment with biocontrol yeast to control postharvest decay of melon

Significant losses in harvested melon can be directly attributable to decay fungi. In the present study, the use of UV-C treatment combined with biocontrol yeast, Pichia cecembensis, was evaluated for their ability to control postharvest decay of melon fruits after they were artificially inoculated with Fusarium oxysporum and Alternaria alternata. Natural infection of fruit was also assessed. As a stand-alone treatment, UV-C or P. cecembensis significantly reduced Fusarium rot and Alternaria rot, and also the level of natural infection on melon fruit, relative to the untreated control. The combination of UV-C or P. cecembensis, however, provided a superior level of decay control on artificially inoculated and naturally infected fruit, compared to either treatment alone. None of the treatments impaired fruit quality. Integrating the use of UV-C treatment with biocontrol yeast has potential as an effective method to control postharvest decay of melon.

Is the extraction by Whatman FTA filter matrix technology and sequencing of large ribosomal subunit D1-D2 region sufficient for identification of clinical fungi?

Although conventional identification of pathogenic fungi is based on the combination of tests evaluating their morphological and biochemical characteristics, they can fail to identify the less common species or the differentiation of closely related species. In addition these tests are time consuming, labour-intensive and require experienced personnel. We evaluated the feasibility and sufficiency of DNA extraction by Whatman FTA filter matrix technology and DNA sequencing of D1-D2 region of the large ribosomal subunit gene for identification of clinical isolates of 21 yeast and 160 moulds in our clinical mycology laboratory. While the yeast isolates were identified at species level with 100% homology, 102 (63.75%) clinically important mould isolates were identified at species level, 56 (35%) isolates at genus level against fungal sequences existing in DNA databases and two (1.25%) isolates could not be identified. Consequently, Whatman FTA filter matrix technology was a useful method for extraction of fungal DNA; extremely rapid, practical and successful. Sequence analysis strategy of D1-D2 region of the large ribosomal subunit gene was found considerably sufficient in identification to genus level for the most clinical fungi. However, the identification to species level and especially discrimination of closely related species may require additional analysis.

Sensitive and rapid RT-qPCR quantification of pathogenic Candida species in human blood

For accurate diagnosis and appropriate treatment of candidiasis, we developed a highly sensitive quantitative RT-PCR (RT-qPCR) system for five Candida species that have been reported to be the major causes of bloodstream fungal infection (Candida albicans, Candida glabrata, Candida tropicalis, Candida parapsilosis, and Candida krusei), together with a system for all pathogenic Candida species. Cells of each fungal species spiked into human peripheral blood (PB) were specifically detected at a lower detection limit of 10(0) cell/1 mL PB by this system using the newly developed specific primer sets targeting 18S or 26S rRNA of the five Candida species, together with the existing group primer set. The total count of the five Candida spp. as the sum of those obtained by using the five species primer sets was equivalent to the count obtained by using the group primer set, indicating that the group set covered the major five Candida spp. in human blood with the same degree of accuracy as the species primer sets. The RT-qPCR counts of the Candida species were in good agreement with CFU counts obtained by their culture on CHROMagar™, with a lower detection limit of 10(0)cell/mL of PB. Candida rRNA molecules were stably stored for at least 7 days at 4°C by keeping the blood specimens in an RNA stabilizing reagent. These results strongly suggest that this sensitive system is useful for accurate and rapid diagnosis of Candida bloodstream infections.

DNA barcoding of fungi causing infections in humans and animals

Correct species identification is becoming increasingly important in clinical diagnostics. Till now, many mycological laboratories rely on conventional phenotypic identification. But this is slow and strongly operator-dependent. Therefore, to improve the quality of pathogen identification, rapid, reliable, and objective identification methods are essential. One of the most encouraging approaches is molecular barcoding using the internal transcribed spacer (ITS) of the rDNA, which is rapid, easily achievable, accurate, and applicable directly from clinical specimens. It relies on the comparison of a single ITS sequence with a curated reference database. The International Society for Human and Animal Mycology (ISHAM) working group for DNA barcoding has recently established such a database, focusing on the majority of human and animal pathogenic fungi (ISHAM-ITS, freely accessible at http://www.isham.org/ or directly from http://its.mycologylab.org). For some fungi the use of secondary barcodes may be necessary.

Intravenous Catheter-Associated Candidemia due to Candida membranaefaciens: The First Iranian Case

The incidence of candidemia due to the uncommon non-albicans Candida species appears to be increasing, and certain species such as Candida (C.) membranaefaciens have been reported in some clinical researches. Vascular catheters are considered the likely culprit for the sudden emergence of hospital-acquired candidemia. The identification of C. membranaefaciens can be problematic in clinical practice owing to its phenotypic resemblance to C. guilliermondii. We report the first case of C. membranaefaciens in Iran, which occurred in a 70-year-old woman, who had coronary artery bypass grafting (CABG). We isolated germ-tube negative yeast from both blood culture and central venous catheter (CVC) tip culture on brain-heart infusion agar, Sabouraud dextrose agar plates, and biphasic brain-heart infusion media bottle; it developed smooth, pink colonies on CHROMagar Candida. By using the polymerase chain reaction and sequencing of theinternal transcribed spacer region of rDNA, we identified C. membranaefaciens. After the removal of the CVC and initiation of Fluconazole treatment, the patient's condition gradually improved and she was discharged from the hospital. The early detection of organisms in the catheter, removal of the catheter, and treatment with anti-fungal antibiotics have an important role in controlling disease and preventing septicemia after CABG. As C. membranaefaciens is an opportunistic Candida species, both clinicians and microbiologists should be aware of the factors that confer fast diagnosis and appropriate treatment.

International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi

Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections and creating new risks for established ones. There is a growing need for a rapid and accurate identification of pathogens to enable early diagnosis and targeted antifungal therapy. Morphological and biochemical identification methods are time-consuming and require trained experts. Alternatively, molecular methods, such as DNA barcoding, a powerful and easy tool for rapid monophasic identification, offer a practical approach for species identification and less demanding in terms of taxonomical expertise. However, its wide-spread use is still limited by a lack of quality-controlled reference databases and the evolving recognition and definition of new fungal species/complexes. An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database under the umbrella of the ISHAM working group on "DNA barcoding of human and animal pathogenic fungi." A new database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool at http://www.isham.org/ and http://its.mycologylab.org/ to rapidly and reliably identify most agents of mycoses, was established. The generated sequences included in the new database were used to evaluate the variation and overall utility of the ITS region for the identification of pathogenic fungi at intra-and interspecies level. The average intraspecies variation ranged from 0 to 2.25%. This highlighted selected pathogenic fungal species, such as the dermatophytes and emerging yeast, for which additional molecular methods/genetic markers are required for their reliable identification from clinical and veterinary specimens.

Molecular identification of uncommon clinical yeast species in Iran

Background and Purpose:

By using advanced detection/identification methods, the list of emerging uncommon opportunistic yeast infections is rapidly expanding worldwide. Our aim in the present study was sequence-based species delineation of previously unidentified yeasts obtained from a clinically yeast collection.

Materials and Methods:

A total of twenty three out of the 855 (5.7%) yeast isolates which formerly remained unidentified by PCR-RFLP method, were subjected to sequence analysis of the entire internal transcribed spacers (ITS) regions of rDNA. The precise species recognition was performed by the comparison of the sequences with the reliable GenBank database.

Results:

Sequencing analysis of the ITS region of the strains revealed several uncommon yeasts that were not reported previously in Iran. The species include Hanseniaspora uvarum, Saccharomyces cerevisiae, Sporidiobolus salmonicolor, Pichia fabianii, Pichia fermentans, Candida famata, Candida inconspicua, Candida maqnoliae, Candida guilliermondii, Candida kefyr, Candida rugosa, Candida lusitaniae, Candida orthopsilosis, and Candida viswanathii.

Conclusion:

We identified several rare clinical isolates selected from a big collection at the species level by ITS-sequencing. As the list of yeast species as opportunistic human fungal infections is increasing dramatically, and many isolates remain unidentified using conventional methods, more sensitive and specific advanced approaches help us to clarify the aspects of microbial epidemiology of the yeast infections.

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.

Genetic diversity of medically important and emerging Candida species causing invasive infection

BACKGROUND

Genetic variation in the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region has been studied among fungi. However, the numbers of ITS sequence polymorphisms in the various Candida species and their associations with sources of invasive fungal infections remain poorly investigated. Here, we characterized the intraspecific and interspecific ITS diversity of Candida spp. strains collected from patients with bloodstream or oroesophageal candidiasis.

METHODS

We selected cultures of representative medically important species of Candida as well as some rare and emerging pathogens. Identification was performed by micromorphology and by biochemical testing using an ID32C system, as well as by the sequencing of rDNA ITS. The presence of intraspecific ITS polymorphisms was characterized based on haplotype networks, and interspecific diversity was characterized based on Bayesian phylogenetic analysis.

RESULTS

Among 300 Candida strains, we identified 76 C. albicans, 14 C. dubliniensis, 40 C. tropicalis, 47 C. glabrata, 34 C. parapsilosis (sensu stricto), 31 C. orthopsilosis, 3 C. metapsilosis, 21 Meyerozyma guilliermondii (C. guilliermondii), 12 Pichia kudriavzevii (C. krusei), 6 Clavispora lusitaniae (C. lusitaniae), 3 C. intermedia, 6 Wickerhamomyces anomalus (C. pelliculosa), and 2 C. haemulonii strains, and 1 C. duobushaemulonii, 1 Kluyveromyces marxianus (C. kefyr), 1 Meyerozyma caribbica (C. fermentati), 1 Pichia norvegensis (C. norvegensis), and 1 Lodderomyces elongisporus strain. Out of a total of seven isolates with inconsistent ID32C profiles, ITS sequencing identified one C. lusitaniae strain, three C. intermedia strains, two C. haemulonii strains and one C. duobushaemulonii strain. Analysis of ITS variability revealed a greater number of haplotypes among C. albicans, C. tropicalis, C. glabrata and C. lusitaniae, which are predominantly related to endogenous sources of acquisition. Bayesian analysis confirmed the major phylogenetic relationships among the isolates and the molecular identification of the different Candida spp.

CONCLUSIONS

Molecular studies based on ITS sequencing are necessary to identify closely related and emerging species. Polymorphism analysis of the ITS rDNA region demonstrated its utility as a genetic marker for species identification and phylogenetic relationships as well as for drawing inferences concerning the natural history of hematogenous infections caused by medically important and emerging Candida species.

Current methods for identifying clinically important cryptic Candida species

In recent years, the taxonomy of the most important pathogenic Candida species (Candida albicans, Candida parapsilosis and Candida glabrata) has undergone profound changes due to the description of new closely-related species. This has resulted in the establishment of cryptic species complexes difficult to recognize in clinical diagnostic laboratories. The identification of these novel Candida species seems to be clinically relevant because it is likely that they differ in virulence and drug resistance. Nevertheless, current phenotypic methods are not suitable to accurately distinguish all the species belonging to a specific cryptic complex and therefore their recognition still requires molecular methods. Since traditional mycological techniques have not been useful, a number of molecular based methods have recently been developed. These range from simple PCR-based methods to more sophisticated real-time PCR and/or MALDI-TOF methods. In this article, we review the current methods designed for discriminating among closely related Candida species by highlighting, in particular, the limits of the existing phenotypic tests and the development of rapid and specific molecular tools for their proper identification.

Synergistic activity of chloroquine with fluconazole against fluconazole-resistant isolates of Candida species

The in vitro activity of chloroquine and the interactions of chloroquine combined with fluconazole against 37 Candida isolates were tested using the broth microdilution, disk diffusion, and Etest susceptibility tests. Synergistic effect was detected with 6 of 9 fluconazole-resistant Candida albicans isolates, with Candida krusei ATCC 6258, and with all 12 fluconazole-resistant Candida tropicalis isolates.

The first reported case of central venous catheter-related fungemia caused by Cryptococcus liquefaciens

We describe a case of central venous catheter-related fungemia caused by Cryptococcus liquefaciens, a non-neoformans and non-gattii Cryptococcus, in a non-HIV patient. A 71-year-old man with diffuse large B-cell lymphoma receiving antineoplastic chemotherapy was febrile approximately 30 weeks after central venous port insertion, and C. liquefaciens was isolated from all three performed blood cultures as well as a central venous catheter tip culture. In vitro antifungal susceptibility tests showed that this yeast isolate was susceptible to low concentrations of amphotericin B, fluconazole, itraconazole and voriconazole yet was resistant to 5-fluorocytosine (MIC: >64 μg/ml), unlike Cryptococcus neoformans. Treatment of the patient with oral and intravenous voriconazole was effective and consistent with the susceptibility tests. Although non-neoformans and non-gattii Cryptococcus spp. are considered non-pathogenic environmental yeast, they may rarely be the causative agents of serious infections in humans, as in the present case.

Comparison of the accuracy of two conventional phenotypic methods and two MALDI-TOF MS systems with that of DNA sequencing analysis for correctly identifying clinically encountered yeasts

We assessed the accuracy of species-level identification of two commercially available matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems (Bruker Biotyper and Vitek MS) and two conventional phenotypic methods (Phoenix 100 YBC and Vitek 2 Yeast ID) with that of rDNA gene sequencing analysis among 200 clinical isolates of commonly encountered yeasts. The correct identification rates of the 200 yeast isolates to species or complex (Candida parapsilosis complex, C. guilliermondii complex and C. rugosa complex) levels by the Bruker Biotyper, Vitek MS (using in vitro devices [IVD] database), Phoenix 100 YBC and Vitek 2 Yeast ID (Sabouraud's dextrose agar) systems were 92.5%, 79.5%, 89%, and 74%, respectively. An additional 72 isolates of C. parapsilosis complex and 18 from the above 200 isolates (30 in each of C. parapsilosis, C. metapsilosis, and C. orthopsilosis) were also evaluated separately. Bruker Biotyper system could accurately identify all C. parapsilosis complex to species level. Using Vitek 2 MS (IVD) system, all C. parapsilosis but none of C. metapsilosis, or C. orthopsilosis could be accurately identified. Among the 89 yeasts misidentified by the Vitek 2 MS (IVD) system, 39 (43.8%), including 27 C. orthopsilosis isolates, could be correctly identified Using the Vitek MS Plus SARAMIS database for research use only. This resulted in an increase in the rate of correct identification of all yeast isolates (87.5%) by Vitek 2 MS. The two species in C. guilliermondii complex (C. guilliermondii and C. fermentati) isolates were correctly identified by cluster analysis of spectra generated by the Bruker Biotyper system. Based on the results obtained in the current study, MALDI-TOF MS systems present a promising alternative for the routine identification of yeast species, including clinically commonly and rarely encountered yeast species and several species belonging to C. parapsilosis complex, C. guilliermondii complex, and C. rugosa complex.

Prospective assessment of FilmArray® technology for the rapid identification of yeast isolated from blood cultures

We prospectively assessed the ability of FilmArray® device to identify fungal species involved in bloodstream infections. It succeeded in identifying 85.7% of isolates. The automated readout of results enabled the rapid initiation of appropriate antifungal therapy. Thus, FilmArray® appeared as a reliable alternative diagnostic method for the most common yeast-like species.

Application of MALDI-TOF MS for requalification of a Candida clinical isolates culture collection

Microbial culture collections underpin biotechnology applications and are important resources for clinical microbiology by supplying reference strains and/or performing microbial identifications as a service. Proteomic profiles by MALDI-TOF MS have been used for Candida spp. identification in clinical laboratories and demonstrated to be a fast and reliable technique for the routine identification of pathogenic yeasts. The main aim of this study was to apply MALDI-TOF MS combined with classical phenotypic and molecular approaches to identify Candida clinical isolates preserved from 1 up to 52 years in a Brazilian culture collection and assess its value for the identification of yeasts preserved in this type of collections. Forty Candida spp. clinical isolates were identified by morphological and biochemical analyses. Identifications were also performed by the new proteomic approach based on MALDI-TOF MS. Results demonstrated 15% discordance when compared with morphological and biochemical analyses. Discordant isolates were analysed by ITS sequencing, which confirmed the MALDI-TOF MS identifications and these strains were renamed in the culture collection catalogue. In conclusion, proteomic profiles by MALDI-TOF MS represents a rapid and reliable method for identifying clinical Candida species preserved in culture collections and may present clear benefits when compared with the performance of existing daily routine methods applied at health centres and hospitals.

Potential association of specific Candida parapsilosis genotypes, bloodstream infections and colonization of health workers' hands

Fungal nosocomial infections continue to be a serious problem among hospitalized patients, decreasing quality of life and adding millions of euros to healthcare costs. The aim of this study was to describe the pattern of fungi associated with the hands of healthcare workers and to genotype Candida parapsilosis isolates in order to understand whether their high clinical prevalence stems from endemic nosocomial genotypes or from the real emergence of epidemiologically-unrelated strains. Approximately 39% (50/129) of healthcare workers were positive for yeasts and among 77 different fungal isolates recovered, C. parapsilosis was the most frequent (44/77; 57%). Twenty-seven diverse genotypes were obtained by microsatellite analysis of 42 selected blood and hand isolates. Most of the isolates from hands showed a new, unrelated, genotype, whereas a particular group of closely related genotypes prevailed in blood samples. Some of the latter genotypes were also found on the hands of healthcare workers, indicating a persistence of these clones within our hospital. C. parapsilosis genotypes from the hands were much more heterogeneous than clinical ones, thus reflecting a high genetic diversity among isolates, which is notably unusual and unexpected for this species.

Development of two molecular approaches for differentiation of clinically relevant yeast species closely related to Candida guilliermondii and Candida famata

The emerging pathogens Candida palmioleophila, Candida fermentati, and Debaryomyces nepalensis are often misidentified as Candida guilliermondii or Candida famata in the clinical laboratory. Due to the significant differences in antifungal susceptibilities and epidemiologies among these closely related species, a lot of studies have focused on the identification of these emerging yeast species in clinical specimens. Nevertheless, limited tools are currently available for their discrimination. Here, two new molecular approaches were established to distinguish these closely related species. The first approach differentiates these species by use of restriction fragment length polymorphism analysis of partial internal transcribed spacer 2 (ITS2) and large subunit ribosomal DNA with the enzymes BsaHI and XbaI in a double digestion. The second method involves a multiplex PCR based on the intron size differences of RPL18, a gene coding for a protein component of the large (60S) ribosomal subunit, and species-specific amplification. These two methods worked well in differentiation of these closely related yeast species and have the potential to serve as effective molecular tools suitable for laboratory diagnoses and epidemiological studies.