Yeast identification in the clinical microbiology laboratory: phenotypical methods

A Cluster of Diutina catenulata Funguria in Patients with Coronavirus Disease 2019 (COVID-19) Hospitalized in a Tertiary Reference Hospital from Rio de Janeiro, Brazil

During the COVID-19 pandemic, fungal infections, especially pulmonary aspergillosis, mucormycosis, and invasive candidiasis, have emerged as a significant health concern. Beyond Candida albicans, the most common cause of invasive candidiasis, other rare ascomycetous yeast species have been described in tertiary care units, potentially posing a broader health threat. We have isolated, from September 2020 to June 2021, nine Diutina catenulata strains from urine samples of six patients. This was intriguing as this fungus had not been previously identified in our institution, nor after June 2021. Therefore, we decided to outline the clinical features of the patients with this rare pathogen, to describe phenotypic characteristics, including antifungal susceptibility profiles, of this yeast species and to identify the genetic makeup through whole-genome sequencing analysis to evaluate if this was a cluster of genetically similar D. catenulata isolates in our institution. The strains were identified through MALDI-TOF MS analyses and Sanger sequencing of two rDNA regions. All patients yielding D. catenulata from urine samples needed ventilator support and used urinary catheters during hospitalization for treatment of COVID-19. None of them had received COVID-19 vaccines. Morphological and biochemical profiles of the nine strains were largely consistent, although fluconazole susceptibility varied, ranging from 4 to 32 μg/mL. Phylogenomic analysis revealed minimal genetic variation among the isolates, with low intrapopulation variation, supported by the identification of only 84 SNPs across all strains. Therefore, we propose that the yeast strains isolated were part of a cluster of D. catenulata funguria in the context of COVID-19.

Novel Chromogenic Medium CHROMagarTM Candida Plus for Detection of Candida auris and Other Candida Species from Surveillance and Environmental Samples: A Multicenter Study

Epidemiological trends show a dramatic increase in the prevalence of fungal infections, and in the isolation of multidrug-resistant species, such as Candida auris. CHROMagar^TM Candida (CC; CHROMagar, Paris, France) and other chromogenic media, which are widely used in the clinical laboratory because they allow a rapid identification of most Candida species. Recently, CHROMagar^TM Candida Plus (CC-Plus; CHROMagar, Paris, France) was developed to detect and differentiate C. auris in addition to other major clinical Candida species, such as C. albicans, C. tropicalis, C. glabrata, or C. krusei. C. auris colonies display a differential light blue color with a blue halo. A multicentric study was designed to evaluate the performance of the CC-Plus medium in the detection of Candida species in patients’ surveillance and environmental samples from three Spanish hospitals with active C. auris outbreaks. A total of 364 patients’ surveillance samples and 212 environmental samples were tested. Samples were inoculated in CC and CC-Plus in parallel, and the plates were read at 24 and 48 h. All recovered colonies were presumptively identified according to colony color described by manufacturer, and the definitive identification was performed by mass spectrometry at 48 h. A total of 134 C. auris isolates were obtained (101 from patients’ surveillance samples, and 33 from environmental samples). Sensitivity, specificity, and predictive positive and negative values were 99.5%, 100%, 100%, and 99.1%, respectively, for the main clinical Candida species, showing that CC-Plus is comparable to CC, with the advantage of being able to differentiate C. auris from C. parapsilosis. Furthermore, CC-Plus was able to detect one C. albicans, one C. glabrata, and eight C. auris that did not grow in CC. Additionally, the yeast colonies were generally larger, suggesting that this novel medium could be a richer medium, and suitable for surveillance and environmental cultures of C. auris and other clinically relevant Candida species.

Characterization, enzymatic activity and biofilm formation of Candida species isolated from goat milk

BACKGROUND

Data regarding yeast microbiota in goat milk is scarce.

AIMS

To isolate and identify species of the genus Candida in milk samples from clinically healthy goats, and evaluate their enzymatic activity and biofilm formation.

METHODS

1092 milk samples from clinically healthy goats were collected and processed. The yeast isolates were identified by phenotypic, methods and their enzymatic activity (phospholipase, hemolysin and protease) and biofilm formation evaluated.

RESULTS

We obtained 221 Candida isolates belonging to six species: Candida kefyr (35.7%), Candida guilliermondii (33%), Candida famata (23.5%), Candida glabrata (5.9%), Candida albicans (1.35%) and Candida parapsilosissensu lato (0.45%). Protease activity was detected in all Candida species while hemolysin activity was only present in C. kefyr, C. guilliermondii, C. famata and C. albicans. Only C. albicans showed phospholipase activity. With the exception of C. parapsilosis sensu lato, all Candida species formed biofilm, with 60.19% of the isolates being poor producers, 9.93% moderate producers, and 1.35% strong producers.

CONCLUSIONS

The milk of clinically healthy goats contains several species of the genus Candida that could play a role as opportunistic pathogens in mastitis.

MALDI-TOF MS Overcomes Misidentification of the Uncommon Human Pathogen Candida famata by Routine Phenotypic Identification Methods

Candida famata has been associated with the identifiable Candida infections that takes place in human and the identification error of this species possibly will result in misinterpretation of antifungal susceptibility and improper diagnosis; which will have a major effect on the prognosis and therapy of patients. Our objective is to correctly identify Candida spp. collected from patients at the intensive care units, New Cairo University teaching hospital in Cairo-Egypt using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Hundred clinically isolated yeast strains were identified using API 20C AUX obtained from patients receiving care at intensive care units. ATB FUNGUS 3 strips were used to detect the minimum inhibitory concentration. Thirty-three non duplicate strains identified as C. famata were subjected to re-identification by MALDI-TOF MS. Our results revealed that isolates were initially identified as C. famata 33%, C. tropicalis 15%, C. albicans 12% and C. parapsillosis 10% using the phenotypic techniques. MALDI-TOF MS analyses results showed that the 33 C. famata isolates are C. tropicalis (n = 29), Trichosporon asahii (n = 2), C. parapsilosis (n = 1), and Aeromonas sobria (n = 1). Antifungal resistance was low in the Candida species, except for reduced susceptibility to itraconazole among C. krusei strains. This report shows that misidentification of C. famata is frequent when using conventional phenotypic methods of identification which result in challenges in treating fungal infections. MALDI-TOF MS is an accurate convenient substitute to classical approaches for fungal identification. In general, antifungal multidrug resistance is uncommon in our studied Candida species and yeast isolates.

The Evolving Landscape of Fungal Diagnostics, Current and Emerging Microbiological Approaches

Invasive fungal infections are increasingly recognized in immunocompromised hosts. Current diagnostic techniques are limited by low sensitivity and prolonged turnaround times. We review emerging diagnostic technologies and platforms for diagnosing the clinically invasive disease caused by Candida, Aspergillus, and Mucorales.

Isolation, identification and genotyping of Candida albicans from Landes geese

In May 2018, Landes geese raised in Weifang, Shandong Province, China, developed a disease characterized by thickened oesophageal mucosa and white, round ulcers. Based on pathogen isolation and identification, differential culture and morphological observations, Candida albicans (C. albicans) was identified as the causative pathogen from the oesophagus of infected geese, and artificial infection experiments were then performed using the isolated strains. In experimental reproduction, the symptoms of infected geese were consistent with those of natural infection, and gosling morbidity and mortality were 75% and 60%, respectively. Re-isolation of the strain from the dead goslings confirmed C. albicans as the causative pathogen of oesophageal ulcers. We further performed internal transcribed space rDNA sequence analysis, ABC genotyping and multi-locus sequence typing analysis. We observed 100% sequence similarity between the two strains, designated as WFCL and WFLQ, which were isolated from different regions, with 100% homology between the strains isolated in the present study and the human-origin C. albicans strains isolated previously from China. The goose-origin strains isolated in this study and the human-origin C. albicans isolates were included in the same branch in phylogenetic trees analysis, indicating that the strain responsible for oesophageal ulcer in geese is closely related to human-origin C. albicans. In addition, based on eBURST analysis of sequence types, goose-origin C. albicans strains were relatively independent in terms of population evolution. To the best of our knowledge, this is the first detailed report on goose oesophageal ulceration caused by C. albicans infection in geese. Considering that C. albicans is an important zoonotic pathogen, this study provides a reference for further studies on avian C. albicans infections and is important for ensuring public health and safety.

Evaluation of a novel chromogenic medium for Candida spp. identification and comparison with CHROMagar™ Candida for the detection of Candida auris in surveillance samples

A shift to Candida non-albicans infections has been noted during the last years, and the emergence of multi-resistant Candida auris has complicated their management. The aim of this study was first to compare the performance of the novel chromogenic medium CHROMagar™ Candida Plus (CHROMagar, France) with CHROMagar™ Candida (Becton Dickinson, Germany) for the presumptive identification of Candida species; and then, to evaluate its utility in the detection of C. auris in surveillance samples. CHROMagar™ Candida Plus showed a good performance compared with the reference medium CHROMagar™ Candida. Sensitivity and specificity were 100% in both media for tested species at 48 h of incubation, except for Candida glabrata and Candida lusitaniae. Furthermore, the new medium allows a reliable presumptive identification of C. auris, as a new specific color for this species is assigned (light blue with a blue halo), obtaining a sensitivity and specificity of 100% at 36 h of incubation.

Saprochaete capitata oropharyngeal infection in a neutropenic patient: unusual presentation

Introduction: Saprochete capitata is unusual etiologic agent in immunocompromised patients, particularly in those with hematologic malignancy and severe neutropenia. Most often, infections of the oral cavity are manifested clinically as oral candidiasis. Invasive forms are rarely described. Observation: a 63-year-old man consulted for pseudomembranous lesions associated with ulcero perforating lesion of the tongue and palatal region ulcerations. All evolving in a context of profound physical deterioration and severe neutropenia. Mycological examination showed Saprochaete capitata. The evolution was favorable with oral voriconazole. Comment: Saprochaete capitata invasive fungal infections have become an important cause of morbidity and mortality, particularly in hematology-oncology patients. Invasive or non-invasive, oropharyngeal involvement with this pathogen should not be underestimated in the neutropenic patient. They are the main starting point for fongemia of this pathogen, which is often fatal. Conclusion: Saprochete capitata is now recognized emerging etiologic agent in patients with hematological malignancy and severe neutropenia. Early detection and diagnosis of these fungal infections could lead to reduced morbidity and mortality, particularly in locally invasive infection.

The emergence of non-albicans candidemia and evaluation of HiChrome Candida differential agar and VITEK2 YST® platform for differentiation of Candida bloodstream isolates in teaching hospital Kandy, Sri Lanka

Background

Candidemia is an emerging hospital-acquired bloodstream infection (BSI). It is common among severely ill and immunocompromised patients. Even following appropriate therapy in candidemia, recent studies reveal relative high mortality (40%). The global incidence of candidemia shows an incline. In Sri Lanka, candida speciation often difficult where basic facilities are less available. We have compared the risk factors, epidemiology, demography, and performance of HiChrome Candida differential agar (HiCA) characteristics with the VITEK2 YST platform for differentiation of Candida albicans (CA) and non-albicans candida (NAC) from blood culture isolate.

Methods

This is a laboratory-based cross-sectional study. Positive aerobic BACTEC blood cultures having yeast were identified using HiCA and VITEK2® platform. Epidemiology, risk factors, and clinical outcomes were compared between CA and NAC bloodstream isolates.

Results

Out of 120 positive yeast samples, VITEK2® has identified 110 (92%) as Candida sp. From that CA-34 (31%) and NAC-76 (69%) were isolated. Candidemia following NCA in neonates (p = 0.02), infants (p = 0.04) and adults (p = 0.02) in ICU and immunocompromised patients were significantly higher. Compared to CA, NAC bacteremia period prevalence (0.00041%) and incidence (0.23 per 100,000-person-years) was significantly high (p = 0.03). NAC 48 (63%) isolates were resistance to azoles. Exposure to antifungals (odds ratio (OR); p = 0.03), prolonged intensive care stay > 14 days (OR-3.3; p = 0.04), having a central venous line for > 8 days (OR-4.3; p = 0.03) and on immunosuppressive treatment (OR-2.4; p = 0.04) was significantly poses risk for NAC candidemia. Sen day mortality was significant among non-albicans cases (p = 0.03) while 30-day mortality was significant among albicans cases (p = 0.04). Compared to VITEK2®, the HiCA method was 93% sensitive and 93% specific in detecting CA.

Conclusion

Compared to CA, candidemia following NAC was high. NAC isolates were having a high percentage of fluconazole and voriconazole resistance. VITEK2 YST® platform provides antifungal susceptibility with minimal inhibitory concentration (MIC). Impact, this would highlight the use of rapid candida identification flat form with MIC to direct appropriate antifungals for candidemia. For that implementation of novel diagnostic facilities like the VITEK2 YST platform at a tertiary care facility is demanding.

Potential of fungi isolated from the dumping sites mangrove rhizosphere soil to degrade polythene

Polythene is the most widely used plastic around the globe. Among the total plastic waste generated, polythene contributes the maximum share (64%). Various strategies/methods are being utilized to deal with the increasing rate of plastic waste, but among all the methods, bioremediation is regarded as the ecofriendly and widely accepted method. In the current investigation, we have attempted to discover the elite polythene deteriorating fungi (isolated from the rhizosphere soil of Avicennia marina). From 12 different eco-geographical locations along the West Coast of India, total 109 fungal isolates were recorded. The polythene deteriorating fungi were screened at varied pH (3.5, 7 and 9.5) based on changes in weight and tensile strength of the treated polythene at ambient temperature with continuous shaking for 60 days. BAYF5 isolate (pH 7) results in maximum reduction in weight (58.51 ± 8.14) whereas PNPF15 (pH 3.5) recorded highest reduction in tensile strength (94.44 ± 2.40). Surprisingly, we have also reported weight gain, with highest percent weight gain (28.41 ± 6.99) with MANGF13 at pH 9.5. To test the reproducibility of the results, the elite polythene degrading fungal isolates based on weight loss and reduction in tensile strength were only used for repetition experiment and the results based on the reduction in tensile strength were found only reproducible. Polythene biodegradation was further confirmed using Scanning Electron Microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR) analysis. The most efficient polythene deteriorating fungal isolates were identified as Aspergillus terreus strain MANGF1/WL and Aspergillus sydowii strain PNPF15/TS using both morphological keys and molecular tools.

Blastoschizomyces capitatus pneumonia in a patient with untreated chronic lymphocytic leukemia

Several cases have been reported of B. capitatus infections in immunocompromised patients. Acute leukemia is the main predisposing factor. Chronic lymphocytic leukemia (CLL) is not usually associated with opportunistic infections. We report a case of pulmonary infection by B. capitatus in a patient with untreated chronic lymphocytic leukemia. Although the patient had a complete recovery, we believe that this report will alert clinicians to consider B. capitatus as possible cause of severe pneumonia in untreated CLL.

Epidemiological investigation of non-albicans Candida species recovered from mycotic mastitis of cows in Yinchuan, Ningxia of China

BACKGROUND

Candida spp. is the vital pathogen involved in mycotic mastitis of cows. However the epidemiology and infection of Candida species in mycotic mastitis of cow in Ningxia province of China has not been explored. In the present study, the epidemiology, antimicrobial susceptibility and virulence-related genes of non-albicans Candida (NAC) species were investigated.

METHODS

A total of 482 milk samples from cows with clinical mastitis in four herds of Yinchuan, Ningxia were collected and used for the isolation and identification of mastic pathogens by phenotypic and molecular characteristics, and matrix-assisted laser desorption ionization-time of flight mass spectrometry. The antimicrobial susceptibility to antifungal agents was also determined by a disk diffusion assay. The presence of virulence-related genes was determined by polymerase chain reaction (PCR).

RESULTS

A total of 60 isolates from nine different Candida species were identified from 256 (60/256, 23.44%) milk samples. The most frequently identified species in cows with clinical mastitis groups were Candida krusei (n = 14) and Candida parapsilosis (n = 6). Others include Candida lipolytica, Candida lusitaniae, Cryptococcus neoformans. But no Candida albicans was identified in this study. Interestingly, All C. krusei isolates (14/14) were resistant to fluconazole, fluorocytosine, itraconazole and ketoconazole, 2 out of 14 C. krusei were resistant to amphotericin, and 8 out of the 14 were resistant to nystatin. Similarly, all six C. parapsilosis isolates were resistant to fluorocytosine, but susceptible to fluconazole, ketoconazole and nystatin; two of the six were resistant amphotericin and itraconazole. Molecularly, all of the C. parapsilosis isolates carried eight virulence-related genes, FKS1, FKS2, FKS3, SAP1, SAP2, CDR1, ERG11 and MDR1. All of the C. krusei isolates contained three virulence-related genes, ERG11, ABC2 and FKS1.

CONCLUSION

These data suggested that Candida species other than C. albicans played a pathogenic role in mycotic mastitis of cows in Yinchuan, Ningxia of China. The high incidence of drug-resistant genes in C. parapsilosis and C. krusei also highlighted a great concern in public and animal health in this region.

Speciation of Candida using CHROMagar in cases with oral epithelial dysplasia and squamous cell carcinoma

Background

Candida albicans is most frequently isolated from oral cavity but identification of other Candida species such as C. tropicalis, C. krusei, C. glabrata & C. dubliniensis is increasing proportionately. A constant rise in immuno-suppressed patients, widening range of recognized pathogens, and resistance to antifungal drugs are contributing factors which stress the need for species identification of Candida, an opportunistic pathogen. Objectives: 1. To detect the prevalence of Candida albicans and Non albicans Candida albicans (NAC) species in the oral cavity of patients with epithelial dysplasia, Oral squamous cell carcinoma (OSCC) and healthy controls. 2. To identify and differentiate Candidal species using CHROMagar, a differential media.

Material and Methods

The study included smears from 50 patients with histopathological confirmation of epithelial dysplasia & OSCC and 50 normal controls. Candida albicans was identified using Sabouraud dextrose agar media (SDA) as primary culture followed by species identification using CHROMagar on the basis of colony color and morphology.

Results

Non albicans candida predominated (66%) over Candida albicans (34%) in speciation on CHROMagar media in the study group. Non albicans Candida species isolated were C. tropicalis (38%), C. glabrata (24%) and 2 cases showing polyfungal population of C. albicans & C. glabrata.

Conclusions

Species level isolation of Candida helps in early identification of resistant non Candida strains and prompt treatment of the cases there by preventing the dissemination of infection in case of immuno-compromised individuals. The data presented also supports the use of CHROMagar Candida as a pertinent media for the rapid identification of Candida species directly from clinical specimens in resource challenged settings, which could be helpful in developing appropriate therapeutic strategy and management of patients. Key words:Candida, CHROMagar, epithelial dysplasia, oral cancer.

Blastoschizomyces capitatus pulmonary infections in immunocompetent patients: case report, case series and literature review

Blastoschizomyces capitatus is an uncommon opportunistic yeast associated with infections in neutropaenic patients secondary to haematological malignancies, with a special predilection for the lungs. Globalisation and population migration impact on the epidemiology of infection with this organism but its effect on the immunocompetent population has rarely been described. We present here a case report, an overview of 11 other cases published between 2000 and 2016, and a comprehensive literature review of Blastoschizomyces pneumonia in the non-immunocompromised. The median age at diagnosis was 68 years (range 40-86 years) and more than half the cases reported a positive history of either current or past tobacco smoking. Six cases had either clinical or radiological evidence of chronic obstructive pulmonary disease and three had a history of prior treated tuberculosis. Fluconazole and itraconazole, alone or in combination, was the most utilised treatment. We conclude that unlike most other invasive yeast species, B. capitatus poses an infectious risk for immunocompetent patients, usually of middle to older age with risk factors for distorted lung architecture. Further research is warranted into the pathophysiology of Blastoschizomyces infections in the immunocompetent, including standardised treatment options.

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.

Auxanographic Carbohydrate Assimilation Method for Large Scale Yeast Identification

INTRODUCTION

The auxanographic carbohydrate assimilation had been an important method for differentiation of yeasts. Prevailing methods described in the literature for carbohydrate assimilation has limited scope for use in large scale yeast identification.

AIM

To optimize the large scale auxanographic carbohydrate assimilation method for yeast identification.

MATERIALS AND METHODS

A modified auxanographic carbohydrate assimilation method was developed and a total of 35 isolates of Candida species comprising of four ATCC (American Type Culture Collection) Candida strains (Candida albicans ATCC 90028, Candida tropicalis ATCC 90018, Candida parapsilosis ATCC 750, Candida krusei ATCC 6258) and 31 clinical isolates of Candida tropicalis (n=13), Candida krusei (n=7), Candida glabrata (n=3), Candida kefyr (n=3), Candida albicans (n=5) were validated. The carbohydrates tested were Glucose, Sucrose, Maltose, Lactose, Cellubiose, Raffinose, Trehalose, Xylose, Galactose and Dulcitol.

RESULTS

A total of 35 Candida species were tested for their carbohydrate assimilative property and the results were consistent with the existing standard protocols. A well circumscribed opaque yeast growth indicated assimilation of the test carbohydrate and translucent to opalescent growth with the outline of initial inoculum alone indicated lack of assimilation. The control plate indicated no growth of the Candida species.

CONCLUSION

The carbohydrate assimilation tests finds utility for yeast diversity studies exploring novel ecological niches. The technique described here facilitates testing of an extended range of carbohydrates and yeasts in a cost effective manner.

Intra-abdominal Candida spp infection in acute abdomen in a quality assurance (QA)-certified academic setting

AIMS

To evaluate the contribution of light microscopy to detecting Candida spp infection in patients with complicated intra-abdominal infections (IAIs) admitted for acute abdomen to a quality assurance (QA)-certified surgical emergency ward.

METHODS

We conducted a retrospective study (2008-2012) of 809 abdominal intraoperative or biopsy tissue specimens obtained from patients admitted with acute abdomen and microbiological samples positive for Candida spp. Demographic data, mortality, comorbidities, specimen type, microscopy results, special histological staining performed, antimicrobial therapy were collected and analysed. Any comments at the multidisciplinary team meeting was recorded in minutes of and approved.

RESULTS

Sixty-six patients with complicated IAIs due to Candida spp were identified (39 male, 27 female, mean±SD age 75±20 years). Candida albicans was isolated in 35 cases and Candida non-albicans spp in 31 cases. Candida spp were isolated from blood in 50% of all selected microbiological specimens. Patients were stratified according to Candida spp (albicans vs non-albicans), underlying cancer disease and no previous antimicrobial administration, and a positive correlation with C. albicans isolation was found (p=0.009 and p=0.048, respectively). Out of 41 cases with microscopic evaluation, we identified yeast forms, pseudohyphae or both, indicative of Candida spp, in 23. Identification of Candida spp in histological specimens was higher in C. albicans cases than in C. non-albicans cases (73% vs 37.5%). Microscopy allowed prompt treatment of all patients.

CONCLUSIONS

Light microscopy still has great diagnostic significance, being a solid QA step. It provides rapid information and clues in patients who may harbour impaired defence mechanisms, concurrent chronic conditions and/or cancer.

Usefulness of CHROMagar Candida Medium, Biochemical Methods--API ID32C and VITEK 2 Compact and Two MALDI-TOF MS Systems for Candida spp. Identification

This study was conducted to compare of the yeasts identification results obtained with two new systems using the MALDI-TOF MS technique with the ones obtained using the routine identification methods of Candida spp. in clinical microbiology laboratories. All 124 Candida spp. isolates were recovered from the routine examination of clinical specimens in microbiological laboratories and collected in the Centre of Quality Control in Microbiology in Warsaw (Poland). Our findings confirm the high agreement (98%) of fungal identification using the standard, biochemistry laboratory methods and mass spectrometry technique.

Prospective evaluation of the chromogenic medium CandiSelect 4 for differentiation and presumptive identification of non-Candida albicans Candida species

Rapid identification of pathogenic yeasts is a crucial step in timely and appropriate antifungal therapy. For diagnostics in the clinical laboratory, simplified alternatives to barcoding are needed. CandiSelect 4 (CS4) medium, a chromogenic medium for isolation of clinical yeasts, allows routine recognition of Candida albicans and presumptive identification of Candida tropicalis, Candida glabrata, and Candida krusei. We evaluated an extension of this method with 46 non-Candida albicans Candida (NCAC) and 7 Malassezia species. The medium supported growth of all species tested and a wide diversity of cultural types were observed. Colony colours were in violet, turquoise (including green and blue), or white tinges. Eight NCAC species produced violet pigmentation similar to that of C. albicans. Most NCAC species, including C. glabrata and C. tropicalis were distributed in the turquoise group. Malassezia species were invariably blue.

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.

Are the Conventional Commercial Yeast Identification Methods Still Helpful in the Era of New Clinical Microbiology Diagnostics? A Meta-Analysis of Their Accuracy

Accurate identification of pathogenic species is important for early appropriate patient management, but growing diversity of infectious species/strains makes the identification of clinical yeasts increasingly difficult. Among conventional methods that are commercially available, the API ID32C, AuxaColor, and Vitek 2 systems are currently the most used systems in routine clinical microbiology. We performed a systematic review and meta-analysis to estimate and to compare the accuracy of the three systems, in order to assess whether they are still of value for the species-level identification of medically relevant yeasts. After adopting rigorous selection criteria, we included 26 published studies involving Candida and non-Candida yeasts that were tested with the API ID32C (674 isolates), AuxaColor (1,740 isolates), and Vitek 2 (2,853 isolates) systems. The random-effects pooled identification ratios at the species level were 0.89 (95% confidence interval [CI], 0.80 to 0.95) for the API ID32C system, 0.89 (95% CI, 0.83 to 0.93) for the AuxaColor system, and 0.93 (95% CI, 0.89 to 0.96) for the Vitek 2 system (P for heterogeneity, 0.255). Overall, the accuracy of studies using phenotypic analysis-based comparison methods was comparable to that of studies using molecular analysis-based comparison methods. Subanalysis of studies conducted on Candida yeasts showed that the Vitek 2 system was significantly more accurate (pooled ratio, 0.94 [95% CI, 0.85 to 0.99]) than the API ID32C system (pooled ratio, 0.84 [95% CI, 0.61 to 0.99]) and the AuxaColor system (pooled ratio, 0.76 [95% CI, 0.67 to 0.84]) with respect to uncommon species (P for heterogeneity, <0.05). Subanalysis of studies conducted on non-Candida yeasts (i.e., Cryptococcus, Rhodotorula, Saccharomyces, and Trichosporon) revealed pooled identification accuracies of ≥98% for the Vitek 2, API ID32C (excluding Cryptococcus), and AuxaColor (only Rhodotorula) systems, with significant low or null levels of heterogeneity (P > 0.05). Nonetheless, clinical microbiologists should reconsider the usefulness of these systems, particularly in light of new diagnostic tools such as matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry, which allow for considerably shortened turnaround times and/or avoid the requirement for additional tests for species identity confirmation.

Species spectrum and antifungal susceptibility profile of vaginal isolates of Candida in Kuwait

OBJECTIVE

The study was undertaken to determine the prevalence of vulvovaginal candidiasis (VVC) among patients with vaginitis, frequency of different Candida species, and their susceptibility profile.

PATIENTS AND METHODS

Over six months period, high vaginal swabs were cultured on Sabouraud's dextrose agar and isolates were identified by culture on CHROMagar Candida and Vitek2 yeast identification system or/and API 20C (BioMerieux, France). Antifungal susceptibility of the Candida isolates was determined by E-test against amphotericin B, flucytosine, fluconazole, voriconazole, posaconazole and caspofungin.

RESULTS

One thousand seven hundred and fifty-two women with vaginitis were screened for the prevalence of Candida spp. Vaginal swab cultures of 231 (13.2%) women yielded Candida spp. The isolation rates of different species were as follows: Candida albicans (73.9%), Candida glabrata (19.8%), Candida kefir (1.94%), Candida tropicalis (0.96%), Candida parapsilosis (0.96%), Candida krusei (0.96%), Candida guilliermondii (0.96%), and Saccharomyces cerevisiae (0.52%). All strains of C. albicans and non-C. albicans were susceptible to most of the antifungal agents tested.

CONCLUSION

The high frequency with which C. albicans was recovered and its azole susceptibility support the continued use of azole agents for empirical therapy of uncomplicated VVC. However, a larger controlled study is required to determine the role of non-C. albicans in recurrent VVC.

Multiple species of Trichosporon produce biofilms highly resistant to triazoles and amphotericin B

Invasive infections caused by Trichosporon spp. have increased considerably in recent years, especially in neutropenic and critically ill patients using catheters and antibiotics. The genus presents limited sensitivity to different antifungal agents, but triazoles are the first choice for treatment. Here, we investigated the biofilm production and antifungal susceptibility to triazoles and amphotericin B of 54 Trichosporon spp. isolates obtained from blood samples (19), urine (20) and superficial mycosis (15). All isolates and 7 reference strains were identified by sequence analysis and phylogenetic inferences of the IGS1 region of the rDNA. Biofilms were grown on 96-well plates and quantitation was performed using crystal violet staining, complemented with Scanning Electron Microscopy (SEM). Susceptibility tests for fluconazole, itraconazole, voriconazole and amphotericin B were processed using the microdilution broth method (CLSI) for planktonic cells and XTT reduction assay for biofilm-forming cells. Our results showed that T. asahii was the most frequent species identified (66.7%), followed by T. faecale (11.1%), T. asteroides (9.3%), T. inkin (7.4%), T. dermatis (3.7%) and one T. coremiiforme (1.8%). We identified 4 genotypes within T. asahii isolates (G1, G3, G4 and G5) and 2 genotypes within T. faecale (G1 and G3). All species exhibited high adhesion and biofilm formation capabilities, mainly T. inkin, T. asteroides and T. faecale. Microscopy images of high biofilm-producing isolates showed that T. asahii presented mainly hyphae and arthroconidia, whereas T. asteroides exhibited mainly short arthroconidia and few filaments. Voriconazole exhibited the best in vitro activity against all species tested. Biofilm-forming cells of isolates and reference strains were highly resistant to all antifungals tested. We concluded that levels of biofilm formation by Trichosporon spp. were similar or even greater than those described for the Candida genus. Biofilm-forming cells were at least 1,000 times more resistant to antifungals than planktonic cells, especially to voriconazole.

Laboratory diagnosis of mucormycosis: current status and future perspectives

ABSTRACT: 

Fungal infections caused by members of the Mucorales order are rapidly progressing and fatal. The importance of mucormycosis has grown in recent years as the number of patients with predisposing factors has increased dramatically. Clinical symptoms are elusive and conventional techniques are often insensitive and unspecific; in particular, cultures are often negative even though direct microscopy is positive. For early diagnosis of the causative agent of disease and subsequently guiding therapy to improving patients’ outcome, molecular assays are promising add-ons. This article provides an overview on current laboratory methods for diagnosing mucormycosis with a special focus on new molecular-based tools. We aim to highlight the pros and cons of various techniques at hand. Given the increase in number and the severity of these infections, molecular approaches for improved diagnosis are highly warranted.

Multi-probe real-time PCR identification of four common Candida species in blood culture broth

We developed a single-tube real-time polymerase chain reaction (PCR) assay with multiple hybridization probes for detecting Candida albicans, C. tropicalis, C. glabrata, and C. parapsilosis. Primers were designed to amplify 18S rRNA gene of the genus Candida, and DNA probes were designed to hybridize two areas of the amplicons. The amplification curves and specific melting peaks of the probes hybridized with PCR product were used for definite species identifications. The reaction specificity was 100 % when evaluating the assay using DNA samples from 21 isolates of fungal and bacterial species. The assay was further evaluated in 129 fungal blood culture broth samples which were culture positive for fungus. Of the 129 samples, 119 were positively identified as: C. albicans (39), C. tropicalis (30), C. parapsilosis (23), C. glabrata (20), Candida spp. (5), and two samples containing mixed C. glabrata/C. albicans and C. glabrata/C. tropicalis. The five Candida spp. were identified by sequencing analysis as C. krusei, C. dubliniensis, C. aquaetextoris, and two isolates of C. athensensis. Of the ten samples which showed negative PCR results, six were Cryptococcus neoformans, and the others were Trichosporon sp., Rhodotorula sp., Fusarium sp., and Penicillium marneffei. Our findings show that the assay was highly effective in identifying the four medically important Candida species. The results can be available within 3 h after positivity of a blood culture broth sample.

Multicenter study evaluating the Vitek MS system for identification of medically important yeasts

The optimal management of fungal infections is correlated with timely organism identification. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is revolutionizing the identification of yeasts isolated from clinical specimens. We present a multicenter study assessing the performance of the Vitek MS system (bioMérieux) in identifying medically important yeasts. A collection of 852 isolates was tested, including 20 Candida species (626 isolates, including 58 C. albicans, 62 C. glabrata, and 53 C. krusei isolates), 35 Cryptococcus neoformans isolates, and 191 other clinically relevant yeast isolates; in total, 31 different species were evaluated. Isolates were directly applied to a target plate, followed by a formic acid overlay. Mass spectra were acquired using the Vitek MS system and were analyzed using the Vitek MS v2.0 database. The gold standard for identification was sequence analysis of the D2 region of the 26S rRNA gene. In total, 823 isolates (96.6%) were identified to the genus level and 819 isolates (96.1%) were identified to the species level. Twenty-four isolates (2.8%) were not identified, and five isolates (0.6%) were misidentified. Misidentified isolates included one isolate of C. albicans (n = 58) identified as Candida dubliniensis, one isolate of Candida parapsilosis (n = 73) identified as Candida pelliculosa, and three isolates of Geotrichum klebahnii (n = 6) identified as Geotrichum candidum. The identification of clinically relevant yeasts using MS is superior to the phenotypic identification systems currently employed in clinical microbiology laboratories.

Candida infections and their prevention

Infections caused by Candida species have been increased dramatically worldwide due to the increase in immunocompromised patients. For the prevention and cure of candidiasis, several strategies have been adopted at clinical level. Candida infected patients are commonly treated with a variety of antifungal drugs such as fluconazole, amphotericin B, nystatin, and flucytosine. Moreover, early detection and speciation of the fungal agents will play a crucial role for administering appropriate drugs for antifungal therapy. Many modern technologies like MALDI-TOF-MS, real-time PCR, and DNA microarray are being applied for accurate and fast detection of the strains. However, during prolonged use of these drugs, many fungal pathogens become resistant and antifungal therapy suffers. In this regard, combination of two or more antifungal drugs is thought to be an alternative to counter the rising drug resistance. Also, many inhibitors of efflux pumps have been designed and tested in different models to effectively treat candidiasis. However, most of the synthetic drugs have side effects and biomedicines like antibodies and polysaccharide-peptide conjugates could be better alternatives and safe options to prevent and cure the diseases. Furthermore, availability of genome sequences of Candida   albicans and other non-albicans strains has made it feasible to analyze the genes for their roles in adherence, penetration, and establishment of diseases. Understanding the biology of Candida species by applying different modern and advanced technology will definitely help us in preventing and curing the diseases caused by fungal pathogens.

Assessment of accuracy of identification of pathogenic yeasts in microbiology laboratories in the United kingdom

Rapid, accurate identification of yeast isolates from clinical samples has always been important given their innately variable antifungal susceptibility profiles. Recently, this has become paramount with the proposed introduction of species-specific interpretive breakpoints for MICs obtained in yeast antifungal susceptibility tests (M. A. Pfaller, D. Andes, D. J. Diekema, A. Espinel-Ingroff, D. Sheehan, and CLSI Subcommittee for Antifungal Susceptibility Testing, Drug Resist. Updat. 13:180-195, 2010). Here, we present the results of a 12-month evaluation of the accuracy of identifications that accompany yeast isolates submitted to the Mycology Reference Laboratory (United Kingdom) for either confirmation of identity or susceptibility testing. In total, 1,781 yeast isolates were analyzed, and the robustness of prior identifications obtained in microbiology laboratories throughout the United Kingdom was assessed using a combination of culture on chromogenic agar, morphology on cornmeal agar, and molecular identification by pyrosequencing. Over 40% of isolates (755) were submitted without any suggested identification. Of those isolates with a prior identification, 100 (9.7%) were incorrectly identified. Error rates ranged from 5.2% (for organisms submitted for antifungal susceptibility testing) to 18.2% (for organisms requiring confirmation of identity) and varied in a strictly species-specific manner. At least 50% of identification errors would be likely to affect interpretation of MIC data, with a possible impact on patient management. In addition, 2.3% of submitted cultures were found to contain mixtures of at least two yeast species. The vast majority of mixtures had gone undetected in the referring laboratory and would have impacted the interpretation of antifungal susceptibility profiles and patient management. Some of the more common misidentifications are discussed according to the identification method employed, with suggestions for avoiding such misinterpretations.

Emergence of Blastoschizomyces capitatus yeast infections, Central Europe

We report 5 cases of disseminated infection caused by Blastoschizomyces capitatus yeast in central Switzerland. The emergence of this yeast in an area in which it is not known to be endemic should alert clinicians caring for immunocompromised patients outside the Mediterranean region to consider infections caused by unfamiliar fungal pathogens.

Evaluation of the commercial rapid trehalose test (GLABRATA RTT) for the point of isolation identification of Candida glabrata isolates in primary cultures

Candidaemias account for 10-20% of nosocomial bloodstream infections depending on the study. Whilst Candida albicans remains the most frequently isolated species, Candida glabrata may be responsible for as many as 10-25% of all candidaemias. Moreover, C. glabrata is generally less susceptible to the azole antifungals than the majority of other pathogenic yeast species. Thus, a rapid test for the specific identification of isolates of C. glabrata would be useful for patient management if it could be performed at point of isolation, on primary cultures grown on standard mycological media directly from patient specimens. Under certain conditions, C. glabrata rapidly hydrolyses trehalose into glucose. The GLABRATA RTT kit allows detection of the preformed enzyme responsible for this action. This study has assessed GLABRATA RTT as an identification tool specifically at point of isolation. Sixty test isolates were evaluated: 39 clinical isolates of C. glabrata identified at the UK Mycology Reference Laboratory, examples of the recently described genetic relatives of C. glabrata, Candida nivariensis (n = 6) and Candida bracarensis (n = 1), and a selection of other common pathogenic yeast species (n = 14). The test provided results within 30 min. Although 77% (30/39) of confirmed C. glabrata isolates were correctly identified by GLABRATA RTT (positive trehalase test), 23% (9/39) of isolates gave negative or equivocal results. All other yeast species gave negative results. The performance of GLABRATA RTT in this study is compared to previous evaluations of the test which employed isolates pre-cultured on specialised media and to other existing conventional identification methodologies.

Comparative evaluation of three commercial identification systems using common and rare bloodstream yeast isolates

The commercial yeast identification systems API ID32C, Auxacolor, and Vitek were evaluated using 251 molecularly identified bloodstream isolates and 2 reference strains, representing a total of 35 species (6 common and 29 rare). Correct identification rates were higher for common species (Auxacolor, 95%; API ID32C, 94%; Vitek, 92%) than for rare species (Auxacolor, 43%; API ID32C, 56%; Vitek, 64%). All systems performed equally among the former, and Vitek performed best among the latter.

Influence of multidrug efflux systems on methylene blue-mediated photodynamic inactivation of Candida albicans

OBJECTIVES

To investigate whether the major fungal multidrug efflux systems (MESs) affect the efficiency of methylene blue (MB)-mediated antimicrobial photodynamic inactivation (APDI) in pathogenic fungi and test specific inhibitors of these efflux systems to potentiate APDI.

METHODS

Candida albicans wild-type and mutants that overexpressed two classes of MESs [ATP-binding cassette (ABC) and major facilitator superfamily (MFS)] were tested for APDI using MB as the photosensitizer with and without addition of MES inhibitors. The uptake and cytoplasm localization of photosensitizer were achieved using laser confocal microscopy.

RESULTS

ABC MES overexpression reduced MB accumulation and APDI killing more than MFS MES overexpression. Furthermore, by combining MB APDI with the ABC inhibitor verapamil, fungal killing and MB uptake were potentiated, while by combining MB APDI with the MFS inhibitor INF(271), fungal killing and MB uptake were inhibited. This latter surprising finding may be explained by the hypothesis that the MFS channel can also serve as an uptake mechanism for MB.

CONCLUSIONS

The ABC pumps are directly implicated in MB efflux from the cell cytoplasm. Both the influx and efflux of MB may be regulated by MFS systems, and blocking this gate before incubation with MB can decrease the uptake and APDI effects. An ABC inhibitor could be usefully combined with MB APDI for treating C. albicans infections.

Molecular identification of closely related Candida species using two ribosomal intergenic spacer fingerprinting methods

Recent changes in the epidemiology of candidiasis highlighted an increase in non- Candida albicans species emphasizing the need for reliable identification methods. Molecular diagnostics in fungal infections may improve species characterization, particularly in cases of the closely related species in the Candida complexes. We developed two PCR/restriction fragment length polymorphism assays, targeting either a part of the intergenic spacer 2 or the entire intergenic spacer (IGS) of ribosomal DNA using a panel of 270 isolates. A part of the intergenic spacer was used for discrimination between C. albicans and C. dubliniensis and between species of the C. glabrata complex (C. glabrata/C. bracarensis/C. nivariensis). The whole IGS was applied to C. parapsilosis, C. metapsilosis, and C. orthopsilosis, and to separate C. famata (Debaryomyces hansenii) from C. guilliermondii (Pichia guilliermondii) and from the other species within this complex (ie, C. carpophila, C. fermentati and C. xestobii). Sharing similar biochemical patterns, Pichia norvegensis and C. inconspicua exhibited specific IGS profiles. Our study confirmed that isolates of C. guilliermondii were frequently mis-identified as C. famata. As much as 67% of the clinical isolates phenotypically determined as C. famata were recognized mostly as true P. guilliermondii. Conversely, 44% of the isolates initially identified as C. guilliermondii were corrected by the IGS fingerprints as C. parapsilosis, C. fermentati, or C. zeylanoides. These two PCR/restriction fragment length polymorphism methods may be used as reference tools [either alternatively or adjunctively to the existing ribosomal DNA (26S or ITS) sequence comparisons] for unambiguous determination of the Candida species for which phenotypic characterization remains problematic.

The effect of cumulative length of hospital stay on the antifungal resistance of Candida strains isolated from critically ill surgical patients

Fluconazole is the first line of therapy for the management of candidiasis. However, fluconazole-resistant strains pose an emerging challenge in everyday clinical practice. In this study, we sought to determine whether cumulative length of hospital stay (CLOS) is a predictive factor for the acquisition of non-susceptible Candida strains to fluconazole. Thirty-three critically ill emergency surgery patients with 56 Candida isolates were enrolled in this prospective study. We divided our isolates according to their minimum inhibitory concentration (MIC) to fluconazole using 8 mcg/ml as a cutoff. We then compared the two groups with respect to basic demographics, antifungal agents prescribed, number of wide-spectrum antibiotics, duration of central venous catheter placement, elapsed time to positive culture, duration of prior hospital stay, and length of hospital stay. Non-susceptible fluconazole samples belonged to patients with a significantly longer prior hospital stay and a longer CLOS (P = 0.02 and 0.01, respectively). The difference between the 2 groups regarding non-albicans strains was statistically significant (P < 0.001). By fitting a non-parametric receiver-operating characteristics (ROC) curve into our analysis, a CLOS ≥ 29 days predicted the occurrence of non-susceptible strains with 90% sensitivity and 79.6% specificity (correct classification 81.5%). A CLOS ≥ 29 days is a strong predictor for the isolation of non-susceptible Candida isolates to fluconazole among critically ill emergency surgery patients. Clinicians should consider the duration of previous hospital stay when deciding on empiric antifungal therapy.

Performance of Chromogenic Candida agar and CHROMagar Candida in recovery and presumptive identification of monofungal and polyfungal vaginal isolates

Chromogenic Candida agar (OCCA) is a novel medium facilitating isolation and identification of Candida albicans, C. tropicalis, and C. krusei, as well as indicating polyfungal population in clinical samples. We compare the performance of OCCA, to CHROMagar Candida (CAC) and Sabouraud chloramphenicol agar (SCA). Vaginal swab samples from 392 women were simultaneously inoculated onto three study media. A total of 161 (41.1%) were found to be positive for fungi of which 140 (87%) were monofungal, and 21 (13%) polyfungal. One-hundred and fifty-seven samples (97.5%) were positive on CAC, 156 (96.9%) on OCCA, 148 (91.9%) on SCA and 144 (89.4%) samples were positive on all three media. The yeasts were identified by conventional methods including germ tube test, microscopic morphology on cornmeal-Tween 80 agar, and the commercial API 20C AUX. The 182 isolates were C. albicans (n = 104), C. glabrata (n = 51), C. krusei (n = 7), C. tropicalis (n = 5), C. famata (n = 3), C. kefyr (n = 3), C. zeylanoides (n = 3), C. colliculosa (n = 2), and other species of Candida (n = 4). Among the 21 polyfungal populations, 20 (95.2%) were detected in OCCA, 14 (66.7%) in CAC, and 13 (61.9%) in CAC and OCCA (P <0.05). Most polyfungal populations (47.6%) yielded C. albicans + C. glabrata. The efficiency of both chromogenic media for C. albicans was >or=92.9% at 72 h. OCCA is more efficient and reliable for rapidly identifying C. albicans and polyfungal populations than CAC. However, CAC is more efficient for identifying C. krusei and C. tropicalis. A chromogenic agar with a higher isolation rate of yeasts and better detection of polyfungal populations than SCA, is suggested as a medium of first choice when available.

Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of clinically important yeast species

We evaluated the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for the rapid identification of yeast species. Using Bruker Daltonics MALDI BioTyper software, we created a spectral database library with m/z ratios of 2,000 to 20,000 Da for 109 type and reference strains of yeast (44 species in 8 genera). The database was tested for accuracy by use of 194 clinical isolates (23 species in 6 genera). A total of 192 (99.0%) of the clinical isolates were identified accurately by MALDI-TOF MS. The MALDI-TOF MS-based method was found to be reproducible and accurate, with low consumable costs and minimal preparation time.

Molecular identification of veterinary yeast isolates by use of sequence-based analysis of the D1/D2 region of the large ribosomal subunit

Conventional methods of yeast identification are often time-consuming and difficult; however, recent studies of sequence-based identification methods have shown promise. Additionally, little is known about the diversity of yeasts identified from various animal species in veterinary diagnostic laboratories. Therefore, in this study, we examined three methods of identification by using 109 yeast samples isolated during a 1-year period from veterinary clinical samples. Comparison of the three methods-traditional substrate assimilation, fatty acid profile analysis, and sequence-based analysis of the region spanning the D1 and D2 regions (D1/D2) of the large ribosomal subunit-showed that sequence analysis provided the highest percent identification among the three. Sequence analysis identified 87% of isolates to the species level, whereas substrate assimilation and fatty acid profile analysis identified only 54% and 47%, respectively. Less-stringent criteria for identification increased the percentage of isolates identified to 98% for sequence analysis, 62% for substrate assimilation, and 55% for fatty acid profile analysis. We also found that sequence analysis of the internal transcribed spacer 2 (ITS2) region provided further identification for 36% of yeast not identified to the species level by D1/D2 sequence analysis. Additionally, we identified a large variety of yeast from animal sources, with at least 30 different species among the isolates tested, and with the majority not belonging to the common Candida spp., such as C. albicans, C. glabrata, C. tropicalis, and the C. parapsilosis group. Thus, we determined that sequence analysis of the D1/D2 region was the best method for identification of the variety of yeasts found in a veterinary population.

Use of CHROMagar Candida for the presumptive identification of Candida species directly from clinical specimens in resource-limited settings

Introduction

Identification of yeast isolated from clinical specimens to the species level has become increasingly important. Ever-increasing numbers of immuno-suppressed patients, a widening range of recognized pathogens, and the discovery of resistance to antifungal drugs are contributing factors to this necessity.

Material and methods

A total of 487 yeast strains were studied for the primary isolation and presumptive identification, directly from clinical specimen. Efficacy of CHROMagar Candida has been evaluated with conventional methods including morphology on Corn meal–tween 80 agar and biochemical methods by using API 20 C AUX.

Results

The result of this study shows that CHROMagar Candida can easily identify three species of Candida on the basis of colonial color and morphology, and accurately differentiate between them i.e. Candida albicans, Candida tropicalis, and Candida krusei. The specificity and sensitivity of CHROMagar Candida for C. albicans calculated as 99%, for C. tropicalis calculated as 98%, and C. krusei it is 100%.

Conclusion

The data presented supports the use of CHROMagar Candida for the rapid identification of Candida species directly from clinical specimens in resource-limited settings, which could be very helpful in developing appropriate therapeutic strategy and management of patients.

Performance of optimized McRAPD in identification of 9 yeast species frequently isolated from patient samples: potential for automation

Background

Rapid, easy, economical and accurate species identification of yeasts isolated from clinical samples remains an important challenge for routine microbiological laboratories, because susceptibility to antifungal agents, probability to develop resistance and ability to cause disease vary in different species. To overcome the drawbacks of the currently available techniques we have recently proposed an innovative approach to yeast species identification based on RAPD genotyping and termed McRAPD (Melting curve of RAPD). Here we have evaluated its performance on a broader spectrum of clinically relevant yeast species and also examined the potential of automated and semi-automated interpretation of McRAPD data for yeast species identification.

Results

A simple fully automated algorithm based on normalized melting data identified 80% of the isolates correctly. When this algorithm was supplemented by semi-automated matching of decisive peaks in first derivative plots, 87% of the isolates were identified correctly. However, a computer-aided visual matching of derivative plots showed the best performance with average 98.3% of the accurately identified isolates, almost matching the 99.4% performance of traditional RAPD fingerprinting.

Conclusion

Since McRAPD technique omits gel electrophoresis and can be performed in a rapid, economical and convenient way, we believe that it can find its place in routine identification of medically important yeasts in advanced diagnostic laboratories that are able to adopt this technique. It can also serve as a broad-range high-throughput technique for epidemiological surveillance.

Epidemiology of Herpes Simplex Virus Infection in Pregnancy: A Pilot Study

Herpes simplex virus (HSV) infection is one of the most common sexually transmitted viral diseases worldwide. HSV type 2 causes most genital herpes and HSV type 1 is usually transmitted via non-sexual contacts. We studied 109 pregnant women between January 2007 and December 2008, in relation to their age, condom use, number of sexual partners, age at first intercourse, parity and smoking habits. The aim of this study is to evaluate the prevalence of HSV cervical infection and HSV co-infection with other genital microorganisms associated with poor neonatal outcome. Our results show that of the 109 outpatients enrolled, 30% were HSV1 and/or HSV2 positive, of whom 30% were infected with both HSV1 and HSV2, 18% were infected with HSV1 alone and 52% with HSV2 alone. A significant association between HSV1 and HSV2 infection was found, and the prevalence of HSV2 infection in women infected with HSV1 was 63%. The prevalence of HSV1/2 varied in the presence of other vaginal microorganisms but a statistical significant association was not found. This pilot study is probably too small to obtain statistically significant results. Nevertheless, using these observed results, we calculated that about 530 patients with comparable features should be enrolled to detect an increase of 50% in HSV infection due to the presence of other genital infections and potential risk factors.