Evaluation of VITEK 2 and RapID yeast plus systems for yeast species identification: experience at a large clinical microbiology laboratory

Retrospective analysis on distribution and antifungal susceptibility profile of Candida in clinical samples: a study from Southern India

Introduction

Candida is one of the rising primary causes of infections connected with health care. However, their distribution and susceptibility patterns vary widely amongst different regions.

Method

The study was carried out to retrospectively analyze the distribution of Candida in various clinical samples, their species types and susceptibility, in a tertiary care hospital, in India for 4 years using the Vitek-2 database.

Results

Candida infection was identified in 751 clinical samples, and the major source of infection was found to be urine samples accounting for about 58.32%. A total of 18 different Candida species were recorded. Non-albicans Candida (NAC) 73.64% (n = 553) predominated Candida albicans 26.36% (n = 198). Candida tropicalis was found to be identified at a higher frequency followed by C. albicans, Candida glabrata and Candida parapsilosis. Candida tropicalis was the only species which were recovered from bile; Candida pelliculosa was recorded merely from blood and Candida lipolytica from urine and blood and not in any other samples. In vaginal swabs, C. albicans accounted for 63.64% (n = 14) compared to NAC 36.36% (n = 8). The susceptibility test revealed that 75.44% (n = 559) isolates were susceptible and 24.56% (n = 182) were resistant to one or more drugs tested. Major resistance was exhibited to flucytosine by C. tropicalis 77.46% (n = 55) compared to C. albicans 11.27% (n = 8). Apart from C. albicans, NAC-C. tropicalis, C. glabrata and Candida krusei showed resistance to echinocandins, and Candida haemulonii to amphotericin-B.

Conclusion

The knowledge of the incidence, resistance and emergence of different species might guide clinicians to select an appropriate antifungal therapy and plan effective strategies to control invasive and systemic Candida infections.

How to Identify Invasive Candidemia in ICU-A Narrative Review

The incidence of invasive fungal infection in ICUs has increased over time, and Candida spp. is the most common cause. Critical care patients are a particular set of patients with a higher risk of invasive fungal infections; this population is characterized by extensive use of medical devices such as central venous lines, arterial lines, bladder catheters, hemodialysis and mechanical intubation. Blood cultures are the gold standard diagnosis; still, they are not an early diagnostic technique. Mannan, anti-mannan antibody, 1,3-β-D-glucan, Candida albicans germ tube antibody, Vitek 2, PNA-FISH, MALDI-TOF, PCR and T2Candida panel are diagnostic promising microbiological assays. Scoring systems are tools to distinguish patients with low and high risk of infection. They can be combined with diagnostic tests to select patients for pre-emptive treatment or antifungal discontinuation. Candidemia is the focus of this narrative review, an approach to contributing factors and diagnosis, with an emphasis on critical care patients.

Gamma-glutamyl transpeptidase-platelet ratio, systemic immune inflammation index, and system inflammation response index in invasive Aspergillosis

OBJECTIVE

Gamma-glutamyl transpeptidase-platelet ratio, system inflammation response index, and systemic immune inflammation index are three systemic immune and inflammation indexes that were investigated for their diagnostic and prognostic proficiencies in cardiovascular diseases and cancers. However, their predictive values for invasive aspergillosis have not yet been studied. The aim of this study was to evaluate Gamma-glutamyl transpeptidase-platelet ratio, system inflammation response index, and systemic immune inflammation index levels and their diagnostic values in invasive aspergillosis.

METHODS

A total of 23 patients with invasive aspergillosis and 23 sex- and age-matched healthy participants were included in this study. Complete blood count parameters and liver function tests were studied. Gamma-glutamyl transpeptidase-platelet ratio, system inflammation response index, and systemic immune inflammation index were calculated.

RESULTS

Leukocyte, neutrophil, lymphocyte, and monocyte levels were statistically significantly higher in IA group (p=0.031, p=0.027, p=0.033, and p=0.001, respectively). In invasive aspergillosis group, platelets were numerically lower; Aspartate transaminase, alanine aminotransferase, and lactic dehydrogenase levels were numerically higher than those in control group but differences between levels were not statistically significant (p>0.05). The γ-glutamyl transpeptidase levels of patients were statistically significantly higher (p=0.007), and in addition, statistically significant differences were found between groups in terms of gamma-glutamyl transpeptidase-platelet ratio, system inflammation response index, and systemic immune inflammation index (p<0.001, p=0.037, p=0.001, respectively). Receiver operating characteristic analysis was performed, and areas under the curves were evaluated. gamma-glutamyl transpeptidase-platelet ratio had the higher area under the curve than systemic immune inflammation index and system inflammation response index (AUC 0.849, 0.798, 0.693, respectively). The results from receiver operating characteristic analysis of the data suggested that the use of a cutoff value of 0.15 for gamma-glutamyl transpeptidase-platelet ratio would be optimum for clinical use to confirm independent predictors of patients with invasive aspergillosis.

CONCLUSIONS

Gamma-glutamyl transpeptidase-platelet ratio is an independent, a useful predictor, and is superior to other evaluated markers in the diagnosis of inflammation in invasive aspergillosis. Gamma-glutamyl transpeptidase-platelet ratio may also be a helpful biomarker for clinicians to follow-up the inflammatory process of these patients.

Species Distribution and Antifungal Susceptibility Pattern of Candida Recovered from Intensive Care Unit Patients, Vietnam National Hospital of Burn (2017-2019)

INTRODUCTION

Candida species is the most common cause of invasive fungal infection. With the wide variation in species distribution and antifungal susceptibility of causative agents, local epidemiological profiles are needed to provide effective guidelines for the treatment of invasive candidiasis.

OBJECTIVE

To find out the species distribution and antifungal susceptibilities of Candida strains isolated from patients in an intensive care unit (ICU) of Vietnam.

METHODS

All patients in ICU of Vietnam National Hospital of Burn with Candida isolation reported from January 2017 to December 2019 were retrospectively studied. Species identification and antifungal susceptibility testing were performed using VITEK 2 Compact. The identification was reconfirmed by sequencing of the internal transcribed spacer regions when needed.

RESULTS

A total of 186 yeasts belonging to ten species were collected. The most common agent was C. tropicalis (45.7%), followed by C. albicans (42.4%), and C. parapsilosis (7.53%). The isolated yeasts showed less susceptibility to fluconazole (resistant rate R 10.7%) than to micafungin, caspofungin, flucytosine and amphotericin B (R 0%, 0.6%, 2.3% and 3.4%, respectively, p < 0.05). C. albicans isolates were more susceptible to fluconazole (R 5.2%) than C. tropicalis (R 15.7%). Resistance to voriconazole was seen only among C. albicans (3.9%) and C. tropicalis isolates (9.9%).

CONCLUSION

Non-albicans species (especially C. tropicalis) is the predominant species, and there is a significant proportion of isolates with reduced susceptibility to azole but not to echinocandin.

Candidal Onychomycosis: Clinicoepidemiological Profile, Prevailing Strains, and Antifungal Susceptibility Pattern-A Study from a Tertiary Care Hospital

Background:

Despite an increasing trend of onychomycosis caused by Candida species in recent years, there is a scarcity of published data.

Objective:

To determine the epidemiological and clinical characteristics of Candida onychomycosis, to identify the prevalent, and perform in-vitro antifungal susceptibility testing (AFST) of the isolates.

Methodology:

A total of 506 consecutive patients with a clinical suspicion of onychomycosis were included in a cross-sectional clinical study. Nail scrapings and clippings were subjected to KOH examination and culture. Species identification and antifungal drug sensitivity testing were done for Candida isolates using Vitek 2YST Compact system using Vitek 2 cards.

Results:

Out of 384 (75.88%) culture-positive cases, dermatophytes were isolated in 58.08%, yeast in 26.30%, and NDM in 12.24%. Of the yeast, Candida albicans was isolated in 59.4% and non-albicans species in 40.59%. AFST showed that most of Candida species exhibited 100% susceptibility to most of the antifungal drugs tested, while intermediate resistance to fluconazole and flucytosine was seen in some non-albicans species (C. krusei, C. glabrata, and C. guilliermondii). Time taken for species identification was 14–18 h (average 15.5 h), while determination of minimum inhibitory concentration took 9–27 h (average 13 h).

Conclusions:

Our study showcases the present scenario of Candida distribution and the resistance patterns of various species afflicting the nail unit. Furthermore, our findings clearly indicate that the carriage of this pathogenic yeast is seen in both healthy individuals as well as with immunosuppression.

Epidemiology of yeast species causing bloodstream infection in Tehran, Iran (2015-2017); superiority of 21-plex PCR over the Vitek 2 system for yeast identification

Introduction. Given the limited number of candidaemia studies in Iran, the profile of yeast species causing bloodstream infections (BSIs), especially in adults, remains limited. Although biochemical assays are widely used in developing countries, they produce erroneous results, especially for rare yeast species.Aim. We aimed to assess the profile of yeast species causing BSIs and to compare the accuracy of the Vitek 2 system and 21-plex PCR.Methodology. Yeast blood isolates were retrospectively collected from patients recruited from two tertiary care training hospitals in Tehran from 2015 to 2017. Relevant clinical data were mined. Identification was performed by automated Vitek 2, 21-plex PCR and sequencing of the internal transcribed spacer region (ITS1-5.8S-ITS2).Results. In total, 137 yeast isolates were recovered from 107 patients. The overall all-cause 30-day mortality rate was 47.7 %. Fluconazole was the most widely used systemic antifungal. Candida albicans (58/137, 42.3 %), Candida glabrata (30/137, 21.9 %), Candida parapsilosis sensu stricto (23/137, 16.8 %), Candida tropicalis (10/137, 7.3 %) and Pichia kudriavzevii (Candida krusei) (4/137, 2.9 %) constituted almost 90 % of the isolates and 10 % of the species detected were rare yeast species (12/137; 8.7 %). The 21-plex PCR method correctly identified 97.1 % of the isolates, a higher percentage than the Vitek 2 showed (87.6 %).Conclusion. C. albicans was the main cause of yeast-derived fungaemia in this study. Future prospective studies are warranted to closely monitor the epidemiological landscape of yeast species causing BSIs in Iran. The superiority of 21-plex PCR over automated Vitek 2 indicates its potential clinical utility as an alternative identification tool use in developing countries.

Identification of medically important yeasts by sequence analysis of the internal transcribed spacer and D1/D2 region of the large ribosomal subunit

BACKGROUND

The prevalence of opportunistic yeast infections has increased in recent decades as the result of an increasing immunocompromised patient population.

AIMS

To evaluate ribosomal RNA (rRNA) gene sequence to identify medically important yeast species, to investigate the performance of both the rRNA gene internal transcribed spacer (ITS) and D1/D2 region in identifying clinically relevant yeasts, and to compare these results with those of a standard phenotypic method.

METHODS

Both regions from 50 yeast strains, comprising 45 clinical isolates and 5 reference strains, were amplified using PCR and then sequenced. The sequences were compared to reference data available from the GenBank database of the National Center for Biotechnology Information using the BLASTn tool.

RESULTS

Using ID32C, 88% (44/50) of all strains were identified accurately at the species level, although 6% were misidentified; two Candida eremophila isolates were identified as Candida glabrata and Candida tropicalis, and one Saprochaete clavata isolate was identified as Saprochaete capitata. Two of the four isolates identified by phenotypic methods as Trichosporon asahii were defined so by analyzing the ITS region, but the remaining two were not distinguishable from closely related species. Based on the D1/D2 region, these four isolates had 100% sequence identity with T. asahii, Trichosporon japonicum, and Trichosporon asteroides. The isolate identified as Trichosporon inkin using ID32C could not be distinguished from Trichosporon ovoides by analyzing the ITS and D1/D2 regions.

CONCLUSIONS

Identifying medically important yeasts by sequencing the ITS and D1/D2 region is a rapid and reliable alternative to conventional identification methods. For a diagnostic algorithm, we suggest a two-step procedure integrating conventional methods (e.g. microscopic morphology on corn meal agar with Tween® 80 and API ID32C®) and sequence analysis of the ITS and D1/D2 region.

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.

[Performance evaluation of Rapid™ Yeast Plus (Remel) system from two different culture media]

Within the genus Candida, Candida albicans is the most commonly isolated species from clinical samples. Due to the emergence of other species which can show a higher index of antifungal resistance, a fast identification of these species is necessary. The aim of this work was to evaluate the performance of the RapID Yeast Plus system from two different subculture media formulations: Sabouraud dextrose agar adjusted by Emmons (the medium is indicated in the equipment insert) and Sabouraud glucose agar, which is the most frequently used in Buenos Aires City laboratories. One hundred and sixty-six clinical sample strains coming from different hospitals belonging to the Mycology Network of Buenos Aires City were studied. From the obtained results, we conclude that the conditions and culture medium indicated by the manufacturer should be followed.

Comparative Evaluation of the BD Phoenix Yeast ID Panel and Remel RapID Yeast Plus System for Yeast Identification

Becton Dickinson Phoenix Yeast ID Panel was compared to the Remel RapID Yeast Plus System using 150 recent clinical yeast isolates and the API 20C AUX system to resolve discrepant results. The concordance rate between the Yeast ID Panel and the RapID Yeast Plus System (without arbitration) was 93.3% with 97.3% (146/150) and 95.3% (143/150) of the isolates correctly identified by the Becton Dickinson Phoenix and the Remel RapID, respectively, with arbitration.

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.

Antifungal susceptibility profiles of bloodstream yeast isolates by Sensititre YeastOne over nine years at a large Italian teaching hospital

Sensititre YeastOne (SYO) is an affordable alternative to the Clinical and Laboratory Standards Institute (CLSI) reference method for antifungal susceptibility testing. In this study, the MICs of yeast isolates from 1,214 bloodstream infection episodes, generated by SYO during hospital laboratory activity (January 2005 to December 2013), were reanalyzed using current CLSI clinical breakpoints/epidemiological cutoff values to assign susceptibility (or the wild-type [WT] phenotype) to systemic antifungal agents. Excluding Candida albicans (57.4% of all isolates [n = 1,250]), the most predominant species were Candida parapsilosis complex (20.9%), Candida tropicalis (8.2%), Candida glabrata (6.4%), Candida guilliermondii (1.6%), and Candida krusei (1.3%). Among the non-Candida species (1.9%), 7 were Cryptococcus neoformans and 17 were other species, mainly Rhodotorula species. Over 97% of Candida isolates were susceptible (WT phenotype) to amphotericin B and flucytosine. Rates of susceptibility (WT phenotype) to fluconazole, itraconazole, and voriconazole were 98.7% in C. albicans, 92.3% in the C. parapsilosis complex, 96.1% in C. tropicalis, 92.5% in C. glabrata, 100% in C. guilliermondii, and 100% (excluding fluconazole) in C. krusei. The fluconazole-resistant isolates consisted of 6 C. parapsilosis complex isolates, 3 C. glabrata isolates, 2 C. albicans isolates, 2 C. tropicalis isolates, and 1 Candida lusitaniae isolate. Of the non-Candida isolates, 2 C. neoformans isolates had the non-WT phenotype for susceptibility to fluconazole, whereas Rhodotorula isolates had elevated azole MICs. Overall, 99.7% to 99.8% of Candida isolates were susceptible (WT phenotype) to echinocandins, but 3 isolates were nonsusceptible (either intermediate or resistant) to caspofungin (C. albicans, C. guilliermondii, and C. krusei), anidulafungin (C. albicans and C. guilliermondii), and micafungin (C. albicans). However, when the intrinsically resistant non-Candida isolates were included, the rate of echinocandin nonsusceptibility reached 1.8%. In summary, the SYO method proved to be able to detect yeast species showing antifungal resistance or reduced susceptibility.

[Evaluation of Vitek 2 for the identification of Candida yeasts]

The aim of this investigation was to evaluate the performance of Vitek 2 YST cards (bioMérieux, Inc., Hazelwood, MO, USA) for the identification of yeasts of the genus Candida. A total of 168 isolates were analyzed and the results were compared to those of the API 20 C AUX (24%) o API ID 32 C (76%) kits (bioMérieux, Marcy L'Etoile, France). Each isolate was grown in chromogenic agar and in corn meal agar (Oxoid, UK) to observe its micromorphology. C. albicans and C. dublininesis were identified by additional biochemical and molecular tests. The agreement observed was 98.3%. Only three isolates were incorrectly identified by Vitek 2: one strain of C .tropicalis and one strain of C. krusei were identified as C. parapsilosis by YST while one strain of C. krusei was identified with low discrimination. The average time for obtaining results was 18.25 h. Vitek 2 is a simple, safe and useful system for the identification of significant Candida species.

Misidentification of Candida guilliermondii as C. famata among strains isolated from blood cultures by the VITEK 2 system

Introduction. The aim of this study was to differentiate between Candida famata and Candida guilliermondii correctly by using matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) and gene sequencing. Methods. Twenty-eight Candida strains from blood cultures that had been identified as C. famata (N = 25), C. famata/C. guilliermondii (N = 2), and C. guilliermondii (N = 1) by the VITEK 2 system using the YST ID card were included. We identified these strains by MALDI-TOF MS and gene sequencing using the 28S rRNA and ITS genes and compared the results with those obtained by the VITEK 2 system. Results. All 28 isolates were finally identified as C. guilliermondii. Sequencing analysis of the 28S rRNA gene showed 99.80%–100% similarity with C. guilliermondii for all 28 strains. The ITS gene sequencing of the strains showed 98.34%–100% homology with C. guilliermondii. By MALDI-TOF, we could correctly identify 21 (75%) of 28 C. guilliermondii isolates. Conclusion. We should suspect misidentification when C. famata is reported by the VITEK 2 system, and we always should keep in mind the possibility of misidentification of any organism when an uncommon species is reported.

Rapid laboratory diagnosis for respiratory infectious diseases by using MALDI-TOF mass spectrometry

It is still challenging to prevent and treat respiratory infectious diseases. One critical step in the successful treatment of respiratory infections is rapid diagnosis by identifying the causative microorganisms in a timely fashion. However, traditional methods for identification of causative agents could not satisfy the need for rapid and accurate testing due to the limitations of technology-used. In recent years, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) has been validated and used for rapid identification of microorganism and for potential discovery of diseases associated biomarkers. We reviewed recent advances of MALDI-TOF-MS as the laboratory diagnostic tool for the rapid laboratory diagnosis of microorganisms associated with respiratory infectious diseases, with the focus on rapid identification of pathogenic bacteria and molecular markers discovery using MALDI-TOF-MS. With the advanced technologies such as MALDI-TOF, early and targeted therapies based on rapid identification of pathogens and could lead to quick and effective treatment of respiratory infections and better patient management.

Extradural spinal cord lesion in a dog: first case study of canine neurological histoplasmosis in Italy

A 7-year-old intact male mixed dog was presented with a history of acute and progressive paraparesis. Abnormal clinical signs consisted of non-ambulatory paraparesis, hind limbs hypertonia and severe thoracolumbar pain. Magnetic resonance imaging demonstrated an isointense in T1 and T2 WI epidural lesion, with good contrast enhancement, extending from T-10 to T-13. Laminectomy was carried out to remove the epidural mass. Histological examination revealed a pyogranulomatous lesion characterized by numerous macrophages containing yeast-like Grocott and PAS-positive bodies. Immunohistochemistry and PCR performed on formalin-fixed paraffin-embedded tissue confirmed Histoplasma capsulatum as the causative agent. H. capsulatum has a worldwide distribution in temperate and subtropical climates but its presence as an autochthonous fungus in Europe is now recognized. To the authors' knowledge this is the first report of canine histoplasmosis in Italy with lesion confined to the central nervous system.

Development and validation of an in-house database for matrix-assisted laser desorption ionization-time of flight mass spectrometry-based yeast identification using a fast protein extraction procedure

In recent studies evaluating the usefulness of the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification of yeasts for the routine diagnosis of fungal infections, preanalytical sample processing has emerged as a critical step for reliable MALDI-TOF MS outcomes, especially when the Bruker Daltonics Biotyper software was used. In addition, inadequate results often occurred due to discrepancies between the methods used for clinical testing and database construction. Therefore, we created an in-house MALDI-TOF MS library using the spectra from 156 reference and clinical yeast isolates (48 species in 11 genera), which were generated with a fast sample preparation procedure. After a retrospective validation study, our database was evaluated on 4,232 yeasts routinely isolated during a 6-month period and fast prepared for MALDI-TOF MS analysis. Thus, 4,209 (99.5%) of the isolates were successfully identified to the species level (with scores of ≥2.0), with 1,676 (39.6%) having scores of >2.3. For the remaining 23 (0.5%) isolates, no reliable identification (with scores of <1.7) was obtained. Interestingly, these isolates were almost always from species uniquely represented or not included in the database. As the MALDI-TOF MS results were, except for 23 isolates, validated without additional phenotypic or molecular tests, our proposed strategy can enhance the rapidity and accuracy of MALDI-TOF MS in identifying medically important yeast species. However, while continuous updating of our database will be necessary to enrich it with more strains/species of new and emerging yeasts, the present in-house MALDI-TOF MS library can be made publicly available for future multicenter studies.

Comparative evaluation of BD Phoenix and vitek 2 systems for species identification of common and uncommon pathogenic yeasts

The BD Phoenix system was evaluated for species-level identification of yeasts (250 clinical isolates) and compared with the Vitek 2 system, using ribosomal internal transcribed spacer (ITS) sequence analysis as the gold standard. Considering only the species included in each system's database, 96.3% (236/245) and 91.4% (224/245) of the isolates were correctly identified by BD Phoenix and Vitek 2, respectively.

Oral microflora and their relation to risk factors in HIV+ patients with oropharyngeal candidiasis

OBJECTIVE

The purpose of this study was to determine the prevalence of oral microflora and association of oral candidiasis and multiple risk factors in HIV(+) patients.

PATIENTS AND METHODS

The present study included 100 HIV-infected patients participated in Imam Khomeini Hospital, Tehran, Iran for Oropharyngeal candidiasis (OPC) and HIV. We assessed the presence or absence of OPC, and samples were obtained from the oral cavity and direct microscopic examination, gram staining and culture on standard microbiological media were performed in all patients. CD4(+) cell count/CD4(+) percentage were also calculated.

RESULTS

The demographic characteristics showed that the patients had a mean age of 32.3 years old, 78% male and 22% female. Patients belonging to 'O(+)' blood group (27%) were more prone to develop OPC. A total of 460 bacterial colonies were obtained and Streptococcus mutans (15.4%) was the most frequently isolated species in the HIV(+) patients, followed by Staphylococcus epidermidis (12.8%) and Corynebacterium (8.7%). In addition, 254 yeasts (from four different genera) were isolated from the patient under study. Candida species (94.4%) were the most frequently obtained genera, followed by Saccharomyces (2.4%), Kluyveromyces and Cryptococcus (1.6% for both) species. Candida albicans (37.2%) was the most common species isolated from HIV(+) patients with OPC and its frequency was significantly higher than that of other Candida species (P<0.05). Candida glabrata, C. dubliniensis, C. tropicalis, C. parapsilosis, C. krusei, C. lusitaniae, C. guilliermondii and C. norvegensis were also identified. Forty percent of the patients had angular cheilitis as the most frequent clinical variant. The mean CD4(+) cell counts were 154.5 cells/μL, with a range of 8 to 611 cells/μL. Thirty percent patients had a CD4(+) cell count between 101 and 200 cells/μL (28.7% of total yeasts isolated). Yeast and bacteria counts did not differ statistically among HIV(+) patients' subgroups with different levels of CD4(+) cells counts.

CONCLUSION

Our results showed that yeasts of the genus Candida were isolated at a comparable rate from the oral cavity of HIV(+) patients and there was no significant difference of the variables CD4(+) cell count and yeast counts. The findings of this study would be helpful in any further study, which, if done prospectively on a large cohort, can be confirmatory.

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.

Fungal diagnostics: review of commercially available methods

Fungi and yeasts are critical causes of acute infection. As such, the detection and identification of these organisms are crucial in the diagnosis of affected patient populations. There is a vast array of commercial tests currently available for diagnostic purposes. These vary from traditional culture and biochemical methods to advanced multiparameter molecular tests. Recent technological advances have driven the development of rapid tests which are complementing and in some cases replacing the more traditional methods of detection. Irrespective of the method used the ultimate goal is timely detection of the infectious agent allowing appropriate treatment and improved outcome for the patient.

Overview of invasive fungal infections

The incidence of invasive fungal infections (IFIs) has seen a marked increase in the last two decades. This is especially evident among transplant recipients, patients suffering from AIDS, in addition to those in receipt of immunosuppressive therapy. Worryingly, this increased incidence includes infections caused by opportunistic fungi and emerging fungal infections which are resistant to or certainly less susceptible than others to standard antifungal agents. As a direct response to this phenomenon, there has been a resolute effort over the past several decades to improve early and accurate diagnosis and provide reliable screening protocols thereby promoting the administration of appropriate antifungal therapy for fungal infections. Early diagnosis and treatment with antifungal therapy are vital if a patient is to survive an IFI. Substantial advancements have been made with regard to both the diagnosis and subsequent treatment of an IFI. In parallel, stark changes in the epidemiological profile of these IFIs have similarly occurred, often in direct response the type of antifungal agent being administered. The effects of an IFI can be far reaching, ranging from increased morbidity and mortality to increased length hospital stays and economic burden.

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.

Internal transcribed spacer region sequence analysis using SmartGene IDNS software for the identification of unusual clinical yeast isolates

Rapid and accurate identification of clinically important yeasts is essential given their inherent differences in antifungal susceptibility. We implemented nucleic acid sequencing for those species that could not be identified by phenotypic methods. Internal Transcribed Spacer region 1 and 2 (ITS1 and ITS2) sequences were investigated using SmartGene IDNS software, an rDNA sequence database and analysis program for microbial identification (ID). Over a 2.5-year period, 2,938 specimens were evaluated. Most (94%) isolates were fully identified by conventional methods, with Candida species accounting for the majority of them. Of the 169 organisms that required molecular analysis, 79% were identified to species level, 19% to genus and 2% remained unresolved. Sequenced isolates encompassed 33 unique species of which approximately half (52%) were common pathogens with atypical biochemical profiles and the remainder were rarer yeast species. A significant proportion (33%) of sequenced organisms displayed elevated MICs to fluconazole. Our experience supports the use of molecular techniques as an adjunct to conventional methods for the identification of medically important yeasts. Susceptibility testing alone may provide valuable treatment information in situations where phenotypic assessments are inconclusive and molecular or proteomic testing is not readily available.

Direct maldi-tof mass spectrometry assay of blood culture broths for rapid identification of Candida species causing bloodstream infections: an observational study in two large microbiology laboratories

We evaluated the reliability of the Bruker Daltonik's MALDI Biotyper system in species-level identification of yeasts directly from blood culture bottles. Identification results were concordant with those of the conventional culture-based method for 95.9% of Candida albicans (187/195) and 86.5% of non-albicans Candida species (128/148). Results were available in 30 min (median), suggesting that this approach is a reliable, time-saving tool for routine identification of Candida species causing bloodstream infection.

Pyrosequencing of a hypervariable region in the internal transcribed spacer 2 to identify clinical yeast isolates

The incidence of invasive fungal infection has increased significantly. A majority of the infections is caused by yeast. Clinically important yeast show species-specific differences in susceptibility to antifungal agents therefore rapid and accurate identification of the pathogen is essential. We aimed to validate pyrosequencing of 40 nucleotides in the internal transcribed spacer 2 (ITS2) for species identification of yeast. Amplification of ITS2 and pyrosequencing of targeted region were performed in 940 clinical isolates of yeast. A local database containing the 40 nucleotide ITS2 sequences of 33 species of medically important yeast was generated using published sequences of type strains. The sequencing results were searched against the local database using the BLAST algorithm to identify the species of yeast. The length of sequences obtained from pyrosequencing averaged between 40-61 nucleotides. Pyrosequencing identified 940 clinical isolates of yeast down to 14 species level, whereby 931 isolates belonged to genus Candida (11 species), four of Saccharomyces cerevisiae, three of Malassezia pachydermatis and two of Rhodotorula mucilaginosa. In addition, intraspecies specific sequence variations in Candida albicans and Candida glabrata were detected. Pyrosequencing of 40 nucleotides in ITS2 is reliable for species identification of yeast. This methodology can contribute to the high quality management of patients with fungal infections.

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.

Uncommon Neosartorya udagawae fungus as a causative agent of severe corneal infection

We report the first documented case of a posttraumatic fungal keratitis caused by Neosartorya udagawae. The patient was empirically treated with fluconazole until a corneal scraping grew an Aspergillus fumigatus-like fungus, and itraconazole therapy was then established. A sequence-based approach assigned the isolate to the species. Five months after completion of antifungal therapy, endophthalmitis occurred and orbital exenteration was necessary.

Misidentification of Candida parapsilosis as C famata in a clinical case of vertebral osteomyelitis

A case of vertebral osteomyelitis involving misidentification of Candida parapsilosis as C famata by the VITEK 2 compact is described. Species-specific primers were used in the polymerase chain reaction to correctly identify the clinical isolate. When uncommon species of Candida are reported using automated systems, heightened clinical suspicion is warranted.

Performance and cost analysis of matrix-assisted laser desorption ionization-time of flight mass spectrometry for routine identification of yeast

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry was compared to phenotypic testing for yeast identification. MALDI-TOF mass spectrometry yielded 96.3% and 84.5% accurate species level identifications (spectral scores, ≥ 1.8) for 138 common and 103 archived strains of yeast. MALDI-TOF mass spectrometry is accurate, rapid (5.1 min of hands-on time/identification), and cost-effective ($0.50/sample) for yeast identification in the clinical laboratory.

Update on the laboratory diagnosis of invasive fungal infections

Recent advances in the management of patients with haematological malignancies and transplant recipients have paralleled an increase in the incidence of fungal diseases due to pathogenic genera such as Candida and Aspergillus and the emergence of less common genera including Fusarium and Zygomycetes. Despite availability of new antifungal agents these opportunistic infections have high mortality. Rapid and reliable species identification is essential for antifungal treatment, but detection of the increasing diversity of fungal pathogens by conventional phenotypic methods remains difficult and time-consuming, and the results may sometimes be inconclusive, especially for unusual species. New diagnostic techniques (e.g., 1,3-beta-d-glucan detection) could improve this scenario, although further studies are necessary to confirm their usefulness in clinical practice.

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.

Early mannan detection in bronchoalveolar lavage fluid with preemptive treatment reduces the incidence of invasive Candida infections in preterm infants

BACKGROUND

Candida colonization is an important predictor for development of invasive fungal infection (IFI). We investigated whether early detection of Candida mannan (Mn) in bronchoalveolar lavage fluid (BALF) reduces IFI among preterm infants.

METHODS

We conducted an observational study of infants with gestational age of < or =28 weeks, where a group undergoing Candida surveillance cultures (pre-Mn detection group) was compared with a group defined after the initiation of routine use of Candida Mn detection in BALF (Mn detection group). Antifungal treatment was started based on positive microbiologic (surveillance culture or Mn-antigen assay) results.

RESULTS

No significant differences were detected when the groups were compared for several predictors of IFI. IFI was observed for 12 (23%) of 51 infants in the pre-Mn detection group, and for 0 (0%) of 29 infants in the Mn detection group (P = 0.003). Surveillance cultures in the pre-Mn detection group became positive at 15.0 +/- 7.2 days after birth, whereas the mean age at time of positive Mn antigen results in the Mn detection group was 4.3 +/- 3.1 days (P < 0.0001). Among 16 infants positive for surveillance cultures, 12 (75%) developed IFI (P < 0.0001).

CONCLUSIONS

This study suggests that Candida Mn detection in BALF may be useful for earlier identification and preemptive therapy targeting preterm infants at high risk of IFI.

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.

Enzymatic substrates in microbiology

Enzymatic substrates are powerful tools in biochemistry. They are widely used in microbiology to study metabolic pathways, to monitor metabolism and to detect, enumerate and identify microorganisms. Synthetic enzymatic substrates have been customized for various microbial assays, to detect an expanding range of both new enzymatic activities and target microorganisms. Recent developments in synthetic enzymatic substrates with new spectral, chemical and biochemical properties allow improved detection, enumeration and identification of food-borne microorganisms, clinical pathogens and multi-resistant bacteria in various sample types. In the past 20 years, the range of synthetic enzymatic substrates used in microbiology has been markedly extended supporting the development of new multi-test systems (e.g., Microscan, Vitek 2, Phoenix) and chromogenic culture media. The use of such substrates enables an improvement in time to detection and specificity over conventional tests that employ natural substrates. In the era of intense developments in molecular biology, phenotypic tests involving enzymatic substrates remain useful to analyse both simple and complex samples. Such tests are applicable to diagnostic and research laboratories all over the world.

Evaluation of new colorimetric vitek 2 yeast identification card by use of different source media

The new colorimetric Vitek 2 YST card was evaluated for identification of yeasts (136 strains) with respect to the influence of different source media. The Vitek 2 YST card achieved satisfactory results for all yeast species tested, with the exception of Candida guilliermondii, Candida norvegensis, Candida parapsilosis, Candida rugosa, and Candida tropicalis. After simple additional tests, 93.7% of all the strains tested were correctly identified. A significant influence of the isolation medium on the identification rate could not be observed.