Use of the VITEK 2 system to identify and test the antifungal susceptibility of clinically relevant yeast species

First report of amphotericin B resistant Candida haemulonii isolated from the ICU of a referral hospital in Indonesia

Background and Objectives

Amphotericin B is a broad-spectrum antifungal agent commonly used to treat Candida haemulonii infection. C. haemulonii was isolated from patients reported to be intrinsically resistant to amphotericin B, encoded by the ERG2 and ERG11 genes. However, there have been limited studies concerning amphotericin B-resistant C. haemulonii in Indonesia. The objective of this study is to explore the phenotypic and genotypic characteristics (ERG2 and ERG11) of C. haemulonii isolated from the ICU of a referral hospital in Indonesia.

Materials and Methods

Identification and susceptibility tests were conducted using VITEK2. Thereafter, DNA was extracted and amplified using conventional PCR followed by DNA sequencing (Sanger method).

Results

The results of the phenotypic susceptibility test showed that all C. haemulonii were resistant to amphotericin B. ERG2 and ERG11 sequences showed the same amino acid sequence and corresponded to references that are resistant to amphotericin B.

Conclusion

The resistant properties of C. haemulonii against amphotericin B found in this study require further exploration, including comparing resistant and sensitive C. haemulonii to amphotericin B. In addition, it is necessary to analyze other genes besides ERG2 and ERG11.

Candida haemulonii Species Complex: A Mini-review

Candida haemulonii species complex (CHSC) are emerging multidrug-resistant yeast pathogens able to cause life-threatening human infections in at-risk populations for invasive candidiasis worldwide. A recent laboratory survey conducted in 12 medical centers found that prevalence rates of Candida haemulonii complex isolates rose from 0.9 to 1.7% along the period between 2008 and 2019. We present a mini-review addressing recent aspects of the epidemiology, diagnosis and therapy of infections due to CHSC.

Differences of clinical characteristics and outcome in proven invasive Trichosporon infections caused by asahii and non-asahii species

BACKGROUND

Trichosporon is an emerging yeast that causes invasive infections in immunocompromised patients experiencing prolonged hospitalisation, indwelling venous catheters and neutropenia.

METHODS

This retrospective observational cohort study analysed invasive Trichosporon infections (ITIs) occurring between January 2005 and December 2022 at three tertiary hospitals and compared the clinical characteristics and prognostic factors of ITIs caused by Trichosporon asahii and non-T. asahii spp. After evaluating 1067 clinical isolates, we identified 46 patients with proven ITIs, defined as cases in which Trichosporon was isolated from blood, cerebrospinal fluid, or sterile tissues.

RESULTS

The patients were separated into T. asahii and non-T. asahii groups containing 25 and 21 patients, respectively, all of which except one were immunocompromised. During this period, both the number of clinical isolates and patients with ITIs (mainly T. asahii) increased; whereas, cases involving non-T. asahii spp. decreased. Compared with the non-T. asahii group, the T. asahii group had more patients with multiple catheters (84% vs. 33%, p = .001) and those receiving renal replacement therapy (48% vs. 14%, p = .005). The all-cause 28-day mortality rate after ITI in the T. asahii group (44%) was significantly higher than in the non-T. asahii group (10%, Log-rank p = .014). The multivariate Cox regression model revealed that T. asahii (reference, non-T. asahii spp.; aHR = 4.3; 95% CI = 1.2-15.2, p = .024) and neutropenia for 5 days or more (aHR = 2.2, 95% CI = 1.5-3.6, p = .035) were independent factors in the 28-day mortality after ITI.

CONCLUSION

The proven ITIs due to T. asahii produced more unfavourable outcomes compared with ITIs caused by non-T. asahii spp.

[Species diversity of the genus Candida in the oral cavity of cancer patients in Barranquilla, Colombia]

Candida spp. was characterized in the oral cavity of cancer patients in a health care center in Barranquilla, Colombia. This is a cross-sectional investigation including 60 oncological patients with oral candidiasis, selected by convenience sampling, from whom samples were subjected to culture in Sabouraud chloramphenicol agar, CHROMagar® Candida and Sabouraud dextrose agar were taken. The antifungal susceptibility profile was then identified and established. Descriptive statistics, Chi square test, and bivariate analysis were conducted using the Statgraphics Centurion XVII software with odds ratio (OR) for the probability of occurrence. A total of 107 Candida strains were identified belonging to 15 species, C. albicans with 23%, C. glabrata with 18%, C. tropicalis 13%, C. krusei 10%, C intermedia, and C. lipolytica with 1.5%. Species other than C. albicans were identified in 77% of the cases. A relationship between reproductive system cancer and C. guilliermondii was identified (p = 0.0001, <0.05) OR: 17.0. Between C. colliculosa and respiratory cancer (p = 0.0003, <0.05) OR 19.5. With regard to antifungal susceptibility, 99% of the identified Candida species were susceptible to the following antifungals: fluconazole, voriconazole, caspofungin, and micafungin. Only one strain of C. krusei was resistant. It is concluded that there was a diversity of Candida species, either single or mixed in cancer patients, which could determine that only one species is not responsible for fungal infection in the oral cavity.

Metagenomic Assessment of the Pathogenic Risk of Microorganisms in Sputum of Postoperative Patients With Pulmonary Infection

Respiratory infections are complicated biological processes associated with an unbalanced microbial community and a wide range of pathogens. To date, robust approaches are still required for distinguishing the pathogenic microorganisms from the colonizing ones in the clinical specimens with complex infection. In this study, we retrospectively analyzed the data of conventional culture testing and metagenomic next-generation sequencing (mNGS) of the sputum samples collected from 50 pulmonary infected patients after cardiac surgery from December 2020 and June 2021 in Ruijin Hospital. Taxonomic classification of the sputum metagenomes showed that the numbers of species belonging to bacteria, fungi, and viruses were 682, 58, and 21, respectively. The full spectrum of microorganisms present in the sputum microbiome covered all the species identified by culture, including 12 bacterial species and two fungal species. Based on species-level microbiome profiling, a reference catalog of microbial abundance detection limits was constructed to assess the pathogenic risks of individual microorganisms in the specimens. The proposed screening procedure detected 64 bacterial pathogens, 10 fungal pathogens, and three viruses. In particular, certain opportunistic pathogenic strains can be distinguished from the colonizing ones in the individual specimens. Strain-level identification and phylogenetic analysis were further performed to decipher molecular epidemiological characteristics of four opportunistic etiologic agents, including Klebsiella pneumoniae, Corynebacterium striatum, Staphylococcus aureus, and Candida albicans. Our findings provide a novel metagenomic insight into precision diagnosis for clinically relevant microbes, especially for opportunistic pathogens in the clinical setting.

Changing Trends of Candida Species and Antifungal Susceptibility Profile of Candida Bloodstream Isolates: A 5-Year Retrospective Survey

Background: Candida species have emerged as one of the most common causes of bloodstream infections (BSIs). There are limited data on the distribution of Candida spp. and susceptibility by year. Objectives: In this study, we analyzed changes in the distribution of Candida spp. and their antifungal susceptibility profiles from blood cultures. Methods: Records from January 2016 to December 2020 were obtained from the microbiology laboratory in Istanbul. Antifungal susceptibility tests were performed using the VITEK 2 compact system and evaluated according to EUCAST breakpoints. A total of 241 unique candidemia episodes were included in this study. Results: Candida albicans was the predominant pathogen (n = 95, 39.42%), followed by C. parapsilosis (n = 82, 34.02%), C. glabrata (n = 18, 7.47%), C. tropicalis (n = 17, 7.05%), C. krusei (n = 15, 6.22%), and other Candida spp. (n = 14, 5.79%). There was no statistically significant difference in the percentage of episodes of Candida spp. After data analysis, a tendency to shift from C. albicans to C. parapsilosis was observed in the period analyzed in this study. Candida albicans was the most common species in intensive care units (ICUs), hematology and hemopoietic stem cell transplantation units, and surgical clinics, with C. parapsilosis predominant in medical clinics. In general, micafungin susceptibility was the highest, and fluconazole was the lowest. There was reduced sensitivity to fluconazole and voriconazole for C. albicans and C. parapsilosis over 5 years. Conclusions: Detecting changes in the distribution of Candida spp. and antifungal susceptibility over time will lead to the selection of appropriate empirical therapy and monitor phenomena of antifungal resistance. Empirical treatment with antifungal agents is associated with high costs, toxicities, and risk of antifungal resistance. Therefore, it is mandatory to determine and monitor Candida spp. and antifungal susceptibility testing to select appropriate antifungal agents.

Antifungal Susceptibility Testing and Identification

The requirement for antifungal susceptibility testing is increasing given the availability of new drugs, increasing populations of individuals at risk for fungal infection, and emerging multiresistant fungi. Rapid and accurate fungal identification remains at the forefront of laboratory efforts to guide empiric therapy. Antifungal susceptibility testing methods have greatly improved, but are subject to variation in results between methods. Careful standardization, validation, and extensive training of users is essential to ensure susceptibility results are clinically useful and interpreted appropriately. Interpretive criteria for many drugs and species are still lacking, but this will continue to evolve.

Virulence Factors and Antifungal Susceptibility Profile of C. tropicalis Isolated from Various Clinical Specimens in Alexandria, Egypt

BACKGROUND

The incidence of candidiasis caused by non-albicans Candida (NAC) species is increasing. Candida tropicalis has emerged as one of the most important NAC species. This study aims to examine the antifungal susceptibility profile and some virulence factors of C. tropicalis isolated from various clinical specimens.

METHODS

A total of 71 C. tropicalis isolates from various clinical specimens (69.01%, 18.31%, 9.86%, and 2.82% of isolates were collected from urine, respiratory samples, blood, and skin and soft tissue infections, respectively) from ICU patients in Alexandria, Egypt. The isolates were identified at species level by CHROMagar Candida and VITEK 2 compact system. Furthermore, the antifungal susceptibility was determined using the VITEK 2 system AST-YS07 card containing different antifungals. Hemolysin, phospholipase, and proteinase activity and biofilm formation were also tested as virulence factors.

RESULTS

Only 30 isolates (42.25%) were non-susceptible (MIC ≥ 4 µg/mL) to fluconazole, of which 28 isolates showed non-susceptibility (MIC ≥ 0.25 µg/mL) to voriconazole. All isolates showed both hemolysin and proteinase activities, while only 9 isolates (12.68%) showed phospholipase production and 70 isolates (98.59%) demonstrated biofilm formation. Strong biofilm production was observed among the blood culture isolates (85.71%), followed by the respiratory and urinary isolates (61.54% and 46.94%, respectively).

CONCLUSIONS

This study sought to provide useful data on the antifungal susceptibility of C. tropicalis isolates from ICU patients suffering from invasive infections with an increased trend towards elevated MICs levels of both fluconazole and voriconazole. Due to the high incidence of systemic candidiasis and antifungal resistance, C. tropicalis is emerging as a serious root of infections. Therefore, early and accurate identification of Candida species along with susceptibility testing is of utmost importance.

Prevalence and Antifungal Susceptibility Profile of Clinically Relevant Candida Species in Postmenopausal Women with Diabetes

The incidence of diabetes mellitus has increased in Saudi Arabia, which has raised the risk of vulvovaginal candidiasis (VVC). This study highlights the prevalence and antifungal susceptibility of Candida species among postmenopausal women with diabetes with symptoms of VVC in Taif, a city in Saudi Arabia. Several diagnostic tools were used to differentiate the yeast isolates, including microscopic examination, culture morphology on CHROM agar, further confirmation with the VITEK 2 system, and ITS1 and ITS4 region sequencing. Antifungal susceptibility of the selected Candida species was determined using the VITEK 2 system (bioMérieux Inc., USA). Out of the 550 high vaginal swabs investigated, 86 specimens were Candida species positive (15.6%) with a significant difference according to age; the positivity in the 45–50 years' age group (12%) was higher than that in the 51–55 years' age group (3.6%). Candida albicans was the most common causative agent in 51 samples (59.3%), followed by C. glabrata in 21 samples (24.41%) and C. krusei in 14 samples (16.27%), with no significant differences between the age groups. Three isolates, including two C. albicans and one C. krusei, exhibited resistance against all the tested antifungal agents. CHROM agar and VITEK 2 were accurate phenotypic tools to identify Candida species with 100% sensitivity and specificity and were consistent with the phylogenetic characterization. The data emphasized the importance of identifying Candida species and their antifungal susceptibility among postmenopausal women with diabetes, highlighting the potential risk posed by diabetes in this age group.

[Identification and susceptibility profile of Candida species isolated from hemocultures in hospitals in ParaguayIdentificação e perfil de sensibilidade de Candida spp. isoladas de hemoculturas em hospitais no Paraguai]

Objetivo.

Reportar las especies identificadas en candidemias aisladas en hospitales del país, su distribución según los grupos etarios y determinar la sensibilidad a fluconazol, voriconazol y anfotericina B.

Métodos.

Estudio retrospectivo de candidemias reportados por siete hospitales al Laboratorio Central de Salud Pública en el período 2010 - 2018. La identificación y el antifungigrama fueron realizados en el sistema automatizado Vitek^®2.

Resultados.

Se informaron 520 casos de candidemias. Las especies prevalentes fueron Candida albicans (34,4%), C. parapsilosis (30,4%), C. tropicalis (25,4%), C. glabrata (4,8%), C. krusei (2,1%). Otras menos frecuentes fueron: C. lusitaniae (1,2%), C. guilliermondii (1%), C. famata (0,3%), C. rugosa (0,2%) y C. kefyr (0,2%). Las candidemias en ancianos (48,5%) y adultos (29,9%) fueron las más prevalentes. C. parapsilosis fue más frecuente en recién nacidos y lactantes y C. tropicalis en pacientes pediátricos. El 2,8 % y 0,6% de C. albicans y el 4,4% y 2,5% de C. parapsilosis fueron resistentes a fluconazol y voriconazol, respectivamente. El 8% de C. glabrata fue resistente a fluconazol y dos aislamientos presentaron una concentración inhibitoria mínima para voriconazol mayor que 0,25 mg/L.

Conclusiones.

Este es el primer reporte de candidemias en hospitales de Paraguay que, junto a otros estudios, permitirá un mejor conocimiento de esta infección en el país.

Antifungal susceptibility testing in Candida species: current methods and promising new tools for shortening the turnaround time

INTRODUCTION

Invasive fungal diseases (IFDs) have received attention as an emerging public health threat, are difficult to diagnose and to treat, and are associated with substantial morbidity and mortality. The standard of care in IFD management requires an early and targeted antifungal treatment, hence covers - amongst others - species identification and antifungal susceptibility testing (AFST).

AREAS COVERED

This review gives an overview of methods currently applied in AFST and highlights promising new tools for shortening the turnaround time focusing on Candida species.

EXPERT OPINION

The performance of the broth microdilution reference methods for AFST is not suitable for daily laboratory practice as they are too labor-intensive and time-consuming. Other conventional approaches such as disk diffusion assays, epsilometer tests, colorimetric or automated approaches are easier in handling, and in part, show good correlations with the reference methods. Promising results for shortening the turnaround time in providing MIC data or resistance detection include matrix-assisted laser desorption/ionization-time of flight mass spectrometer (MALDI-TOF MS) assisted AFST, molecular-based techniques and modified conventional approaches applying direct inoculation methods. These underlying AFST concepts are promising but in part completely different, have their own advantages and disadvantages, and need further clinical validation.

Risk factors for candidaemia in hospitalized patients with liver cirrhosis: a multicentre case-control-control study

OBJECTIVES

The aim of this study was to evaluate the risk factors for candidaemia in patients with liver cirrhosis.

METHODS

This was a case-control-control (1:2:2) study performed in four Italian tertiary centres from 2006 to 2015. Cases were patients with liver cirrhosis developing candidaemia. For every case of candidaemia we enrolled two additional patients undergoing blood cultures for suspected infection yielding isolation of a bacterial pathogen (control A) and two additional patients undergoing blood cultures for suspected infection yielding negative results (control B). Patients were matched according to age, sex and model for end stage liver disease at hospital admission.

RESULTS

During the study period 90 cases, 180 controls A and 180 controls B were included. At multivariate analysis assessed by means of multinomial conditional regression models, factors independently associated with candidaemia were previous (<30 days) acute-on-chronic liver failure (relative risk ratio (RRR) 2.22 (95% confidence interval (CI) 1.09-4.54), p = 0.046), previous(<30 days) gastrointestinal endoscopy (RRR 2.38 (95% CI 1.19-4.78) p = 0.014), previous(<30 days) antibiotic treatment for at least 7 days (RRR 2.74 (95% CI 1.00-7.48), p = 0.049), presence of central venous catheter (RRR 2.77 (95% CI 1.26-6.09, p = 0.011), total parenteral nutrition (RRR 3.90 (95% CI 1.62-9.40), p = 0.002) at infection onset and length of in-hospital stay >15 days (RRR 4.63 (95% CI 2.11-10.18), p <0.001] Conversely, rifaximin treatment was associated with lower rate of candidaemia (RRR 0.38 (95% CI 0.19-0.77), p = 0.007). Multivariable analysis for 30-day mortality showed that patients with isolation of Candida spp. from blood cultures had worse outcome when compared with controls even though the difference did not reach a statistical significance (hazard ratio 1.64 (95% 0.97-2.75) p = 0.06).

CONCLUSIONS

We identified previous antibiotic use, gastrointestinal endoscopy or acute-on-chronic liver failure and presence of central venous catheter especially for parenteral nutrition as independent factors associated with candidaemia. Surprisingly, chronic rifaximin use was a protective factor.

Candida Bloodstream Infection: Changing Pattern of Occurrence and Antifungal Susceptibility over 10 Years in a Tertiary Care Saudi Hospital

Background

Candida has emerged as one of the most important pathogens that cause bloodstream infection (BSI).Understanding the current Candida BSI trends, the dominant species causing disease and the mortality associated with this infection are crucial to optimize therapeutic and prophylaxis measures.

Objectives

To study the epidemiology and to evaluate the risk factors, prognostic factors, and mortality associated with candidemia and to compare these findings with previously published studies from Saudi Arabia.

Design

A retrospective medical record review.

Setting

Tertiary hospital in Riyadh.

Patients and Methods

The analysis included all cases of Candida blood stream infection who are >18 years old over the period from 2013 to 2018. Continuous variables were compared using the parametric T-test while categorical variables were compared using the Chi-squared test.

Main Outcome Measure

Incidence, resistance, and hospital outcomes in Candida blood stream infection.

Sample Size

324 patients.

Results

Three hundred and twenty-four episodes of Candida blood stream infections were identified. Median age of patients was 49.7 SD ± 28.1 years, and 53% of patients were males. More than half of the patients had an underlying disease involving the abdomen or laparotomy, 78% had an indwelling intravenous catheter, and 62% had suffered a bacterial infection within 2 weeks prior to candidemia. Candida albicans represents 33% of all isolates with decreasing trend overtime. There was an increase in the number of nonalbicans Candida overtime with Candida tropicalis in the lead (20%). Use of broad spectrum antibiotics (82%), prior ICU admission (60%) and use of central venous catheters (58%) were the most prevalent predisposing factors of candidemia. Azole resistance was variable overtime. Resistance to caspofungin remained very low (1.9%). Fourteen days crude mortality was 37% for ICU patients and 26.7% in non-ICU patients, while hospital crude mortality was 64.4% and 46.7%, respectively.

Conclusion

There is an increasing trend of nonalbicans Candida blood stream infection. Fluconazole resistance remained low to C. albicans. Most isolates remain susceptible to caspofungin, voriconazole, and amphotericin B. Candida bloodstream infection is associated with high 14-day hospital mortality.

Species distribution and antifungal susceptibility among clinical isolates of Candida parapsilosis complex from India

BACKGROUND

Candida parapsilosis is recognized as a species complex: Candida parapsilosis sensu stricto, Candida orthopsilosis and Candida metapsilosis are three distinct but closely related species.

AIMS

To determine the species and antifungal susceptibility of members of the C. parapsilosis complex, isolated from clinical samples.

METHODS

Isolates identified as C. parapsilosis complex by VITEK^® 2 system were included. Antifungal susceptibility test was done using the VITEK^® 2 semi-automated system. The distribution of the species in the complex was determined by multiplex PCR.

RESULTS

Among the seventy-seven C. parapsilosis complex isolates, C. parapsilosis sensu stricto (57.1%) was the commonest species, followed by C. orthopsilosis (40.2%) and C. metapsilosis (2.5%). All three species were susceptible to amphotericin B, caspofungin and micafungin. Among C. parapsilosis sensu stricto isolates, 16% were resistant to fluconazole while 2.2% showed dose dependent susceptibility. Also, 18.2% of C. parapsilosis sensu stricto isolates showed dose dependent susceptibility to voriconazole.

CONCLUSIONS

C. parapsilosis sensu stricto was the most commonly isolated member of the C. parapsilosis complex and it showed high resistance to fluconazole. A high prevalence of C. orthopsilosis (40.2%) was also noted.

Vulvovaginal candidiasis: species distribution of Candida and their antifungal susceptibility pattern

BACKGROUND

Vulvovaginal candidiasis is a global issue of concern due to its association with economic costs, sexually transmitted infections, and ascending genital tract infection. The aim of this study was to determine species distribution and antifungal susceptibility pattern of Candida species causing vulvovaginal candidiasis.

METHODS

A cross sectional study was conducted from November 2015 to December 2016 at the Family Guidance Association of Ethiopia. Vaginal swabs collected from study subjects that were clinically diagnosed with vulvovaginal candidiasis were cultured. Yeast identification and antifungal susceptibility testing were determined by the automated VITEK 2 compact system. The association of vulvovaginal candidiasis with possible risk factors was assessed and analyzed using SPSS version 20.

RESULTS

The overall prevalence of vulvovaginal candidiasis was 41.4%. The association of vulvovaginal candidiasis was statistically significant with previous genital tract infection (p = 0.004), number of life-time male sex partners (p = .037), and number of male sex partners in 12 month (p = 0.001). Of 87 Candida isolates recovered, 58.6% were C. albicans while 41.4% were non-albicans Candida species. The highest overall drug resistance rate of Candida species was observed against fluconazole (17.2%), followed by flycytosine (5.7%). All Candida isolates were 100% susceptible to voriconazole, caspofungin, and micafungin. C. albicans, was 100% susceptible to all drugs tested except fluconazole and flycytosine with a resistance rate of 2% each drug. C. krusei, was 100 and 33.3% resistant to fluconazole and flycytosine, respectively.

CONCLUSIONS

High prevalence rate of vulvovaginal candidiasis and observation of high prevalence rate of non-albicans Candida species in the present study substantiate, the importance of conducting continuous epidemiological surveys to measure changes in species distribution from C. albicans to non-albicans Candida species in Ethiopia. Although, fluconazole still appeared to be active against all isolates of C. albicans and non-albicans Candida species high resistance rate of C. krusei against the drug may demonstrate a search for alternative antifungal drugs when treating vulvovaginal candidiasis caused by C. krusei.

Antifungal susceptibility profile of diferent yeasts isolates from wild animals, cow's milk with subclinical mastitis and hospital environment

Yeast infections have acquired great importance due to increasing frequency in immunocompromised patients or patients undergoing invasive diagnostic and therapeutic techniques, and also because of its high morbidity and mortality. At the same time, it has been seen an increase in the emergence of new pathogenic species difficult to diagnose and treat. The aim of this study was to determine the in vitro susceptibility of 89 yeasts from different sources against the antifungals amphotericin B, voriconazole, fluconazole and flucytosine, using the VITEK® 2 Compact system. The antifungal susceptibility was performed automatically by the Vitek® 2 Compact system. The origin of the yeasts was: Group 1 - microbiota of wild animals (W) (26/89), 2 - cow's milk with subclinical mastitis (M) (27/89) and 3 - hospital enviorment (H) (36/89). Of the 89 yeasts submitted to the Vitek® 2 test, 25 (20.9%) were resistant to fluconazole, 11 (12.36%) to amphotericin B, 3 (3.37%) to voriconazole, and no sample was resistant to flucytosine. Regarding the minimum inhibitory concentration (MIC), fluconazole showed an MIC between 1 and 64 mg/mL for the three groups, voriconazole had an MIC between 0.12 and 8 mg/mL, amphotericin B had an MIC between 0.25 and 4 mg/mL for group H and group W respectively, between 0.25 and 16 mg/mL for group M and flucytosine had an MIC equal to 1μg/mL for all groups. The yeasts isolated from the H group showed the highest resistance to fluconazole 12/89 (13.49%), followed by group W (7.87%) and group M (5.62%). The more resistant group to voriconazole was followed by the M and H groups, the W group showed no resistance to this antifungal. Group H was the least resistant (2.25%) to amphotericin.

SUSCEPTIBILITY TEST FOR FUNGI: CLINICAL AND LABORATORIAL CORRELATIONS IN MEDICAL MYCOLOGY

During recent decades, antifungal susceptibility testing has become standardized and nowadays has the same role of the antibacterial susceptibility testing in microbiology laboratories. American and European standards have been developed, as well as equivalent commercial systems which are more appropriate for clinical laboratories. The detection of resistant strains by means of these systems has allowed the study and understanding of the molecular basis and the mechanisms of resistance of fungal species to antifungal agents. In addition, many studies on the correlation of in vitro results with the outcome of patients have been performed, reaching the conclusion that infections caused by resistant strains have worse outcome than those caused by susceptible fungal isolates. These studies have allowed the development of interpretative breakpoints for Candida spp. and Aspergillus spp., the most frequent agents of fungal infections in the world. In summary, antifungal susceptibility tests have become essential tools to guide the treatment of fungal diseases, to know the local and global disease epidemiology, and to identify resistance to antifungals.

Identification and Antifungal Susceptibility Testing of Candida Species: A Comparison of Vitek-2 System with Conventional and Molecular Methods

Background:

Candida infection is a major cause of morbidity and mortality in immunocompromised patients; an accurate and early identification is a prerequisite need to be taken as an effective measure for the management of patients. The purpose of this study was to compare the conventional identification of Candida species with identification by Vitek-2 system and the antifungal susceptibility testing (AST) by broth microdilution method with Vitek-2 AST system.

Materials and Methods:

A total of 172 Candida isolates were subjected for identification by the conventional methods, Vitek-2 system, restriction fragment length polymorphism, and random amplified polymorphic DNA analysis. AST was carried out as per the Clinical and Laboratory Standards Institute M27-A3 document and by Vitek-2 system.

Results:

Candida albicans (82.51%) was the most common Candida species followed by Candida tropicalis (6.29%), Candida krusei (4.89%), Candida parapsilosis (3.49%), and Candida glabrata (2.79%). With Vitek-2 system, of the 172 isolates, 155 Candida isolates were correctly identified, 13 were misidentified, and four were with low discrimination. Whereas with conventional methods, 171 Candida isolates were correctly identified and only a single isolate of C. albicans was misidentified as C. tropicalis. The average measurement of agreement between the Vitek-2 system and conventional methods was >94%. Most of the isolates were susceptible to fluconazole (88.95%) and amphotericin B (97.67%). The measurement of agreement between the methods of AST was >94% for fluconazole and >99% for amphotericin B, which was statistically significant (P < 0.01).

Conclusion:

The study confirmed the importance and reliability of conventional and molecular methods, and the acceptable agreements suggest Vitek-2 system an alternative method for speciation and sensitivity testing of Candida species infections.

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.

Current methods for identifying clinically important cryptic Candida species

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