Yeast identification in routine clinical microbiology laboratory and its clinical relevance

Biodetection Strategies for Selective Identification of Candidiasis

Fungi are among the predominant pathogens seen in a greater proportion of infections acquired in healthcare settings. A common fungus that causes infections in medical settings is Candida species. Hospitalized patients who suffer from fungal diseases such as candidiasis and candidemia often have elevated rates of mortality and morbidity. It is evident that longer hospital stays have the possibility of bacterial and fungal recurrence and also have a negative economic impact. If left untreated, a Candida infection can spread to other organs and cause a systemic infection that can result in sepsis. Clinicians can treat patients quickly when fungal infections are timely detected, this enhances the results of clinical trials. Developing novel, sensitive, and quick methods for detecting Candida species is imperative. Conventional detection techniques are unsuitable for clinical settings and point-of-care systems as they require expensive equipment and take a longer detection time. This review examines a few of the most widely used biosensor systems for the detection of Candida species, their sensitivity, and the limit of detection. It focuses on various biorecognition elements used and follows utilization and advances in nanotechnology in the context of sensing. In addition to enabling general analysis and quick real-time analysis, crucial for detecting Candida species, biosensors provide an intriguing alternative to more conventional techniques.

Comparison of Candida colonization in intensive care unit patients with and without COVID-19: First prospective cohort study from Turkey

Candida species are the primary cause of fungal infections in intensive care units (ICUs). Despite the increasing prevalence of Candida-related infections, monitoring the progression of these infections from colonization in COVID-19 ICU patients lacks sufficient information. This study aims prospectively to compare 62 COVID-19 and 60 non-COVID-19 ICU patients from admission to discharge in terms of colonization development, rates, isolated Candida species, risk factors, and Candida infections during hospitalization. A total of 1464 samples were collected at specific time intervals from various body sites [mouth, skin (axilla), rectal, and urine]. All samples were inoculated onto CHROMagar Candida and CHROMagar Candida Plus media, and isolates identified using MALDI-TOF MS. COVID-19 patients exhibited significantly higher colonization rates in oral, rectal, and urine samples compared to non-COVID-19 patients, (p < 0.05). Among the Candida species, non-albicans Candida was more frequently detected in COVID-19 patients, particularly in oral (75.8%-25%; p < 0.001) and rectal regions (74.19% - 46.66%; p < 0.05). Colonization with mixed Candida species was also more prevalent in the oropharyngeal region (p < 0.05). Mechanical ventilation and corticosteroid use emerged as elevated risk factors among COVID-19 patients (p < 0.05). Despite the colonization prevalence, both COVID-19-positive and negative patients exhibited low incidences of Candida infections, with rates of 9.67% (n = 6/62) and 6.67% (n = 3/60), respectively. Consequently, although Candida colonization rates were higher in COVID-19 ICU patients, there was no significant difference in Candida infection development compared to the non-COVID-19 group. However, the elevated rate of non-albicans Candida isolates highlights potential future infections, particularly given their intrinsic resistance in prophylactic or empirical treatments if needed. Additionally, the high rate of mixed colonization emphasizes the importance of using chromogenic media for routine evaluation.

Candiduria-Study of Virulence Factors and Its Antifungal Susceptibility Pattern in Tertiary Care Hospital

Background The increased incidence of candiduria in hospitalized patients is due to the use of indwelling devices, long-term antibiotics, parenteral nutrition, and immunocompromised status of the patient. In this study, an attempt was made to speciate, characterize, and determine the antifungal susceptibility pattern of Candida isolated from urinary tract infections (UTIs).

Materials and Methods A total of 70 Candida isolates were obtained from urine samples. The isolated Candida species were studied for the production of virulence factors like phospholipase, protease activities, hemolysin, and biofilm production. Antifungal susceptibility testing of the isolated yeasts was done using Mueller-Hinton agar supplemented with 0.5 mg/mL methylene blue by E-test method for amphotericin B, fluconazole, caspofungin, and voriconazole.

Results Out of 70 isolates, Candida tropicalis was the most frequently isolated species (65.7%), followed by Candida albicans (14.3%), Candida glabrata (7.1%), Candida krusei (5.7%), Candida parapsilosis (4.3%), and Candida dubliniensis (2.9%). A total of 37.1% were biofilm producers, 62.9% showed proteinase activity, 38.6% were phospholipase positive, and 58.6% isolates showed hemolytic activity. Antifungal susceptibility profile of Candida species showed 38.6, 25.7, 15.7, and 12.9% resistance to amphotericin B, fluconazole, caspofungin, and voriconazole, respectively.

Conclusion A rising trend in isolation of non-albicans Candida from urinary isolates was noticed, which was statistically significant when comparing catheterized and noncatheterized urinary isolates from our study. However, there was no statistically significant difference when different virulence factor expressions were compared among Candida spp. isolated from catheterized and noncatheterized urinary samples. Due to this rise in non-albicans Candida species causing UTI that are intrinsically resistant to certain antifungal agents like azoles and increasing incidence of antifungal resistance, it is essential to monitor the antifungal susceptibility profile of Candida species causing candiduria.

Epidemiology, laboratory diagnosis and clinical aspects of fungal pulmonary infections in 384 patients hospitalized in pulmonary units in Guilan province, Iran

Background and Objectives:

The respiratory tract is the most common site for developing fungal infections. People who have a weakened immune system are more susceptible to respiratory system involvement with fungi. Fungal infections of the respiratory tract are largely unrecognized and their true burden is elusive. Therefore, the aim of the current study was to evaluate the clinical spectrum, demographic characteristics, risk factors, and etiology of fungal respiratory infections in 384 patients hospitalized in pulmonary units of Razi hospital, Guilan province, Iran.

Materials and Methods:

A total of 384 lung specimens (192 Bronchoalveolar lavages (BAL) and 192 sputa) were obtained from patients who met the inclusion criteria. All samples were analyzed by direct microscopy and culture. Fungal identification was accomplished by internal transcribed spacer (ITS) and beta-tubulin sequencing. Also, in patients suspected to invasive pulmonary aspergillosis BAL specimens were tested for galactomannan (GM) antigen. According to the host factors (clinical symptoms, radiology findings and predisposing factors which were defined as inclusion criteria), and the positive results in direct examination, culture and serology (GM for aspergillosis) the infection was confirmed.

Results:

Fungal respiratory infection was confirmed in 137 cases (35.67%) including 86 (62.77%) males and 51 (37.23%) females and the highest prevalence of infection was found in the age group of 46–72 years (n=75, 54.74%). Cough (n=129, 94.16%), dyspnea (n=111, 81.02%), purulent sputum (n=85, 62.04%) and weight loss (n=77, 56.2%) were the predominant symptoms. Tuberculosis (n=34, 24.81%), taking chemotherapy regimen (n=30, 21.89%) and diabetes mellitus (n=27, 19.70%) were the predominant underlying conditions. Candida albicans (37.22%) and Candida tropicalis (21.89%) represent the two most commonly isolated species in the current study. Furthermore, according to revised EORTC/MSG (2008) definitions for invasive fungal infections, from 5 cases of pulmonary aspergillosis, 2 (40%) cases of probable invasive pulmonary aspergillosis (IPA) and 3 (60%) cases of possible IPA were diagnosed.

Conclusion:

According to the results of this study, infected infants with congenital CMV infection could identify at early stage by testing Guthrie cards (within 21 days of life). Furthermore, since there is a lack of CMV knowledge in our population, educating and effective counseling by obstetricians/gynecologists to the pregnant women are recommended.

Fungal Isolates of the Respiratory Tract in Symptomatic Patients Hospitalized in Pulmonary Units: A Mycological and Molecular Epidemiologic Study

Introduction

Fungal respiratory infections are being recognized with increasing frequency in parallel with an expanding population of immunocompromised patients. In most cases, colonization is the first step in the progression to pulmonary fungal infection. This study was designed to evaluate the distribution of fungal elements in the respiratory tract of symptomatic patients hospitalized in pulmonary units.

Methods

This descriptive cross-sectional study was carried out over a period of two years, from October 2017 to October 2019 in Guilan province, located in Iran’s northern region. In the current study, bronchoalveolar lavage or sputum specimens were collected. All samples were analyzed by direct microscopy using KOH 10% and culture. Fungal identification was accomplished by internal transcribed spacer (ITS) and beta-tubulin sequencing. Also, in patients suspected of invasive pulmonary aspergillosis, BAL specimens were tested for galactomannan (GM) antigen.

Results

A total of 384 lung specimens (192 bronchoalveolar lavage (BAL) and 192 sputum samples) were obtained from symptomatic patients hospitalized in pulmonary units. Of these, 137 (35.67%) were positive in direct examination and culture. Among the 137 positive cases, most isolates were from male patients 86 (62.77%) and most of them were between 46 and 72 years. Candida albicans (37.22%) and Candida tropicalis (21.89%) represent the two most commonly isolated species in the current study. Cough (94.16%), dyspnea (81.02%), purulent sputum (62.04%) and weight loss (56.2%) were the predominant symptoms and tuberculosis (24.81%), chemotherapy (21.89%) and diabetes mellitus (19.70%) were the predominant underlying conditions. Also, 5 cases of invasive pulmonary aspergillosis and 1 case of mucormycosis were diagnosed.

Conclusion

Candida albicans was the most common fungal species isolated from symptomatic patients hospitalized in pulmonary units. Tuberculosis, chemotherapy and diabetes mellitus were important underlying conditions for pulmonary fungal colonization and/or infection.

A study on biofilm production and antifungal drug resistance among Candida species from vulvovaginal and bloodstream infections

Introduction

Candida species, one among the opportunistic fungi, has become a common pathogen causing vaginal thrush and nosocomial bloodstream infections (BSIs). This study aims to evaluate the prevalence and antifungal susceptibility of various Candida species and slime production by Candida species in BSIs and vulvovaginal candidiasis (VVC).

Materials and methods

A total of 176 samples were collected for a period of 1 year. Anti-fungal susceptibility testing and biofilm production testing were performed by the Kirby-Bauer method and crystal violet assay, respectively.

Results

Out of 176 samples, 74 (42%) were from BSIs and 102 (58%) were from VVC. The biofilm production was comparatively high in blood isolates, 55 (74%), than cervical isolates, 45 (44%). Increase in the trends of non-albicans Candida (NAC) species was seen in our setup. Good susceptibility rates were seen among Candida species, 82.38% to voriconazole and an increasing resistance pattern of 26.13% to fluconazole.

Conclusion

Speciation of Candida becomes important as the prevalence of NAC is increasing. Antifungal susceptibility testing by the disk diffusion method is cost effective and should be adopted in routine testing as there is an increasing azole resistance, especially in invasive NAC infections. In this study, there was no correlation of antifungal drugs with the biofilm production.

Antifungal Susceptibility and Biofilm Production of Candida spp. Isolated from Clinical Samples

Objective

The study aims to speciate clinical Candida isolates and detect their biofilm-forming ability and antifungal resistance.

Methods

All the Candida spp. isolated from different clinical samples like pus, urine, blood, and body fluid were included in the study. Biofilm production was tested by the microtiter plate method. Antifungal susceptibility was studied by the disk diffusion method. Patient's demographic details such as age, sex, and clinical information were collected. Presence of other risk factors such as diabetes mellitus, history of antibiotic use, and any urinary tract instrumentations was also recorded.

Results

Among 90 Candida species isolated, most predominant species was found to be C. albicans (45.5%) followed by C. tropicalis (28.88%), C. krusei (20%), C. glabrata (3.33%), and C. parapsilosis (2.22%). Candida spp. were isolated from urine (43%), BAL/sputum (18.88%), high vaginal swab (8.88%), suction tips (7.77%), blood and wound swabs (6.66%), pus (3.33%), bile aspirate (2.22%), and deep tissue (1.11%). A larger number of females were affected than males, and the age group of 51 to 60 years was more susceptible to candidiasis. A higher number of C. albicans isolates produced biofilm followed by C. parapsilosis, C. tropicalis, and C. krusei. However, C. glabrata showed no biofilm production in our study. All Candida isolates were 100% sensitive to amphotericin B. Voriconazole was the next effective drug with 81.11% susceptibility. 24.44% of strains were resistant to fluconazole.

Conclusion

Speciation of Candida isolates, detection of ability to form the biofilm, and monitoring of antifungal susceptibility testing are necessary for appropriate treatment.

A Fatal Case of Candida auris and Candida tropicalis Candidemia in Neutropenic Patient

We report a fatal case of Candida auris that was involved in mixed candidemia with Candida tropicalis, isolated from the blood of a neutropenic patient. Identification of both isolates was confirmed by amplification and sequencing of internal transcribed spacer and D1/D2 domain of large subunit in rRNA gene. Antifungal susceptibility test by E-test method revealed that C. auris was resistant to amphotericin B, anidulafungin, caspofungin, fluconazole, itraconazole and voriconazole. On the other hand, C. tropicalis was sensitive to all antifungal tested. The use of chromogenic agar as isolation media is vital in detecting mixed candidemia.

Advances in Candida detection platforms for clinical and point-of-care applications

Invasive candidiasis remains one of the most serious community and healthcare-acquired infections worldwide. Conventional Candida detection methods based on blood and plate culture are time-consuming and require at least 2-4 days to identify various Candida species. Despite considerable advances for candidiasis detection, the development of simple, compact and portable point-of-care diagnostics for rapid and precise testing that automatically performs cell lysis, nucleic acid extraction, purification and detection still remains a challenge. Here, we systematically review most prominent conventional and nonconventional techniques for the detection of various Candida species, including Candida staining, blood culture, serological testing and nucleic acid-based analysis. We also discuss the most advanced lab on a chip devices for candida detection.

Rapid detection of Candida species in bronchoalveolar lavage fluid from patients with pulmonary symptoms

Candida species, especially C. albicans, are commensals on human mucosal surfaces, but are increasingly becoming one of the important invasive pathogens as seen by a rise in its prevalence in immunocompromised patients and in antibiotic consumption. Thus, an accurate identification of Candida species in patients with pulmonary symptoms can provide important information for effective treatment. A total of 75 clinical isolates of Candida species were obtained from the bronchoalveolar lavage fluid of both immunocompromised and immunocompetent patients with pulmonary symptoms. Candida cultures were identified based on nuclear ribosomal Internal Transcribed Spacer (ITS1-ITS2 rDNA) sequence analysis by polymerase chain reaction–restriction fragment length polymorphisms (PCR-RFLP). Molecular identification indicated that the isolates belonged predominantly to C. albicans (52%), followed by C. tropicalis (24%), C. glabrata (14.7%), C. krusei (5.3%), C. parapsilosis (1.3%), C. kefyr (1.3%) and C. guilliermondii (1.3%). Given the increasing complexity of disease profiles and their management regimens in diverse patients, rapid and accurate identification of Candida species can lead to timely and appropriate antifungal therapy.

Candiduria in Catheter Associated Urinary Tract Infection with Special Reference to Biofilm Production

INTRODUCTION

Urinary tract infections as a result of Candida species are becoming increasingly common in hospital settings. The association is higher in patients with prolonged urinary catheterization and also various pre-disposing factors.

AIM

This study was done to look into the significance of candiduria in the catheterized patients and to perform microbial catheterization of yeast and biofilm detection by tube method to guide treatment protocol.

MATERIALS AND METHODS

This is a prospective study. One hundred urine samples were collected over a period of 3 months. Specimens included were those of patients presenting with nosocomial Urinary tract infection (UTI) after 72 hours of hospitalization. The urine samples obtained were immediately processed in microbiology laboratory by semi-quantitative method as per standard protocol. All yeast isolates were stored for further microbial characterization. Biofilm production was detected by tube method.

RESULTS

In the present study we observed that out of 100 samples obtained from catheterized patients presenting with nosocomial UTI 26% were caused by Candida species. Among the 26 Candida isolates 16 (61.53%) were non albicans Candida and 10(38.47%) were Candida albicans. Out 26 Candida isolates, 14(53.84%) of the candida isolates were found to produce biofilm. Biofilm production was found to occur more frequently among non albicans Candida 10(62.5%) than Candida albicans 4(40.0%).

CONCLUSION

The present study reiterates the presence of candiduria in catheterized patients. Non-albicans candida speices are replacing candida albicans as the predominant pathogen for nosocomial UTI. It was also observed that Biofilm formation is seen more frequently with non albicans candida species than with Candida albicans.

Performance of chromogenic media for Candida in rapid presumptive identification of Candida species from clinical materials

Background:

In perspective of the worldwide increase in a number of immunocompromised patients, the need for identification of Candida species has become a major concern. The development of chromogenic differential media, introduced recently, facilitate rapid speciation. However, it can be employed for routine mycology workup only after an exhaustive evaluation of its benefit and cost effectiveness. This study was undertaken to evaluate the benefit and cost effectiveness of chromogenic media for speciation of Candida clinical isolates.

Materials and Methods:

Sputum samples of 382 patients were screened for the presence of Candida spp. by Gram stain and culture on sabouraud dextrose agar. Candida species were identified using Gram stain morphology, germ tube formation, cornmeal agar with Tween-80, sugar fermentation tests and morphology on HiCrome Candida differential agar. All the Candida isolates were inoculated on HiCrome Candida agar (HiMedia, Mumbai, India).

Results:

The sensitivity and specificity of HiCrome agar for identification of Candida albicans were 90% and 96.42%, respectively whereas sensitivity and specificity of carbohydrate fermentation test were 86.67% and 74.07%, respectively. Sensitivity and specificity values of HiCrome agar for detection of C. albicans, Candida parapsilosis and Candida glabrata were above 90%.

Conclusions:

We found HiCrome agar has high sensitivity and specificity comparable to that of the conventional method. In addition, use of this differential media could significantly cut down the turnaround time as well as cost of sample processing.

Distribution of different yeasts isolates among trauma patients and comparison of accuracy in identification of yeasts by automated method versus conventional methods for better use in low resource countries

INTRODUCTION

As most trauma patients require long-term hospital stay and long-term antibiotic therapy, the risk of fungal infections in such patients is steadily increasing. Early diagnosis and rapid treatment is life saving in such critically ill trauma patients.

AIMS

To see the distribution of various species of Candida among trauma patients and compare the accuracy, rapid identification and cost effectiveness between VITEK 2, CHROMagar and conventional methods.

SETTINGS AND DESIGN

Retrospective laboratory-based surveillance study performed over a period of 52 months (January 2009 to April 2013) at a level I trauma centre in New Delhi, India.

MATERIALS AND METHODS

All microbiological samples positive for Candida were processed for microbial identification using standard methods. Identification of Candida was done using chromogenic medium and by automated VITEK 2 Compact system and later confirmed using the conventional method. Time to identification in both was noted and accuracy compared with conventional method.

STATISTICAL ANALYSIS

Performed using the SPSS software for Windows (SPSS Inc. Chicago, IL, version 15.0). P values calculated using χ2 test for categorical variables. A P<0.05 was considered significant.

RESULTS

Out of 445 yeasts isolates, Candida tropicalis (217, 49%) was the species that was maximally isolated. VITEK 2 was able to correctly identify 354 (79.5%) isolates but could not identify 48 (10.7%) isolates and wrongly identified or showed low discrimination in 43 (9.6%) isolates but CHROM agar correctly identified 381 (85.6%) isolates with 64 (14.4%) misidentification. Highest rate of misidentification was seen in C. tropicalis and C. glabrata (13, 27.1% each) by VITEK 2 and among C. albicans (9, 14%) by CHROMagar.

CONCLUSIONS

Though CHROMagar gives identification at a lower cost compared with VITEK 2 and are more accurate, which is useful in low resource countries, its main drawback is the long duration taken for complete identification.

Identifying Candida and other yeast-like fungi: utility of an identification algorithm in resource limited setting

AIM

The increasing recovery rates of unusual yeasts with innate drug resistance make accurate identification crucial for successful therapy and infection control measures. The current study was undertaken to study the utility of CHROMagar Candida (CC) and evaluate an identification algorithm, using germ tube test (GT), CC and a commercial identification kit, API ID 32C.

SETTINGS AND DESIGN

The prospective study was carried out at a private laboratory in Mumbai, India.

MATERIALS AND METHODS

Identification of 533 yeast and yeast like isolates was carried out using an identification algorithm, comprising of the GT, CC and API tests.

RESULTS

CC was useful to detect mixed cultures. We were able to identify 393/533, i.e. 73.7 % of isolates using GT and CC Tests only. This was because C. albicans and C. tropicalis, which can be reliably identified using CC, constituted 75.2 % of the isolates. We were unable to identify 140 isolates, i.e. 26.3 %, using GT and CC tests only and performed additional testing using API ID 32C. CC was not found to be reliable in identifying C. krusei.

CONCLUSION

The diverse identification profile obtained in our study substantiates the need for all diagnostic microbiology laboratories to be better prepared for identifying unusual yeasts. Though GT or CC testing cannot alone suffice for identification of all clinically encountered Candida and yeast-like fungi, use of GT, CC and automated identification systems in a step-wise algorithm can enable the same in a more cost effective manner.

Changing trends of vulvovaginal candidiasis

INTRODUCTION

Vulvovaginal candidiasis is one of the most common infections seen in women.

MATERIALS AND METHODS

A total of 300 symptomatic women were studied. High vaginal swabs collected from each patient were processed by Gram stain, culture on Sabourauds dextrose agar and CHROM agar plates. Isolates were identified and speciated using conventional methods and by the color of the colonies on the CHROM agar. Antifungal susceptibility was performed by disc diffusion method for fluconazole (25 μg) and voriconazole (1 μg) discs as per Clinical and Laboratory Standards Institute (CLSI) guidelines.

RESULTS

Vulvovaginal candidiasis was found in 53 (17.7%) of cases. Gram stain was positive in 22 (41.41%) of culture positives. Speciation of isolates by conventional and CHROM agar methods showed similar results. C. albicans 35 (66.0%) was the most common species isolated followed by C. tropicalis 14 (26.4%), C. krusei 2 (3.8%), C. parapsilosis and C. glabrata in 1 (1.9%) case each. Sensitivity to fluconazole was found in 91.4% of C. albicans, 57.1% of C. tropicalis and 50.0% of C. krusei. Sensitivity to voriconazole was seen in 91.4% of C. albicans, 85.7% of C. tropicalis and 50.0% of C. krusei. C. parapsilosis and C. glabrata were found sensitive only to voriconazole.

CONCLUSION

CHROM agar has the advantage of being rapid, simple and cost effective method as compared to conventional methods in speciation of Candida. Routine susceptibility testing of Candida isolates help in selecting the most appropriate antifungal agent for vulvovaginal candidiasis.

The spectrum and aetiology of mycotic infections from a tertiary care hospital from Western part of India

BACKGROUND

In the past few years, there has been an increase in infections caused by fungal aetiology. This is mainly due to increase in sizes of populations which are at risk. Also, fungi which were previously considered as non-pathogenic have been increasingly implicated. Hence, this study was taken up.

AIM

To assess the magnitude of mycotic infections in this set up. To assess the spectrum of fungi which are involved in various infections.

MATERIAL AND METHODS

Total 704 samples taken over two and half period were included. They consisted of various samples like sputum, blood, urine, sterile body fluids, corneal scrapings. These were processed by conventional mycological techniques. These included direct microscopy after Gram staining and KOH mount, culture on Sabouraud's dextrose agar (SDA), corn meal agar, brain heart infusion (BHI), brain heart infusion agar (BHIA) and others, as required. For non-albicans Candida, the automated Vitek 2 C system was used. Various moulds and yeasts were identified up to genus level and species level.

RESULTS

Of 704 samples, 336 (48%) were positive for fungal culture. Of these, 244 isolates were yeast like fungi, 81 were moulds, 7 were yeasts and 4 were dimorphic. Among blood stream infections, non-albicans Candida were the commonest isolates. In the urine samples, C. albicans was the commonest isolate. From corneal scrapings, only moulds and dimorphic fungi were isolated.

CONCLUSION

Incidence of non- albicans Candidal infections is increasing. Culture and identification of mycotic infections is essential for commencement of suitable antifungal therapy.