Comparison of four commercially available chromogenic media to identify Candida albicans and other medically relevant Candida species

Investigation of multi-drug resistant Candida auris using species-specific molecular markers in immunocompromised patients from a tertiary care hospital in Quetta, Pakistan

INTRODUCTION

Candida auris is an emerging multidrug-resistant pathogen responsible for nosocomial infections worldwide, characterized by high mortality rates and significant challenges in detection due to frequent misidentification. Classified by the WHO as a pathogen of critical importance since it exhibits resistance to multiple antifungal agents, particularly fluconazole, and is highly transmissible in healthcare settings. Conventional detection methods often lack the accuracy required for effective infection control. This study aimed to conduct inferential and molecular analyses of C. auris and other yeast species infecting immunocompromised patients in the Special and Intensive Care Units (SCU and ICU) of a tertiary care hospital in Quetta, Pakistan. In this region, C. auris remains rarely studied and is frequently misdiagnosed by clinical staff due to limited awareness and diagnostic challenges. Notably, no prior research has been conducted on C. auris in Quetta. The study also sought to develop reliable diagnostic methods suitable for resource-limited settings, addressing a critical gap in healthcare infrastructure.

MATERIALS AND METHODS

Samples (150 each) from the ear, axilla, groin, and saliva of SCU/ICU patients were collected and processed on yeast malt agar, with preliminary identification using Brilliance Candida Agar (BCA) and CHROMagar Candida Plus (CCP). Advanced techniques, including PCR amplification of ITS regions, DNA sequencing, RFLP with Msp1, MALDI-TOF, Vitek 2, and species-specific primers, were used for identification. Antifungal susceptibility to fluconazole, amphotericin B, and voriconazole were also assessed.

RESULTS

The culture test revealed that 42.6% samples were positive for yeast infections. In addition to detecting Candida auris in 4 cultures, chromogenic media identified 6 other Candida species: C. albicans, C. dubliniensis, C. glabrata, C. krusei, C. parapsilosis, and C. tropicalis. Further validation through advanced techniques, including molecular diagnostics and MALDI-TOF, enabled the identification of additional species: C. famata, C. kefyr, C. lusitaniae, and Meyerozyma (Candida) guilliermondii. Out of all identified yeast species C. dubliniensis was the most common, followed by C. albicans and C. tropicalis, with the highest infection rates observed in saliva samples. Antifungal Susceptibility Tests (AST) revealed that C. auris isolates were resistant to Fluconazole, Amphotericin B, and Voriconazole, highlighting multidrug resistance. This study represents the first report of novel multidrug-resistant C. auris from Quetta, Pakistan, indicating that C. auris is prevalent among ICU and SCU patients. Novel species specific primers targeting phospholipase B, topoisomerase II, CDR and 18s genes were designed in our laboratory and not previously reported in earlier studies, proved highly effective for the rapid identification of Candida species. The established protocol using these primers is recommended for implementation in resource-limited laboratory settings. The statistical analysis demonstrated significant correlations between Candida species infection (dependent variable) and several independent factors (variables) emphasizing the importance of targeted diagnostics and intervention strategies.

Performance of common primary and chromogenic culture media for MALDI-TOF MS identification of clinically relevant yeasts

Timely and accurate identification of yeasts is essential for adequate treatment, considering the increase in antifungal resistance of some species, particularly for C. auris. Current matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) manufacturer's protocol for identification of yeasts requires 24- to 72-h cultivation on Sabouraud dextrose media (SAB), but not some of the mainstay primary culture media used in mycology such as inhibitory mold agar (IMA), Mycosel, CHROMagar Candida Plus, and CHROMagar Candida. As culture media can influence MALDI-TOF MS identification results, this study evaluated the accuracy and performance of identification of clinically relevant yeasts on these first-line media using the VITEK-MS MALDI-TOF MS system.IMPORTANCEIn this study, a panel of 140 strains (21 species) was used to assess the performance of the selected media. Although not in the manufacturer's list of accepted media, IMA and chromogenic media are suitable for the identification of yeasts on the VITEK-MS systems. CHROMagar Candida Plus allowed the identification of 135/140 isolates tested after 24-h incubation similar to SAB reference media (137/140). Yeast isolates that grew on Mycosel selective media were also reliably identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. VITEK-MS system with IVD database V3.2 correctly identified C. auris strains to the species level on CHROMagar Candida Plus alleviating the need for subcultivation and reduced turnaround time (24-72 h) to identification for patient screening.

Prevalence of Closely Related Candida albicans Species among Patients with Vulvovaginal Candidiasis in Southern Poland Based on the hwp1 Gene Amplification

Candida albicans remains the most common species isolated from women with vulvovaginal candidiasis. However, closely related species such as Candida africana and Candida dubliniensis may also occur, although they are often misidentified. The aim of the study was to confirm the phenotypic identification of C. albicans and its closely related species isolated from women with genital tract infections by amplification of the hwp1 (hyphal wall protein 1) gene in a PCR assay. We report a detailed molecular identification of C. albicans and its closely related species among 326 patients in the Małopolska region, Poland. Initial phenotypic identifications were confirmed by amplification of the hwp1 gene. Based on molecular analysis, we revealed 307 strains (94.17%) as C. albicans and 17 as C. dubliniensis (5.22%). No strain of C. africana was detected. Two patients h ad co-infection with C. albicans and C. dubliniensis (0.61%). A PCR assay targeting the hwp1 gene was reliable for correctly identifying species among the C. albicans complex.

Identification of Pathogenic and Opportunistic Yeasts in Pigeon Excreta by MALDI-TOF Mass Spectrometry and Their Prevalence in Chon Buri Province, Thailand

Pigeon excreta can cause environmental and public health issues, particularly in urban and public areas. They are reservoirs of several human pathogens including fungi, bacteria, and viruses. Epidemiological data of pathogenic and opportunistic yeasts in pigeon droppings in Chon Buri, one of the most reputable tourist cities of Thailand, are scarce. The present study aimed to identify yeasts in pigeon droppings by MALDI-TOF mass spectrometry, and to study their prevalence in Chon Buri, Thailand. A total of 200 pigeon fecal samples were collected randomly from all 11 districts of Chon Buri. A sum of 393 yeast-like colonies were isolated on Sabourand's dextrose agar and CHROMagar media. These isolates were further confirmed for their species by MALDI-TOF MS. Twenty-four yeast species belonging to 11 different genera were identified in pigeon fecal samples. Candida spp., predominantly C. krusei (14.32%), were the most prevalent yeast species. Other yeast species, including C. glabrata (12.73%), C. metapsilosis (11.93%), Lodderomyces elongisporus (10.87%), C. tropicalis (7.16%), C. albicans (5.83%), and Cryptococcus neoformans (4.77%) were identified. This study provides valuable epidemiological data and diversity of yeasts in pigeon droppings in Chon Buri, Thailand, and also supports the use of MALDI-TOF MS for yeast identification and epidemiological surveillance.

Similarities and Differences among Species Closely Related to Candida albicans: C. tropicalis, C. dubliniensis, and C. auris

Although Candida species are widespread commensals of the microflora of healthy individuals, they are also among the most important human fungal pathogens that under certain conditions can cause diseases (candidiases) of varying severity ranging from mild superficial infections of the mucous membranes to life-threatening systemic infections. So far, the vast majority of research aimed at understanding the molecular basis of pathogenesis has been focused on the most common species—Candida albicans. Meanwhile, other closely related species belonging to the CTG clade, namely, Candida tropicalis and Candida dubliniensis, are becoming more important in clinical practice, as well as a relatively newly identified species, Candida auris. Despite the close relationship of these microorganisms, it seems that in the course of evolution, they have developed distinct biochemical, metabolic, and physiological adaptations, which they use to fit to commensal niches and achieve full virulence. Therefore, in this review, we describe the current knowledge on C. tropicalis, C. dubliniensis, and C. auris virulence factors, the formation of a mixed species biofilm and mutual communication, the environmental stress response and related changes in fungal cell metabolism, and the effect of pathogens on host defense response and susceptibility to antifungal agents used, highlighting differences with respect to C. albicans. Special attention is paid to common diagnostic problems resulting from similarities between these species and the emergence of drug resistance mechanisms. Understanding the different strategies to achieve virulence, used by important opportunistic pathogens of the genus Candida, is essential for proper diagnosis and treatment.

Fungal infections diagnosis - Past, present and future

Despite the scientific advances observed in the recent decades and the emergence of new methodologies, the diagnosis of systemic fungal infections persists as a problematic issue. Fungal cultivation, the standard method that allows a proven diagnosis, has numerous disadvantages, as low sensitivity (only 50% of the patients present positive fungal cultures), and long growth time. These are factors that delay the patient's treatment and, consequently, lead to higher hospital costs. To improve the accuracy and quickness of fungal infections diagnosis, several new methodologies attempt to be implemented in clinical microbiology laboratories. Most of these innovative methods are independent of pathogen isolation, which means that the diagnosis goes from being considered proven to probable. In spite of the advantage of being culture-independent, the majority of the methods lack standardization. PCR-based methods are becoming more and more commonly used, which has earned them an important place in hospital laboratories. This can be perceived now, as PCR-based methodologies have proved to be an essential tool fighting against the COVID-19 pandemic. This review aims to go through the main steps of the diagnosis for systemic fungal infection, from diagnostic classifications, through methodologies considered as "gold standard", to the molecular methods currently used, and finally mentioning some of the more futuristic approaches.

Violet colonies of Talaromyces marneffei produce on CHROMagar candida medium

In the present report, we describe an unusual case of mixed infection of Candida albicans and Talaromyces marneffei in the oral cavity and oropharynx with cutaneous involvement. On the CHROMagar Candida plate, green colonies (identified as C. albicans) and tiny violet colonies (identified as T. marneffei) grew from the throat swab after incubation for 96 hours. 10 clinical isolates of T. marneffei were used to verify their color production on CHROMagar Candida. All colonies were violet on the fourth, seventh and ninth day incubated at 37 °C. T. marneffei appears violet on the CHROMagar Candida plate, but it may be easily ignored because of its slow growth and small colony size, especially after incubation for 48 hours. Therefore, when using CHROMagar Candida plate to detect specimens in AIDS patients, special attention must be paid to detect non-yeasts such as T. marneffei for up to 96 hours.

Performance of Two Novel Chromogenic Media for the Identification of Multidrug-Resistant Candida auris Compared with Other Commercially Available Formulations

Non-albicans Candida species are emerging in the nosocomial environment, with the multidrug-resistant (MDR) species Candida auris being the most notorious example. Consequently, rapid and accurate species identification has become essential. The objective of this study was to evaluate five commercially available chromogenic media for the presumptive identification of C. auris Two novel chromogenic formulations, CHROMagar Candida Plus (CHROMagar) and HiCrome C. auris MDR selective agar (HiMedia), and three reference media, CandiSelect (Bio-Rad), CHROMagar Candida (CHROMagar), and Chromatic Candida (Liofilchem), were inoculated with a collection of 9 genetically diverse C. auris strains and 35 strains from closely related comparator species. After 48 h of incubation, the media were evaluated for their ability to detect and identify C. auris All media had the same limitations in the differentiation of the more common species Candida dubliniensis and Candida glabrata Only on CHROMagar Candida Plus did C. auris colonies develop a species-specific coloration. Nevertheless, the closely related pathogenic species Candida pseudohaemulonii and Candida vulturna developed a similar appearance as C. auris on this medium. CHROMagar Candida Plus was shown to be superior in the detection and identification of C. auris, with 100% inclusivity for C. auris compared to 0% and 33% for the reference media and HiCrome C. auris MDR selective agar, respectively. Although C. vulturna and C. pseudohaemulonii can cause false positives, CHROMagar Candida Plus was shown to be a valuable addition to the plethora of mostly molecular methods for C. auris detection and identification.

The Use of MALDI-TOF Mass Spectrometry to Analyze Commensal Oral Yeasts in Nursing Home Residents

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid and accurate method to identify microorganisms in clinical laboratories. This study isolates yeast-like microorganisms in the oral washes that are collected from non-bedridden nursing home residents, using CHROMagar Candida plates, and identifies them using Bruker MALDI-TOF MS. The ribosomal DNA sequences of the isolates are then examined. Three hundred and twenty yeast isolates are isolated from the oral washes. Candida species form the majority (78.1%), followed by Trichosporon/Cutaneotrichosporon species (8.8%). Bruker MALDI-TOF MS gives a high-level confidence, with a log(score) value of ≥1.8, and identifies 96.9% of the isolates. There are six inconclusive results (1.9%), and those sequences are verified as rare clinical species, including Candida ethanolica, Cutaneotrichosporon jirovecii, Exophiala dermatitidis, and Fereydounia khargensis. Almost all of the isolates have a regular color on the CHROMagar Candida plates. If the colonies are grouped by color on the plates, a specific dominant yeast species is present in each color group, except for purple or orange isolates. In conclusion, MALDI-TOF MS is verified as a fast, accurate and practical method to analyze oral yeasts in elderly subjects.