Evaluating a semi-nested PCR to support histopathology reports of fungal rhinosinusitis in formalin-fixed paraffin-embedded tissue samples

Screening Candida auris through a multiplex stepwise PCR algorithm directly from clinical samples of patients suspected of otomycosis in south of Iran; Detection of five cases

BACKGROUND

Otomycosis is an infection of the external auditory canal caused by molds and yeasts with descending frequency. Laboratory diagnosis is usually confirmed by microscopy and culture. However, they are not specific enough to reliably differentiate the causative agents, especially for rare pathogens such as Candida auris. The purpose of the current study was to the molecular screening of C. auris species from direct clinical samples of patients with suspected otomycosis in Southern of Iran.

MATERIALS AND METHODS

A total of 221 ear aspirates collected from 221 patients with suspected otomycosis over a four-year period. All the ear aspirations were examined with pan-fungal primers, then those with a positive result was included in two separate reaction mixtures simultaneously to identify the most clinically relevant Aspergillus and Candida species. The validity of positive samples for C. auris was assessed by sequencing.

RESULTS

Of the 189 pan-fungal positive PCRs, 78 and 39 specimens contained Aspergillus spp. and Candida spp., respectively. Furthermore, 65 specimens showed simultaneous positive bands in both Candida and Aspergillus species-specific multiplex PCR including five samples/patients with positive result for C. auris (5/189; 2.6%). Four out of five cases with C. auris species-specific PCR were reconfirmed by sequencing, while none were positive for C. auris in culture.

CONCLUSION

Unfortunately, due to high treatment failure rates of antifungal classes against C. auris species, rapid and accurate identification of patients colonised with C. auris is critical to overcome the challenge of preventing transmission. This PCR assay can be successfully applied for rapid and accurate detection of C. auris directly in patient samples and is able to differentiate C. auris from closely related Candida species.

Rapid detection of Mucorales based on recombinase polymerase amplification and real-time PCR

Mucormycosis, an invasive fungal disease with severe consequences, poses a significant threat to immunocompromised individuals. However, the timely and accurate identification of Mucorales infection continues to present difficulties. In this study, novel detection techniques utilizing recombinase polymerase amplification (RPA) and quantitative real-time polymerase chain reaction (qPCR) were developed, specifically targeting the mitochondrial rnl gene, in order to address this challenge. The specificity of the RPA and qPCR assay was assessed by adding genomic DNAs extracted from 14 non-targeted strains, as well as human and mouse blood. No false-positive results were observed. Additionally, genomic DNAs from 13 species in five genera of order Mucorales were tested and yielded positive results in both methods. To further evaluate the sensitivity of the assays, DNAs from Rhizopus oryzae, Mucor racemosus, Absidia glauca, Rhizomucor miehei, and Cunninghamella bertholletiae were utilized, with concentrations ranging from 1 ng/μL to 1 fg/μL. The limit of detection (LoD) for the RPA assay was determined to be 1 pg., with the exception of Rhizomucor miehei which had a LoD of 1 ng. The LoD for the qPCR assay varied between 10 fg and 1 pg., depending on the specific species being tested. Sensitivity analysis conducted on simulated clinical samples revealed that the LoD for RPA and qPCR assays were capable of detecting DNA extracted from 103 and 101 colony forming units (CFU) conidia in 200 μL of blood and serum, respectively. Consequently, the real-time RPA and qPCR assays developed in this study exhibited favorable sensitivity and specificity for the diagnosis of mucormycosis.

A Comprehensive Review of Identification Methods for Pathogenic Yeasts: Challenges and Approaches

Given the increasing incidence of yeast infections and the presence of drug-resistant isolates, accurate identification of the pathogenic yeasts is essential for the management of yeast infections. In this review, we tried to introduce the routine and novel techniques applied for yeast identification. Laboratory identification methods of pathogenic yeast are classified into three categories; I. conventional methods, including microscopical and culture-base methods II. biochemical/physiological-processes methods III. molecular methods. While conventional and biochemical methods require more precautions and are not specific in some cases, molecular diagnostic methods are the optimum tools for diagnosing pathogenic yeasts in a short time with high accuracy and specificity, and having various methods that cover different purposes, and affordable costs for researchers. Nucleotide sequencing is a reference or gold standard for identifying pathogenic yeasts. Since it is an expensive method, it is not widely used in developing countries. However, novel identification techniques are constantly updated, and we recommend further studies in this field. The results of this study will guide researchers in finding more accurate diagnostic method(s) for their studies in a short period of time.

Molecular identification and antifungal susceptibility profiles of etiologic agents of oral candidiasis among HIV-positive patients: A multicenter study

Background and Purpose

Human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) is a serious risk factor for oral candidiasis (OC). In this regard, the present study aimed to investigate the frequency of Candida species collected from the oropharyngeal cavity of HIV-positive patients and the sensitivity of these isolates to antifungal drugs.

Materials and Methods

Oral samples were collected from 169 HIV-positive patients. In addition to culture-based methods, a molecular assay via the polymerase chain reaction-restriction fragment length polymorphism method was applied to identify isolates using the MspI restriction enzyme. The disk diffusion method determined the susceptibility of isolated yeasts to common antifungal drugs according to the CLSI M44-A2 protocol.

Results

In total, 81 participants (47.92%) were positive for OC, and Candida albicans was the most prevalent yeast (53.98%). The median age of patients was 36 years old (IQR=10.5; 17-59), and it was found that women are 27% more susceptible to HIV-associated OC (OR=1.268; 95% CI: 0.685-2.348). Patients who received antifungal therapy had a 97.3% reduced chance for OC (OR: 0.027; 95% CI: 0.008-0.091; P-value: 0.000). Antifungal therapy reduced the risk of OC by 97.3% (OR=0.027; 95% CI=0.008-0.091; P=0.000), and antiretroviral therapy decreased the chance of OC 4.42 times (OR=4.423; 95% CI=1.697-11.528; P=0.002). The resistance rates for antifungals, namely fluconazole, ketoconazole, itraconazole, amphotericin B, and nystatin were 15.93%, 8.85%, 7.96%, 5.31%, and 4.42%, respectively.

Conclusion

Although several decades have passed since the emergence of HIV/AIDS, little information is available about fungal colonization and infections in this population. Further investigations are suggested using novel and reference molecular identification methods, such as matrix-assisted laser desorption ionization time-of-flight mass spectrometry and sequencing, respectively. In addition, more reliable methods for antifungal susceptibility testing are recommended.