Molecular characterization of Alternaria alternata causing ocular infection: detection of IGS-RFLP intraspecific polymorphism

Molecular identification and genetic variation of Alternaria species isolated from tomatoes using ITS1 sequencing and inter simple sequence repeat methods

Background and Purpose:

Alternaria is one of the most abundant fungi that exists in numerous places around the world. This saprophytic fungus causes diseases in plants and accounts for the spoilage of cereals in warehouses. The aim of this study was to identify Alternaria isolates based on their morphological characteristics and internal transcribed spacer ribosomal RNA (ITS rRNA) sequencing method. To this end, genetic diversity in the isolates was also examined using inter simple sequence repeat (ISSR) markers.

Materials and Methods:

To conduct this research, a total of 60 tomato samples with black spots were collected from supermarkets in Khorramabad City, Iran, in the winter of 2017. The specimens were cultured on a potato dextrose agar medium. After the purification of the fungus by the single-spore method, the identification of the species was carried out using morphological characteristics and ITS rRNA sequencing by polymerase chain reaction. The genetic diversity of the identified species with four primers was evaluated using the ISSR marker.

Results:

Based on the sequencing of the ITS1 region, all the isolates were identified as A. alternata. Cluster diagrams for the ISSR marker were classified into six distinct groups. The mean polymorphism information content was obtained as 0.35, indicating the effectiveness of the primers in the separation of the isolates.

Conclusion:

The sequencing of ITS1 led to the identification of Alternaria species that are morphologically similar. The production of various mycotoxins by A. Alternata species leads to the contamination of livestock and human food. Regarding this, the investigation of the genetic diversity of A. alternata species using the ISSR marker would facilitate the identification of suitable and effective strategies for controlling the fungal and mycotoxin contamination of human nutrition.

Characterization and pathogenicity of Alternaria spp. strains associated with grape bunch rot during post-harvest withering

Alternaria is a fungal agent of grape bunch rot which occurs during withering, a process which produces passito style wines. Seven isolates of Alternaria spp. were characterized using morphological examination, genotypic analysis and pathogenicity. Six of these isolates produced conidiophores and conidia displaying sporulation patterns typical of the Alternaria alternata species-group. Variability in colony morphology and growth on different media was observed. Phylogenetic analysis of internal transcribed spacer (ITS) sequences clustered all isolates within a monophyletic clade, while intergenic spacer region (IGS)-RFLP profiles were congruent with those of A. alternata and Alternaria arborescens. RAPD-PCR proved helpful in discriminating between strains. To assay strain pathogenicity, grape berries were infected while undergoing withering conditions at different temperatures. Disease capacity was found to be strain dependent and varied consistently between the most and least aggressive strains. This study has provided interesting information on polymorphism within Alternaria spp. populations in withered grapes and on understanding the saprophytic role of this fungus during the post-harvest dehydrating process.

PCR for the molecular diagnosis of mycotic keratitis

Mycotic keratitis, an infection of the cornea caused by fungi, is a medical emergency, with patients presenting with considerable pain and distress. For effective management of the condition, a specific diagnosis must be made rapidly to permit early initiation of antifungal therapy. Currently, direct microscopic examination and culture of corneal material constitute the 'gold standard' for diagnosis. However, rapid, sensitive yet specific tests are needed to detect a small number of, or nonviable, fungi. PCR has many potential advantages when used as a diagnostic aid for mycotic keratitis; the present review covers these advantages, and possible limitations. An expert assessment is also made of studies that have used PCR for the diagnosis of mycotic keratitis. The review concludes with a Five-year view of the potential impact of PCR in management of mycotic keratitis.

Phaeohyphomycosis due to Alternaria infectoria: a single-center experience with utility of PCR for diagnosis and species identification

The term phaeohyphomycosis refers to a rare group of fungal infections characterized by the presence of dark-walled hyphae or yeast-like cells in affected tissues. Herein, we report on the clinical and epidemiological characteristics of six cases of phaeohyphomycosis due to Alternaria spp. that occurred in our hospital over a 30-month period (from January 2008 to June 2010). Interestingly, whereas histopathological examinations were positive and fungal cultures yielded molds in all cases, mycological identification using conventional phenotypic methods was never possible despite prolonged incubation of the isolates. Identification of Alternaria infectoria species complex was obtained for each isolate by amplification and sequencing of the internal transcribed spacer of the ribosomal DNA (ITS rDNA). All patients had favourable outcomes following the introduction of azole-based antifungal therapy. This case series describes the clinical course of these six patients and highlights the utility of molecular identification to help in the identification of the etiologic agent when classical mycological methods have failed.

Evaluation of molecular diagnosis in fungal keratitis. Ten years of experience

Purpose

The aims of this study were to assess the utility of polymerase chain reaction (PCR) in diagnosing fungal keratitis in the last decade in our center and to review the molecular diagnosis of mycotic keratitis.

Methods

A retrospective nonrandomized investigation was undertaken at Vissum Corporación Instituto Oftalmologico de Alicante to evaluate 27 corneal samples of 20 patients with proven fungal keratitis from January 2000 to December 2009. Corneal samples (21 corneal scrapings, 5 biopsies, and 1 cornea) were evaluated by Gram stain or calcofluor stain, culture, and PCR. The detection and molecular identification were carried out by DNA amplification and sequencing of the internal transcribed spacer and 5.8S rRNA region from the corneal samples.

Results

PCR detected all the samples that were positive by conventional methods. Four samples were positive by PCR and showed negative results by culture and stain. Combination of microscopy and culture gave positive results in 21 of the 27 samples of patients with mycotic keratitis. Stains showed a 66.7% of positive results, culture showed 59.3%, and PCR showed 92.6%. The time taken for PCR assay was 4 to 8 h whereas positive fungal cultures took 1 to 35 days. Identification at species level by molecular methods was possible in all cases except one. Identification at species level by conventional methods only was possible in eight cases.

Conclusions

PCR not only proved to be an effective rapid method for the diagnosis of fungal keratitis but was also more sensitive than stain and culture methods. Fungal PCR must be added as the screening diagnosis test when an early mycotic keratitis is suspected. Molecular identification is the gold standard technique for the identification of corneal fungal pathogens.

Molecular identification of phaeohyphomycosis due to Alternaria infectoria in a patient with acute myeloid leukemia--a case report

We report the case of a 15-year old with acute myeloid leukemia who developed breakthrough invasive fungal rhinitis. The fungus was identified as Alternaria infectoria by polymerase chain reaction (PCR) and successfully treated by surgical excision and combination antifungal therapy, emphasizing the utility of fungal PCR in timely diagnosis of invasive fungal infections.