Postmortem diagnosis of Fusarium panophthalmitis by the polymerase chain reaction

Metagenomic analysis for detecting Fusarium solani in a case of fungal keratitis

PURPOSE

To report a difficult-to-identify case of keratitis due to Fusarium solani, diagnosed with the help of exhaustive gene analysis.

CASE

A 47-year-old woman attended our hospital with a refractory corneal ulcer associated with contact lens wear in her left eye that had appeared two weeks earlier. On her initial visit, slit lamp examination revealed a small double-ringed irregular hyphate ulcer in the center of the cornea, which had no epithelial defect, suggesting fungal infection. Microscopic visualization and culture of corneal scrapings were performed repeatedly, but the results were negative. Despite intensive antifungal treatment, infiltration of the cornea worsened and therapeutic keratoplasty was performed. Specimens from a corneal button were microbiologically and histologically negative for microorganisms. During irrigation of the anterior chamber with amphotericin B, aspirated corneal infiltrations were submitted for culture and metagenomic analysis. Genes belonging to F. solani were identified by metagenomic analysis, and an isolate presumed to be a Fusarium species was cultured. Genotypic identification of the isolates confirmed F. solani.

CONCLUSION

The detection of microorganisms, especially fungi, can be extremely difficult. In difficult-to-culture cases, metagenomic analysis seems to be a promising technique for the identification of microbial pathogens.

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.

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.

Diagnosis of Aspergillus fumigatus endophthalmitis from formalin fixed paraffin-embedded tissue by polymerase chain reaction-based restriction fragment length polymorphism

New molecular biological technique of Polymerase Chain Reaction (PCR) based Restriction Fragment Length Polymorphism (RFLP) can identify the species from paraffin-embedded tissue section. We demonstrated Aspergillus fumigatus fungus by PCR-based RFLP technique from paraffin section of an eyeball of an eight- month-old child removed for endogenous endophthalmitis.

Advances in the molecular diagnosis of ochratoxin A–producing fungi

Ochratoxin A (OTA) is detected worldwide in various food and feed sources. The compound is produced by Penicillium nordicum and P. verrucosum, as well as by various species within the sections Nigri and Circumdati of the genus Aspergillus, with A. ochraceus and A. carbonarius known to be the predominant producers. Recently, various pairs of PCR primers based on AFLP, RFLP, RAPD and the calmodulin gene were developed to set up novel diagnostic approaches for OTA producers in the Aspergillus and Penicillium genera. Real-time PCR assays based on well-characterized genomic sequences in A. ochraceus and P. nordicum have also been set up. Since the application of such assays to the analysis of contaminated sample material was demonstrated in only a few cases, future studies should be focused on applying such methods in rapid, robust and user-friendly applications, and implementing them in HACCP concepts. The recent detection and characterization of OTA biosynthetic pathway genes in the Penicillium genus is an important step towards understanding what mechanisms influence production of the toxin in order to redesign production processes in the food and feed industry and to keep de-novo synthesis to a minimum.

Current perspectives on ophthalmic mycoses

Fungi may infect the cornea, orbit and other ocular structures. Species of Fusarium, Aspergillus, Candida, dematiaceous fungi, and Scedosporium predominate. Diagnosis is aided by recognition of typical clinical features and by direct microscopic detection of fungi in scrapes, biopsy specimens, and other samples. Culture confirms the diagnosis. Histopathological, immunohistochemical, or DNA-based tests may also be needed. Pathogenesis involves agent (invasiveness, toxigenicity) and host factors. Specific antifungal therapy is instituted as soon as the diagnosis is made. Amphotericin B by various routes is the mainstay of treatment for life-threatening and severe ophthalmic mycoses. Topical natamycin is usually the first choice for filamentous fungal keratitis, and topical amphotericin B is the first choice for yeast keratitis. Increasingly, the triazoles itraconazole and fluconazole are being evaluated as therapeutic options in ophthalmic mycoses. Medical therapy alone does not usually suffice for invasive fungal orbital infections, scleritis, and keratitis due to Fusarium spp., Lasiodiplodia theobromae, and Pythium insidiosum. Surgical debridement is essential in orbital infections, while various surgical procedures may be required for other infections not responding to medical therapy. Corticosteroids are contraindicated in most ophthalmic mycoses; therefore, other methods are being sought to control inflammatory tissue damage. Fungal infections following ophthalmic surgical procedures, in patients with AIDS, and due to use of various ocular biomaterials are unique subsets of ophthalmic mycoses. Future research needs to focus on the development of rapid, species-specific diagnostic aids, broad-spectrum fungicidal compounds that are active by various routes, and therapeutic modalities which curtail the harmful effects of fungus- and host tissue-derived factors.

Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens

Advances in molecular technology show great potential for the rapid detection and identification of fungi for medical, scientific and commercial purposes. Numerous targets within the fungal genome have been evaluated, with much of the current work using sequence areas within the ribosomal DNA (rDNA) gene complex. This section of the genome includes the 18S, 5.8S and 28S genes which code for ribosomal RNA (rRNA) and which have a relatively conserved nucleotide sequence among fungi. It also includes the variable DNA sequence areas of the intervening internal transcribed spacer (ITS) regions called ITS1 and ITS2. Although not translated into proteins, the ITS coding regions have a critical role in the development of functional rRNA, with sequence variations among species showing promise as signature regions for molecular assays. This review of the current literature was conducted to evaluate clinical approaches for using the fungal ITS regions as molecular targets. Multiple applications using the fungal ITS sequences are summarized here including those for culture identification, phylogenetic research, direct detection from clinical specimens or the environment, and molecular typing for epidemiological investigations. The breadth of applications shows that ITS regions have great potential as targets in molecular-based assays for the characterization and identification of fungi. Development of rapid and accurate amplification-based ITS assays to diagnose invasive fungal infections could potentially impact care and improve outcome for affected patients.

Specific detection of fusarium species in blood and tissues by a PCR technique

Fusarium species are opportunistic nosocomial pathogens that often cause fatal invasive mycoses. We designed a primer pair that amplifies by PCR a fragment of a gene coding for the rRNA of Fusarium species. The DNAs of the main Fusarium species and Neocosmospora vasinfecta but not the DNAs from 11 medically important fungi were amplified by these primers. The lower limit of detection of the PCR system was 10 fg of Fusarium solani DNA by ethidium bromide staining. To test the ability of this PCR system to detect Fusarium DNA in tissues, we developed a mouse model of disseminated fusariosis. Using the PCR, we detected Fusarium DNA in mouse tissues and in spiked human blood. Furthermore, F. solani, Fusarium moniliforme, and Fusarium oxysporum were testing by random amplified polymorphic DNA (RAPD) analysis. The bands produced by RAPD analysis were purified, cloned, and sequenced. The information was used to design primer pairs that selectively amplified one or several Fusarium species. The method developed may be useful for the rapid detection and identification of Fusarium species both from culture and from clinical samples.

Diagnosis of Fusarium keratitis in an animal model using the polymerase chain reaction

AIMS/BACKGROUND

The purpose of this study was apply the polymerase chain reaction (PCR) to develop a sensitive, specific, and rapid test to diagnose Fusarium keratitis. Fusarium is the most common cause of fungal corneal infection in some parts of the world. It is often difficult to establish that a keratitis is due to fungal infection.

METHODS

Fusarium solani keratitis was induced in three eyes of three rabbits by injection of a suspension of the fungus into the anterior corneal stroma. In one rabbit the contralateral eye served as a control. From four to 28 days after inoculation, the corneas were scraped for culture, then scraped and swabbed for PCR analysis. The PCR was performed with primers directed against a portion of the Fusarium cutinase gene, and the presence or absence of this amplified target sequence was determined by agarose gel.

RESULTS

The amplified DNA sequence was detected in 25 of 28 samples from the corneas infected with Fusarium, for a sensitivity of 89%. Only three of the 14 samples from these eyes with Fusarium keratitis were positive by culture, for a sensitivity of 21%. Seven of eight control samples were negative by the PCR based test, for a specificity of 88%.

CONCLUSION

This PCR based test holds promise of being an effective method of diagnosing Fusarium keratitis as well as Fusarium infections at other sites.

Immunohistologic identification of Aspergillus spp. and other hyaline fungi by using polyclonal fluorescent antibodies

Isolation and identification of pathogenic Aspergillus and Fusarium spp. from clinical materials provide the most accurate means for establishing a diagnosis of infections by these molds. Such efforts, however, are not always successful. Histologic diagnosis also has its limitations. In vivo the hyphae of Aspergillus and Fusarium spp. are very similar and their in situ manifestations are not pathognomonic. To improve the histologic diagnosis of infections by Aspergillus and Fusarium species, we developed polyclonal fluorescent-antibody reagents to Aspergillus fumigatus and Fusarium solani and evaluated their diagnostic utilities. Our studies revealed that A. fumigatus and F. solani share epitopes not only with one another but also with other Aspergillus and Fusarium spp. as well as with Paecilomyces lilacinus and Pseudallescheria boydii. Adsorption of the A. fumigatus conjugate with cells of Fusarium proliferatum and F. solani and F. solani antiserum with cells of Aspergillus flavus resulted in reagents that distinguished Aspergillus spp. from Fusarium spp. but that still cross-stained P. lilacinus and P. boydii. Adjunctive use of a specific P. boydii conjugate enabled the identification of Aspergillus spp., Fusarium spp., P. lilacinus, and P. boydii in formalin-fixed tissue sections from 19 humans with culture-proven cases of mycotic infection.