Rapid method for detection of Aspergillus 5S ribosomal RNA using a genus-specific oligonucleotide probe

A Practical Guide to the Role of Ancillary Techniques in the Diagnosis of Infectious Agents in Fine Needle Aspiration Samples

Fine needle aspiration samples and small biopsies provide a minimally invasive diagnostic modality for mass lesions. When an infectious process is suspected based on initial evaluation, ancillary techniques can assist in making a specific diagnosis. Here we review the cytopathology that should prompt additional testing and review the availability and interpretation of special stains, immunohistochemistry, and in situ hybridization. In addition, this review addresses when special cultures may be necessary and the use of newer molecular techniques for pathogen identification.

In situ hybridization for fungal ribosomal RNA sequences in paraffin-embedded tissues using biotin-labeled locked nucleic acid probes

Ribosomal RNAs (rRNA) are conserved, abundant species-specific sequences that are used for phylogenetically classifying organisms. Due to their abundance and species specificity, rRNA sequences have been established as optimal targets for in situ hybridization (ISH). ISH for rRNA sequences using DNA oligonucleotide probes has been utilized to detect a variety of fungi in paraffin tissues. However, ISH with some oligonucleotide DNA probes produces weak signals, and applications for nucleotide modification may be useful to enhance hybridization signal. ISH with LNA probes has been shown to result in improved ISH signal. A protocol for LNA ISH with biotin-labeled LNA oligonucleotide probes is described.

In situ hybridization for rRNA sequences in anatomic pathology specimens, applications for fungal pathogen detection: a review

Fungal infections are a frequent occurrence in medical practice due to increasing numbers of immunosuppressed patients. New antifungal medications have been developed and it has become evident that different fungi require different treatments as some are intrinsically resistant to these drugs. Thus, it is imperative that pathologists recognize the limitations of histopathologic diagnosis regarding speciation of fungal infections and advocate for the use of different techniques that can help define the genus and species of the fungus present in the specimen they are studying. In this review we present the use of in situ hybridization as an important adjunct for the diagnosis of fungal diseases, the different techniques that have been used for fungal identification, and the limitations that these techniques have.

In situ hybridization for specific fungal organisms in acute invasive fungal rhinosinusitis

Acute invasive fungal rhinosinusitis (AIFRS) most commonly occurs in immunosuppressed patients. The identification of fungal subtypes is important for management, and cultures can be negative. We studied 55 specimens from 23 patients with AIFRS (Rhizopus sp, 6; Aspergillus sp, 8; Fusarium sp, 1; Alternaria sp, 1; and culture negative, 7) using in situ hybridization (ISH) with biotin-labeled oligonucleotide probes targeting Aspergillus sp, Fusarium sp, Rhizopus sp, and a sequence identified in dematiaceous fungi. Ribosomal RNA preservation was established by using a pan-fungal probe. Nucleic acid preservation was seen in 18 patients (33 specimens [60%]). ISH using the specific fungal probes highlighted the respective fungal organisms in all culture-positive cases with adequate negative controls. Of the 7 culture-negative AIFRS cases, 4 had preserved fungal sequences. Of these cases, 2 additional cases of Aspergillus and 1 additional case of dematiaceous species were identified. In our study, 60% of AIFRS cases had fungal nucleic acid preservation. ISH can effectively identify fungi in AIFRS. ISH for specific fungal pathogens may aid in species identification in specimens with negative cultures.

In situ hybridization for Coccidioides immitis 5.8S ribosomal RNA sequences in formalin-fixed, paraffin-embedded pulmonary specimens using a locked nucleic acid probe: a rapid means for identification in tissue sections

Coccidioides immitis/Coccidioides posadasii are common causes of pulmonary infection in certain geographic areas, and are highly infectious when working with culture isolates in the laboratory. Rapid techniques to accurately identify this pathogen in tissues may be of benefit for diagnosis and in limiting the exposure of laboratory personnel to this agent. Locked nucleic acids (LNA) are modified nucleotides in which a ribonucleoside is linked between the 2'-oxygen and the 4'-carbon atoms with a methylene unit. LNA oligonucleotides exhibit increased thermal stability and make excellent probes for in situ hybridization (ISH). In this study, ISH utilizing a biotin-labeled LNA probe targeting Coccidioides sp. ribosomal RNA sequences in 6 formalin-fixed, paraffin-embedded pulmonary tissue specimens from 6 patients with culture positive or histologic findings suggestive of Coccidioides sp. infection is described. The cultures of the pulmonary specimens confirmed C. immitis in 3 of 6 patients. The ISH procedure with the LNA probe was positive in all 6 cases, although the number of organisms that were highlighted varied from rare to numerous. ISH with a biotin-labeled DNA probe of the same sequence was positive in 4 of the 6 cases and the signal intensity and number of organisms was much less than that observed with the LNA probe. Negative control tissues containing a variety of different fungal pathogens including Aspergillus sp., Fusarium sp., Blastomyces dermatitidis, Candida sp, Histoplasma capsulatum, and Zygomyces did not hybridize with the LNA and DNA probes. ISH with an LNA oligonucleotide probe targeting Coccidioides sp. ribosomal RNA is useful for rapid ISH. ISH could be rapidly performed when fungal pathogens are observed in tissue but cultures are negative or have not been performed.

In situ detection of aspergillus 18s ribosomal RNA Sequences using a terminally biotinylated locked nucleic acid (LNA) probe

Locked nucleic acids (LNA) are modified nucleotides where a ribonucleoside is linked between the 2'-oxygen and the 4'-carbon atoms with a methylene unit. LNA oligonucleotides exhibit increased thermal stability toward complementary DNA and RNA with characteristically higher melting temperatures. In situ hybridization (ISH) using LNA oligonucleotide probes targeting fungal ribosomal RNA (rRNA) sequences has not been described. This study details an ISH procedure by using a biotin-labeled LNA probe targeting Aspergillus spp.18s rRNA sequences. A genus-specific 3' terminally biotin-labeled oligonucleotide probe was commercially synthesized by using a mixture of DNA (60%) and LNA (40%). A rapid, 2-hour, nonisotopic ISH procedure was developed and performed on 20 culturally proven formalin-fixed, paraffin-embedded (FFPE) cases of Aspergillus spp. By ISH, the LNA probe effectively detected Aspergillus spp. rRNA sequences in all specimens. Compared with a DNA probe with the same sequence, the LNA probe produced a stronger signal. ISH with the Aspergillus-specific LNA probe was negative on culture-proven cases of other fungal pathogens including Zygomyces and Fusarium. ISH with an LNA oligonucleotide probe targeting Aspergillus 18s rRNA sequences is useful for rapidly detecting Aspergillus spp. in paraffin-embedded tissue specimens. This test could be used when fungal pathogens are observed in tissue but cultures are negative or have not been performed. ISH with LNA probes may be useful for detecting a variety of fungal pathogens in formalin-fixed, paraffin-embedded tissue specimens.

Differentiation of Fusarium from Aspergillus species by colorimetric in situ hybridization in formalin-fixed, paraffin-embedded tissue sections using dual fluorogenic-labeled LNA probes

Fusarium and Aspergillus are 2 genera of fungal pathogens that can result in devastating disease particularly in immunosuppressed hosts. In tissue sections, these organisms can be extremely difficult to distinguish from one another. To differentiate between these 2 pathogens, a rapid (<3 hours) ribosomal RNA (rRNA) in situ hybridization (ISH) protocol using dual fluorogenic-labeled oligonucleotide probes composed of a mixture of DNA and locked nucleic acids (LNAs) was developed. This assay was able to differentiate between Aspergillus and Fusarium in formalin-fixed, paraffin-embedded tissue sections. ISH targeting rRNA can be used to identify the species of fungal pathogens in surgical pathology material and may be useful when pathogens are histologically observed but cultures are negative or have not been performed. ISH with dual-labeled LNA probes may be useful for detecting a variety of fungal pathogens in formalin-fixed, paraffin-embedded tissue specimens.

Application of in situ hybridization to tissue sections for identification of molds causing invasive fungal infection

The present article describes our studies to know the usefulness of in situ hybridization (ISH) to identify various kinds of mold observed in tissue sections and / or cytological preparations from the lesions of patients with invasive fungal infection. To establish the precise procedure for ISH in formalin-fixed and paraffin-embedded sections, various pretreatments were attempted. The condition finally chosen is written here providing a favorable outcome regarding to both intensity and specificity of signals on outline of molds observed in the tissue sections when specimens were treated with both heat and proteinase K and, solutions were adjusted to higher pH value.Therefore, usefulness of promising probes, two each DNA and peptide nucleic acid (PNA) were verified with a favorable pretreatment condition, using lungs of mice experimentally infected and / or those obtained from autopsies with invasive mold infection. As the result, DNA probes targeting alkaline proteinase (ALP) gene and retrotransposon Afut-1 gene of Aspergillus fumigatus showed specific signal intensity for the Aspergillus species and A. fumigatus, respectively. PNA probes for Candida albicans and the Fusarium species also showed satisfactory specificity. We wish to emphasize that ISH can be a valuable tool to identify medically important molds in formalin-fixed and paraffin-embedded tissue sections or cytological preparations.

[Deep seated mycosis diagnosed at hospital pathology division]

A pathological diagnosis can be a decisive diagnosis for deep-seated mycosis. HE stain is used to look for structural changes of the infected lesion and then various special stains are used to visualize the fungus in sections. When viability of the fungus is low, it is faintly stained with HE or PAS. Grocott stain can clearly demonstrate the fungus regardless of viability. Overstaining and understaining sometimes occur. Grocott stain is not suitable to detect structural changes of an infected lesion. Cell walls of Cryptococcus and dematiaceous fungi are stained brown with Fontana-Masson stain because of the existence of melanin. However, it is noteworthy that some Aspergillus and zygomycetes also turn brown with this stain. Fungiflora Y with a fluorescence microscope can readily demonstrate most fungal hyphae except zygomycetes. Immunohistochemistry with antibody against various fungi and in situ hybridization are useful to confirm a fungal genus on paraffin sections. Furthermore, probes to detect specific species of Aspergillus for in situ hybridization are now available.

The use of MUC5B antibody in identifying the fungal type of fungal sinusitis

Fungal sinusitis is an opportunistic fungal infection. Candida albicans, Aspergillus spp, and Mucorales, the most common pathogenic fungi, differ in both prognosis and therapy. Early diagnosis and differentiation between the subtypes therefore are pivotal for adequate treatment. This report describes a diagnostic immunohistochemical method that is able to distinguish these types of fungi. Formalin-fixed paraffin-embedded blocks of 89 fungal sinusitis specimens (12 C albicans, 52 Aspergillus spp, and 25 Mucorales) and 21 cultures (5 C albicans, 11 Aspergillus spp, and 5 Mucorales) were stained with MUC2, MUC5AC, and MUC5B antibodies. The immunohistochemical staining results of paraffin-embedded samples for MUC5B were successful in 100% and 92.3% of the C albicans and Aspergillus spp samples, respectively. Only 4.0% of the Mucorales parafin sections were found positive, demonstrating a significant difference in detection from C albicans and Aspergillus spp (P < .001). MUC5B expressions for cultures showed that it stained 100% and 90.9% for C albicans and Aspergillus spp, respectively, but negative for Mucorales. The expressions of MUC2 and MUC5AC for both paraffin-embedded samples and cultures were negative. The present study demonstrates the ability of an MUC5B antibody to distinguish C albicans and Aspergillus spp from Mucorales and its use as a diagnostic tool in fungal sinusitis.

Fungal infections of the spine

Fungal infections of the spine are relatively uncommon. Fungi such as Coccidioides immitis and Blastomyces dermatitidis are limited to specific geographical areas whereas cryptococcus, candida, and aspergillus are found worldwide. Candida and aspergillus are normal commensals of the body and produce disease in susceptible organisms when they gain access to the vascular system through intravenous lines, during implantation of prosthetic devices, or during surgery. For the other fungi, spinal involvement usually is the result of hematogenous or direct spread of organisms from an initial pulmonary source of infection. Involvement of the vertebral bodies can lead to vertebral compression fractures and gross deformity of the spine. Spread of infection along the anterior longitudinal ligament can lead to psoas or paravertebral abscesses. Early recognition of the disease requires a high index of suspicion, proper travel history, and a detailed physical examination. Treatment relies on the prompt institution of appropriate pharmacotherapy and constant monitoring of clinical progress. Resistance to medical therapy, spinal instability, and neurologic deficits are indications for débridement and stabilization with spinal fusion. Prognosis depends on the premorbid state of the patient, the type of fungal organism, and the timing of treatment.

LEVEL OF EVIDENCE

Level V (expert opinion). Please see the Guidelines for Authors for a complete description of levels of evidence.

Validation and Clinical Application of Molecular Methods for the Identification of Molds in Tissue

BACKGROUND

Invasive fungal infections due to less-common molds are an increasing problem, and accurate diagnosis is difficult.

METHODS

We used our previously established molecular method, which allows species identification of molds in histological tissue sections, to test sequential specimens from 56 patients with invasive fungal infections who were treated at our institution from 1982 to 2000.

RESULTS

The validity of the method was demonstrated with the establishment of a molecular diagnosis in 52 cases (93%). Confirmation of the causative organism was made in all cases in which a mold had been cultured from the tissue specimen. Less-common molds were identified in 7% of cases and appear to be an increasing problem.

CONCLUSIONS

Our previously established method has proven to be of value in determining the incidence of invasive infection caused by less-common molds. Institutions should continue to pursue diagnosis of invasive fungal infections by means of tissue culture and microbiologic analysis.

Rapid differentiation of Aspergillus species from other medically important opportunistic molds and yeasts by PCR-enzyme immunoassay

We developed a PCR-based assay to differentiate medically important species of Aspergillus from one another and from other opportunistic molds and yeasts by employing universal, fungus-specific primers and DNA probes in an enzyme immunoassay format (PCR-EIA). Oligonucleotide probes, directed to the internal transcribed spacer 2 region of ribosomal DNA from Aspergillus flavus, Aspergillus fumigatus, Aspergillus nidulans, Aspergillus niger, Aspergillus terreus, Aspergillus ustus, and Aspergillus versicolor, differentiated 41 isolates (3 to 9 each of the respective species; P < 0.001) in a PCR-EIA detection matrix and gave no false-positive reactions with 33 species of Acremonium, Exophiala, Candida, Fusarium, Mucor, Paecilomyces, Penicillium, Rhizopus, Scedosporium, Sporothrix, or other aspergilli tested. A single DNA probe to detect all seven of the most medically important Aspergillus species (A. flavus, A. fumigatus, A. nidulans, A. niger, A. terreus, A. ustus, and A. versicolor) was also designed. Identification of Aspergillus species was accomplished within a single day by the PCR-EIA, and as little as 0.5 pg of fungal DNA could be detected by this system. In addition, fungal DNA extracted from tissues of experimentally infected rabbits was successfully amplified and identified using the PCR-EIA system. This method is simple, rapid, and sensitive for the identification of medically important Aspergillus species and for their differentiation from other opportunistic fungi.

Immunoproliferative small intestinal disease associated with Campylobacter jejuni

BACKGROUND

Immunoproliferative small intestinal disease (also known as alpha chain disease) is a form of lymphoma that arises in small intestinal mucosa-associated lymphoid tissue (MALT) and is associated with the expression of a monotypic truncated immunoglobulin alpha heavy chain without an associated light chain. Early-stage disease responds to antibiotics, suggesting a bacterial origin. We attempted to identify a causative agent.

METHODS

We performed polymerase chain reaction (PCR), DNA sequencing, fluorescence in situ hybridization, and immunohistochemical studies on intestinal-biopsy specimens from a series of patients with immunoproliferative small intestinal disease.

RESULTS

Analysis of frozen intestinal tissue obtained from an index patient with immunoproliferative small intestinal disease who had a dramatic response to antibiotics revealed the presence of Campylobacter jejuni. A follow-up retrospective analysis of archival intestinal-biopsy specimens disclosed campylobacter species in four of six additional patients with immunoproliferative small intestinal disease.

CONCLUSIONS

These results indicate that campylobacter and immunoproliferative small intestinal disease are associated and that C. jejuni should be added to the growing list of human pathogens responsible for immunoproliferative states.

In situ hybridization for the differentiation of Aspergillus, Fusarium, and Pseudallescheria species in tissue section

Identification of fungi in tissue sections can be difficult. In particular, species of Aspergillus, Fusarium, and Pseudallescheria all appear as septate, branched hyphae. However, their differentiation can have significant clinical implications, as the latter two groups are often resistant to commonly used antifungal agents. In situ hybridization may assist in rapidly distinguishing these organisms in the absence of available culture. Oligonucleotide DNA probes were directed against the 5S, 18S, or 28S rRNA sequences of three groups of fungi with a high degree of specificity for each. Probes were tested on 26 formalin-fixed, paraffin-embedded tissue specimens, each with culture-proven involvement by one of these organisms: Fusarium species, n = 12; Pseudallescheria boydii, n = 5; Aspergillus species, n = 9 ( probe set validated in an earlier study). Accuracy of both ISH and morphology was compared with culture. Morphologic examination (GMS and PAS) showed a greater sensitivity in detecting fungi (100%) as compared with in situ hybridization (84.6%). When detected, however, DNA probes allowed definitive identification of organisms. While there was no ability to distinguish between the three groups of organisms by morphologic features, ISH probes showed 100% positive predictive value (PPV, 19/19 organisms identified correctly). No cross-reactivity was observed when the probes were tested against other genera (100% specificity). Furthermore, the use of ISH allowed the detection of mixed fungal infections involving multiple organism types in two cases, demonstrating another advantage over morphology. In situ hybridization, directed against rRNA sequences, provides a rapid and accurate technique for distinguishing commonly encountered, nonpigmented filamentous fungi in histologic sections. While less sensitive than morphology, ISH is highly accurate and may help to distinguish between organisms that have similar or identical morphologic features by light microscopy.

New molecular methods to study gene functions in Candida infections

Candida albicans has become a model system for human pathogenic fungi in clinical research, mainly due to the increasing number of Candida infections. Molecular techniques to study C. albicans virulence properties have been improved over the last few years, despite difficulties in genetic manipulation of this fungus. Some of the recent achievements from our own laboratory or from other groups are described in this article. The molecular analysis of the recently identified ATP-dependent transporter Mlt1 using the green fluorescent protein (GFP) as reporter for protein localization and the dominant MPAR gene as a selection marker for gene inactivation provides an example for the study of gene functions in C. albicans.

Current status of nonculture methods for diagnosis of invasive fungal infections

The incidence of invasive fungal infections has increased dramatically in recent decades, especially among immunocompromised patients. However, the diagnosis of these infections in a timely fashion is often very difficult. Conventional microbiologic and histopathologic approaches generally are neither sensitive nor specific, and they often do not detect invasive fungal infection until late in the course of disease. Since early diagnosis may guide appropriate treatment and prevent mortality, there has been considerable interest in developing nonculture approaches to diagnosing fungal infections. These approaches include detection of specific host immune responses to fungal antigens, detection of specific macromolecular antigens using immunologic reagents, amplification and detection of specific fungal nucleic acid sequences, and detection and quantitation of specific fungal metabolite products. This work reviews the current status and recent developments as well as problems in the design of nonculture diagnostic methods for invasive fungal infections.

In situ hybridization for the identification of filamentous fungi in tissue section

Identification of fungi in tissue sections can be difficult because of limited biopsy tissue with only a few organisms present, or mycelial elements may be the only forms present, rendering common organism types indistinguishable from one another. In situ hybridization may assist in the rapid and accurate identification of such fungi. In this study, DNA probes were directed against the 5S or 18S ribosomal RNA sequences of three groups of fungi with a high degree of specificity for each. Two of the three, Aspergillus and Zygomycetes species, are usually seen in tissue purely in their hyphal forms. The third, Candida species is seen less commonly as predominantly mycelial elements. Probes were tested on 61 formalin-fixed, paraffin-embedded tissue specimens, each with culture-proven involvement by one of these organisms (Candida species, n = 21; Aspergillus species, n = 27; Zygomycetes, n = 13). Accuracy of both in situ hybridization (ISH) and morphology, based on the examination of Grocott methanamine silver (GMS)- and periodic acid-Schiff (PAS)-stained slides, was compared with culture. The results showed that morphologic examination (GMS and PAS) showed a slightly greater sensitivity in detecting the presence of fungi (98%) compared with in situ hybridization (95%). DNA probes, however, were more accurate in correctly identifying those organisms present. Although ISH specific probes showed 97% positive predictive value (PPV), examination of GMS-and PAS-stained slides had an 86% PPV when compared with culture-based identification methods. These results show that ISH, directed against ribosomal RNA, provides a rapid and accurate technique for the identification of mycelial fungal organisms in histologic tissue sections. Its primary use lies in the ability to accurately distinguish between organisms that have similar or identical morphologic features by light microscopy.

In situ hybridization for the identification of yeastlike organisms in tissue section

The identification of yeast and yeastlike organisms in tissue sections can be very difficult. Biopsy tissues may be limited, with only occasional organisms present. In addition, several common species have overlapping histologic features. Deoxyribonucleic acid probes were designed to detect both the 18S and 28S ribosomal ribonucleic acid sequences of five fungal organisms with a high degree of specificity for each fungus. Each of these organisms--Blastomyces dermatitidis, Coccidioides immitis, Cryptococcus neoformans, Histoplasma capsulatum, and Sporothrix schenckii--can be manifested histologically as round, yeastlike structures, often within a similar size range. Probes were tested against 98 archived, formalin-fixed, paraffin-embedded tissue specimens, each of which had culture-proved involvement by one of these organisms. Assessment of accuracy was based on the presence of yeastlike organisms in consecutive Grocott's methanemine silver (GMS)-stained tissue sections, and agreement with culture results. The results indicated that GMS had a greater overall sensitivity in detecting fungal organisms (95.9%) compared with in situ hybridization (ISH; 82.7%). ISH with oligonucleotide deoxyribonucleic acid probes, however, was more specific, with all species-specific probes yielding 100% specificity (compared with 96.2-100% specificity based on morphology alone). ISH also had a higher positive predictive value (100% in all cases) compared with GMS (83.3-100%). In addition, four cases with rare organisms present (4.1% of cases tested) were detected by ISH but not by GMS staining. These results show that ISH, directed against ribosomal ribonucleic acid, provides a rapid, accurate technique for the identification of yeastlike organisms in histologic tissue sections. Its primary strength lies in the ability to speciate organisms accurately that are too few or atypical to identify based solely on morphologic features.

Immunochemical detection of molds: a review

Molds are widely distributed in nature and cause deterioration of foods and feeds. Their mycotoxins can adversely affect human and animal health. Suitable assays for molds, therefore, are required to implement control and regulatory strategies and to develop appropriate feeding regimens for mold-infested feeds. Many different types of mold assays have been used, most of which are not reproducible or accurate. However, the immunoassays, particularly enzyme-linked immunosorbent assays (ELISAs), can be especially useful. Among these, assays that detect the water-soluble extracellular secretions of fungi, the exoantigens, are generally able to detect fungi at the genus or species level, whereas the heat-stable polysaccharides tend to be specific for one or more genus of fungi. Several species and genus (genera)-specific ELISAs have been developed using monoclonal or polyclonal antibodies against exoantigens and heat-stable polysaccharides from a wide range of fungi, including Aspergillus, Penicillium, and Fusarium species. Other assays have been developed that nonspecifically detect mold in food or feed, some using antibodies against a mixture of antigens from different fungi. These assays are highly sensitive, are easy to perform, and provide an index of the amount of mold present in the sample. Further refinement of these assays should facilitate their widespread use by food and feed processors, regulatory agencies, taxonomists, and research scientists.

Detection of Aspergillus ribosomal RNA using biotinylated oligonucleotide probes

Aspergillosis continues to be a devastating disease entity that results in significant mortality in immunosuppressed patients. Rapid diagnosis is often required to initiate appropriate therapy. Although the histopathologist may be able to visualize fungal organisms in tissue specimens, the histology of Aspergillus species may overlap with a variety of fungi, so diagnosis often relies on fungal cultures that can take weeks to complete. Recently, an in situ hybridization assay targeting Aspergillus 5S ribosomal RNA (rRNA) was reported. This assay proved to be useful when fungal cultures were negative or not performed but when fungi compatible with Aspergillus species were identified in tissue sections. That study was performed to compare the probe described in the previous study (5S-1 probe) with two other probes specific for Aspergillus. Two customly designed 21- and 23-base oligonucleotide probes complementary to 5S (5S-2 probe) and 18S (18S-1 probe) rRNA of Aspergillus were synthesized and labeled with multiple biotin moieties at the 3' termini. By GenBank analysis, the sequence of the 18S-1 probe was shown to have 90% to 100% homology to Aspergillus fumigatus group, Aspergillus flavus, Aspergillus niger, Aspergillus terreus, Aspergillus parasiticus, Aspergillus tamarii, and Aspergillus glaucus group; the 5S-2 probe was homologous to Aspergillus flavus, Aspergillus niger, Aspergillus nidulans, Aspergillus awamori, and Aspergillus wentii. In situ hybridization was performed on 43 cases of Aspergillus infection including 41 localized aspergillomas in the lung, brain, sinonasal tract, and ear, and 2 cases of invasive aspergillosis involving pleura and soft tissue of the scapular region. The results were compared with those obtained using a previously reported 5S-1 probe. In situ hybridization was positive in 38, 38, and 40 cases with the 5S-1, 5S-2, and 18S-1 probes, respectively. The 18S-1 probe was most useful because of a wider detection spectrum. In situ hybridization for Aspergillus rRNA provides a useful means for rapidly and accurately identifying Aspergillus in tissues and may be useful if fungal organisms suggestive of Aspergillus species are present but if cultures are negative or have not been performed.

In situ hybridization for Aspergillus and Penicillium in allergic fungal sinusitis: a rapid means of speciating fungal pathogens in tissues

Allergic fungal sinusitis (AFS) is a serious form of sinonasal fungal disease that is commonly associated with Aspergillus or Dematiaceous fungi. This study was performed to determine the incidence of Aspergillus or Penicillium in AFS by using in situ hybridization (ISH) for Aspergillus and Penicillium ribosomal RNA (rRNA). The Fontana-Masson melanin stain (FMMS) was also used to detect pigmented fungi (A. niger and Dematiaceous fungi). ISH was performed on 26 patients: 17 AFS cases with histologic evidence of fungi, 5 AFS cases without histologic evidence of fungi, 3 cases of invasive fungal sinusitis (IFS), and 1 case of fungus ball. Nine AFS specimens with histologic evidence of fungi were ISH positive. Positivity was also noted in two of three IFS cases, while no staining was seen in the fungus ball and in six AFS specimens without fungi demonstrable by silver stains. Six ISH-positive cases were FMMS positive, suggesting A. niger. Five ISH-negative AFS specimens were FMMS positive, suggesting Dematiaceous fungi. In summary, many AFS patients in our institution demonstrate Aspergillus/Penicillium organisms. Ancillary techniques may help identify fungi responsible for AFS if cultures are negative or not performed. ISH for rRNA is a useful means for rapidly speciating fungi in human tissues.

Pulmonary tuberculosis associated with invasive pseudallescheriasis

A 54-year-old woman with pulmonary tuberculosis developed pneumonia caused by Scedosporium apiospermum, the asexual stage of the fungus Pseudallescheria boydii. Mycobacterium tuberculosis and P boydii were cultured in BAL fluid. The patient cleaned swimming pools in a spa health resort and was highly exposed to fungal conidia. She was successfully treated with antituberculosis drugs, miconazole nitrate and ketoconazole, leading to remission of her pulmonary infection. Invasive pulmonary pseudallescheriasis associated with tuberculosis is an unusual finding, especially in an immunocompetent individual.

Simple detection of the 5S ribosomal RNA of Pneumocystis carinii using in situ hybridisation

AIMS

To investigate the effectiveness of digoxigenin incorporated double stranded DNA probes produced by the polymerase chain reaction (PCR), for the detection of Pneumocystis carinii, using in situ hybridisation (ISH).

METHODS

Formalin fixed, paraffin wax embedded sections of 26 human lung samples from 11 patients with P carinii pneumonia (PCP), and 15 with various types of fungal and viral pneumonia, were obtained during necropsy or transbronchial lung biopsy. Three additional PCP induced rat lung samples were also tested. PCR probes were prepared using the digoxigenin labelling mixture, and they were amplified from the DNA of a PCP induced rat lung after administration of dexamethasone, on the basis that 5S ribosomal RNA sequences are identical in human and rat P carinii. ISH was performed using this probe, and visualised using the digoxigenin nucleic acid detection kit. An immunohistochemical study using anti-human Pneumocystis monoclonal antibody was also carried out in parallel.

RESULTS

ISH positively stained eight (of eight) lung necropsy specimens from patients with PCP, three (of three) transbronchial lung biopsy specimens from patients with PCP, and none of the three PCP induced rat lung specimens. In contrast, none of the specimens from patients with pneumonia caused by Aspergillus sp (n = 5), Candida sp (n = 4), Cryptococcus sp (n = 2), mucormycosis (n = 2), or cytomegalovirus (n = 2) were positive on ISH or immunohistochemistry.

CONCLUSIONS

Using a digoxigenin labelled PCR probe for the entire 5S rRNA sequence in conjunction with conventional staining, ISH is highly reactive and specific for the diagnosis of PCP.

Detection of Pneumocystis carinii by in situ hybridization in the lungs of immunosuppressed rats

In situ hybridization was performed to detect rat Pneumocystis carinii in the lung sections. Rats were immunosuppressed by weekly subcutaneous injection of 10 mg/kg methylprednisolone. On the 6th, 8th and 9th week of immunosuppression, the lungs were removed and fixed in 10% neutral formalin. A 22 base oligonucleotide probe complementary to P. carinii 5S ribosomal RNA was commercially synthesized and its 3' terminal was labeled with biotin. In situ hybridization was performed utilizing manual capillary action technology on the Microprobe system. P. carinii were detected along the luminal surface of alveolar pneumocytes, in exudate of alveolar cavities, and also in secretory material of bronchioles. In the 6th week group, positive reaction was observed focally in the peripheral region of the lung sections, but the reaction was observed diffusely in the 8th or 9th week groups. In comparison with Grocott's methenamine silver stain, in situ hybridization technique can detect the organism rapidly, and can detect trophic forms very well. Furthermore, no nonspecific reaction with other pathogenic fungi and protozoa was recognized. Therefore, in situ hybridization can be a good technique to detect P. carinii in the lungs of infected rats.

The spectrum of orbital aspergillosis: a clinicopathological review

Orbital aspergillosis is an uncommon but serious infection that may first present to the ophthalmologist. Usually arising from the paranasal sinuses, it may present in manifold ways within the orbit. Some presentations, such as optic nerve involvement, can respond to systemic corticosteroids, leading to delays in diagnosis and possibly iatrogenic potentiation of the infectious process. In this review, pertinent clinical and radiographic findings are discussed, and the literature is summarized. Classic approaches to therapy include local treatment, debridement, and systemic amphotericin B. We review novel approaches to treating orbital aspergillosis and detail a flow-chart for its management. Four patients from the spectrum of orbital aspergillosis are also described: initially presenting as an infection of an exenteration socket, a complex dacryocystitis, and optic nerve tumor, and post-operative periorbital swelling. Physicians should be familiar with the clinical spectrum of disease and the variable presentation of this infection, as early diagnosis and rapid institution of appropriate therapy are crucial elements in the management of invasive aspergillosis. In the neutropenic or otherwise immunocompromised patient, a high index of suspicion must be maintained as delays in diagnosis of fulminant aspergillosis may lead to overwhelming and rapidly progressive infection. Obtaining adequate diagnostic material for pathological and microbiological examination is critical. Newer methods of therapy, particularly itraconazole and liposomal amphotericin B, may be beneficial in selected patients.

Universal fungus-specific primer systems and group-specific hybridization oligonucleotides for 18S rDNA

We designed two primer systems that amplify a fragment of the gene coding for the small ribosomal subunit (18S rRNA). A broadly reactive, yet fungus-specific, primer cocktail comprises two previously published primers, TR1 and TR2, which specifically amplify dermatophytes, and two newly designed primers, CA1 and AF2, which specifically amplify Candida and Aspergillus respectively. This primer cocktail amplifies a DNA fragment of approximately 578 basepairs (bp) in length (from position 838 to 1415), which contains variable, possibly species-specific regions (V5, partly V7). Another newly designed primer, UF1 (universal fungal primer 1), along with the eukaryotic primer S3 amplifies a 926-bp fragment (from position 263 to 1188) that includes the variable regions V3, V4 and V5. Both primer systems amplified DNA from Saccharomyces cerevisiae, Candida albicans, Cryptococcus neoformans, Aspergillus fumigatus, Penicillium marneffei, Fusarium oxysporum and Trichophyton mentagrophytes, but not the DNA from Prototheca zopfii, Escherichia coli or humans. The previously published oligonucleotides TR and HC, which are specific for dermatophytes and Histoplasma respectively, and the newly designed group-specific oligonucleotides, CA and AF, hybridized with T. mentagrophytes, Histoplasma capsulatum, C. albicans and A. fumigatus respectively, but not with the other six fungi or with the three controls.

The pathology of fungal disease in the lung

The gross and histological appearance of pulmonary mycotic disease is rarely pathognomonic for a particular entity. Tissue obtained through an invasive procedure is usually necessary for a specific diagnosis. Pathological diagnosis is directed by the pattern of inflammation and based on the morphological identification of fungi. The interventional radiologist plays a critical role in the diagnosis of pulmonary mycoses by obtaining additional material for culture. An open and inquisitive collaboration between the radiologist and pathologist can improve diagnostic accuracy for both specialists.