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

Coccidioidomycosis in Nonhuman Primates: Pathologic and Clinical Findings

Coccidioidomycosis in nonhuman primates has been sporadically reported in the literature. This study describes 22 cases of coccidioidomycosis in nonhuman primates within an endemic region, and 79 cases of coccidioidomycosis from the veterinary literature are also reviewed. The 22 cases included baboons ( n = 10), macaques ( n = 9), and chimpanzees ( n = 3). The majority died or were euthanized following episodes of dyspnea, lethargy, or neurologic and locomotion abnormalities. The lungs were most frequently involved followed by the vertebral column and abdominal organs. Microscopic examination revealed granulomatous inflammation accompanied by fungal spherules variably undergoing endosporulation. Baboons represented a large number of cases presented here and had a unique presentation with lesions in bone or thoracic organs, but none had both intrathoracic and extrathoracic lesions. Although noted in 3 cases in the literature, cutaneous infections were not observed among the 22 contemporaneous cases. Similarly, subclinical infections were only rarely observed (2 cases). This case series and review of the literature illustrates that coccidioidomycosis in nonhuman primates reflects human disease with a varied spectrum of presentations from localized lesions to disseminated disease.

Challenges in the Diagnosis of Invasive Fungal Infections in Immunocompromised Hosts

Purpose of review

The expanding population of immunocompromised patients coupled with the recognition of a growing number of different species of fungi responsible for diseases in such hosts makes the diagnosis of invasive fungal infection (IFI) a challenging task. The recent advances and challenges in the diagnosis of IFI in the setting of immunocompromised hosts are reviewed. The advantages and limitations of histopathology and the role of culture-independent methods, such as those based on the use of nucleic acids applied to fresh and formalin-fixed, paraffin-embedded sections, besides culture- and non-culture-based diagnostic methods, to obtain a timely and correct diagnosis of IFI are highlighted.

Recent findings

The therapeutic implications of identifying the genus and species of the fungus present in the specimen with the molecular diagnostics applied to tissue specimens are reviewed. No method alone is efficient in correctly identifying fungi and it is essential to combine the traditional histochemical staining with molecular methods to achieve a rapid and genus-/species-specific diagnosis of IFI.

Summary

We review the recent findings and challenges in the hystopathologic diagnosis of IFI in the setting of immunocompromised hosts. Non method alone is efficient in correctly identify fungi and pathologists should combine classic staining with molecular methods to achieve a rapid and genus/species fungal diagnosis.

Histopathology of fungal diseases of the lung

Fungal pneumonias can be a diagnostic problem. However, their recognition is important as they can pose a significant health risk, especially in the immunocompromised host. While many of these infections are accompanied by necrotizing or non-necrotizing granulomas, some might be characterized by cellular interstitial pneumonia, intra-alveolar frothy material or only minimal inflammatory change. Much of the tissue reaction is dependent on the immune status of the patient and the type of fungal organism. While many of the fungi can be identified in tissue, especially if using histochemical stains such as Grocott's Methenamine Silver (GMS) stain and/or Periodic Acid Schiff (PAS) stain, in some cases, these stains are negative and the organisms can only be identified in cultures or using special techniques such as PCR or fungal serology. Some fungi can be accurately identified in tissue based on morphologic features; others require culture for exact classification. Knowledge about immune status, geographic region and social history of the patient are helpful in identifying the fungus and, therefore, detailed clinical and travel histories are important. In this manuscript we aim to describe the most common fungal infections that occur in the lung, their morphologic features, and differential diagnoses.

Identification of fungal pathogens in Formalin-fixed, Paraffin-embedded tissue samples by molecular methods

The etiology of invasive fungal infections (IFI) is incompletely understood due to diagnostic limitations including insensitivity of cultures and failure of histopathology to discriminate between different species. This diagnostic gap precludes the optimal use of antifungals, leading to adverse patient outcomes. The identification of fungal pathogens from Formalin-fixed, Paraffin-embedded tissue (FFPE) blocks by molecular methods is emerging as an alternative approach to study the etiology of IFI. PCR assays, including species specific- and broadrange fungal tests are used with FFPE samples from patients with proven IFI. Fungal species identification is achieved in 15-90% of the samples. This heterogeneity may be explained by the samples studied. However, comparison of different studies is impaired, as controls ruling out false positive-, false negative test results or PCR inhibition are frequently not reported. Studies using in situ hybridization also vary in the clinical samples included and the targeted fungi. In addition, target sequences, the probe chemistry and the detection of hybridization signals also account for the differences in diagnostic sensitivity. Using both approaches in parallel yields additive insights, potentially leading to a superior identification of fungal etiology and awareness of the limitations of both molecular diagnostic approaches.

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.

Molecular and nonmolecular diagnostic methods for invasive fungal infections

Invasive fungal infections constitute a serious threat to an ever-growing population of immunocompromised individuals and other individuals at risk. Traditional diagnostic methods, such as histopathology and culture, which are still considered the gold standards, have low sensitivity, which underscores the need for the development of new means of detecting fungal infectious agents. Indeed, novel serologic and molecular techniques have been developed and are currently under clinical evaluation. Tests like the galactomannan antigen test for aspergillosis and the β-glucan test for invasive Candida spp. and molds, as well as other antigen and antibody tests, for Cryptococcus spp., Pneumocystis spp., and dimorphic fungi, have already been established as important diagnostic approaches and are implemented in routine clinical practice. On the other hand, PCR and other molecular approaches, such as matrix-assisted laser desorption ionization (MALDI) and fluorescence in situ hybridization (FISH), have proved promising in clinical trials but still need to undergo standardization before their clinical use can become widespread. The purpose of this review is to highlight the different diagnostic approaches that are currently utilized or under development for invasive fungal infections and to identify their performance characteristics and the challenges associated with their use.

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.

LNA probes substantially improve the detection of bacterial endosymbionts in whole mount of insects by fluorescent in-situ hybridization

Background

Detection of unculturable bacteria and their localization in the host, by fluorescent in-situ hybridization (FISH), is a powerful technique in the study of host-bacteria interaction. FISH probes are designed to target the 16 s rRNA region of the bacteria to be detected. LNA probes have recently been used in FISH studies and proven to be more efficient. To date no report has employed LNA probes for FISH detection of bacterial endosymbiont in the whole mount tissues. Further, though speculated, bacteriocytes have not been reported from males of Bemisia tabaci.

Results

In this study, we compared the efficiency in detecting bacteria by fluorescent DNA oligonucleotides versus modified probes containing Locked Nucleic Acid (LNA) substitution in their structure. We used the insect Bemisia tabaci as the experimental material since it carried simultaneous infection by two bacteria: one a primary endosymbiont, Portiera (and present in more numbers) while the other a secondary endosymbiont Arsenophonus (and present in less numbers). Thus a variation in the abundance of bacteria was expected. While detecting both the bacteria, we found a significant increase in the signal whenever LNA probes were used. However, the difference was more pronounced in detecting the secondary endosymbiont, wherein DNA probes gave weak signals when compared to LNA probes. Also, signal to noise ratio for LNA probes was higher than DNA probes. We found that LNA considerably improved sensitivity of FISH, as compared to the commonly used DNA oligonucleotide probe.

Conclusion

By employing LNA probes we could detect endosymbiotic bacteria in males, which have never been reported previously. We were able to detect bacteriocytes containing Portiera and Arsenophonus in the males of B. tabaci. Thus, employing LNA probes at optimized conditions will help to significantly improve detection of bacteria at the lowest concentration and may give a comprehensible depiction about their specific distribution within samples.

Laryngeal coccidioidomycosis with vocal fold paralysis

We present the case of a 52-year-old woman with recurrent disseminated coccidioidomycosis involving the larynx that was associated with vocal fold paralysis. The diagnosis was confirmed by histologic biopsy, and the patient had an excellent response to systemic antifungal treatment. However, her vocal fold motion did not return. We also review the current world literature.

Comparison of quantitative real time PCR with Sequencing and ribosomal RNA-FISH for the identification of fungi in formalin fixed, paraffin-embedded tissue specimens

Background

Identification of the causative agents of invasive fungal infections (IFI) is critical for guiding antifungal therapy. Cultures remain negative in a substantial number of IFI cases. Accordingly, species identification from formalin fixed, paraffin embedded (FFPE) tissue specimens by molecular methods such as fluorescence in situ hybridisation (FISH) and PCR provides an appealing approach to improve management of patients.

Methods

We designed FISH probes targeting the 28S rRNA of Aspergillus and Candida and evaluated them with type strains. Fluorescence microscopy (FM), using FISH probes and quantitative broad-range fungal PCR targeting the rRNA gene were applied to FFPE tissue specimens from patients with proven IFI in order to explore benefits and limitations of each approach.

Results

PCR followed by sequencing identified a broad spectrum of pathogenic fungi in 28 of 40 evaluable samples (70%). Hybridisation of FISH probes to fungal rRNA was documented in 19 of 40 tissue samples (47.5%), including 3 PCR negative samples with low fungal burden. The use of FISH was highly sensitive in invasive yeast infections, but less sensitive for moulds. In samples with hyphal elements, the evaluation of hybridisation was impaired due to autofluorescence of hyphae and necrotic tissue background.

Conclusions

While PCR appears to be more sensitive in identifying the causative agents of IFI, some PCR negative and FISH positive samples suggest that FISH has some potential in the rapid identification of fungi from FFPE tissue samples.

Role of histology in the diagnosis of infectious causes of granulomatous lung disease

PURPOSE OF REVIEW

Histologic examination and microbiologic cultures are the gold standards for the diagnosis of infectious granulomatous lung diseases. Although biopsies require invasive procedures, they often yield information that cannot be obtained by other methods. The aims of this article are to outline the major infections that cause granulomatous inflammation in the lung and to familiarize clinicians with the utility of histologic examination in their diagnosis.

RECENT FINDINGS

The histopathologic features of acute pulmonary histoplasmosis and granulomatous Pneumocystis pneumonia have been described in detail, the relative contributions of histology and microbiologic cultures in the diagnosis of blastomycosis have been delineated, and Cryptococcus gattii has emerged as a significant cause of granulomatous pulmonary nodules.

SUMMARY

The major infectious causes of granulomatous lung disease are mycobacteria and fungi. Histologic examination is particularly important in the diagnosis of pulmonary granulomatous infections when clinical, radiologic and serologic findings are nonspecific. Histology and microbiology play complementary but distinct roles in diagnosis. For organisms that grow slowly in cultures, histology has the additional advantage of being able to provide a rapid diagnosis.