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

What every neuropathologist needs to know: Update on neuro infectious disease workups and consultation resources

Efficient histopathological diagnosis of central nervous system infections can be challenging but is critical for therapeutic decision making in cases for which less invasive blood or cerebrospinal fluid testing has been unrevealing. A wide variety of bacteria, fungi, viruses, and parasites can cause infections, particularly in immunocompromised individuals. Histological findings may be nonspecific or overlap with noninfectious inflammatory conditions. To minimize wasted tissue and time, a systematic approach is recommended in which: (1) relevant patient history (eg, comorbidities, travel and other exposures, and immune status) and radiological findings are reviewed, (2) a preliminary differential diagnosis based on this information and on inflammatory patterns and visualization of potential microorganisms on hematoxylin and eosin stains is generated, (3) special stains, immunohistochemistry, in situ hybridization, or molecular testing (pathogen-specific or broad-spectrum) are used for confirmation and further classification, and (4) correlation with culture results and other laboratory testing is performed to arrive at a final integrated diagnosis. Discrepancies between molecular and histological findings are often due to contamination and require careful evaluation to avoid treatment of false positives. Consultation with infectious disease pathologists or public health reference laboratories may be needed to confirm diagnoses of unusual organisms or when specialized testing is required.

Atypical Skull-Base Osteomyelitis: Comprehensive Review and Multidisciplinary Management Viewpoints

Atypical skull-base osteomyelitis is a rare but fatal disease that usually involves infection of the ethmoid, sphenoid, occipital, or temporal bones that form the skull base. Unlike typical (so-called otogenic), atypical skull-base osteomyelitis has no otogenic cause. Instead, some authors call atypical skull-base osteomyelitis sinonasal, since the infection most often originates from the nose and paranasal sinuses. Diagnosing and treating this disease is challenging. To assist in managing atypical skull-base osteomyelitis, a review of the most recent literature, with patient cases and multidisciplinary perspectives from otolaryngologists, neurosurgeons, radiologists, infectious disease specialists, pathologists, and clinical microbiologists, is provided in this paper.

Molecular Techniques for Genus and Species Determination of Fungi From Fresh and Paraffin-Embedded Formalin-Fixed Tissue in the Revised EORTC/MSGERC Definitions of Invasive Fungal Infection

The EORTC/MSGERC have revised the definitions for proven, probable, and possible fungal diseases. The tissue diagnosis subcommittee was tasked with determining how and when species can be determined from tissue in the absence of culture. The subcommittee reached a consensus decision that polymerase chain reaction (PCR) from tissue, but not immunohistochemistry or in situ hybridization, can be used for genus or species determination under the new EORTC/MSGERC guidelines, but only when fungal elements are identified by histology. Fungal elements seen in tissue samples by histopathology and identified by PCR followed by sequencing should fulfill the definition of a proven fungal infection, identified to genus/species, even in the absence of culture. This summary discusses the issues that were deliberated by the subcommittee to reach the consensus decision and outlines the criteria a laboratory should follow in order to produce data that meet the EORTC/MSGERC definitions.

Diagnostic performance of immunohistochemistry for the aspergillosis and mucormycosis

OBJECTIVE

To investigate the accuracy of immunohistochemistry (IHC) tests for distinguishing between mucormycosis and aspergillosis and compare the clinical characteristics of mucormycosis patients according to galactomannan (GM) results.

METHODS

We evaluated diagnostic performance of IHC test with tissue sections of patients with culture-proven invasive fungal infection. In addition, we conducted PCR assay with tissue sections of mucormycosis patients with positive GM results to evaluate the possibility of co-infection.

RESULTS

In culture-proven mucormycosis (n = 13) and aspergillosis (n = 20), the sensitivity and specificity of IHC test were both 100% for mucormycosis and 85% and 100%, respectively, for aspergillosis. Among the 53 patients who met the modified criteria for proven mucormycosis and had GM assay results, 24 (45%) were positive. Compared with those with negative GM results (n = 29), mucormycosis patients with positive GM results had significantly higher incidence of gastrointestinal tract infections (6/24 [25%] vs 0/29 [0%], P = .006) and were more likely to be histomorphologically diagnosed as aspergillosis (7/24 [29%] vs 2/29 [7%], P = .06). PCR assay amplified both Aspergillus- and Mucorales-specific DNA in 6 of these 24 cases.

CONCLUSIONS

Immunohistochemistry tests seem useful for compensating for the limitations of histomorphologic diagnosis in distinguishing between mucormycosis and aspergillosis. Some proven mucormycosis patients with positive GM results had histopathology consistent with aspergillosis and gastrointestinal mucormycosis. In addition, about one quarter of these patients revealed the evidence of co-infection with aspergillosis by PCR assay.

In situ hybridization for the localization of two pepino mosaic virus isolates in mixed infections

In situ hybridization (ISH) is an informative and relatively accessible technique for the localization of viral genomes in plant tissue and cells. However, simultaneous visualization of related plant viruses in mixed infections may be limited by the nucleotide similarity in the genomes and the single chromogenic detection over the same sample preparation. To address this issue, we used two Pepino mosaic virus isolates and performed ISH over consecutive serial cross-sections of paraffin-embedded leaf samples of single and mixed infected Nicotiana benthamiana plants. Moreover, the probe design was optimized to reduce cross-hybridisation, and co-localization was based on the overlapping of consecutive cross-sections from mixed infected leaves; thus, our results showed that both Pepino mosaic virus isolates co-localized in the same leaf tissue. In turn, both isolates were localized in the cytoplasm of the same cells. These results provide valuable information for studying mixed infections in plants by using a simple ISH procedure that is accessible to any pathology laboratory.

[New microbiological techniques]

Microbiological diagnostic procedures have changed rapidly in recent years. This is especially true in the field of molecular diagnostics. Classical culture-based techniques are still the gold standard in many areas; however, they are already complemented by automated and also molecular techniques to guarantee faster and better quality results. The most commonly used techniques include real-time polymerase chain reaction (RT-PCR) based systems and nucleic acid hybridization. These procedures are used most powerfully from direct patient samples or in assays to detect the presence of nonculturable or fastidious organisms. Further techniques such as DNA sequencing are not yet used routinely for urological samples and can be considered experimental. However, in conjunction with dropping prices and further technical developments, these techniques promise to be used much more in the near future. Regarding bacterial identification from culture, mass spectrometry (MALDI-TOF MS) has become the technique of choice in recent years especially in Europe. It has tremendously shortened the time to result. This is now going to be extended to antibiotic susceptibility testing. This is of paramount importance in view of ever rising antimicrobial resistance rates. Techniques described in this review offer a faster and better microbiological diagnosis. Such continuous improvements are critical especially in times of cost pressure and rising antimicrobial resistance rates. It is in our interest to provide the best possible care for patients and in this regard a good and effective communication between the laboratory and the clinician is of vital importance.

Identification of Fungal Pathogens in Tissue Samples from Patients with Proven Invasive Infection by Fluorescence In Situ Hybridization

Identification of fungal pathogens in clinical samples by hybridization with short oligonucleotide probes is increasingly used in the diagnosis of invasive fungal infections. Rapid and specific fungal identification has been documented in different diagnostic settings allowing for specific patient management. Identification of fungal pathogens in formalin-fixed, paraffin-embedded tissue samples appears to be rewarding as these materials are stored in pathology archives offering an insight into the etiology of deep fungal infections that is often not achieved by non-molecular tests. In contrast to PCR based methods, amplification of target sequences is unnecessary limiting the potential for contamination and localization within infected tissue is possible helping to distinguish between colonization and infection.

In situ hybridization for the detection of rust fungi in paraffin embedded plant tissue sections

BACKGROUND

Rust fungi are obligate pathogens with multiple life stages often including different spore types and multiple plant hosts. While individual rust pathogens are often associated with specific plants, a wide range of plant species are infected with rust fungi. To study the interactions between these important pathogenic fungi and their host plants, one must be able to differentiate fungal tissue from plant tissue. This can be accomplished using the In situ hybridization (ISH) protocol described here.

RESULTS

To validate reproducibility using the ISH protocol, samples of Chrysanthemum × morifolium infected with Puccinia horiana, Gladiolus × hortulanus infected with Uromyces transversalis and Glycine max infected with Phakopsora pachyrhizi were tested alongside uninfected leaf tissue samples. The results of these tests show that this technique clearly distinguishes between rust pathogens and their respective host plant tissues.

CONCLUSIONS

This ISH protocol is applicable to rust fungi and potentially other plant pathogenic fungi as well. It has been shown here that this protocol can be applied to pathogens from different genera of rust fungi with no background staining of plant tissue. We encourage the use of this protocol for the study of plant pathogenic fungi in paraffin embedded sections of host plant tissue.

Conidial heads (Fruiting Bodies) as a hallmark for histopathological diagnosis of angioinvasive aspergillosis

Aspergillosis is a mycosis that afflicts immunocompetent and immunocompromised hosts; among the former it exhibits different clinical pictures, and among the latter the infection renders an invasive form of the disease. The histologic diagnosis of invasive aspergillosis is somewhat challenging mostly because of some morphological similarities between other fungi. However, when present, the conidial heads are pathognomonic of aspergillosis. The authors present the case of a 68-year-old woman who was submitted to autologous hematopoietic stem cell transplantation in the pursuit of multiple myeloma treatment. The post-transplantation period was troublesome with the development of severe neutropenia, human respiratory syncytial virus pneumonia, and disseminated aspergillosis, which was suspected because of a positive serum galactomannan antigen determination, and resulted in a fatal outcome. The autopsy findings showed diffuse alveolar damage associated with angioinvasive pulmonary aspergillosis with numerous hyphae and conidial heads in the lung parenchyma histology. The authors call attention to the aid of autopsy in confirming the diagnosis of this deep mycosis, since only the research of the galactomannan antigen may be insufficient and uncertain due to its specificity and of the possibility of false-positive results.

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.

[Identification of fungal pathogens in tissue samples using fluorescence in situ hybridization]

Deep fungal infections are associated with significant mortality despite the availability of new antifungal agents. The identification of causative fungi is important to define successful antifungal therapies as agents differ in the in vitro susceptibility. Characterization of tissue morphology and cultivation from tissue provide important clues to patient management. Molecular techniques such as PCR-based assays are increasingly being used to identify agents of invasive fungal infections. However, potential contamination limits the use when ubiquitous fungi are targeted. Hybridization with fluorescently labeled probes targeting the ribosomal RNA of fungi is emerging as an alternative identification strategy. Using conserved or variable regions of the rRNA as targets, group or species-specific probes can be synthesized to identify fungal pathogens and localize them in the infectious process. These techniques have been successfully applied to deep fungal infections due to different agents in various organ samples.

Comparison between cytologic examination of fungi in bronchial washings and bronchoalveolar lavage specimens and culture: a review of 100 cases with emphasis on diagnostic pitfalls

INTRODUCTION

Microbiology culture is the "gold standard" for diagnosis of fungal infections; however, culture has a lengthy turnaround time. A more timely assessment is possible with cytology and Gomori-methamine silver (GMS) staining.

MATERIALS AND METHODS

A total of 100 respiratory tract specimens with a positive fungal Gomori-methamine silver stain and corresponding culture were selected. The cytology slides were reviewed for factors contributing to discrepant results. Specimens were classified as 2 types of variances: interpretative and sampling. Concordant diagnoses were also evaluated.

RESULTS

Eighty-two cases had fungal organisms that grew in culture. The remaining 18 cases were composed solely of fungal organisms that did not grow in culture (17 cases with Pneumocystis jirovecii; 1 case with Pityrosporum ovale). These 18 cases were excluded from the variance analysis. Thirty-three of 82 cases (40%) had concordant cytology and microbiology results, whereas 49 cases were discrepant. Variances were both sampling (41 cases) and interpretive (8 cases). Interpretive variances were predominantly Aspergillus species misinterpreted as Candida. Difficulty identifying true septate hyphae was the major contributing factor for misinterpretation.

CONCLUSIONS

Cytologic evaluation of respiratory specimens remains a useful preemptive diagnostic tool in the rapid diagnosis of fungal infection. Cytology samples significantly contribute to the diagnosis of respiratory fungi. However, interpretive variances between Aspergillus and Candida organisms are common. Awareness of the characteristic features that distinguish fungal organisms can further improve the diagnostic utility of cytology.