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

Detection of Gram-positive and Gram-negative bacteria in brain abscesses by 16S rRNA in situ hybridization

In situ hybridization (ISH) staining of bacterial 16S ribosomal RNA (rRNA) is an alternative to standard histological stains (eg, Gram, Warthin-Starry), and may improve the diagnosis of bacterial brain abscesses. To evaluate the utility of 16S rRNA ISH, a 10-year retrospective cohort was assembled from a large academic medical center. Results of histological stains, cultures, and 16S rRNA sequencing were extracted from reports, and new Gram and 16S rRNA ISH stains were performed. Histologically identifiable bacteria were present in 40/63 (63%) cases and 38/57 (67%) were associated with positive cultures. Overall, 16S rRNA ISH was positive in 18/63 (29%) cases, including 16/37 (43%) with positive Gram stains, 12/38 (32%) positive by culture, and 4/8 (50%) positive by sequencing. 16S rRNA ISH highlighted bacteria in 14/40 (35%) cases with Gram-positive organisms and 9/17 (53%) with Gram-negative organisms (including 6 polymicrobial cases). Compared to a composite gold standard of Gram stain and culture, the sensitivity and specificity of 16S rRNA ISH were 35% and 93%, respectively. While sensitivity is relatively low, 16S rRNA ISH may be useful for distinguishing real organisms from artifacts and for identifying brain abscess cases suitable for 16S rRNA sequencing.

The clinical laboratory evolution in coccidioidomycosis detection: Future perspectives

Coccidioidomycosis is a systemic disease caused by the fungi Coccidioides immitis and C. posadasii. It is a prevalent disease in arid regions with high temperatures and low precipitations in America. Coccidioidomycosis is a highly endemic disease of US-Mexico border states but commonly underdiagnosed. The diagnosis of coccidiomycosis is not easy due to the lack of specific symptoms; it is usually an integral approach, including clinical laboratory tests as an essential part of the diagnosis. Nevertheless, despite various laboratory tests available, affordability can be a limitation, mainly in developing countries. This review's objectives are 1) to learn the different laboratory approaches that arose and their application for clinical diagnosis; 2) to discuss their advantages and weaknesses, and finally, 3) propose what is on the horizon for future advances in clinical laboratory diagnosis of coccidioidomycosis. It has been a long way in laboratory tests evolution to detect coccidioidomycosis from tissue microscopy to Real-Time PCR. However, there is a delay in technology adoption for Coccidioides spp. detection in the clinical laboratory. The molecular Point of Care Testing (POCT) technology has reached us in our trench while research in PCR variants stills on-going. None of the currently existing scientific literature in coccidioidomycosis research has mentioned it. However, this trend in infectious and non-infectious disease diagnosis will continue in that way in order to offer better options for an easy and fast diagnosis. Undoubtedly, the implementation of molecular POCT for Coccidioides spp. would save resources in health care attention and improve access to diagnostic tools.

Clinical Significance and Histologic Characterization of Histoplasma Granulomas

OBJECTIVES

To clarify the clinical significance and degree of resolution (ie, grade) of Histoplasma granulomas in routinely reviewed surgical pathology specimens and the clinical outcomes of patients with this diagnosis, with an emphasis on those not receiving antifungal therapy.

METHODS

We performed a retrospective medical record, laboratory data, and surgical pathology slide review of patients with Histoplasma granulomas following institutional review board approval.

RESULTS

Clinical, pathologic, and laboratory data from 62 patients with Histoplasma granulomas were available for review. Of these, 1 of 19 (5%) fungal cultures, 4 of 12 (33%) fungal serologic studies, 0 of 9 Histoplasma urinary antigen tests, and 0 of 2 Histoplasma serum antigen tests were positive. All but 3 of the Histoplasma granulomas were either in the resolving (grade 2) or resolved (grade 3) stage of resolution. None of the patients, including those who did not receive antifungal therapy after the histologic diagnosis, developed progressive or disseminated histoplasmosis.

CONCLUSIONS

These findings, which are supportive of clinical guidelines, suggest that patients with old, hyalinized Histoplasma granulomas do not benefit from further laboratory studies or antifungal therapy. The proposed grading of Histoplasma granulomas informs clinicians of the stage of resolution of an excised lesion, which informs therapeutic decisions and thus is recommended.

Comparative aspects of laboratory testing for the detection of Toxoplasma gondii and its differentiation from Neospora caninum as the etiologic agent of ovine abortion

Histologic examination of aborted material is an essential component in the diagnosis of ovine toxoplasmosis. However, the detection of Toxoplasma gondii in histologic sections, and its differentiation from the closely related protozoan Neospora caninum, is challenging. We developed a chromogenic in situ hybridization (ISH) assay for the identification of T. gondii in paraffin-embedded tissue samples. We examined retrospectively the archived placental tissue of 200 sheep abortion submissions for the presence of T. gondii by immunohistochemistry (IHC), ISH, and real-time PCR (rtPCR). All placental samples that tested positive for T. gondii by rtPCR (9 of 200) were also positive by IHC, with inconclusive IHC staining in an additional 7 rtPCR-negative cases. Further testing for N. caninum of all 200 placentas by rtPCR revealed 7 Neospora-positive cases. T. gondii ISH was positive in 4 of 9 IHC-positive samples and 1 of the 7 N. caninum rtPCR-positive samples. Real-time PCR was used as the reference standard for specificity and sensitivity calculations regarding placenta samples. Specificity of ISH and IHC was 99% and 96-100%, respectively. The sensitivity of ISH (44%) was quite low compared to IHC (100%). The exclusive use of ISH for the detection of T. gondii, and thus for the diagnosis of ovine toxoplasmosis, was not acceptable. However, combined with rtPCR, both ISH and IHC can be useful detection methods to improve histologic evaluation by visualizing the parasite within tissue sections.

The utility of real-time polymerase chain reaction in detecting Coccidioides immitis among clinical specimens in the Central California San Joaquin Valley

Coccidioidomycosis, the fungal infection caused by dimorphic Coccidioides species, is typically diagnosed by histopathologic identification of spherules, by culture, or by serology. These tests are reliable but time-intensive, delaying diagnosis and treatment. Rapid real-time polymerase chain reaction (RT-PCR) can be performed and was validated to identify Coccidioides immitis using an in-house developed assay for the Becton Dickinson molecular instrument (BD MAXTM). These studies were performed using patient samples that had been shown to be positive on previously set up fungal cultures. To evaluate this new RT-PCR test in the clinical setting, we conducted a retrospective chart review of patients (N = 1160) who underwent Coccidioides PCR (Cocci PCR) on clinical samples between March 1, 2014, and Dec 31, 2016. We abstracted clinical, microbiologic, serologic, radiographic, treatment, and follow-up data. Specimens of cerebrospinal fluid (CSF), bronchioalveolar lavage fluid (BAL), lung tissue biopsy (LTB), sputum, and pleural fluid were evaluated to determine sensitivity and specificity. Of the 113 specimens that tested positive for Cocci PCR, all had clinical disease defined by traditional clinical criteria, yielding 100% specificity. Overall sensitivity was 74% versus 46% for fungal culture and was available in 4 hours rather than 1-2 weeks. Sensitivities varied by source material and clinical setting. CSF had a sensitivity of 59%, BAL for acute pneumonia 91%, sputum for acute pneumonia 94%, pleural fluid 86%, but LTB for lung nodules only 44%. Overall positive predictive value (PPV) was 100%, while negative predictive value (NPV) was 96%, but again this varied by specimen and clinical setting. Our experience with clinical testing of >1160 specimens over 2-3 years shows we can utilize this technology to improve our ability to diagnose disease but that the sensitivity varies by specimen source and clinical setting.

In situ hybridization: Introduction to techniques, applications and pitfalls in the performance and interpretation of assays

In situ hybridization (ISH) has become a common laboratory technique used for the analysis of gene expression and for the localization of specific DNA and RNA molecules in cells. Many different methods of performing ISH have been described. These techniques have evolved into important tools in basic scientific research and in clinical diagnoses. One of the goals of ISH is to localize gene sequences in situ and to visualize the products within cells while preserving cell integrity. This allows for meaningful anatomical and histological interpretation of the localized product(s) within heterogeneous tissues. Because of the possibility of false positive and false negative results that may occur with ISH assays, familiarity with the pathophysiology of the molecules that are analyzed and the cellular processes involved as well as with limitations of the assays can help to avoid erroneous diagnoses with clinical specimens.

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.

A case of pulmonary blastomycosis in a common eland (Taurotragus oryx)

This case report describes for the first time pulmonary blastomycosis in a captive common eland (Taurotragus oryx). The animal has been in captivity for over 14 years and the clinical signs observed before death were non-specific. The carcass was examined grossly and histologically using special stains. There were yellowish, firm and gritty nodules of varying sizes (0.5–2 cm in diameter) on the pleura, in the lung, mediastinal lymph nodes and pericardium. The nodules showed pyogranulomatous inflammation and broad based budding yeast (PAS, Giemsa positive and ZN negative) consistent with Blastomyces dermatitidis. Regular screening of soil and environment including animals in captivity should be encouraged to avert possible spread of the mold in favourable conditions. Public awareness should be improved on fungal diseases.

Lung Infections

A review of pulmonary infections of all types with diagnostic and morphological features.

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.

Detection of Pneumocystis infections by in situ hybridization in lung samples of Austrian pigs with interstitial pneumonia

Pneumocystis carinii f. sp. suis is a fungus multiplying in the respiratory tract of pigs which occasionally is associated with interstitial pneumonia. Identification of Pneumocystis in tissue samples is considered difficult and there are only scarce data on its occurrence in European pigs. This investigation presents an in situ hybridization (ISH) procedure for identification of Pneumocystis spp. in paraffin wax embedded tissue samples and its application for labeling the agent in lung samples of pigs with interstitial pneumonia. Thirty-two out of 100 lung samples from pigs on Austrian farms were identified as positive, five of them with multiple, 12 with moderate and 15 with few organisms but Grocott’s methenamine silver staining demonstrated that only 20 cases were unequivocally positive for Pneumocystis carinii. In addition to interstitial pneumonia Pneumocystis-positive pigs were more frequently affected with granulomatous pneumonia than Pneumocystis-negative pigs. Frequently concurrent infections with different viral or bacterial lung pathogens were noted but there was no positive correlation between Pneumocystis- and PCV-2-infections. With other infections, no clear-cut differences between Pneumocystis-positive and Pneumocystis-negative animals were found. This study shows that Pneumocystis infections occur frequently in Austrian pigs with interstitial pneumonia. It remains to be shown which are the factors triggering severe multiplication and whether infection with Pneumocystis alone is able to induce lung disease in pigs.

Development and evaluation of nucleic acid-based techniques for an auxiliary diagnosis of invasive fungal infections in formalin-fixed and paraffin-embedded (FFPE) tissues

Notwithstanding the advantages of providing definitive diagnoses, the identification of fungi based on histopathological determination can be difficult and may lead to a pit of diagnoses. Therefore, the establishment of an auxiliary diagnostic method for use in routine pathological laboratories is desirable and should improve the above situation. Our previous studies have shown the superiority of in situ hybridization (ISH) for the detection of pathogenic fungi in histological specimens. This review focuses on the usefulness of ISH in the detection and identification of pathogenic fungi from formalin-fixed and paraffin-embedded (FFPE) tissue sections, and provides an overview of ISH for the diagnosis of fungal infection and retrospective autopsy analysis using molecular procedures. Based on the above, peptide nucleic acid (PNA) probes were shown to be superior in terms of the detection of target fungi and useful since histopathological diagnosis has the potential danger of being incorrect in the identification of fungi. In conclusion, we wish to emphasize that histopathological diagnosis in combination with molecular methods such as ISH and polymerase chain reaction (PCR) of FFPE samples should enhance the accuracy of identification in relation to fungi.

Molecular diagnosis of endemic and invasive mycoses: advances and challenges

The diagnosis of endemic and invasive fungal disease remains challenging. Molecular techniques for identification of fungi now play a significant and growing role in clinical mycology and offer distinct advantages as they are faster, more sensitive and more specific. The aim of this mini-review is to provide an overview of the state of the art of molecular diagnosis of endemic and invasive fungal diseases, and to emphasize the challenges and current need for standardization of the different methods. The European Aspergillus PCR Initiative (EAPCRI) has made significant progress in developing a standard for Aspergillus polymerase chain reaction (PCR), but recognizes that the process will not be finished until clinical utility has been established in formal and extensive clinical trials. Similar efforts should be implemented for the diagnosis of the other mycoses in order to fully validate the current methods or reinforce the need to design new ones. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012).

Pulmonary mycoses diagnosed using exfoliative cytology: infection or colonization?

OBJECTIVES

Flexible bronchoscopy with exfoliative cytology is an important tool for the diagnosis of pulmonary fungal infections. The question of colonization versus true fungal infection is of critical importance.

STUDY DESIGN

A 5-year retrospective analysis of all cases of pulmonary fungal infection diagnosed using exfoliative cytology was performed. Clinical, radiological, bronchoscopy and histopathology findings were recorded.

RESULTS

A total of 69 cases of mycoses were retrieved. The most common fungal organism identified was Aspergillus followed by Candida and Pneumocystis. Most cases of Aspergillus and Candida in cytological specimens presented as a pulmonary mass or endobronchial growth and were diagnosed as carcinomas in biopsy specimens, thus representing colonization. All cases of Pneumocystis with bilateral ground glass infiltrates and cryptococcosis with parenchymal mass lesion in radiology represented true infection. Histoplasma was identified in pleural fluid from a known case of lung carcinoma.

CONCLUSION

Aspergillus and Candida species are the most common fungal organisms. Most of these represent colonization of malignant growths. However, true fungal infections may also present as mass lesions and may masquerade malignancy clinically. Fluid cytological examination is an important diagnostic modality for pulmonary mycoses; however, it is important to correlate results with clinical, bronchoscopy and biopsy findings for accurate diagnosis and appropriate management.

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.

Applying a real-time PCR assay for Histoplasma capsulatum to clinically relevant formalin-fixed paraffin-embedded human tissue

A real-time PCR assay to detect Histoplasma capsulatum in formalin-fixed, paraffin-embedded (FFPE) tissue is described. The assay had an analytical sensitivity of 6 pg/μl of fungal DNA, analytical specificity of 100%, and clinical sensitivity of 88.9%. This proof-of-concept study may aid in the diagnosis of histoplasmosis from FFPE tissue.

Necrotizing granulomatous inflammation: what does it mean if your special stains are negative?

Necrotizing granulomas are commonly encountered in surgically resected specimens. The majority will be proven infectious with special stains for microorganisms. These need to be distinguished from other granulomatous processes such as Wegener's granulomatosis (WG). Although there may be histological overlap between these different processes, the identification of a true necrotizing vasculitis is specific to WG in the context of necrotizing granulomas. Otherwise, the combination of histological features should lead to a specific diagnosis. Despite a thorough histological examination and assessments of special stains, a significant proportion of necrotizing granulomas will appear infectious with no obvious infectious etiology. There are only few clinically available ancillary tests that can be performed on paraffin-embedded tissue and include real-time PCR for tuberculous mycobacteria. Despite correlation with clinical, serological and other microbiological studies, some necrotizing granulomas remain unexplained. Patients with such granulomas appear not to require any additional treatment and do experience a favorable outcome.

Diagnostic dilemmas in retinitis and endophthalmitis

Visual loss in infectious posterior uveitis or panuveitis can occur if proper therapy is delayed because of diagnostic uncertainty. Some disorders, such as acute retinal necrosis and bacterial endophthalmitis, can be rapidly progressive, and therefore require prompt and accurate diagnosis to guide initial therapy. Other more slowly evolving infections, such as toxoplasmic chorioretinitis or fungal endophthalmitis, can be worsened by empiric use of corticosteroids without specific antimicrobial coverage. Key ocular diagnostic features are helpful but highly variable with overlap with both non-infectious uveitis and neoplastic masquerades, even for key signs such as hypopyon. Close examination of the fundus with attention to color, location, size, border, and opacity of lesions and associated arteriolitis or frosted branch angiitis is helpful in the diagnosis of chorioretinitis. Ultrasonography is an important tool in the evaluation of eyes with suspected endophthalmitis, especially those with intracapsular infection or focal infected deposits. Testing of intraocular fluid can be extremely useful but suffers from inaccessibility, poor sensitivity, and test selections dependent on a presumptive diagnosis, which may be wrong. The dilemma for clinician is to make the correct diagnosis of a rare, blinding, variegated disease quickly enough to intercede with specific therapy or to apply empiric therapy in a sufficiently skilled manner to avert disaster and confirm the diagnosis by response to treatment. When non-infectious uveitis is in the differential, empiric corticosteroids must sometimes be used, at great risk, if clinical examination, ancillary testing, and any available intraocular diagnostic tests have failed to confirm a diagnosis.

Biopsy procedures for molecular tissue diagnosis of invasive fungal infections

The incidence of invasive fungal infections (IFI) has increased substantially and the epidemiology has changed dramatically in recent years. Candida albicans is still most important, but non-albicans species, Aspergillus species, Glomeromycota (formerly Zygomycetes) and Fusarium species are an increasing cause of IFIs. Due to this growing diversity, the identification of the causative organism to genus and species level is important to perform best and adequate treatment. The early, sensitive and specific detection of IFIs remains challenging and current conventional methods are limited. The golden standard for the definite diagnosis of proven pulmonary infection remains either histopathologic, cytopathologic or direct tissue examination. Invasive procedures are necessary to obtain reliable specimens and biopsies may be taken percutaneously, bronchoscopically, via open surgery or via video-assisted thorascopic surgery. Molecular methods, like PCR or in situ hybridization, are a promising diagnostic tool for rapid and reliable species identification and should be performed in addition to microscopic examination and culture to increase the sensitivity for the diagnosis of IFI. Combining culture, microscopy, serology, and PCR in lung tissues and/or bronchial samples will increase the diagnostic yield by 99%. Here, we give an overview of biopsy procedures for molecular tissue diagnosis of IFI.

Histopathologic diagnosis of fungal infections in the 21st century

Fungal infections are becoming more frequent because of expansion of at-risk populations and the use of treatment modalities that permit longer survival of these patients. Because histopathologic examination of tissues detects fungal invasion of tissues and vessels as well as the host reaction to the fungus, it is and will remain an important tool to define the diagnostic significance of positive culture isolates or results from PCR testing. However, there are very few instances where the morphological characteristics of fungi are specific. Therefore, histopathologic diagnosis should be primarily descriptive of the fungus and should include the presence or absence of tissue invasion and the host reaction to the infection. The pathology report should also include a comment stating the most frequent fungi associated with that morphology as well as other possible fungi and parasites that should be considered in the differential diagnosis. Alternate techniques have been used to determine the specific agent present in the histopathologic specimen, including immunohistochemistry, in situ hybridization, and PCR. In addition, techniques such as laser microdissection will be useful to detect the now more frequently recognized dual fungal infections and the local environment in which this phenomenon occurs.

Candida glabrata and Candida albicans co-infection of an in vitro oral epithelium

BACKGROUND

Candida albicans is regarded as the leading of candidosis. However, Candida glabrata has emerged as an important pathogen of oral mucosa, occurring both singly or in mixed species infections, often with C. albicans. Compared with C. albicans, little is known about the role of C. glabrata in oral infection. The aim of this study was to examine single and mixed species infection of oral epithelium involving C. glabrata and establish its ability to invade and damage tissue.

METHODS

A reconstituted human oral epithelium (RHOE) was infected only with C. glabrata, or simultaneously with C. glabrata and C. albicans. The ability of both species to invade the tissue was examined using species specific peptide nucleic acid (PNA) probe hybridization and confocal laser scanning microscopy. Epithelial damage was assessed by measuring lactate dehydrogenase (LDH) activity.

RESULTS

Candida glabrata strains were able to colonize the RHOE, in a strain dependent manner. Candida glabrata single infection after 12 h, generally revealed no invasion of the RHOE, which contrasted with extensive tissue invasion demonstrated by C. albicans. Mixed infection showed that C. albicans enhanced the invasiveness of C. glabrata, and led to increased LDH release by the RHOE, which paralleled the observed histological damage.

CONCLUSIONS

The results obtained demonstrating enhanced invasion and increased tissue damage caused by mixed C. glabrata and C. albicans infections have important clinical significance and highlight the need to identify Candida species involved in oral candidosis.

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.

Clinical and laboratory update on blastomycosis

Blastomycosis is endemic in regions of North America that border the Great Lakes and the St. Lawrence River, as well as in the Mississippi River and Ohio River basins. Men are affected more often than women and children because men are more likely to participate in activities that put them at risk for exposure to Blastomyces dermatitidis. Human infection occurs when soil containing microfoci of mycelia is disturbed and airborne conidia are inhaled. If natural defenses in the alveoli fail to contain the infection, lymphohematogenous dissemination ensues. Normal host responses generate a characteristic pyogranulomatous reaction. The most common sites of clinical disease are the lung and skin; osseous, genitourinary, and central nervous system manifestations follow in decreasing order of frequency. Blastomycosis is one of the great mimickers in medicine; verrucous cutaneous blastomycosis resembles malignancy, and mass-like lung opacities due to B. dermatitidis often are confused with cancer. Blastomycosis may be clinically indistinguishable from tuberculosis. Diagnosis is based on culture and direct visualization of round, multinucleated yeast forms that produce daughter cells from a single broad-based bud. Although a long course of amphotericin B is usually curative, itraconazole is also highly effective and is the mainstay of therapy for most patients with blastomycosis.

Granulomatous lung disease: an approach to the differential diagnosis

CONTEXT

Granulomas are among the most commonly encountered abnormalities in pulmonary pathology and often pose a diagnostic challenge. Although most pathologists are aware of the need to exclude an infection in this setting, there is less familiarity with the specific histologic features that aid in the differential diagnosis.

OBJECTIVE

To review the differential diagnosis, suggest a practical diagnostic approach, and emphasize major diagnostically useful histologic features. This review is aimed at surgical pathologists who encounter granulomas in lung specimens.

DATA SOURCES

Pertinent recent and classic peer-reviewed literature retrieved from PubMed (US National Library of Medicine) and primary material from the institutions of both authors.

CONCLUSIONS

Most granulomas in the lung are caused by mycobacterial or fungal infection. The diagnosis requires familiarity with the tissue reaction as well as with the morphologic features of the organisms, including appropriate interpretation of special stains. The major noninfectious causes of granulomatous lung disease are sarcoidosis, Wegener granulomatosis, hypersensitivity pneumonitis, hot tub lung, aspiration pneumonia, and talc granulomatosis.

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.

In situ hybridization for the differentiation of Actinomyces and Nocardia in tissue sections

The specific identification of filamentous bacteria in tissue sections can be difficult. The filamentous bacteria Actinomyces and Nocardia often produce similar host responses and single bacterial organisms seem morphologically similar; however, their differentiation may be clinically significant. In situ hybridization (ISH) may assist in the rapid and accurate identification of these microorganisms. In this study, DNA probes were directed against the variable regions of 16S ribosomal RNA genes of multiple Actinomyces and Nocardia spp. Probes were tested on 26 formalin-fixed, paraffin-embedded tissue specimens, each of which contained diagnostic foci of filamentous bacteria confirmed by both Gram and Grocott methenamine silver stains. On the basis of histology and clinical features, cases were classified as Actinomyces-related, n = 13 with 6 culture-proven cases and Nocardia-related, n = 13 with 11 culture-proven cases. Using this classification, all cases were assessed for cross-reactivity using other species-specific probes and probe specificity was determined. Overall, Gram and Grocott methenamine silver histochemical stains (100% sensitivity) were more sensitive than ISH (77% sensitivity for both Actinomyces and Nocardia probes). The slender caliber of filamentous bacteria was a limitation for ISH interpretation and necessitated careful examination of some slides. Probes demonstrated 100% specificity for identifying both species, 100% positive predictive value and 81% negative predictive value. No mixed infections were observed. This study demonstrates that ISH is highly specific for distinguishing between Actinomyces and Nocardia spp. in tissue sections. Although histochemical stains demonstrate greater sensitivity for organism detection, ISH is a rapid and specific technique that is especially useful for evaluating culture-negative or clinically unsuspected cases of filamentous bacterial infection.

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.

Specific in situ visualization of the pathogenic endophytic fungus Aciculosporium take, the cause of witches' broom in bamboo

The endophytic fungus Aciculosporium take (Ascomycota; Clavicipitaceae) causes continuous shoot growth in bamboo. The colonized shoot eventually results in witches' broom formation but maintains normal leaf arrangement and branching pattern. To analyze the mechanism of well-regulated symptom development, the location of the fungal endophytic hyphae in host tissues was visualized. A colorimetric in situ hybridization technique using a species-specific oligonucleotide probe targeting the 18S rRNA of A. take was used. In situ hybridization was performed on tissue sections of diseased shoots with or without external signs of fungal colonization. Specific signals were detected in intercellular spaces of the bamboo tissues. Most signals were detected in the shoot apical meristem and the leaf primordia. In addition, fewer signals were detected in the lateral buds, juvenile leaves, and stems. These results indicate that A. take grows endophytically, particularly in the shoot apical meristem of the host. The location of A. take hyphae suggests that the mechanism of symptom development can be explained by the action of exogenous fungal auxin, which continuously induces primordium initiation within the host.

Challenges and pitfalls of morphologic identification of fungal infections in histologic and cytologic specimens: a ten-year retrospective review at a single institution

Despite the advantages of providing an early presumptive diagnosis, fungal classification by histopathology can be difficult and may lead to diagnostic error. To assess the accuracy of histologic diagnosis of fungal infections vs culture ("gold standard"), we performed a 10-year retrospective review at our institution. Of the 47 of 338 positive mold and yeast cultures with concurrent surgical pathology evaluation without known history of a fungal infection, 37 (79%) were correctly identified based on morphologic features in histologic and/or cytologic specimens. The 10 discrepant diagnoses (21%) included misidentification of septate and nonseptate hyphal organisms and yeast forms. Errors resulted from morphologic mimics, use of inappropriate terminology, and incomplete knowledge in mycology. The accuracy did not correlate with preceding antifungal therapy (P = .14) or use of special stains (P = .34) and was not operator-dependent. Among 8 discrepancies with clinical follow-up available, 2 potential adverse clinical consequences resulted. While histopathologic identification of fungi in tissue sections and cytologic preparations is prone to error, implementation of a standardized reporting format should improve diagnostic accuracy and prevent adverse outcomes.

Identification of Aspergillus species in oral tissue samples of patients with hematologic malignancies by in situ hybridization: a preliminary report

PURPOSE

A definitive diagnosis of invasive oral aspergillosis can be difficult because the culturing of tissue samples frequently fails to isolate Aspergillus species. In addition, the mycelial elements of Aspergillus species seen in tissue sections are histopathologically indistinguishable from those of non-Aspergillus species. We analyzed the usefulness of a DNA probe directed against the alkaline proteinase (ALP) gene of Aspergillus fumigatus for the identification of Aspergillus species by the in situ hybridization (ISH) technique in patients with oral mycosis.

PATIENTS AND METHODS

The ALP probe was tested on tissue specimens from 16 patients with hematologic malignancies who had invasive, orofacial fungal infections and a positive culture for one of the following organisms: Aspergillus species in 13 patients (A. flavus in 10, A. terreus in 2, and A. fumigatus in 1), and Exophiala dermatitis, Trichoderma longibrachiatum, and Candida albicans in 1 patient each. In situ hybridization with the ALP probe was performed using formalin-fixed, paraffin-embedded tissue samples.

RESULTS

The ALP probe showed a strong reaction with specimens from all 13 patients who had culture-proven aspergillosis specimens attributable to A. flavus, A. terreus, and A. fumigatus. On the other hand, the ALP probe showed no cross-reactivity with other fungi (Exophiala dermatitis, Trichoderma longibrachiatum, and Candida albicans).

CONCLUSION

These findings indicate that ISH using an ALP probe may increase the accuracy of diagnosing invasive oral aspergillosis in immunocompromised patients, and facilitate the provision of adequate antifungal treatment.

Real-time PCR method for detection of zygomycetes

Zygomycete infections can be devastating in immunocompromised hosts. Difficulties in the histopathologic differentiation of this class from other filamentous fungi (e.g., Aspergillus spp., Fusarium spp.) may lead to delays in diagnosis and initiation of appropriate treatment, thereby significantly affecting patient outcome. A real-time PCR assay was developed to detect species of the zygomycete genera Absidia, Apophysomyces, Cunninghamella, Mucor, Rhizopus, and Saksenaea in culture and tissue samples. Primers and fluorescence resonance energy transfer hybridization probes were designed to detect a 167-bp conserved region of the multicopy zygomycete cytochrome b gene. A plasmid containing target sequence from Mucor racemosus was constructed as a positive control. The analytical sensitivity of the assay is 10 targets/mul, and a specificity panel consisting of other filamentous fungi, yeasts (Candida spp.), and bacteria demonstrated no cross-reactivity in the assay. The clinical sensitivity and specificity of the assay from culture isolates were 100% (39/39) and 92% (59/64), respectively. Sensitivity and specificity determined using a limited number of fresh tissue specimens were both 100% (2/2). The sensitivity seen with formalin-fixed, paraffin-embedded tissues was 56% (35/62), and the specificity was 100% (19/19). The speed, sensitivity, and specificity of the PCR assay indicate that it is useful for the rapid and accurate detection of zygomycetes.

Molecular diagnostics for the detection and characterization of microbial pathogens

New and advanced methods of molecular diagnostics are changing the way we practice clinical microbiology, which affects the practice of medicine. Signal amplification and real-time nucleic acid amplification technologies offer a sensitive and specific result with a more rapid turnaround time than has ever before been possible. Numerous methods of postamplification analysis afford the simultaneous detection and differentiation of numerous microbial pathogens, their mechanisms of resistance, and the construction of disease-specific assays. The technical feasibility of these assays has already been demonstrated. How these new, often more expensive tests will be incorporated into routine practice and the impact they will have on patient care remain to be determined. One of the most attractive uses for such techniques is to achieve a more rapid characterization of the infectious agent so that a narrower-spectrum antimicrobial agent may be used, which should have an impact on resistance patterns.

Yeast identification--past, present, and future methods

The focus of this review is the evolution of biochemical phenotypic yeast identification methods with emphasis on conventional approaches, rapid screening tests, chromogenic agars, comprehensive commercial methods, and the eventual migration to genotypic methods. As systemic yeast infections can be devastating and resistance is common in certain species, accurate identification to the species level is paramount for successful therapy and appropriate patient care.