In situ hybridisation for the identification of Helicobacter pylori in paraffin wax embedded tissue

Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review

Early identification of microbial pathogens is essential for rational and conservative antibiotic use especially in the case of known regional resistance patterns. Here, we describe fluorescence in situ hybridization (FISH) as one of the rapid methods for easy identification of microbial pathogens, and its advantages and disadvantages for the diagnosis of pathogens in human infections in the laboratory diagnostic routine. Binding of short fluorescence-labeled DNA or nucleic acid-mimicking PNA probes to ribosomes of infectious agents with consecutive analysis by fluorescence microscopy allows identification of bacterial and eukaryotic pathogens at genus or species level. FISH analysis leads to immediate differentiation of infectious agents without delay due to the need for microbial culture. As a microscopic technique, FISH has the unique potential to provide information about spatial resolution, morphology and identification of key pathogens in mixed species samples. On-going automation and commercialization of the FISH procedure has led to significant shortening of the time-to-result and increased test reliability. FISH is a useful tool for the rapid initial identification of microbial pathogens, even from primary materials. Among the rapidly developing alternative techniques, FISH serves as a bridging technology between microscopy, microbial culture, biochemical identification and molecular diagnostic procedures.

In situ hybridization to detect and identify Burkholderia pseudomallei in human melioidosis

Burkholderia pseudomallei causes a potentially fatal infection called melioidosis. We have developed a nonfluorescent, colorimetric in situ hybridization assay using a specific probe to target 16s rRNA of B. pseudomallei in formalin-fixed, paraffin-embedded infected tissues for diagnostic purposes and to study infectious disease pathology. A 63-base pair DNA probe was synthesized and labeled with digoxigenin by PCR. Probe specificity was confirmed by BLAST analysis and by testing on appropriate microbial controls. The in situ hybridization assay was specifically and consistently positive for B. pseudomallei, showing strongly and crisply stained, single bacillus and bacilli clusters in mainly inflamed tissues in seven human acute melioidosis cases and experimentally infected mouse tissues. Intravascular and extravascular bacilli were detected in both intracellular and extracellular locations in various human organs, including lung, spleen, kidney, liver, bone marrow, and aortic mycotic aneurysm, particularly in the inflamed areas. Intravascular, intracellular bacteria in melioidosis have not been previously reported. Although the identity of infected intravascular leukocytes has to be confirmed, extravascular, intracellular bacilli appear to be found mainly within macrophages and neutrophils. Rarely, large intravascular, extracellular bacillary clusters/emboli could be detected in both human and mouse tissues. B. cepacia and non-Burkholderia pathogens (16 microbial species) all tested negative. Nonpathogenic B. thailandensis showed some cross-hybridization but signals were less intense. This in situ hybridization assay could be usefully adapted for B. pseudomallei identification in other clinical specimens such as pus and sputum.

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.

Increased rate of Helicobacter pylori infection detected by PCR in biopsies with chronic gastritis

Histology is considered a sensitive method for detection of Helicobacter pylori, in gastric biopsies. We investigated the diagnostic potential of qualitative nested (nPCR) and quantitative PCR (qPCR) for detection of H. pylori using different primers on 126 archived gastric biopsies with inflammation and correlated the inflammatory changes with the presence and density of bacteria. H. pylori was detected in 42.8% biopsies by histology and PCR, an additional 15 samples were positive exclusively by PCR: nPCR was positive in all histologically positive samples, but qPCR failed to detect H. pylori in 10 biopsies. The inflammatory score was significantly higher in biopsies positive for H. pylori only by PCR showed a significant higher inflammatory score compared with negative biopsies (mean of neutrophils score, 1.60 vs. 0.90, P < 0.01; mean of mononuclear cells score, 2.27 vs. 1.67, P < 0.01), whereas the inflammatory score was similar compared with biopsies positive for H. pylori by histology (mean of neutrophils score, 1.60 vs. 1.56, not significant; mean of mononuclear cells score, 2.27 vs. 2.20, not significant). A weak correlation between inflammatory score and the density of H. pylori detected by histology was observed. The mean values of H. pylori DNA were significantly higher in histologic-positive than in histologic negative biopsies. We have shown that PCR can detect H. pylori in about 20% of histologic-negative gastric biopsies, indicating the clinical relevance of H. pylori detection by PCR in biopsies with characteristic inflammatory changes.

In situ localisation of Yersinia enterocolitica by catalysed reported deposition signal amplification

AIM

The sensitive detection of pathogenic Yersinia enterocolitica in paraffin embedded tissue sections by in situ hybridisation (ISH).

METHODS

Y enterocolitica infected cell lines, rat spleens, and patient biopsy specimens were used to compare conventional ISH, immune fluorescence assay (IFA) detection, and catalysed reporter deposition (CARD) signal amplification ISH.

RESULTS

CARD-ISH was shown to be more sensitive then conventional ISH and had a comparable sensitivity to IFA. In contrast to IFA, CARD-ISH preserved good tissue morphology.

CONCLUSIONS

CARD-ISH appeared to be a fast and sensitive ISH method for detecting Y enterocolitica in routinely processed tissue sections. Application of this method allows the combination of routine detection and cellular localisation of the pathogen within the infected tissue.

Polymerase chain reaction for the detection of Helicobacter pylori in formaldehyde-sublimate fixed, paraffin-embedded gastric biopsies

To improve morphologic detail and immunohistochemical staining, mercuric chloride-containing fixatives such as formaldehyde-sublimate (FS) has been widely used as an alternative for neutral buffered formalin. FS-fixed, paraffin-embedded tissue, however, is considered to be an unreliable source of DNA. We used an adapted DNA-extraction method for FS-fixed, paraffin-embedded tissue. In all cases tested we obtained amplifiable DNA with polymerase chain reaction (PCR), after FS-fixation and after fixation in neutral buffered formalin as well. A PCR assay for the 16S-rRNA region of Helicobacter pylori was developed amplifying a fragment of 145 bp. The specificity of this PCR assay was tested on a range of different microorganisms. PCR was performed on 46 archival FS-fixed paraffin-embedded gastric biopsies. The results were compared with histologic examination and with immunohistochemical detection using a polyclonal antibody against H. pylori. Both PCR and immunohistochemistry are very sensitive methods for the detection of H. pylori. A PCR offers the possibility of additional subtyping in archival FS-fixed, paraffin-embedded tissue.

In situ hybridization and its diagnostic applications in pathology

In situ hybridization (ISH) is a technique by which specific nucleotide sequences are identified in cells or tissue sections. These may be endogenous, bacterial or viral, DNA or RNA. On the basis of research applications, the technique is now being translated into diagnostic practice, mainly in the areas of gene expression, infection and interphase cytogenetics. Diagnostic applications are most often based on short nucleotide sequences (oligomers) labelled with non-isotopic reporter molecules, and sites of binding may be localized by histochemical or immunohistochemical methods. The technique can be applied to routinely fixed and processed tissues; with some targets, it is even possible to obtain hybridization in autopsy material. ISH has been used to detect messenger RNA (mRNA) as a marker of gene expression, where levels of protein storage are low; for example, to confirm an endocrine tumour as the source of excess hormone production. Its application in infectious diseases has to date been mainly in viral infections, such as the typing of human papillomavirus (HPV) or the detection of Epstein-Barr virus by the presence of small nuclear RNAs (EBERs). The expression of mRNAs for histone proteins has been used to detect cells in S phase, and related methods may be applied to detect apoptotic cells. Using probes to chromosome-specific sequences, it is possible to detect aneuploidy, and to document changes in specific chromosomes, which may have prognostic significance in some tumours, such as B-cell chronic lymphatic leukaemia. Using sequence-specific probes, translocations can be identified, such as the t(11;12) of Ewing's sarcoma. This review presents an outline of the technique of in situ hybridization and discusses areas of current and potential diagnostic application.

Oral carriage of Helicobacter pylori: a review

Helicobacter pylori is a microaerophilic, motile bacterium, especially adapted to life in the human stomach. The presence of H. pylori in the stomach is strongly associated with chronic gastritis and ulcer disease and is a risk factor for gastric cancers. The microorganism may be transmitted orally and has been detected in dental plaque, saliva, and feces, but the hypothesis that oral microflora may be a permanent reservoir of H. pylori is still controversial. A review of the literature suggests that the recovery of H. pylori in the mouth is probably intermittent, associated with gastroesophageal reflux but not with specific oral disease. Nonetheless, the PCR identification of oral H. pylori may become helpful, particularly in cases of gastritis or ulcer relapse after antimicrobial therapy. Eradication of oral H. pylori by local medication or periodontal procedures would rely on the precise identification of its ecological niche. Within family groups, prophylactic methods should be practiced to avoid oral carriage of H. pylori. The risk of iatrogenic transmission during dental care, however, is already circumscribed by standard professional hygiene procedures.

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.

Detection of Helicobacter pylori in gastric biopsy and resection specimens

AIMS

To compare the sensitivity of detecting Helicobacter pylori in gastric biopsy and resection specimens using tinctorial and silver impregnation stains, immunohistochemistry and the polymerase chain reaction (PCR).

METHODS

Formalin fixed, paraffin wax embedded tissue from 33 gastric biopsy specimens (26 showing chronic gastritis and seven showing low grade mucosa associated lymphoid tissue (MALT) lymphoma) together with blocks of uninvolved mucosa from gastrectomy specimens for MALT lymphoma (five cases) were studied. Consecutive sections were stained using haematoxylin and eosin, Giemsa, the Warthin-Starry silver stain, and a polyclonal antibody directed against H pylori using an immunoperoxidase technique following heat induced antigen retrieval. PCR analysis of DNA extracted from a further section was carried out using primers which amplified a 411 base pair fragment of the urease A gene.

RESULTS

H pylori was detected in 14 (37%) sections stained with haematoxylin and eosin, 21 (55%) with Giemsa, 23 (61%) with Warthin-Starry, and 25 (66%) stained with the antibody. Seventeen (45%) cases were positive on PCR. Immunohistochemistry was positive in all cases in which H pylori was detected by other methods.

CONCLUSION

Immunohistochemistry using an immunoperoxidase technique following heat induced antigen retrieval for detecting H pylori in gastric biopsy and resection specimens is highly sensitive and easy to use.