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Identification of Pneumocystis jirovecii with Fluorescence In-Situ Hybridization (FISH) in Patient Samples-A Proof-of-Principle. J Fungi (Basel) 2021; 8:jof8010013. [PMID: 35049953 PMCID: PMC8778293 DOI: 10.3390/jof8010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022] Open
Abstract
In resource-limited settings, where pneumocystosis in immunocompromised patients is infrequently observed, cost-efficient, reliable, and sensitive approaches for the diagnostic identification of Pneumocystis jirovecii in human tissue samples are desirable. Here, an in-house fluorescence in situ hybridization assay was comparatively evaluated against Grocott’s staining as a reference standard with 30 paraffin-embedded tissue samples as well as against in-house real-time PCR with 30 respiratory secretions from immunocompromised patients with clinical suspicion of pneumocystosis. All pneumocystosis patients included in the study suffered from HIV/AIDS. Compared with Grocott’s staining as the reference standard, sensitivity of the FISH assay was 100% (13/13), specificity was 41% (7/17), and the overall concordance was 66.7% with tissue samples. With respiratory specimens, sensitivity was 83.3% (10/12), specificity was 100% (18/18), and the overall concordance was 93.3% as compared with real-time PCR. It remained unresolved to which proportions sensitivity limitations of Grocott’s staining or autofluorescence phenomena affecting the FISH assay accounted for the recorded reduced specificity with the tissue samples. The assessment confirmed Pneumocystis FISH in lung tissue as a highly sensitive screening approach; however, dissatisfying specificity in paraffin-embedded biopsies calls for confirmatory testing with other techniques in case of positive FISH screening results. In respiratory secretions, acceptable sensitivity and excellent specificity were demonstrated for the diagnostic application of the P. jirovecii-specific FISH assay.
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González-Pérez M, Martins S, Manhita A, Caldeira AT, Pereira A. Coumarin Amine-Reactive DYE C392STP: an Efficient Building Block to Synthesize Single Labeled Oligonucleotides with Application as Fish Probes. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820010068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Reitz A, Poppert S, Rieker M, Frickmann H. Evaluation of FISH for Blood Cultures under Diagnostic Real-Life Conditions. Eur J Microbiol Immunol (Bp) 2018; 8:135-141. [PMID: 30719330 PMCID: PMC6348703 DOI: 10.1556/1886.2018.00024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 09/18/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The study assessed a spectrum of previously published in-house fluorescence in-situ hybridization (FISH) probes in a combined approach regarding their diagnostic performance with incubated blood culture materials. METHODS Within a two-year interval, positive blood culture materials were assessed with Gram and FISH staining. Previously described and new FISH probes were combined to panels for Gram-positive cocci in grape-like clusters and in chains, as well as for Gram-negative rod-shaped bacteria. Covered pathogens comprised Staphylococcus spp., such as S. aureus, Micrococcus spp., Enterococcus spp., including E. faecium, E. faecalis, and E. gallinarum, Streptococcus spp., like S. pyogenes, S. agalactiae, and S. pneumoniae, Enterobacteriaceae, such as Escherichia coli, Klebsiella pneumoniae and Salmonella spp., Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Bacteroides spp. RESULTS A total of 955 blood culture materials were assessed with FISH. In 21 (2.2%) instances, FISH reaction led to non-interpretable results. With few exemptions, the tested FISH probes showed acceptable test characteristics even in the routine setting, with a sensitivity ranging from 28.6% (Bacteroides spp.) to 100% (6 probes) and a specificity of >95% in all instances. CONCLUSION If sophisticated rapid diagnostic methods like mass spectrometry from blood culture materials are not available, FISH provides an option for rapid differentiation for laboratories in resource-limited settings.
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Affiliation(s)
- Annalena Reitz
- University Hospital of the Goethe University, Frankfurt/Main, Germany
| | - Sven Poppert
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,Faculty of Medicine, University Basel, Basel, Switzerland
| | | | - Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany.,Institute for Medical Microbiology, Virology and Hygiene, University Hospital Rostock, Rostock, Germany
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Frickmann H, Zautner AE, Moter A, Kikhney J, Hagen RM, Stender H, Poppert S. Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review. Crit Rev Microbiol 2017; 43:263-293. [PMID: 28129707 DOI: 10.3109/1040841x.2016.1169990] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
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.
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Affiliation(s)
- Hagen Frickmann
- a German Armed Forces Hospital of Hamburg, Department of Tropical Medicine at the Bernhard Nocht Institute , Hamburg , Germany
| | - Andreas Erich Zautner
- b Department of Medical Microbiology, University Medical Center Göttingen , Göttingen , Germany
| | - Annette Moter
- c University Medical Center Berlin, Biofilmcenter at the German Heart Institute Berlin , Berlin , Germany
| | - Judith Kikhney
- c University Medical Center Berlin, Biofilmcenter at the German Heart Institute Berlin , Berlin , Germany
| | - Ralf Matthias Hagen
- a German Armed Forces Hospital of Hamburg, Department of Tropical Medicine at the Bernhard Nocht Institute , Hamburg , Germany
| | | | - Sven Poppert
- e Institute for Medical Microbiology, Justus-Liebig-University Giessen , Giessen , Germany
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Da Silva RM, Da Silva Neto JR, Santos CS, Frickmann H, Poppert S, Cruz KS, Koshikene D, De Souza JVB. Evaluation of fluorescence in situ hybridisation (FISH) for the detection of fungi directly from blood cultures and cerebrospinal fluid from patients with suspected invasive mycoses. Ann Clin Microbiol Antimicrob 2015; 14:6. [PMID: 25637361 PMCID: PMC4322816 DOI: 10.1186/s12941-015-0065-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/18/2015] [Indexed: 11/16/2022] Open
Abstract
The aim of this study was to evaluate the diagnostic performance of in-house FISH (fluorescence in situ hybridisation) procedures for the direct identification of invasive fungal infections in blood cultures and cerebrospinal fluid (CSF) samples and to compare these FISH results with those obtained using traditional microbiological techniques and PCR targeting of the ITS1 region of the rRNA gene. In total, 112 CSF samples and 30 positive blood cultures were investigated by microscopic examination, culture, PCR-RFLP and FISH. The sensitivity of FISH for fungal infections in CSF proved to be slightly better than that of conventional microscopy (India ink) under the experimental conditions, detecting 48 (instead of 46) infections in 112 samples. The discriminatory powers of traditional microbiology, PCR-RFLP and FISH for fungal bloodstream infections were equivalent, with the detection of 14 fungal infections in 30 samples. However, the mean times to diagnosis after the detection of microbial growth by automated blood culture systems were 5 hours, 20 hours and 6 days for FISH, PCR-RFLP and traditional microbiology, respectively. The results demonstrate that FISH is a valuable tool for the identification of invasive mycoses that can be implemented in the diagnostic routine of hospital laboratories.
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Affiliation(s)
| | | | | | - Hagen Frickmann
- Department of Tropical Medicine at the Bernhard Nocht Institute, German Armed Forces Hospital of Hamburg, Hamburg, Germany.
| | - Sven Poppert
- Institute of Medical Microbiology, Justus-Liebig-University Giessen, Giessen, Germany.
| | - Kátia Santana Cruz
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil.
| | | | - João Vicente Braga De Souza
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil. .,Biotecnólogo/Tecnologista Pleno III, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Sociedade, Ambiente e Saúde, Laboratório de Micologia, Av. André Araújo, 2936, Aleixo, Manaus, AM, CEP 69060-001, Brazil.
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da Silva RM, da Silva Neto JR, Santos CS, Cruz KS, Frickmann H, Poppert S, Koshikene D, de Souza JVB. Fluorescent in situ hybridization of pre-incubated blood culture material for the rapid diagnosis of histoplasmosis. Med Mycol 2014; 53:160-4. [DOI: 10.1093/mmy/myu080] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Albertin W, Chasseriaud L, Comte G, Panfili A, Delcamp A, Salin F, Marullo P, Bely M. Winemaking and bioprocesses strongly shaped the genetic diversity of the ubiquitous yeast Torulaspora delbrueckii. PLoS One 2014; 9:e94246. [PMID: 24718638 PMCID: PMC3981792 DOI: 10.1371/journal.pone.0094246] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 03/14/2014] [Indexed: 11/19/2022] Open
Abstract
The yeast Torulaspora delbrueckii is associated with several human activities including oenology, bakery, distillery, dairy industry, etc. In addition to its biotechnological applications, T. delbrueckii is frequently isolated in natural environments (plant, soil, insect). T. delbrueckii is thus a remarkable ubiquitous yeast species with both wild and anthropic habitats, and appears to be a perfect yeast model to search for evidence of human domestication. For that purpose, we developed eight microsatellite markers that were used for the genotyping of 110 strains from various substrates and geographical origins. Microsatellite analysis showed four genetic clusters: two groups contained most nature strains from Old World and Americas respectively, and two clusters were associated with winemaking and other bioprocesses. Analysis of molecular variance (AMOVA) confirmed that human activities significantly shaped the genetic variability of T. delbrueckii species. Natural isolates are differentiated on the basis of geographical localisation, as expected for wild population. The domestication of T. delbrueckii probably dates back to the Roman Empire for winemaking (∼ 1900 years ago), and to the Neolithic era for bioprocesses (∼ 4000 years ago). Microsatellite analysis also provided valuable data regarding the life-cycle of the species, suggesting a mostly diploid homothallic life. In addition to population genetics and ecological studies, the microsatellite tool will be particularly useful for further biotechnological development of T. delbrueckii strains for winemaking and other bioprocesses.
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Affiliation(s)
- Warren Albertin
- Univ. de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
- Biolaffort, Bordeaux, France
| | - Laura Chasseriaud
- Univ. de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
- Biolaffort, Bordeaux, France
| | - Guillaume Comte
- Univ. de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
| | - Aurélie Panfili
- Univ. de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
| | - Adline Delcamp
- INRA, UMR Biodiversité Gènes et Ecosystèmes, PlateForme Génomique, Cestas, France
| | - Franck Salin
- INRA, UMR Biodiversité Gènes et Ecosystèmes, PlateForme Génomique, Cestas, France
| | - Philippe Marullo
- Univ. de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
- Biolaffort, Bordeaux, France
| | - Marina Bely
- Univ. de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
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