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Muzny CA, Cerca N, Elnaggar JH, Taylor CM, Sobel JD, Van Der Pol B. State of the Art for Diagnosis of Bacterial Vaginosis. J Clin Microbiol 2023; 61:e0083722. [PMID: 37199636 PMCID: PMC10446871 DOI: 10.1128/jcm.00837-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023] Open
Abstract
Bacterial vaginosis (BV) is the most common cause of vaginal discharge among reproductive-age women. It is associated with multiple adverse health outcomes, including increased risk of acquisition of HIV and other sexually transmitted infections (STIs), in addition to adverse birth outcomes. While it is known that BV is a vaginal dysbiosis characterized by a shift in the vaginal microbiota from protective Lactobacillus species to an increase in facultative and strict anaerobic bacteria, its exact etiology remains unknown. The purpose of this minireview is to provide an updated overview of the range of tests currently used for the diagnosis of BV in both clinical and research settings. This article is divided into two primary sections: traditional BV diagnostics and molecular diagnostics. Molecular diagnostic assays, particularly 16S rRNA gene sequencing, shotgun metagenomic sequencing, and fluorescence in situ hybridization (FISH), are specifically highlighted, in addition to multiplex nucleic acid amplification tests (NAATs), given their increasing use in clinical practice (NAATs) and research studies (16S rRNA gene sequencing, shotgun metagenomic sequencing, and FISH) regarding the vaginal microbiota and BV pathogenesis. We also provide a discussion of the strengths and weaknesses of current BV diagnostic tests and discuss future challenges in this field of research.
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Affiliation(s)
- Christina A. Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nuno Cerca
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal
| | - Jacob H. Elnaggar
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Christopher M. Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Jack D. Sobel
- Division of Infectious Diseases, Wayne State University, Detroit, Michigan, USA
| | - Barbara Van Der Pol
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Scheuermann-Poley C, Wiessner A, Kikhney J, Gatzer R, Müller M, Stichling M, Moter A, Willy C. Fluorescence In Situ Hybridization as Diagnostic Tool for Implant-associated Infections: A Pilot Study on Added Value. PLASTIC AND RECONSTRUCTIVE SURGERY-GLOBAL OPEN 2023; 11:e4994. [PMID: 37360245 PMCID: PMC10287136 DOI: 10.1097/gox.0000000000004994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 03/23/2023] [Indexed: 06/28/2023]
Abstract
Implant-associated infections are a devastating complication in surgery. Especially in infections with biofilm-forming microorganisms, the identification of the causing microorganism remains a challenge. However, the classification as biofilm is not possible with conventional polymerase chain reaction or culture-based diagnostics. The aim of this study was to evaluate the additional value of fluorescence in situ hybridization (FISH) and nucleic acid amplification technique (FISHseq) to discuss a diagnostic benefit of the culture-independent methods and to map spatial organization of pathogens and microbial biofilms in wounds. Methods In total, 118 tissue samples from 60 patients with clinically suspected implant-associated infections (n = 32 joint replacements, n = 24 open reduction and internal fixation, n = 4 projectiles) were analyzed using classic microbiological culture and culture-independent FISH in combination with polymerase chain reaction and sequencing (FISHseq). Results In 56 of 60 wounds, FISHseq achieved an added value. FISHseq confirmed the result of cultural microbiological examinations in 41 of the 60 wounds. In 12 wounds, one or more additional pathogens were detected by FISHseq. FISHseq could show that the bacteria initially detected by culture corresponded to a contamination in three wounds and could exclude that the identified commensal pathogens were a contamination in four other wounds. In five wounds, a nonplanktonic bacterial life form was detected. Conclusions The study revealed that FISHseq gives additional diagnostic information, including therapy-relevant findings that were missed by culture. In addition, nonplanktonic bacterial life forms could also be detected with FISHseq, albeit less frequently than previously indicated.
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Affiliation(s)
- Catharina Scheuermann-Poley
- From the Trauma & Orthopedic Surgery, Septic & Reconstructive Surgery, Research and Treatment Centre Septic Defect Wounds, Federal Armed Forces of Germany, Bundeswehr (Military) Academic Hospital, Berlin, Germany
| | - Alexandra Wiessner
- Biofilmcenter, Institute for Microbiology, Infectious Diseases, and Immunology, Charité – University Medicine Berlin and MoKi Analytics GmbH, Berlin, Germany
| | - Judith Kikhney
- Biofilmcenter, Institute for Microbiology, Infectious Diseases, and Immunology, Charité – University Medicine Berlin and MoKi Analytics GmbH, Berlin, Germany
| | - Renate Gatzer
- Department of Microbiology, Federal Armed Forces of Germany, Bundeswehr (Military) Academic Hospital, Berlin, Germany
| | - Martin Müller
- Department of Microbiology, Federal Armed Forces of Germany, Bundeswehr (Military) Academic Hospital, Berlin, Germany
| | - Marcus Stichling
- From the Trauma & Orthopedic Surgery, Septic & Reconstructive Surgery, Research and Treatment Centre Septic Defect Wounds, Federal Armed Forces of Germany, Bundeswehr (Military) Academic Hospital, Berlin, Germany
| | - Annette Moter
- Biofilmcenter, Institute for Microbiology, Infectious Diseases, and Immunology, Charité – University Medicine Berlin and MoKi Analytics GmbH, Berlin, Germany
| | - Christian Willy
- From the Trauma & Orthopedic Surgery, Septic & Reconstructive Surgery, Research and Treatment Centre Septic Defect Wounds, Federal Armed Forces of Germany, Bundeswehr (Military) Academic Hospital, Berlin, Germany
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Mendonça A, Carvalho-Pereira J, Franco-Duarte R, Sampaio P. Optimization of a Quantitative PCR Methodology for Detection of Aspergillus spp. and Rhizopus arrhizus. Mol Diagn Ther 2022; 26:511-525. [PMID: 35710958 PMCID: PMC9202985 DOI: 10.1007/s40291-022-00595-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2022] [Indexed: 11/25/2022]
Abstract
Introduction Multiplex quantitative polymerase chain reaction (qPCR) methods for the detection of Aspergillus spp. based only on SYBR Green and melting curve analysis of PCR products are difficult to develop because most targets are located within ITS regions. The aim of this study was to adapt our previously developed methodology based on a multiplex PCR assay coupled with GeneScan analysis to provide a qPCR method. Methods A SYBR Green-based real-time PCR assay was optimized to detect A. fumigatus, A. flavus, A. niger, A. terreus, and R. arrhizus in a multiplex assay and applied to cultured fungi and spiked plasma. Results Different melting temperatures allowed identification of all five pathogens and discrimination between them, even in samples with low amounts of fungal gDNA (from 1.3 to 33.0 pg/μL), which has been reported previously as problematic. No false-positive results were obtained for non-target species, including bacteria and human DNA. This method allowed detection of fungal pathogens in human plasma spiked with fungal DNA and in coinfections of A. niger/R. arrhizus. Discussion This work provides evidence for the use of a qPCR multiplex method based on SYBR Green and melting curve analysis of PCR products for the detection of A. fumigatus, A. flavus, A. niger, A. terreus, and R. arrhizus. The proposed method is simpler and less expensive than available kits based on fluorescent probes and can be used for aiding diagnosis of the most relevant invasive filamentous fungi, particularly in low-income health care institutions. Supplementary Information The online version contains supplementary material available at 10.1007/s40291-022-00595-1.
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Affiliation(s)
- Alexandre Mendonça
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal
| | - Joana Carvalho-Pereira
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal
| | - Ricardo Franco-Duarte
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.
| | - Paula Sampaio
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal
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Mendonça A, Santos H, Franco-Duarte R, Sampaio P. Fungal infections diagnosis - Past, present and future. Res Microbiol 2022; 173:103915. [PMID: 34863883 PMCID: PMC8634697 DOI: 10.1016/j.resmic.2021.103915] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/19/2021] [Accepted: 11/26/2021] [Indexed: 01/07/2023]
Abstract
Despite the scientific advances observed in the recent decades and the emergence of new methodologies, the diagnosis of systemic fungal infections persists as a problematic issue. Fungal cultivation, the standard method that allows a proven diagnosis, has numerous disadvantages, as low sensitivity (only 50% of the patients present positive fungal cultures), and long growth time. These are factors that delay the patient's treatment and, consequently, lead to higher hospital costs. To improve the accuracy and quickness of fungal infections diagnosis, several new methodologies attempt to be implemented in clinical microbiology laboratories. Most of these innovative methods are independent of pathogen isolation, which means that the diagnosis goes from being considered proven to probable. In spite of the advantage of being culture-independent, the majority of the methods lack standardization. PCR-based methods are becoming more and more commonly used, which has earned them an important place in hospital laboratories. This can be perceived now, as PCR-based methodologies have proved to be an essential tool fighting against the COVID-19 pandemic. This review aims to go through the main steps of the diagnosis for systemic fungal infection, from diagnostic classifications, through methodologies considered as "gold standard", to the molecular methods currently used, and finally mentioning some of the more futuristic approaches.
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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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K. Hussain K, Malavia D, M. Johnson E, Littlechild J, Winlove CP, Vollmer F, Gow NAR. Biosensors and Diagnostics for Fungal Detection. J Fungi (Basel) 2020; 6:E349. [PMID: 33302535 PMCID: PMC7770582 DOI: 10.3390/jof6040349] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 12/14/2022] Open
Abstract
Early detection is critical to the successful treatment of life-threatening infections caused by fungal pathogens, as late diagnosis of systemic infection almost always equates with a poor prognosis. The field of fungal diagnostics has some tests that are relatively simple, rapid to perform and are potentially suitable at the point of care. However, there are also more complex high-technology methodologies that offer new opportunities regarding the scale and precision of fungal diagnosis, but may be more limited in their portability and affordability. Future developments in this field are increasingly incorporating new technologies provided by the use of new format biosensors. This overview provides a critical review of current fungal diagnostics and the development of new biophysical technologies that are being applied for selective new sensitive fungal biosensors to augment traditional diagnostic methodologies.
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Affiliation(s)
- Khalil K. Hussain
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; (D.M.); (E.M.J.)
| | - Dhara Malavia
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; (D.M.); (E.M.J.)
| | - Elizabeth M. Johnson
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; (D.M.); (E.M.J.)
- UK National Mycology Reference Laboratory (MRL), Public Health England South-West, Science Quarter Southmead Hospital, Southmead, Bristol BS10 5NB, UK
| | - Jennifer Littlechild
- Biocatalysis Centre, University of Exeter, The Henry Wellcome Building for Biocatalysis, Stocker Road, Exeter EX4 4QD, UK;
| | - C. Peter Winlove
- Department of Physics and Astronomy, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter EX4 4QD, UK;
| | - Frank Vollmer
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK;
| | - Neil A. R. Gow
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; (D.M.); (E.M.J.)
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Pinheiro BG, Hahn RC, de Camargo ZP, Rodrigues AM. Molecular Tools for Detection and Identification of Paracoccidioides Species: Current Status and Future Perspectives. J Fungi (Basel) 2020; 6:E293. [PMID: 33217898 PMCID: PMC7711936 DOI: 10.3390/jof6040293] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/01/2020] [Accepted: 11/05/2020] [Indexed: 12/14/2022] Open
Abstract
Paracoccidioidomycosis (PCM) is a mycotic disease caused by the Paracoccidioides species, a group of thermally dimorphic fungi that grow in mycelial form at 25 °C and as budding yeasts when cultured at 37 °C or when parasitizing the host tissues. PCM occurs in a large area of Latin America, and the most critical regions of endemicity are in Brazil, Colombia, and Venezuela. The clinical diagnosis of PCM needs to be confirmed through laboratory tests. Although classical laboratory techniques provide valuable information due to the presence of pathognomonic forms of Paracoccidioides spp., nucleic acid-based diagnostics gradually are replacing or complementing culture-based, biochemical, and immunological assays in routine microbiology laboratory practice. Recently, taxonomic changes driven by whole-genomic sequencing of Paracoccidioides have highlighted the need to recognize species boundaries, which could better ascertain Paracoccidioides taxonomy. In this scenario, classical laboratory techniques do not have significant discriminatory power over cryptic agents. On the other hand, several PCR-based methods can detect polymorphisms in Paracoccidioides DNA and thus support species identification. This review is focused on the recent achievements in molecular diagnostics of paracoccidioidomycosis, including the main advantages and pitfalls related to each technique. We discuss these breakthroughs in light of taxonomic changes in the Paracoccidioides genus.
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Affiliation(s)
- Breno Gonçalves Pinheiro
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (B.G.P.); (Z.P.d.C.)
| | - Rosane Christine Hahn
- Laboratory of Mycology/Research, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, Mato Grosso 78060900, Brazil;
- Federal University of Mato Grosso, Júlio Muller University Hospital, Mato Grosso 78048902, Brazil
| | - Zoilo Pires de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (B.G.P.); (Z.P.d.C.)
- Department of Medicine, Discipline of infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
| | - Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (B.G.P.); (Z.P.d.C.)
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O'Connor E, Coates CJ, Eastwood DC, Fitzpatrick DA, Grogan H. FISHing in fungi: Visualisation of mushroom virus X in the mycelium of Agaricus bisporus by fluorescence in situ hybridisation. J Microbiol Methods 2020; 173:105913. [DOI: 10.1016/j.mimet.2020.105913] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 12/15/2022]
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Mourad A, Perfect JR. What Can the Clinical Mycology Laboratory Do for Clinicians Today and Tomorrow? CURRENT CLINICAL MICROBIOLOGY REPORTS 2017. [DOI: 10.1007/s40588-017-0061-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Bassetti M, Garnacho-Montero J, Calandra T, Kullberg B, Dimopoulos G, Azoulay E, Chakrabarti A, Kett D, Leon C, Ostrosky-Zeichner L, Sanguinetti M, Timsit JF, Richardson MD, Shorr A, Cornely OA. Intensive care medicine research agenda on invasive fungal infection in critically ill patients. Intensive Care Med 2017; 43:1225-1238. [PMID: 28255613 DOI: 10.1007/s00134-017-4731-2] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 02/16/2017] [Indexed: 12/11/2022]
Abstract
PURPOSE To describe concisely the current standards of care, major recent advances, common beliefs that have been contradicted by recent trials, areas of uncertainty, and clinical studies that need to be performed over the next decade and their expected outcomes with regard to Candida and Aspergillus infections in non-neutropenic patients in the ICU setting. METHODS A systematic review of the medical literature taking account of national and international guidelines and expert opinion. RESULTS Severe invasive fungal infections (IFIs) are becoming increasingly frequent in critically ill patients. Approximately 80% of IFIs are due to Candida spp. and 0.3-19% to Aspergillus spp. Recent observations emphasize the necessity of building a worldwide sentinel network to monitor the emergence of new fungal species and changes in susceptibility. Robust data on the attributable mortality are essential for the design of clinical studies with mortality endpoints. Although early antifungal therapy for Candida has been recommended in patients with risk factors, sepsis of unknown cause, and positive Candida serum biomarkers [β-1 → 3-D-glucan (BDG) and Candida albicans germ tube antibody (CAGTA)], its usefulness and influence on outcome need to be confirmed. Future studies may specifically address the optimal diagnostic and therapeutic strategies for patients with abdominal candidiasis. Better knowledge of the pharmacokinetics of antifungal molecules and tissue penetration is a key issue for intensivists. Regarding invasive aspergillosis, further investigation is needed to determine its incidence in the ICU, its relationship with influenza outbreaks, the clinical impact of rapid diagnosis, and the significance of combination treatment. CONCLUSIONS Fundamental questions regarding IFI have to be addressed over the next decade. The clinical studies described in this research agenda should provide a template and set priorities for the clinical investigations that need to be performed.
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Affiliation(s)
- Matteo Bassetti
- Infectious Diseases Clinic, Santa Maria Misericordia Hospital, University of Udine, Udine, Italy. .,Clinica Malattie Infettive, Azienda Sanitaria Universitaria Integrata, Presidio Ospedaliero Santa Maria della Misericordia, Piazzale S. Maria della Misericordia, n. 15, 33100, Udine, Italy.
| | - Jose Garnacho-Montero
- Unidad Clínica de Cuidados Intensivos, Hospital Universitario Virgen Macarena and Institute of Biomedicine of Seville, IBiS/CSIC/University of Seville, seville, Spain
| | - Thierry Calandra
- Infectious Diseases Service, Department of Medicine, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Bartjan Kullberg
- Department of Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - George Dimopoulos
- Department of Critical Care, University Hospital ATTIKON, National and Kapodistrian University of Athens, Athens, Greece
| | - Elie Azoulay
- Medical Intensive Care Unit, Hôpital Saint-Louis, ECSTRA Team, Biostatistics and Clinical Epidemiology, Paris Diderot Sorbonne University, Paris, France
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Daniel Kett
- Division of Pulmonary and Critical Care Medicine, The Leonard M. Miller School of Medicine at the University of Miami, Miami, FL, USA
| | - Cristobal Leon
- Intensive Care Unit, Hospital Universitario de Valme, Universidad de Sevilla, Seville, Spain
| | | | | | - Jean-Francois Timsit
- 1UMR1137-IAMETeam 5, Decision Sciences in Infectious Disease Prevention, Control and Care, Paris Diderot University-Inserm, Sorbonne Paris Cité and 2AP-HP, Medical and Infectious Diseases ICU, Bichat Hospital, Paris, France
| | - Malcom D Richardson
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Andrew Shorr
- Pulmonary and Critical Care Medicine, Medstar Washington Hospital Center, Washington, USA
| | - Oliver A Cornely
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Clinical Trials Centre Cologne (ZKS Köln), Department I of Internal Medicine, German Centre for Infection Research (DZIF), University of Cologne, Cologne, 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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Identification of Fungal Pathogens in Tissue Samples from Patients with Proven Invasive Infection by Fluorescence In Situ Hybridization. Methods Mol Biol 2016. [PMID: 27837511 DOI: 10.1007/978-1-4939-6515-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
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.
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Batra V, Khararjian A, Wheat J, Zhang SX, Crain B, Baras A. From suspected Creutzfeldt-Jakob disease to confirmed histoplasma meningitis. BMJ Case Rep 2016; 2016:bcr-2016-214937. [PMID: 27389723 DOI: 10.1136/bcr-2016-214937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A 77-year-old man with chronic obstructive lung disease who was on steroids, presented to the hospital after a fall with subacute headaches and ataxia. During the patient's hospital course, his clinical condition deteriorated with myoclonic jerks, fevers and severe encephalopathy. An extensive workup, including EEG, brain MRI and lumbar puncture, revealed possible Creutzfeldt-Jakob disease. Unfortunately, the patient failed to improve and died 12 days after admission. A brain-only autopsy revealed he had acute histoplasma meningitis with patchy superficial cerebritis.
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Affiliation(s)
- Vivek Batra
- Department of Community Physicians, Johns Hopkins, Columbia, Maryland, USA
| | - Armen Khararjian
- Department of Pathology, Johns Hopkins, Baltimore, Maryland, USA
| | | | | | - Barbara Crain
- Department of Pathology, Johns Hopkins, Baltimore, Maryland, USA
| | - Alexander Baras
- Department of Pathology, Johns Hopkins, Baltimore, Maryland, USA
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