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Riebold D, Mahnkopf M, Wicht K, Zubiria-Barrera C, Heise J, Frank M, Misch D, Bauer T, Stocker H, Slevogt H. Axenic Long-Term Cultivation of Pneumocystis jirovecii. J Fungi (Basel) 2023; 9:903. [PMID: 37755011 PMCID: PMC10533121 DOI: 10.3390/jof9090903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/18/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023] Open
Abstract
Pneumocystis jirovecii, a fungus causing severe Pneumocystis pneumonia (PCP) in humans, has long been described as non-culturable. Only isolated short-term experiments with P. jirovecii and a small number of experiments involving animal-derived Pneumocystis species have been published to date. However, P. jirovecii culture conditions may differ significantly from those of animal-derived Pneumocystis, as there are major genotypic and phenotypic differences between them. Establishing a well-performing P. jirovecii cultivation is crucial to understanding PCP and its pathophysiological processes. The aim of this study, therefore, was to develop an axenic culture for Pneumocystis jirovecii. To identify promising approaches for cultivation, a literature survey encompassing animal-derived Pneumocystis cultures was carried out. The variables identified, such as incubation time, pH value, vitamins, amino acids, and other components, were trialed and adjusted to find the optimum conditions for P. jirovecii culture. This allowed us to develop a medium that produced a 42.6-fold increase in P. jirovecii qPCR copy numbers after a 48-day culture. Growth was confirmed microscopically by the increasing number and size of actively growing Pneumocystis clusters in the final medium, DMEM-O3. P. jirovecii doubling time was 8.9 days (range 6.9 to 13.6 days). In conclusion, we successfully cultivated P. jirovecii under optimized cell-free conditions in a 70-day long-term culture for the first time. However, further optimization of the culture conditions for this slow grower is indispensable.
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Affiliation(s)
- Diana Riebold
- Research Centre of Medical Technology and Biotechnology (FZMB), 99947 Bad Langensalza, Germany; (M.M.); (J.H.)
| | - Marie Mahnkopf
- Research Centre of Medical Technology and Biotechnology (FZMB), 99947 Bad Langensalza, Germany; (M.M.); (J.H.)
| | - Kristina Wicht
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, B-9000 Gent, Belgium;
| | - Cristina Zubiria-Barrera
- Respiratory Infection Dynamics Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (C.Z.-B.); (H.S.)
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, German Center for Lung Research (DZL), BREATH, 30625 Hannover, Germany
| | - Jan Heise
- Research Centre of Medical Technology and Biotechnology (FZMB), 99947 Bad Langensalza, Germany; (M.M.); (J.H.)
| | - Marcus Frank
- Medical Biology and Electron Microscopy Centre (EMZ), University Medicine Rostock, 18057 Rostock, Germany;
| | - Daniel Misch
- Lungenklinik Heckeshorn, Helios Klinikum Emil-von-Behring, 14165 Berlin, Germany; (D.M.); (T.B.)
| | - Torsten Bauer
- Lungenklinik Heckeshorn, Helios Klinikum Emil-von-Behring, 14165 Berlin, Germany; (D.M.); (T.B.)
| | - Hartmut Stocker
- Clinic for Infectiology, St. Joseph’s Hospital Berlin, 12101 Berlin, Germany;
| | - Hortense Slevogt
- Respiratory Infection Dynamics Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (C.Z.-B.); (H.S.)
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, German Center for Lung Research (DZL), BREATH, 30625 Hannover, Germany
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Cushion MT, Tisdale-Macioce N, Sayson SG, Porollo A. The Persistent Challenge of Pneumocystis Growth Outside the Mammalian Lung: Past and Future Approaches. Front Microbiol 2021; 12:681474. [PMID: 34093506 PMCID: PMC8174303 DOI: 10.3389/fmicb.2021.681474] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022] Open
Abstract
The pathogenic fungi in the genus, Pneumocystis, have eluded attempts to continuously grow them in an ex vivo cultivation system. New data from transcriptomic and genomic sequencing studies have identified a myriad of absent metabolic pathways, helping to define their host obligate nature. These nutrients, factors, and co-factors are acquired from their mammalian host and provide clues to further supplementation of existing media formulations. Likewise, a new appreciation of the pivotal role for the sexual cycle in the survival and dissemination of the infection suggests that Pneumocystis species are obligated to undergo mating and sexual reproduction in their life cycle with a questionable role for an asexual cycle. The lack of ascus formation in any previous cultivation attempts may explain the failure to identify a sustainable system. Many characteristics of these ascomycetes suggest a biotrophic existence within the lungs of the mammalian hosts. In the present review, previous attempts at growing these fungi ex vivo are summarized. The significance of their life cycle is considered, and a list of potential supplements based on the genomic and transcriptomic studies is presented. State of the art technologies such as metabolomics, organoids, lung-on-a chip, and air lift cultures are discussed as potential growth systems.
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Affiliation(s)
- Melanie T Cushion
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Medical Research Service, Cincinnati Veterans Affairs Medical Center, Cincinnati, OH, United States
| | - Nikeya Tisdale-Macioce
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Medical Research Service, Cincinnati Veterans Affairs Medical Center, Cincinnati, OH, United States
| | - Steven G Sayson
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Medical Research Service, Cincinnati Veterans Affairs Medical Center, Cincinnati, OH, United States
| | - Aleksey Porollo
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
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Abstract
PURPOSE OF REVIEW Pneumocystis pneumonia (PCP) is a frequent opportunistic infection associated with a high mortality rate. PCP is of increasing importance in non-HIV immunocompromised patients, who present with severe respiratory distress with low fungal loads. Molecular detection of Pneumocystis in broncho-alveolar lavage (BAL) has become an important diagnostic tool, but quantitative PCR (qPCR) needs standardization. RECENT FINDINGS Despite a high negative predictive value, the positive predictive value of qPCR is moderate, as it also detects colonized patients. Attempts are made to set a cut-off value of qPCR to discriminate between PCP and colonization, or to use noninvasive samples or combined strategies to increase specificity. SUMMARY It is easy to set a qPCR cut-off for HIV-infected patients. In non-HIV IC patients, a gain in specificity could be obtained by combining strategies, that is, qPCR on BAL and a noninvasive sample, or qPCR and serum beta-1,3-D-glucan dosage.
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Pneumocystosis and quantitative PCR. Med Mal Infect 2018; 48:474-480. [DOI: 10.1016/j.medmal.2018.04.396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 09/06/2017] [Accepted: 04/25/2018] [Indexed: 12/24/2022]
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Martínez Lamas L, Pérez Rodríguez MT, Álvarez Ramos I, Bouza Soage ME, Figueroa Lamas MP, Álvarez Fernández M. Role of Pneumocystis jirovecii in patients with different pulmonary underlying condition using a nested-PCR. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2018; 31:336-343. [PMID: 29956896 PMCID: PMC6172691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/07/2018] [Accepted: 05/11/2018] [Indexed: 11/17/2022]
Abstract
OBJECTIVE The prevalence of Pneumocystis jirovecii colonization and its role in pulmonary disease remains unclear. PCR methods have shown an improved sensitivity in the detection of this fungus. It has been suggested that the PCR results be combined with another test such as IFA to create a diagnostic algorithm. METHODS A multiplex nested-PCR procedure with a 16S rRNA gene as the internal amplification control was evaluated to determine the role of P. jirovecii in pulmonary disease. RESULTS A 20% of the 199 bronchoalveolar lavage samples were PCR-positive, 13.5% samples were PCR-inhibited, and the rate of Pneumocystis-colonisation was 6.4%. The sensitivity, specificity, positive predictive value and negative predictive value of the nested-PCR were 100%, 93%, 70% and 100%, respectively. The sensitivity of the nested-PCR was higher than the current "gold standard" immunofluorescence assay (IFA) (p< 0.0001). PCR-negative and PCR-positive patients did not show any clinical or radiological differences in the medical variables studied. CONCLUSIONS PCR could help the diagnosis of Pneumocystis pulmonary disease given the high negative predictive value of the technique. P. jirovecii DNA can frequently be detected in healthy population, so the analysis of the patient medical history is critical to make the correct clinical decision.
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Affiliation(s)
- L Martínez Lamas
- Lucía Martínez Lamas, Hospital Meixoeiro. EOXI Vigo, C/Camiño do Miexoeiro s/n, CP: 36200 Vigo. Pontevedra. Galicia. Spain.
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Rudramurthy SM, Sharma M, Sharma M, Rawat P, Ghosh A, Venkatesan L, Aggarwal R, Singh M, Chakrabarti A. Reliable differentiation of Pneumocystis pneumonia from Pneumocystis colonisation by quantification of Major Surface Glycoprotein gene using real-time polymerase chain reaction. Mycoses 2017; 61:96-103. [DOI: 10.1111/myc.12708] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 09/21/2017] [Accepted: 09/21/2017] [Indexed: 12/01/2022]
Affiliation(s)
- Shivaprakash M. Rudramurthy
- Department of Medical Microbiology; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Megha Sharma
- Department of Medical Microbiology; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Madhubala Sharma
- Department of Medical Microbiology; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Pankaj Rawat
- Department of Medical Microbiology; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Anup Ghosh
- Department of Medical Microbiology; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Lakshmishree Venkatesan
- Department of Medical Microbiology; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Ritesh Aggarwal
- Department of Pulmonary Medicine; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Meenu Singh
- Department of Pediatrics; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology; Postgraduate Institute of Medical Education and Research; Chandigarh India
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Iturra PA, Rojas DA, Pérez FJ, Méndez A, Ponce CA, Bonilla P, Bustamante R, Rodríguez H, Beltrán CJ, Vargas SL. Progression of Type 2 Helper T Cell-Type Inflammation and Airway Remodeling in a Rodent Model of Naturally Acquired Subclinical Primary Pneumocystis Infection. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 188:417-431. [PMID: 29169991 DOI: 10.1016/j.ajpath.2017.10.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/03/2017] [Accepted: 10/19/2017] [Indexed: 12/25/2022]
Abstract
Subclinical primary Pneumocystis infection is the most common pulmonary infection in early infancy, making it important to determine whether it damages the lung. Pneumocystis peaks at 2 to 5 months of age, when respiratory morbidity coincidently increases. We have documented that Pneumocystis increases mucus production in infant lungs, and animal models reveal lung lesions that warrant characterization. Herein, immunocompetent rats infected at birth with Pneumocystis by cohabitation, to resemble community-acquired infection, underwent lung assessments at 45, 60, and 75 days of age. Lungs fixed by vascular perfusion to prevent collapse during necropsy were used for morphometry evaluations of mucus production, airway epithelial thickening, perivascular and peribronchiolar inflammation, and structural airway remodeling. Changes in these histologic features indicate lung disease. Selected immune markers were assessed in parallel using fresh-frozen lung tissue from sibling rats of the same cages. Sequential activation of NF-κB and an increased Gata3/T-bet mRNA level ratio, consistent with a type 2 helper T-cell-type inflammatory response, and subacute fibrosis were recognized. Therefore, documenting subclinical Pneumocystis infection induces lung disease in the immunocompetent host. Taken together with the peak age of primary Pneumocystis infection, results warrant investigating the clinical impact of this often subclinical infection on the severity of respiratory diseases in early infancy. This model can also be used to assess the effects of airway insults, including coinfections by recognized respiratory pathogens.
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Affiliation(s)
- Pablo A Iturra
- Microbiology and Mycology Program, Biomedical Sciences Institute, University of Chile School of Medicine, Santiago, Chile
| | - Diego A Rojas
- Microbiology and Mycology Program, Biomedical Sciences Institute, University of Chile School of Medicine, Santiago, Chile
| | - Francisco J Pérez
- Microbiology and Mycology Program, Biomedical Sciences Institute, University of Chile School of Medicine, Santiago, Chile
| | - Andrea Méndez
- Microbiology and Mycology Program, Biomedical Sciences Institute, University of Chile School of Medicine, Santiago, Chile
| | - Carolina A Ponce
- Microbiology and Mycology Program, Biomedical Sciences Institute, University of Chile School of Medicine, Santiago, Chile
| | - Paula Bonilla
- Microbiology and Mycology Program, Biomedical Sciences Institute, University of Chile School of Medicine, Santiago, Chile
| | - Rebeca Bustamante
- Microbiology and Mycology Program, Biomedical Sciences Institute, University of Chile School of Medicine, Santiago, Chile
| | - Héctor Rodríguez
- Anatomy and Developmental Biology Program, Biomedical Sciences Institute, University of Chile School of Medicine, Santiago, Chile
| | - Caroll J Beltrán
- Gastroenterology Division, University Hospital, University of Chile School of Medicine, Santiago, Chile
| | - Sergio L Vargas
- Microbiology and Mycology Program, Biomedical Sciences Institute, University of Chile School of Medicine, Santiago, Chile.
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Alanio A, Gits-Muselli M, Guigue N, Desnos-Ollivier M, Calderon EJ, Di Cave D, Dupont D, Hamprecht A, Hauser PM, Helweg-Larsen J, Kicia M, Lagrou K, Lengerova M, Matos O, Melchers WJG, Morio F, Nevez G, Totet A, White LP, Bretagne S. Diversity of Pneumocystis jirovecii Across Europe: A Multicentre Observational Study. EBioMedicine 2017; 22:155-163. [PMID: 28705464 PMCID: PMC5552205 DOI: 10.1016/j.ebiom.2017.06.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/13/2017] [Accepted: 06/28/2017] [Indexed: 12/30/2022] Open
Abstract
Pneumocystis jirovecii is an airborne human-specific ascomycetous fungus responsible for Pneumocystis pneumonia (PCP) in immunocompromised patients, affecting >500,000 patients per year (www.gaffi.org). The understanding of its epidemiology is limited by the lack of standardised culture. Recent genotyping data suggests a limited genetic diversity of P. jirovecii. The objective of the study was to assess the diversity of P. jirovecii across European hospitals and analyse P. jirovecii diversity in respect to clinical data obtained from the patients. Genotyping was performed using six already validated short tandem repeat (STR) markers on 249 samples (median: 17 per centre interquartile range [11-20]) from PCP patients of 16 European centres. Mixtures of STR markers (i.e., ≥2 alleles for ≥1 locus) were detected in 67.6% (interquartile range [61.4; 76.5]) of the samples. Mixture was significantly associated with the underlying disease of the patient, with an increased proportion in HIV patients (78.3%) and a decreased proportion in renal transplant recipients (33.3%) (p<0.001). The distribution of the alleles was significantly different (p<0.001) according to the centres in three out of six markers. In analysable samples, 201 combinations were observed corresponding to 137 genotypes: 116 genotypes were country-specific; 12 in two; six in three; and two in four and one in five countries. Nine genotypes were recorded more than once in a given country. Genotype 123 (Gt123) was significantly associated with France (14/15, p<0.001) and Gt16 with Belgium (5/5, p<0.001). More specifically, Gt123 was observed mainly in France (14/15/16 patients) and in renal transplant patient (13/15). Our study showed the wide population diversity across Europe, with evidence of local clusters of patients harbouring a given genotype. These data suggest a specific association between genotype and underlying disease, with evidence of a different natural history of PCP in HIV patients and renal transplant recipients.
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Affiliation(s)
- Alexandre Alanio
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Institut Pasteur, CNRS, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, URA3012, Paris, France.
| | - Maud Gits-Muselli
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Nicolas Guigue
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France
| | - Marie Desnos-Ollivier
- Institut Pasteur, CNRS, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, URA3012, Paris, France
| | - Enrique J Calderon
- CIBER de Epidemiología y Salud Pública, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío, CSIC, Universidad de Sevilla, Spain
| | - David Di Cave
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Italy
| | - Damien Dupont
- Hospices Civils de Lyon, Institut des Agents Infectieux, Parasitologie Mycologie, Hôpital de la Croix-Rousse, Integrative Physiology of the Brain Arousal Systems, Centre de Recherche en Neurosciences de Lyon, INSERM U1028-CNRS UMR 5292, Faculté de Médecine, Université Claude Bernard Lyon 1, Lyon F-69000, France
| | - Axel Hamprecht
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Germany
| | - Philippe M Hauser
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Jannik Helweg-Larsen
- Department of Infectious Diseases, Rigshospitalet-Copenhagen University Hospital, Copenhagen, Denmark
| | - Marta Kicia
- Department of Biology & Medical Parasitology, Wroclaw Medical University, Wroclaw, Poland
| | - Katrien Lagrou
- Department of Microbiology and Immunology, Catholic University Leuven, Leuven, Belgium and National Reference Centre for Mycosis, Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Martina Lengerova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Olga Matos
- TB, HIV and Opportunistic Diseases and Pathogens, Global Health and Tropical Medicine, Lisboa, Portugal; Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Willem J G Melchers
- Department of medical microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Florent Morio
- Parasitology and Mycology laboratory, Nantes University Hospital, Nantes, France
| | - Gilles Nevez
- University of Brest, GEIHP EA 3142, Laboratory of Parasitology and Mycology, Brest University Hospital, Brest, France
| | - Anne Totet
- University of Picardy-Jules Verne, EA 4285 UMR-I 01 INERIS, Department of Parasitology and Mycology, Amiens University Hospital, Amiens, France
| | - Lewis P White
- Public Health Wales, Microbiology Cardiff, UHW, Heath Park, Cardiff, UK
| | - Stéphane Bretagne
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Institut Pasteur, CNRS, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, URA3012, Paris, France
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Lahmer T, da Costa CP, Held J, Rasch S, Ehmer U, Schmid RM, Huber W. Usefulness of 1,3 Beta-D-Glucan Detection in non-HIV Immunocompromised Mechanical Ventilated Critically Ill Patients with ARDS and Suspected Pneumocystis jirovecii Pneumonia. Mycopathologia 2017; 182:701-708. [PMID: 28378239 DOI: 10.1007/s11046-017-0132-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 03/26/2017] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Pneumocystis jirovecii pneumonia (PCP) is a major cause of disease in immunocompromised individuals. Diagnosis is typically obtained by microscopy and/or PCR. For ambiguous PCR results, we evaluated the new biomarker 1,3-Beta-D-Glucan (BDG). METHODS BDG serum levels were assessed and correlated to PCR results in immunosuppressed patients with ARDS. RESULTS 11 (22%) out of 50 patients had suspected PCP. APACHE II (26 vs. 24; p < 0.002), SOFA score (16 vs. 14; p < 0.010) and mortality rate (34 vs. 69% p < 0.004; 34 vs. 80% p < 0.003) were significantly altered in patients with positive (pPCR) and slightly positive (spPCR) PCJ PCR as compared to patients with no-PCP (nPCP). BDG levels were significantly lower in patients with nPCP (86; 30-315 pg/ml) than in patients with pPCR (589; 356-1000 pg/ml; p < 0.001) and spPCP (398; 297-516 pg/ml; p < 0.004) referring to the cutoff in this study for PCP of 275 pg/ml. An overall sensitivity (S) of 92% (95% CI 86-96%) and specificity (SP) of 84% (95% CI 79-85%) for PCP were found for the BDG Fungitell assay. In detail, S of 98% (95% CI 94-100%) and SP of 86% (95% CI 82-92%) for pPCP and S of 98% (95% CI 96-100%) and SP of 88% (95% CI 86-96%) for spPCO were found. CONCLUSION Serum BDG levels were strongly elevated in PCP, and the negative predictive value is high. BDG could be used as a preliminary test for patients with suspected PCP, especially in patients with slightly positive PCR results.
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Affiliation(s)
- Tobias Lahmer
- II. Medizinische Klinik und Poliklinik, Klinikum rechts der Isar der Technischen Universität München, Ismaninger Str. 22, 81675, Munich, Germany.
| | - Clarissa Prazeres da Costa
- Institut für Medizinische Mikrobiologie, Immunologie und HygieneTechnische Universität München, Munich, Germany
| | - Jürgen Held
- Mikrobiologisches Institut, Universitätsklinik Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Sebastian Rasch
- II. Medizinische Klinik und Poliklinik, Klinikum rechts der Isar der Technischen Universität München, Ismaninger Str. 22, 81675, Munich, Germany
| | - Ursula Ehmer
- II. Medizinische Klinik und Poliklinik, Klinikum rechts der Isar der Technischen Universität München, Ismaninger Str. 22, 81675, Munich, Germany
| | - Roland M Schmid
- II. Medizinische Klinik und Poliklinik, Klinikum rechts der Isar der Technischen Universität München, Ismaninger Str. 22, 81675, Munich, Germany
| | - Wolfgang Huber
- II. Medizinische Klinik und Poliklinik, Klinikum rechts der Isar der Technischen Universität München, Ismaninger Str. 22, 81675, Munich, Germany
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Chaubey KK, Gupta RD, Gupta S, Singh SV, Bhatia AK, Jayaraman S, Kumar N, Goel A, Rathore AS, Sahzad, Sohal JS, Stephen BJ, Singh M, Goyal M, Dhama K, Derakhshandeh A. Trends and advances in the diagnosis and control of paratuberculosis in domestic livestock. Vet Q 2016; 36:203-227. [PMID: 27356470 DOI: 10.1080/01652176.2016.1196508] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Paratuberculosis (pTB) is a chronic granulomatous enteritis caused by Mycobacterium avium subsp. paratuberculosis (MAP) in a wide variety of domestic and wild animals. Control of pTB is difficult due to the lack of sensitive, efficacious and cost-effective diagnostics and marker vaccines. Microscopy, culture, and PCR have been used for the screening of MAP infection in animals for quite a long time. Besides, giving variable sensitivity and specificity, these tests have not been considered ideal for large-scale screening of domestic livestock. Serological tests like ELISA easily detects anti-MAP antibodies. However, it cannot differentiate between the vaccinated and infected animals. Nanotechnology-based diagnostic tests are underway to improve the sensitivity and specificity. Newer generation diagnostic tests based on recombinant MAP secretory proteins would open new paradigm for the differentiation between infected and vaccinated animals and for early detection of the infection. Due to higher seroreactivity of secretory proteins vis-à-vis cellular proteins, the secretory proteins may be used as marker vaccine, which may aid in the control of pTB infection in animals. Secretory proteins can be potentially used to develop future diagnostics, surveillance and monitoring of the disease progression in animals and the marker vaccine for the control and eradication of pTB.
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Affiliation(s)
- Kundan Kumar Chaubey
- a Microbiology Laboratory, Animal Health Division , Central Institute for Research on Goats , Mathura , India.,b Department of Microbiology and Immunology , GLA University , Mathura , India
| | - Rinkoo Devi Gupta
- c Department of Life sciences and Biotechnology , South Asian University , New Delhi , India
| | - Saurabh Gupta
- a Microbiology Laboratory, Animal Health Division , Central Institute for Research on Goats , Mathura , India.,b Department of Microbiology and Immunology , GLA University , Mathura , India
| | - Shoor Vir Singh
- a Microbiology Laboratory, Animal Health Division , Central Institute for Research on Goats , Mathura , India
| | - Ashok Kumar Bhatia
- b Department of Microbiology and Immunology , GLA University , Mathura , India
| | - Sujata Jayaraman
- d Amity Institutes of Microbial Technology , Amity University , Jaipur , India
| | - Naveen Kumar
- a Microbiology Laboratory, Animal Health Division , Central Institute for Research on Goats , Mathura , India
| | - Anjana Goel
- b Department of Microbiology and Immunology , GLA University , Mathura , India
| | - Abhishek Singh Rathore
- c Department of Life sciences and Biotechnology , South Asian University , New Delhi , India
| | - Sahzad
- a Microbiology Laboratory, Animal Health Division , Central Institute for Research on Goats , Mathura , India
| | - Jagdip Singh Sohal
- d Amity Institutes of Microbial Technology , Amity University , Jaipur , India
| | - Bjorn John Stephen
- a Microbiology Laboratory, Animal Health Division , Central Institute for Research on Goats , Mathura , India
| | - Manju Singh
- a Microbiology Laboratory, Animal Health Division , Central Institute for Research on Goats , Mathura , India
| | - Manish Goyal
- e Division of Parasitology , Central Drug Research Institute , Lucknow , India
| | - Kuldeep Dhama
- f Pathology Division , Indian Veterinary Research Institute (IVRI) , Bareilly , India
| | - Abdollah Derakhshandeh
- g Department of Pathobiology, School of Veterinary Medicine , Shiraz University , Shiraz , Iran
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Ma L, Chen Z, Huang DW, Kutty G, Ishihara M, Wang H, Abouelleil A, Bishop L, Davey E, Deng R, Deng X, Fan L, Fantoni G, Fitzgerald M, Gogineni E, Goldberg JM, Handley G, Hu X, Huber C, Jiao X, Jones K, Levin JZ, Liu Y, Macdonald P, Melnikov A, Raley C, Sassi M, Sherman BT, Song X, Sykes S, Tran B, Walsh L, Xia Y, Yang J, Young S, Zeng Q, Zheng X, Stephens R, Nusbaum C, Birren BW, Azadi P, Lempicki RA, Cuomo CA, Kovacs JA. Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts. Nat Commun 2016; 7:10740. [PMID: 26899007 PMCID: PMC4764891 DOI: 10.1038/ncomms10740] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/13/2016] [Indexed: 02/07/2023] Open
Abstract
Pneumocystis jirovecii is a major cause of life-threatening pneumonia in immunosuppressed patients including transplant recipients and those with HIV/AIDS, yet surprisingly little is known about the biology of this fungal pathogen. Here we report near complete genome assemblies for three Pneumocystis species that infect humans, rats and mice. Pneumocystis genomes are highly compact relative to other fungi, with substantial reductions of ribosomal RNA genes, transporters, transcription factors and many metabolic pathways, but contain expansions of surface proteins, especially a unique and complex surface glycoprotein superfamily, as well as proteases and RNA processing proteins. Unexpectedly, the key fungal cell wall components chitin and outer chain N-mannans are absent, based on genome content and experimental validation. Our findings suggest that Pneumocystis has developed unique mechanisms of adaptation to life exclusively in mammalian hosts, including dependence on the lungs for gas and nutrients and highly efficient strategies to escape both host innate and acquired immune defenses.
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Affiliation(s)
- Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Zehua Chen
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Da Wei Huang
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Geetha Kutty
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Mayumi Ishihara
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
| | - Honghui Wang
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Amr Abouelleil
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Lisa Bishop
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Emma Davey
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Rebecca Deng
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Xilong Deng
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Lin Fan
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Giovanna Fantoni
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Michael Fitzgerald
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Emile Gogineni
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Jonathan M. Goldberg
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Grace Handley
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Xiaojun Hu
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Charles Huber
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Xiaoli Jiao
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Kristine Jones
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Joshua Z. Levin
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Yueqin Liu
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Pendexter Macdonald
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Alexandre Melnikov
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Castle Raley
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Monica Sassi
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Brad T. Sherman
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Xiaohong Song
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Sean Sykes
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Bao Tran
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Laura Walsh
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Yun Xia
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Jun Yang
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Sarah Young
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Qiandong Zeng
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Xin Zheng
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Robert Stephens
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Chad Nusbaum
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Bruce W. Birren
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
| | - Richard A. Lempicki
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Christina A. Cuomo
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Joseph A. Kovacs
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
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Quantitative real-time PCR (qPCR) for Eimeria tenella replication--Implications for experimental refinement and animal welfare. Parasitol Int 2015; 64:464-70. [PMID: 26141544 PMCID: PMC4534708 DOI: 10.1016/j.parint.2015.06.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 11/21/2022]
Abstract
The Eimeria species are highly pathogenic parasites of chickens. Research aimed at reducing their impact is hindered by a lack of non-subjective, quantitative, tools to measure parasite replication in the host. The time-consuming, and often time-sensitive, nature of existing approaches precludes their use in large-scale genetic, epidemiological, and evolutionary analyses. We have used quantitative real-time PCR (qPCR) to accurately quantify Eimeria tenella in chicken tissue and shown this to be more efficient and sensitive than traditional methodologies. We tested four chicken-specific reference qPCR assays and found beta-actin (actb) to be optimal for sample normalisation. In an experimental setting, chickens were inoculated with 500, 1500, or 4500 E. tenella oocysts and parasite replication and the impact of infection measured by i) qPCR analysis of DNA extracted from caecal tissues collected at five and eight days post-infection (dpi), ii) faecal oocyst counts (FOCs) on samples taken from six to eight dpi, and iii) lesion scoring on caeca collected post-mortem at five and eight dpi. Quantitative real-time PCR test results indicated a significant dose-dependent increase in parasite numbers among study groups for samples collected five dpi (i.e., prior to gametogony) (R2 = 0.994) (p < 0.002) but not in those from day eight (after most oocyst shedding) (R2 = 0.006) (p > 0.379). A strong dose-dependent increase in parasite replication and severity of infection was also revealed by FOC (R2 = 0.997) and lesion scoring. Importantly, qPCR offers substantial improvements for animal welfare via improved statistical power and reduced group sizes in experimental studies. The described qPCR method overcomes subjective limitations of coproscopic quantification, allows reproducible medium- to high-throughput examination of tissues, faeces, and oocysts, and is a valuable tool for determining the impact of Eimeria infections in both experimental and field settings. Quantitative PCR indicates significant dose-dependent increases in parasites. More sensitive measure of parasite replication than faecal oocyst count/lesion score Significant implications for animal welfare and experiment refinement (3R's) Support studies focusing on the genetic basis of resistance/susceptibility Major implications for investigations of key aspects of Eimeria biology and control
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Martin SI, Fishman JA. Pneumocystis pneumonia in solid organ transplantation. Am J Transplant 2013; 13 Suppl 4:272-9. [PMID: 23465020 DOI: 10.1111/ajt.12119] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- S I Martin
- Division of Infectious Diseases and Comprehensive Transplant Center at The Ohio State University, Wexner Medical Center, Columbus, OH, USA.
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Ma L, Huang DW, Cuomo CA, Sykes S, Fantoni G, Das B, Sherman BT, Yang J, Huber C, Xia Y, Davey E, Kutty G, Bishop L, Sassi M, Lempicki RA, Kovacs JA. Sequencing and characterization of the complete mitochondrial genomes of three Pneumocystis species provide new insights into divergence between human and rodent Pneumocystis. FASEB J 2013; 27:1962-72. [PMID: 23392351 DOI: 10.1096/fj.12-224444] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Pneumocystis jirovecii is an important opportunistic pathogen associated with AIDS and other immunodeficient conditions. Currently, very little is known about its nuclear and mitochondrial genomes. In this study, we sequenced the complete mitochondrial genome (mtDNA) of this organism and its closely related species Pneumocystis carinii and Pneumocystis murina by a combination of sequencing technologies. Our study shows that P. carinii and P. murina mtDNA share a nearly identical number and order of genes in a linear configuration, whereas P. jirovecii has a circular mtDNA containing nearly the same set of genes but in a different order. Detailed studies of the mtDNA terminal structures of P. murina and P. carinii suggest a unique replication mechanism for linear mtDNA. Phylogenetic analysis supports a close association of Pneumocystis species with Taphrina, Saitoella, and Schizosaccharomyces, and divergence within Pneumocystis species, with P. murina and P. carinii being more closely related to each other than either is to P. jirovecii. Comparative analysis of four complete P. jirovecii mtDNA sequences in this study and previously reported mtDNA sequences for diagnosing and genotyping suggests that the current diagnostic and typing methods can be improved using the complete mtDNA data. The availability of the complete P. jirovecii mtDNA also opens the possibility of identifying new therapeutic targets.
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Affiliation(s)
- Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, 10 Center Dr., Bethesda, MD 20892, USA.
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15
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Cavallini Sanches EM, Ferreiro L, Andrade CP, Pacheco SM, Almeida LL, Spanamberg A, Wissmann G. Pneumocystis sp. in bats evaluated by qPCR. J Mycol Med 2013; 23:47-52. [PMID: 23380373 DOI: 10.1016/j.mycmed.2012.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 11/20/2012] [Accepted: 11/27/2012] [Indexed: 10/27/2022]
Abstract
Molecular techniques have revealed a high prevalence of Pneumocystis colonization in wild mammals. Accurate quantification of Pneumocystis sp. is essential for the correct interpretation of many research experiments investigating this organism. The objectives of this study were to detect the presence of Pneumocystis sp. in bats by qPCR, and to distinguish colonization from infection. Probes and primers for real time PCR (qPCR) were designed based on the gene of major surface glycoprotein (MSG) of Pneumocystis sp., in order to analyze 195 lung tissue samples from bats captured (2007-2009). All samples were also analyzed by nested PCR, using oligonucleotide primers designed for the gene encoding the mitochondrial small subunit rRNA (mtSSU rRNA) to confirm the results. The qPCR assay was standardized using a standard curve made with the DNA extracted from bronchoalveolar lavage positive for Pneumocystis jirovecii. The average Ct was found to be between 13 and 14 (calibration curve) for the detection of infection with Pneumocystis sp. and above these values for colonization. It was considered as negative samples the ones that had Ct values equal to 50. Out of the total 195 samples, 47 (24.1%) bat lung DNA samples were positive for Pneumocystis sp. by qPCR. The most common bat species found were: Tadarida brasiliensis (23.4%), Histiotus velatus (17.0%), Desmodus rotundus (14.9%) and Molossus molossus (8.5%). The average cycle threshold of the positive samples (bats) was 25.8 and standard deviation was 1.7. The DNA samples with Ct values greater than 14 suggest that these animals might be colonized by Pneumocystis sp. Results obtained in this study demonstrated the usefulness of the qPCR procedure for identification of Pneumocystis sp. and for distinction between its colonizing or infectious status in bats.
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Affiliation(s)
- E M Cavallini Sanches
- Setor de Micologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
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16
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Validation of the MycAssay Pneumocystis kit for detection of Pneumocystis jirovecii in bronchoalveolar lavage specimens by comparison to a laboratory standard of direct immunofluorescence microscopy, real-time PCR, or conventional PCR. J Clin Microbiol 2012; 50:1856-9. [PMID: 22422855 DOI: 10.1128/jcm.05880-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pneumocystis jirovecii pneumonia is a significant cause of morbidity and mortality in AIDS patients as well as those with non-HIV immunosuppressive diseases. To aid diagnosis, the commercial MycAssay Pneumocystis real-time PCR assay (Myconostica, Ltd., Manchester, United Kingdom) targeting the mitochondrial ribosomal large subunit (mtLSU) has been developed to detect P. jirovecii in bronchoalveolar lavage (BAL) specimens. Here, we validated this assay against a laboratory standard of direct immunofluorescence microscopy, a cdc2 real-time PCR assay, or conventional PCR and sequencing of mtLSU. While more sensitive than any of these three assays analyzed individually, the MycAssay Pneumocystis assay demonstrated 100% sensitivity, 100% specificity, a 100% negative predictive value, and a 100% positive predictive value for detecting the presence of P. jirovecii in BAL specimens compared to the laboratory standard. Of note, two samples with positive cycle threshold (C(T)) values according to the MycAssay Pneumocystis assay lacked exponential amplification curves and thus were deemed negative. Also negative according to the laboratory standard, these samples highlight the importance of examining the amplification curves, in addition to noting the C(T) values, when interpreting positive results. Comparison of the MycAssay Pneumocystis assay to a laboratory standard establishes this assay to be a highly sensitive and specific method for the detection of P. jirovecii in bronchoalveolar lavage specimens. The approach may also be useful for the clinical laboratory validation of other sensitive real-time PCR assays.
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Clinical significance of quantifying Pneumocystis jirovecii DNA by using real-time PCR in bronchoalveolar lavage fluid from immunocompromised patients. J Clin Microbiol 2011; 50:227-31. [PMID: 22162560 DOI: 10.1128/jcm.06036-11] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Quantitative PCR (qPCR) is more sensitive than microscopy for detecting Pneumocystis jirovecii in bronchoalveolar lavage (BAL) fluid. We therefore developed a qPCR assay and compared the results with those of a routine immunofluorescence assay (IFA) and clinical data. The assay included automated DNA extraction, amplification of the mitochondrial large-subunit rRNA gene and an internal control, and quantification of copy numbers with the help of a plasmid clone. We studied 353 consecutive BAL fluids obtained for investigation of unexplained fever and/or pneumonia in 287 immunocompromised patients. No qPCR inhibition was observed. Seventeen (5%) samples were both IFA and qPCR positive, 63 (18%) were IFA negative and qPCR positive, and 273 (77%) were both IFA and qPCR negative. The copy number was significantly higher for IFA-positive/qPCR-positive samples than for IFA-negative/qPCR-positive samples (4.2 ± 1.2 versus 1.1 ± 1.1 log(10) copies/μl; P < 10(-4)). With IFA as the standard, the qPCR assay sensitivity was 100% for ≥2.6 log(10) copies/μl and the specificity was 100% for ≥4 log(10) copies/μl. Since qPCR results were not available at the time of decision-making, these findings did not trigger cotrimoxazole therapy. Patients with systemic inflammatory diseases and IFA-negative/qPCR-positive BAL fluid had a worse 1-year survival rate than those with IFA-negative/qPCR-negative results (P < 10(-3)), in contrast with solid-organ transplant recipients (P = 0.88) and patients with hematological malignancy (P = 0.26). Quantifying P. jirovecii DNA in BAL fluids independently of IFA positivity should be incorporated into the investigation of pneumonia in immunocompromised patients. The relevant threshold remains to be determined and may vary according to the underlying disease.
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18
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Duan YN, Yi LH, Chen JL, Zhu DD, Wang JX, Feng JR, Qin YW, Zhu Y. Protective effect of DNA vaccine with the gene encoding 55kDa antigen fragment against Pneumocystis carinii in mice. ASIAN PAC J TROP MED 2011; 4:353-6. [PMID: 21771675 DOI: 10.1016/s1995-7645(11)60102-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 04/27/2011] [Accepted: 05/05/2011] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE To evaluate the protective effect of DNA vaccine with the gene encoding 55kDa antigen fragment of Pneumocystis carinii (P. carinii) against P. carinii in mice. METHODS The fragment of the antigen within p55(p55-582) was cloned. Then recombinant plasmid was constructed based on the eukaryotic expression vector pcDNA3.1(+). BALB/c mice were used as experimental models to examine the immunogenicity of pcDNA3.1(+)-p55-582. ELISA and RT-PCR were used to evaluate the role of this kind of DNA vaccine. RESULTS The results of western blot indicated that the recombinant DNA[pcDNA3.1(+)-p55-582] could be expressed correctly and had antigenicity in transfected COS-7 cells. ELISA and RT-PCR showed that pcDNA3.1(+)-p55-582 elicited antibody production, stimulated lymphocyte proliferation and provided partial protection by reducing the P. carinii burden. CONCLUSIONS The data demonstrate that pcDNA3.1(+)-p55-582 might be potent vaccination that can afford the partial protection for the immunized animals.
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Affiliation(s)
- Yi-nong Duan
- Department of Parasitology and Microbiology, School of Medicine, Nantong University, Nantong, Jiangsu Province, 226001, China.
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Döşkaya M, Caner A, Değirmenci A, Wengenack NL, Yolasığmaz A, Turgay N, Özensoy Töz S, Gürüz Y. Degree and frequency of inhibition in a routine real-time PCR detecting Pneumocystis jirovecii for the diagnosis of Pneumocystis pneumonia in Turkey. J Med Microbiol 2011; 60:937-944. [PMID: 21459903 DOI: 10.1099/jmm.0.030775-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Routine laboratory diagnosis of Pneumocystis jirovecii is currently achieved by PCR in almost all laboratories with sufficient equipment due to its high sensitivity and specificity compared to staining methods. A current issue that limits the reliability and sensitivity of PCR is the degree of inhibition caused by inhibitory substances in respiratory samples. The present study aimed to analyse the degree and frequency of inhibition in real-time PCR detecting P. jirovecii in respiratory specimens submitted to a Pneumocystis pneumonia (PcP) diagnosis laboratory in Ege University Medical School, Turkey. Between July 2009 and December 2010, 76 respiratory specimens [63 bronchoalveolar lavage (BAL) fluid, 10 sputum samples, two tracheal aspiration fluid and one thoracentesis fluid] obtained from 69 PcP-suspected patients were investigated for the presence of P. jirovecii using real-time PCR targeting the cdc2 gene. Of these samples, 42 of the specimens were stained and examined by microscopy according to the request of the clinicians. PCR was positive in 15 specimens in the initial run. Of the remaining 61 samples, 41 of them were negative with positive internal inhibition controls (i.e. true-negative group). The frequency of inhibition in the initial run was 26.31 % (20/76) as determined by spiked negative controls. All of the inhibited samples were resolved after 1 : 2, 1 : 5, 1 : 10 and 1 : 20 dilutions. P. jirovecii was detected by PCR in two inhibited specimens after retesting with diluted samples which were also positive by microscopy. The incidence of P. jirovecii in respiratory specimens was 22.36 % (17/76) as determined by real-time PCR and 7.14 % (3/42) by microscopy. Overall, the incidence of P. jirovecii in respiratory samples was 23.68 % (18/76) as detected by both methods. In conclusion, inclusion of spiked positive controls in each sample and retesting with diluted samples to resolve inhibition increased the reliability of the real-time PCR assay in terms of determining false-negative results and influencing the treatment of the patient. Furthermore, results of the present study determined for the first time the frequency and degree of inhibition in a real-time PCR detecting P. jirovecii in respiratory specimens during routine diagnosis of PcP.
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Affiliation(s)
- Mert Döşkaya
- Department of Parasitology, Ege University Medical School, Bornova/Izmir 35100, Turkey
| | - Ayşe Caner
- Department of Parasitology, Ege University Medical School, Bornova/Izmir 35100, Turkey
| | - Aysu Değirmenci
- Department of Parasitology, Ege University Medical School, Bornova/Izmir 35100, Turkey
| | - Nancy L Wengenack
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic and Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Ayşegül Yolasığmaz
- Department of Parasitology, Ege University Medical School, Bornova/Izmir 35100, Turkey
| | - Nevin Turgay
- Department of Parasitology, Ege University Medical School, Bornova/Izmir 35100, Turkey
| | - Seray Özensoy Töz
- Department of Parasitology, Ege University Medical School, Bornova/Izmir 35100, Turkey
| | - Yüksel Gürüz
- Department of Parasitology, Ege University Medical School, Bornova/Izmir 35100, Turkey
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Lau A, Chen S, Sleiman S, Sorrell T. Current status and future perspectives on molecular and serological methods in diagnostic mycology. Future Microbiol 2009; 4:1185-222. [DOI: 10.2217/fmb.09.70] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Invasive fungal infections are an important cause of infectious morbidity. Nonculture-based methods are increasingly used for rapid, accurate diagnosis to improve patient outcomes. New and existing DNA amplification platforms have high sensitivity and specificity for direct detection and identification of fungi in clinical specimens. Since laboratories are increasingly reliant on DNA sequencing for fungal identification, measures to improve sequence interpretation should support validation of reference isolates and quality control in public gene repositories. Novel technologies (e.g., isothermal and PNA FISH methods), platforms enabling high-throughput analyses (e.g., DNA microarrays and Luminex® xMAP™) and/or commercial PCR assays warrant further evaluation for routine diagnostic use. Notwithstanding the advantages of molecular tests, serological assays remain clinically useful for patient management. The serum Aspergillus galactomannan test has been incorporated into diagnostic algorithms of invasive aspergillosis. Both the galactomannan and the serum β-D-glucan test have value for diagnosing infection and monitoring therapeutic response.
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Affiliation(s)
- Anna Lau
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia
| | - Sharon Chen
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia and Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Sue Sleiman
- Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Tania Sorrell
- Centre for Infectious Diseases & Microbiology, Westmead Hospital, Darcy and Hawkesbury Roads, Westmead, NSW 2145, Australia
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Complexity of the MSG gene family of Pneumocystis carinii. BMC Genomics 2009; 10:367. [PMID: 19664205 PMCID: PMC2743713 DOI: 10.1186/1471-2164-10-367] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 08/07/2009] [Indexed: 11/17/2022] Open
Abstract
Background The relationship between the parasitic fungus Pneumocystis carinii and its host, the laboratory rat, presumably involves features that allow the fungus to circumvent attacks by the immune system. It is hypothesized that the major surface glycoprotein (MSG) gene family endows Pneumocystis with the capacity to vary its surface. This gene family is comprised of approximately 80 genes, which each are approximately 3 kb long. Expression of the MSG gene family is regulated by a cis-dependent mechanism that involves a unique telomeric site in the genome called the expression site. Only the MSG gene adjacent to the expression site is represented by messenger RNA. Several P. carinii MSG genes have been sequenced, which showed that genes in the family can encode distinct isoforms of MSG. The vast majority of family members have not been characterized at the sequence level. Results The first 300 basepairs of MSG genes were subjected to analysis herein. Analysis of 581 MSG sequence reads from P. carinii genomic DNA yielded 281 different sequences. However, many of the sequence reads differed from others at only one site, a degree of variation consistent with that expected to be caused by error. Accounting for error reduced the number of truly distinct sequences observed to 158, roughly twice the number expected if the gene family contains 80 members. The size of the gene family was verified by PCR. The excess of distinct sequences appeared to be due to allelic variation. Discounting alleles, there were 73 different MSG genes observed. The 73 genes differed by 19% on average. Variable regions were rich in nucleotide differences that changed the encoded protein. The genes shared three regions in which at least 16 consecutive basepairs were invariant. There were numerous cases where two different genes were identical within a region that was variable among family members as a whole, suggesting recombination among family members. Conclusion A set of sequences that represents most if not all of the members of the P. carinii MSG gene family was obtained. The protein-changing nature of the variation among these sequences suggests that the family has been shaped by selection for protein variation, which is consistent with the hypothesis that the MSG gene family functions to enhance phenotypic variation among the members of a population of P. carinii.
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Screening Pneumocystis carinii pneumonia in non–HIV-infected immunocompromised patients using polymerase chain reaction. Diagn Microbiol Infect Dis 2009; 64:396-401. [DOI: 10.1016/j.diagmicrobio.2009.04.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2009] [Revised: 04/09/2009] [Accepted: 04/14/2009] [Indexed: 11/23/2022]
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23
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FUJISAWA T, SUDA T, MATSUDA H, INUI N, NAKAMURA Y, SATO J, TOYOSHIMA M, NAKANO Y, YASUDA K, GEMMA H, HAYAKAWA H, CHIDA K. Real-time PCR is more specific than conventional PCR for induced sputum diagnosis of Pneumocystispneumonia in immunocompromised patients without HIV infection. Respirology 2009; 14:203-9. [DOI: 10.1111/j.1440-1843.2008.01457.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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24
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Detection of Pneumocystis jirovecii by Two Staining Methods and Two Quantitative PCR Assays. Infection 2008; 37:261-5. [DOI: 10.1007/s15010-008-8027-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Accepted: 06/24/2008] [Indexed: 11/26/2022]
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25
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[Pnemocystis jiroveci pneumonia: Comparison between conventional PCR and staining techniques]. ACTA ACUST UNITED AC 2008; 57:373-7. [PMID: 19038508 DOI: 10.1016/j.patbio.2008.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Accepted: 09/30/2008] [Indexed: 11/21/2022]
Abstract
Diagnosis of pneumocystis pneumonia is usually based on clinical features and X-rays photography and confirmed in the laboratory by visualisation of Pneumocystis organisms in stained preparations of respiratory specimens using several techniques (Gomori-Grocott, May-Grünwald Giemsa, bleu de toluidine O). Actually, PCR has considerably increased sensitivity of detection of Pneumocystis. The aim of this study is to compare conventional PCR results to those of staining techniques (Gomori-Grocott, May-Grünwald Giemsa) in addition to the X-ray and clinical findings in order to evaluate the contribution of each method. Sixty-four respiratory specimens were collected from 54 immuno-compromised patients with clinical symptoms of pulmonary infection. We diagnosed pneumocystis pneumonia in 16 patients according to staining techniques and/or typical clinical and radiological findings and/or response to treatment. Of the 15 patients, 14 were positive by PCR and only five were positive by direct examination, yielding a sensitivity and specificity of 93.3 and 87.1% for PCR and 33.3 and 100% for staining techniques. Conventional PCR provides a sensitive and objective method for the detection Pneumocystis jiroveci from less invasive sample.
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26
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Rodríguez-Tudela JL, Cuesta I, Gómez-López A, Alastruey-Izquierdo A, Bernal-Martínez L, Cuenca-Estrella M. Pruebas moleculares en el diagnóstico micológico. Enferm Infecc Microbiol Clin 2008; 26 Suppl 13:47-53. [PMID: 19100167 DOI: 10.1157/13128780] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Kocjan BJ, Seme K, Poljak M. Detection and differentiation of human papillomavirus genotypes HPV-6 and HPV-11 by FRET-based real-time PCR. J Virol Methods 2008; 153:245-9. [PMID: 18722474 DOI: 10.1016/j.jviromet.2008.07.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 06/24/2008] [Accepted: 07/23/2008] [Indexed: 11/26/2022]
Abstract
A real-time PCR (RT-PCR) assay was developed based on fluorescence resonance energy transfer (FRET) hybridization probe technology, allowing very sensitive and specific detection of HPV-6 and HPV-11, reliable differentiation of HPV-6 and HPV-11, as well as prototypic and non-prototypic HPV-6 genomic variants, in a single PCR reaction. The primers and probe were designed on the basis of multiple alignments of 74 HPV-6 E2 gene sequences and 20 HPV-11 E2 gene sequences. Testing on defined plasmid standards showed that the RT-PCR allowed simple and reliable identification of HPV-6 and HPV-11 using type specific amplification followed by probe-specific post-amplification dissociation analysis. Sensitivity, assessed by probit analysis at a 95% detection level, was 42.9, 43.4, and 25.3 DNA copies per assay for prototypic and non-prototypic HPV-6 variants and HPV-11, respectively. The results obtained by the developed assay on 51 HPV DNA-negative samples and 149 HPV DNA-positive samples, including 81 HPV-6 positive samples (19 prototypic and 62 non-prototypic HPV-6 variants), 28 HPV-11 positive samples, 10 samples of HPV-44 and HPV-74 (the closest relatives of HPV-6 and HPV-11) and 30 samples of 15 other important alpha HPV, showed complete agreement with those obtained with the INNO-LiPA human papillomavirus (HPV) Genotyping Assay and HPV-6 E2 and E6 gene sequencing.
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Affiliation(s)
- Bostjan J Kocjan
- Institute of Microbiology and Immunology, Faculty of Medicine, Ljubljana, Slovenia
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29
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Salvador RB, Cuenca-Estrella M, Márquez MVD, Gadea Gironés I. El diagnóstico molecular en las infecciones parasitarias y fúngicas. Enferm Infecc Microbiol Clin 2008; 26 Suppl 9:50-7. [DOI: 10.1016/s0213-005x(08)76541-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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30
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Blake DP, Qin Z, Cai J, Smith AL. Development and validation of real-time polymerase chain reaction assays specific to four species of Eimeria. Avian Pathol 2008; 37:89-94. [DOI: 10.1080/03079450701802248] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Damer P. Blake
- a Enteric Immunology Group , Institute for Animal Health , Compton , Berkshire , RG20 7NN , UK
| | - Zonghua Qin
- b Guangdong Academy of Agricultural Sciences , Institute of Veterinary Medicine , Guangzhou , 510640 , China
| | - Jianping Cai
- b Guangdong Academy of Agricultural Sciences , Institute of Veterinary Medicine , Guangzhou , 510640 , China
| | - Adrian L. Smith
- a Enteric Immunology Group , Institute for Animal Health , Compton , Berkshire , RG20 7NN , UK
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31
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Abstract
Pneumocystis is a genus containing many species of non-culturable fungi, each of which infects a different mammalian host. Pneumonia caused by Pneumocystis is a problem in immunodeficient humans, but not in normal humans. Nevertheless, it appears that Pneumocystis organisms cannot survive and proliferate outside of their mammalian hosts, suggesting that Pneumocystis parasitizes immunocompetent mammals. Residence in immunocompetent hosts may rely on camouflage perpetrated by antigenic variation. In P. carinii, which is found in rats, there exist three families of genes that appear to be designed to create antigenic variation. One gene family, which encodes the major surface glycoprotein (MSG), contains nearly 100 members. Expression of the MSG family is controlled by restricting transcription to the one gene that is linked to a unique expression site. Changes in the sequence of the MSG gene linked to the expression site occur and appear to be caused by recombination with MSG genes not at the expression site. Preliminary evidence suggests that gene conversion is the predominant recombination mechanism.
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Affiliation(s)
- James R Stringer
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, Ohio 45267-0524, USA.
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32
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Larsen HH, von Linstow ML, Lundgren B, Høgh B, Westh H, Lundgren JD. Primary pneumocystis infection in infants hospitalized with acute respiratory tract infection. Emerg Infect Dis 2007; 13:66-72. [PMID: 17370517 PMCID: PMC2725833 DOI: 10.3201/eid1301.060315] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Acquisition of Pneumocystis jirovecii infection early in life has been confirmed by serologic studies. However, no evidence of clinical illness correlated with the primary infection has been found in immunocompetent children. We analyzed 458 nasopharyngeal aspirates from 422 patients hospitalized with 431 episodes of acute respiratory tract infection (RTI) by using a real-time PCR assay. In 68 episodes in 67 infants, P. jirovecii was identified. The odds ratio (95% confidence interval) of a positive signal compared with the first quartile of age (7-49 days) was 47.4 (11.0-203), 8.7 (1.9-39.7), and 0.6 (0.1-6.7) for infants in the second (50-112 days), third (113-265 days), and fourth (268-4,430 days) age quartiles, respectively. Infants with an episode of upper RTI (URTI) were 2.0 (1.05-3.82) times more likely to harbor P. jirovecii than infants with a lower RTI. P. jirovecii may manifest itself as a self-limiting URTI in infants, predominantly those 1.5-4 months of age.
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33
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Keely SP, Linke MJ, Cushion MT, Stringer JR. Pneumocystis murina MSG gene family and the structure of the locus associated with its transcription. Fungal Genet Biol 2007; 44:905-19. [PMID: 17320432 PMCID: PMC2063445 DOI: 10.1016/j.fgb.2007.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Revised: 12/26/2006] [Accepted: 01/03/2007] [Indexed: 11/20/2022]
Abstract
Analysis of the Pneumocystis murina MSG gene family and expression-site locus showed that, as in Pneumocystis carinii, P. murina MSG genes are arranged in head-to-tail tandem arrays located on multiple chromosomes, and that a variety of MSG genes can reside at the unique P. murina expression site. Located between the P. murina expression site and attached MSG gene is a block of 132 basepairs that is also present at the beginning of MSG genes that are not at the expression site. The center of this sequence block resembles the 28 basepair CRJE of P. carinii, but the block of conserved sequence in P. murina is nearly five times longer than in P. carinii, and much shorter than in P. wakefieldiae. These data indicate that the P. murina expression-site locus has a distinct structure.
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Affiliation(s)
- Scott P Keely
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45220, USA
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34
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Linssen CFM, Jacobs JA, Beckers P, Templeton KE, Bakkers J, Kuijper EJ, Melchers WJG, Drent M, Vink C. Inter-laboratory comparison of three different real-time PCR assays for the detection of Pneumocystis jiroveci in bronchoalveolar lavage fluid samples. J Med Microbiol 2006; 55:1229-1235. [PMID: 16914653 DOI: 10.1099/jmm.0.46552-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pneumocystis jirovecipneumonia (PCP) is an opportunistic infection affecting immunocompromised patients. While conventional diagnosis of PCP by microscopy is cumbersome, the use of PCR to diagnose PCP has great potential. Nevertheless, inter-laboratory validation and standardization of PCR assays is lacking. The aim of this study was to evaluate the inter-laboratory agreement of three independently developed real-time PCR assays for the detection ofP. jiroveciin bronchoalveolar lavage fluid samples. Therefore, 124 samples were collected in three tertiary care laboratories (Leiden University Medical Center, Maastricht Infection Center and Radboud University Nijmegen Medical Centre) and were tested by both microscopy and real-time PCR. Of 41 samples positive forP. jiroveciby microscopy, 40 were positive in all three PCR assays. The remaining sample was positive in a single assay only. Out of 83 microscopy-negative samples, 69 were negative in all three PCR assays. The other 14 samples were found positive, either in all three assays (n=5), in two (n=2) or in one of the assays (n=7). The data demonstrate high inter-laboratory agreement among real-time PCR assays for the detection ofP. jiroveci.
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Affiliation(s)
- Catharina F M Linssen
- Department of Medical Microbiology, Maastricht Infection Center (MINC), University Hospital Maastricht, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Jan A Jacobs
- Department of Medical Microbiology, Maastricht Infection Center (MINC), University Hospital Maastricht, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Pieter Beckers
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre (RUNMC), PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Kate E Templeton
- Department of Medical Microbiology, Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Judith Bakkers
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre (RUNMC), PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre (RUNMC), PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Marjolein Drent
- Department of Respiratory Medicine, University Hospital Maastricht, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Cornelis Vink
- Department of Medical Microbiology, Maastricht Infection Center (MINC), University Hospital Maastricht, PO Box 5800, 6202 AZ Maastricht, The Netherlands
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35
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Arcenas RC, Uhl JR, Buckwalter SP, Limper AH, Crino D, Roberts GD, Wengenack NL. A real-time polymerase chain reaction assay for detection of Pneumocystis from bronchoalveolar lavage fluid. Diagn Microbiol Infect Dis 2006; 54:169-75. [PMID: 16423488 DOI: 10.1016/j.diagmicrobio.2005.08.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2005] [Accepted: 08/08/2005] [Indexed: 11/19/2022]
Abstract
Pneumocystis jiroveci is an important cause of pneumonia in immunocompromised individuals. This organism cannot be cultured, and therefore, diagnosis relies on microscopic identification of the organism using stains or antibodies. Although simple, these tests are insensitive and require expertise for accurate interpretation. We developed a real-time polymerase chain reaction (PCR) assay that provides sensitive and objective detection of Pneumocystis from bronchoalveolar lavage fluid. Primers and fluorescence resonance energy transfer probes were developed that target the cdc2 gene of P. jiroveci. Assay sensitivity is 6 copies of target per microliter of sample. No cross-reactivity occurs with other pathogens, and the PCR assay has a 21% increase in clinical sensitivity as compared with Calcofluor white staining. The real-time PCR assay provides a sensitive, rapid, and objective method for the detection of Pneumocystis from bronchoalveolar lavage fluid.
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Affiliation(s)
- Rodney C Arcenas
- Division of Clinical Microbiology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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36
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Espy MJ, Uhl JR, Sloan LM, Buckwalter SP, Jones MF, Vetter EA, Yao JDC, Wengenack NL, Rosenblatt JE, Cockerill FR, Smith TF. Real-time PCR in clinical microbiology: applications for routine laboratory testing. Clin Microbiol Rev 2006; 19:165-256. [PMID: 16418529 PMCID: PMC1360278 DOI: 10.1128/cmr.19.1.165-256.2006] [Citation(s) in RCA: 800] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Real-time PCR has revolutionized the way clinical microbiology laboratories diagnose many human microbial infections. This testing method combines PCR chemistry with fluorescent probe detection of amplified product in the same reaction vessel. In general, both PCR and amplified product detection are completed in an hour or less, which is considerably faster than conventional PCR detection methods. Real-time PCR assays provide sensitivity and specificity equivalent to that of conventional PCR combined with Southern blot analysis, and since amplification and detection steps are performed in the same closed vessel, the risk of releasing amplified nucleic acids into the environment is negligible. The combination of excellent sensitivity and specificity, low contamination risk, and speed has made real-time PCR technology an appealing alternative to culture- or immunoassay-based testing methods for diagnosing many infectious diseases. This review focuses on the application of real-time PCR in the clinical microbiology laboratory.
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Affiliation(s)
- M J Espy
- Mayo Clinic, 200 First St. SW, Hilton 470, Rochester, MN 55905, USA.
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37
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Brancart F, Rodriguez-Villalobos H, Fonteyne PA, Peres-Bota D, Liesnard C. Quantitative TaqMan PCR for detection of Pneumocystis jiroveci. J Microbiol Methods 2005; 61:381-7. [PMID: 15767014 DOI: 10.1016/j.mimet.2005.01.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2004] [Revised: 12/30/2004] [Accepted: 01/04/2005] [Indexed: 10/25/2022]
Abstract
We developed a quantitative real-time PCR assay for detection and quantification of Pneumocystis jiroveci in bronchoalveolar lavage (BAL) specimens based on primers and probe targeting the gene encoding beta-tubulin. The assay was able to detect 50 DNA copies per ml of a standard plasmid containing the target sequence. The intra- and interassay coefficients of variation were 0.46%-4.27% and 0.05-2.00% over 5 log(10) values. Fifty-seven controls of human, viruses, bacteria and fungi DNA samples were amplified and found negative. Fifty-three BAL samples sent to the laboratory for diagnosis of pneumocystosis were prospectively investigated by real-time PCR and direct microscopic examinations (DME) using Giemsa stain and direct immunofluorescence. All PCR negative samples were negative by microscopy. Among the 24 (45%) BAL found PCR positive, 8 were positive by microscopy (35%). The copy numbers of the target gene were between 4.4 x 10(3) and 2.8 x 10(6) per ml for the microscopically positive samples and between 8 and 9.2 x 10(3) per ml for the microscopically negative samples. In conclusion, we developed a rapid, sensitive and specific real time PCR for the diagnosis and quantification of Pneumocystis jiroveci in BAL samples.
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Affiliation(s)
- Françoise Brancart
- Laboratory of Microbiology, Erasme Hospital-ULB, 808 Route de Lennik, 1070 Brussels, Belgium.
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38
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Linke MJ, Rebholz S, Collins M, Tanaka R, Cushion MT. Noninvasive method for monitoring Pneumocystis carinii pneumonia. Emerg Infect Dis 2004; 9:1613-6. [PMID: 14720405 PMCID: PMC3034349 DOI: 10.3201/eid0912.030270] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The progression of Pneumocystis carinii pneumonia was temporally monitored and quantified by real-time polymerase chain reaction of P. carinii–specific DNA in oral swabs and lung homogenates from infected rats. DNA levels correlated with the number of P. carinii organisms in the rats’ lungs, as enumerated by microscopic methods. This report is the first of a noninvasive, antemortem method that can be used to monitor infection in a host over time.
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Affiliation(s)
| | - Sandy Rebholz
- University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Margaret Collins
- University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Reiko Tanaka
- University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Melanie T. Cushion
- Veterans Affairs Medical Center, Cincinnati, Ohio, USA
- University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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39
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Falsey AR, Formica MA, Treanor JJ, Walsh EE. Comparison of quantitative reverse transcription-PCR to viral culture for assessment of respiratory syncytial virus shedding. J Clin Microbiol 2003; 41:4160-5. [PMID: 12958241 PMCID: PMC193781 DOI: 10.1128/jcm.41.9.4160-4165.2003] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Respiratory syncytial virus (RSV) has recently been recognized as a serious pathogen in elderly and immunocompromised adults. Diagnosis of acute infection in adults is often difficult due to the insensitivity of viral culture, and reverse transcription-PCR (RT-PCR) is a more sensitive alternative. The relationship of quantitative RT-PCR to viable virus has never been studied for RSV. Therefore, we compared a quantitative real-time RT-PCR with viral culture to assess viral load in adult volunteers challenged with the RSV A2 strain. Twelve of 13 volunteers were infected, and there was a high correlation (r = 0.84) between quantitative RT-PCR and viral titer by cell culture. However, RT-PCR was more sensitive, with 73 of 169 (43%) samples positive compared to 58 (34%) samples positive by culture. The correlation between the two tests was highest early in the course of viral shedding (r = 0.91, days 0 to 6), whereas during days 7 to 13, there was more variability (r = 0.70). All subjects were culture negative by day 11, whereas one subject remained RT-PCR positive on day 12. All subjects were RT-PCR negative at day 28 postinfection. Quantitative RT-PCR has an excellent correlation with viral titers, as measured by culture, and should be a useful tool for future studies addressing viral load and disease pathogenesis.
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Affiliation(s)
- Ann R Falsey
- Department of Medicine. Infectious Disease Unit, Rochester General Hospital, University of Rochester School of Medicine and Dentistry, Rochester, New York 14621, USA.
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40
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Kutty G, Huang SN, Kovacs JA. Characterization of thioredoxin reductase genes (trr1) from Pneumocystis carinii and Pneumocystis jiroveci. Gene 2003; 310:175-83. [PMID: 12801645 DOI: 10.1016/s0378-1119(03)00549-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We have characterized the thioredoxin reductase (trr1) genes from Pneumocystis carinii and Pneumocystis jiroveci, and have demonstrated that multiple copies of an approximately 500 base pair fragment of the trr1 gene are present in P. carinii, but not in P. jiroveci. Thioredoxin reductases encoded by the full-length genes have predicted molecular weights of approximately 35,000 and show high homology to yeast Trr1. An NADPH-binding domain with a putative redox active site CAVC as well as an flavin-adenine dinucleotide-binding domain are highly conserved in both proteins, which were 85% identical. The multicopy trr1 gene fragments in P. carinii are not transcribed or expressed. Duplication of the gene fragment likely occurred in conjunction with duplication of the kexin homologue, protease-1, which is located immediately upstream of the trr1 gene. Thioredoxin reductase, an enzyme implicated in the growth, survival and pathogenicity of certain microbes, could be a potential target for therapeutic intervention in Pneumocystis infection.
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MESH Headings
- Amino Acid Sequence
- Ascomycota/enzymology
- Ascomycota/genetics
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- Fungal Proteins/genetics
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Fungal
- Molecular Sequence Data
- Pneumocystis/enzymology
- Pneumocystis/genetics
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Schizosaccharomyces/enzymology
- Schizosaccharomyces/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Thioredoxin-Disulfide Reductase/genetics
- Thioredoxin-Disulfide Reductase/metabolism
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Affiliation(s)
- Geetha Kutty
- Critical Care Medicine Department, Warren G. Magnuson Clinical Center, National Institutes of Health, Building 10, Room 7D43, MSC 1662, Bethesda, MD 20892-1662, USA
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