1
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Brown L, Rautemaa-Richardson R, Mengoli C, Alanio A, Barnes RA, Bretagne S, Chen SCA, Cordonnier C, Donnelly JP, Heinz WJ, Jones B, Klingspor L, Loeffler J, Rogers TR, Rowbotham E, White PL, Cruciani M. Polymerase Chain Reaction on Respiratory Tract Specimens of Immunocompromised Patients to Diagnose Pneumocystis Pneumonia: A Systematic Review and Meta-analysis. Clin Infect Dis 2024; 79:161-168. [PMID: 38860786 PMCID: PMC11259226 DOI: 10.1093/cid/ciae239] [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] [Received: 11/06/2023] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND This meta-analysis examines the comparative diagnostic performance of polymerase chain reaction (PCR) for the diagnosis of Pneumocystis pneumonia (PCP) on different respiratory tract samples, in both human immunodeficiency virus (HIV) and non-HIV populations. METHODS A total of 55 articles met inclusion criteria, including 11 434 PCR assays on respiratory specimens from 7835 patients at risk of PCP. QUADAS-2 tool indicated low risk of bias across all studies. Using a bivariate and random-effects meta-regression analysis, the diagnostic performance of PCR against the European Organisation for Research and Treatment of Cancer-Mycoses Study Group definition of proven PCP was examined. RESULTS Quantitative PCR (qPCR) on bronchoalveolar lavage fluid provided the highest pooled sensitivity of 98.7% (95% confidence interval [CI], 96.8%-99.5%), adequate specificity of 89.3% (95% CI, 84.4%-92.7%), negative likelihood ratio (LR-) of 0.014, and positive likelihood ratio (LR+) of 9.19. qPCR on induced sputum provided similarly high sensitivity of 99.0% (95% CI, 94.4%-99.3%) but a reduced specificity of 81.5% (95% CI, 72.1%-88.3%), LR- of 0.024, and LR+ of 5.30. qPCR on upper respiratory tract samples provided lower sensitivity of 89.2% (95% CI, 71.0%-96.5%), high specificity of 90.5% (95% CI, 80.9%-95.5%), LR- of 0.120, and LR+ of 9.34. There was no significant difference in sensitivity and specificity of PCR according to HIV status of patients. CONCLUSIONS On deeper respiratory tract specimens, PCR negativity can be used to confidently exclude PCP, but PCR positivity will likely require clinical interpretation to distinguish between colonization and active infection, partially dependent on the strength of the PCR signal (indicative of fungal burden), the specimen type, and patient population tested.
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Affiliation(s)
- Lottie Brown
- Institute of Infection and Immunity, St George's University and St Georges University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Riina Rautemaa-Richardson
- Mycology Reference Centre Manchester and Department of Infectious Diseases, Manchester Academic Health Science Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust and Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - Carlo Mengoli
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Instituto Superiore Di Sanita, Rome, Italy
| | | | - Rosemary A Barnes
- Department of Infection, Immunity and Biochemistry and School of Medicine, University of Cardiff, United Kingdom
| | - Stéphane Bretagne
- Université Paris Cité, Parasitology-Mycology Laboratory, Hôpital Saint-Louis, APHP, Paris, France
| | - Sharon C A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, Australia
| | - Catherine Cordonnier
- Haematology and Stem Cell Transplant Department, Henri Mondor Hospital, and University Paris-Est-Créteil, Créteil, France
| | - J Peter Donnelly
- Fungal PCR Initiative, a working group of the International Society of Human and Animal Mycology, Verona, Italy
| | - Werner J Heinz
- Med. Clinic II, Caritas Hospital Bad Mergentheim, Germany
| | - Brian Jones
- Institute of Infection, Immunity and Inflammation, University of Glasgow, United Kingdom
| | - Lena Klingspor
- Karolinska Institutet, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Juergen Loeffler
- Medizinische Klinik II, Labor WÜ4i, Universitätsklinikum Würzburg, Germany
| | - Thomas R Rogers
- Discipline of Clinical Microbiology, Trinity College Dublin, St James’s Hospital Campus, Dublin, Ireland
| | - Eleanor Rowbotham
- Mycology Reference Centre Manchester and Department of Infectious Diseases, Manchester University, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester
| | - P Lewis White
- Public Health Wales Mycology Reference Laboratory, Public Health Wales Microbiology Cardiff, University Hospital of Wales, and Centre for Trials Research/Division of Infection and Immunity, Cardiff University, United Kingdom
| | - Mario Cruciani
- Fungal PCR Initiative, a working group of the International Society of Human and Animal Mycology, Verona, Italy
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2
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Xing F, Deng C, Luo Z, Zou S, Liu M, Ye H, Sun L, Tsang CC, Lo SKF, Lau SKP, Woo PCY. Rapid Diagnosis of Pneumocystis jirovecii Pneumonia and Respiratory Tract Colonization by Next-Generation Sequencing. Mycopathologia 2024; 189:38. [PMID: 38704795 PMCID: PMC11070382 DOI: 10.1007/s11046-024-00849-y] [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] [Received: 01/05/2024] [Accepted: 03/30/2024] [Indexed: 05/07/2024]
Abstract
OBJECTIVES To describe the epidemiology of Pneumocystis jirovecii pneumonia and colonization diagnosed by next-generation sequencing (NGS) and explore the usefulness of the number of P. jirovecii sequence reads for the diagnosis of P. jirovecii pneumonia. METHODS We examined the NGS results for P. jirovecii in respiratory samples collected from patients and analysed their clinical, radiological and microbiological characteristics. RESULTS Among 285 respiratory samples collected over a 12-month period (January to December 2022), P. jirovecii sequences were detected in 56 samples from 53 patients. Fifty (94.3%) of the 53 patients were HIV-negative. Following our case definitions, 37 (69.8%) and 16 (30.2%) of the 53 patients had P. jirovecii infection and colonization respectively. P. jirovecii infection was associated with presence of underlying disease with immunosuppression (94.6% vs 18.8%, P < 0.05), positive serum 1,3-β-D-glucan (41.2% vs 0%, P < 0.01) and higher number of P. jirovecii sequence reads (P < 0.005). In contrast, P. jirovecii colonization was associated with the male sex (93.8% vs 54.1%, P < 0.01), another definitive infectious disease diagnosis of the respiratory tract (43.8% vs 2.7%, P < 0.001) and higher survival (100% vs 67.6%, P < 0.01). Although P. jirovecii pneumonia was associated with higher number of P. jirovecii reads in respiratory samples, only a sensitivity of 82.14% and a specificity of 68.75% could be achieved. CONCLUSION Detection of P. jirovecii sequences in respiratory samples has to be interpreted discreetly. A combination of clinical, radiological and laboratory findings is still the most crucial in determining whether a particular case is genuine P. jirovecii pneumonia.
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Affiliation(s)
- Fanfan Xing
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Chaowen Deng
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Zhendong Luo
- Department of Radiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Shan Zou
- Department of Adult Intensive Care, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Min Liu
- Department of Respiratory Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Haiyan Ye
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Linlin Sun
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Chi-Ching Tsang
- School of Medical and Health Sciences, Tung Wah College, Homantin, Hong Kong, China
| | - Simon K F Lo
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Susanna K P Lau
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Patrick C Y Woo
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
- Doctoral Program in Translational Medicine and Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.
- The iEGG and Animal Biotechnology Research Center, National Chung Hsing University, Taichung 402, Taiwan.
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3
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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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4
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Almeida-Siva F, Almeida-Paes R, Serra-Damasceno L, Motta-Santos E, Ferreira LC, Pereira-Quintella L, De Faria Ferreira M, De Medeiros-Muniz M, Zancopé-Oliveira RM. The conventional diagnosis challenge: Real-time PCR and nested PCR correlation with the scoring system for individuals at high-risk of Pneumocystis jirovecii pneumonia. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2023; 43:255-266. [PMID: 37721900 PMCID: PMC10599712 DOI: 10.7705/biomedica.7020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/25/2023] [Indexed: 09/20/2023]
Abstract
INTRODUCTION Pneumocystis jirovecii is an opportunistic fungus that affects mainly people living with HIV (CD4 cell count lower than 200 cells/ml) and other immunosuppressed patients. Since P. jirovecii does not grow on routine mycological media, diagnosis of P. jirovecii pneumonia relies on indirect evidence of its presence in respiratory samples. OBJECTIVES To associate the results of direct immunofluorescence and two molecular methods with a score to predict P. jirovecii pneumonia in patients with AIDS. MATERIALS AND METHODS A prospective study was conducted with 40 patients. A respiratory sample collected before treatment was subjected to direct immunofluorescence using the Merifluor kit, to nested PCR targeting the mitochondrial large subunit ribosomal RNA, and to the VIASURE real-time PCR kit. RESULTS These three techniques revealed P. jirovecii in 6, 12, and 15 samples, respectively. All positive samples by direct immunofluorescence were positive by nested PCR, and all positive samples by nested PCR amplified by real-time PCR. There was a statistically significant association between the P. jirovecii pneumonia score and the molecular methods. Two patients were early diagnosed and responded well to treatment. CONCLUSION Molecular methods, especially real-time PCR, are recommended for early diagnosis of P. jirovecii pneumonia in AIDS patients.
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Affiliation(s)
- Fernando Almeida-Siva
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil.
| | - Rodrigo Almeida-Paes
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil.
| | - Lisandra Serra-Damasceno
- Hospital São José de Doenças Infecciosas, Fortaleza, Ceará, Brasil; Departamento de Saúde Comunitária, Faculdade de Medicina, Universidade Federal do Ceará, Fortaleza, Ceará, Brasil.
| | - Edwiges Motta-Santos
- Laboratório de Medicina Intensiva, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil.
| | - Luiz Claudio Ferreira
- Serviço de Anatomia Patológica, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil.
| | - Leonardo Pereira-Quintella
- Serviço de Anatomia Patológica, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil.
| | - Marcela De Faria Ferreira
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil; Serviço Ambulatorial do Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil.
| | - Mauro De Medeiros-Muniz
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil.
| | - Rosely M Zancopé-Oliveira
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil.
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5
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Ruiz-Ruiz S, Ponce CA, Pesantes N, Bustamante R, Gatti G, San Martin V, Gutierrez M, Bórquez P, Vargas SL, Magne F, Calderón EJ, Pérez-Brocal V, Moya A. A Real-Time PCR Assay for Detection of Low Pneumocystis jirovecii Levels. Front Microbiol 2022; 12:787554. [PMID: 35087490 PMCID: PMC8787145 DOI: 10.3389/fmicb.2021.787554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Here we report a new real-time PCR assay using SYBR Green which provides higher sensitivity for the specific detection of low levels of Pneumocystis jirovecii. To do so, two primer sets were designed, targeting the family of genes that code for the most abundant surface protein of Pneumocystis spp., namely the major surface glycoproteins (Msg), and the mitochondrial large subunit rRNA (mtLSUrRNA) multicopy gene, simultaneously detecting two regions. PCR methods are instrumental in detecting these low levels; however, current nested-PCR methods are time-consuming and complex. To validate our new real-time Msg-A/mtLSUrRNA PCR protocol, we compared it with nested-PCR based on the detection of Pneumocystis mitochondrial large subunit rRNA (mtLSUrRNA), one of the main targets used to detect this pathogen. All samples identified as positive by the nested-PCR method were found positive using our new real-time PCR protocol, which also detected P. jirovecii in three nasal aspirate samples that were negative for both rounds of nested-PCR. Furthermore, we read both rounds of the nested-PCR results for comparison and found that some samples with no PCR amplification, or with a feeble band in the first round, correlated with higher Ct values in our real-time Msg-A/mtLSUrRNA PCR. This finding demonstrates the ability of this new single-round protocol to detect low Pneumocystis levels. This new assay provides a valuable alternative for P. jirovecii detection, as it is both rapid and sensitive.
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Affiliation(s)
- Susana Ruiz-Ruiz
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, València, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBEResp), Instituto de Salud Carlos III, Madrid, Spain
| | - Carolina A Ponce
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Nicole Pesantes
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, València, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBEResp), Instituto de Salud Carlos III, Madrid, Spain
| | - Rebeca Bustamante
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Gianna Gatti
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | | | | | | | - Sergio L Vargas
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Fabien Magne
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Enrique J Calderón
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBEResp), Instituto de Salud Carlos III, Madrid, Spain.,Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), and Universidad de Sevilla, Seville, Spain
| | - Vicente Pérez-Brocal
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, València, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBEResp), Instituto de Salud Carlos III, Madrid, Spain
| | - Andrés Moya
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, València, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBEResp), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biología Integrativa de Sistemas (I2Sysbio), Universitat de València and Consejo Superior de Investigaciones Científicas (CSIC), València, Spain
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6
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Friaza V, de Armas Y, Capó V, Morilla R, Plascencia-Hernández A, Pérez-Gómez HR, Iglesias E, Fonte L, de la Horra C, Calderón EJ. Multilocus Genotyping of Pneumocystis jirovecii from Deceased Cuban AIDS Patients Using Formalin-Fixed and Paraffin-Embedded Tissues. J Fungi (Basel) 2021; 7:jof7121042. [PMID: 34947024 PMCID: PMC8706017 DOI: 10.3390/jof7121042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022] Open
Abstract
The results of the genotypic characterization of Pneumocystis jirovecii are described in lung tissue samples from 41 Cubans who died of AIDS with pneumocystosis between 1995 and 2008. Histological sections of the lung preserved as formalin-fixed and paraffin-embedded tissue were examined. PCR amplification and nucleotide sequencing of the two mitochondrial genes (large and small) of the pathogen allowed verification of a predominance of genotype 3 (85T/248C) of the large mitochondrial gene and genotype 3 (160A/196T) of the small mitochondrial gene over a period of 14 years (1995–2008). These results suggest that the 85T/248C//160A/196T genotype circulates with the highest frequency (81.3%) among AIDS patients in Cuba. Multilocus analysis indicates a limited circulation of pathogen genotypes on the island with the existence of a clonal genotype with an epidemic structure. Furthermore, it appears that circulating strains of P. jirovecii have not developed mutations related to sulfonamide resistance. Taken together, the data in this study revealed important elements about pneumocystosis in Cuban patients dying of AIDS and the usefulness of formalin-fixed and paraffin-embedded samples to carry out molecular epidemiology studies of P. jirovecii.
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Affiliation(s)
- Vicente Friaza
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (V.F.); (R.M.); (E.J.C.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
| | - Yaxsier de Armas
- Department of Clinical Microbiology Diagnostic, Hospital Center of Institute of Tropical Medicine “Pedro Kourí”, 11400 Havana, Cuba;
- Pathology Department, Hospital Center of Institute of Tropical Medicine “Pedro Kourí”, 11400 Havana, Cuba;
| | - Virginia Capó
- Pathology Department, Hospital Center of Institute of Tropical Medicine “Pedro Kourí”, 11400 Havana, Cuba;
| | - Rubén Morilla
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (V.F.); (R.M.); (E.J.C.)
| | - Arturo Plascencia-Hernández
- Centro Universitario de Ciencias para la Salud, Universidad de Guadalajara, 44100 Guadalajara, Mexico; (A.P.-H.); (H.R.P.-G.)
| | - Héctor R. Pérez-Gómez
- Centro Universitario de Ciencias para la Salud, Universidad de Guadalajara, 44100 Guadalajara, Mexico; (A.P.-H.); (H.R.P.-G.)
| | - Enrique Iglesias
- Centro de Ingeniería Genética y Biotecnología, Departamento de Vacunas, 10600 Havana, Cuba;
| | - Luis Fonte
- Parasitology Department, Institute of Tropical Medicine “Pedro Kourí”, 11400 Havana, Cuba;
| | - Carmen de la Horra
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (V.F.); (R.M.); (E.J.C.)
- Correspondence:
| | - Enrique J. Calderón
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (V.F.); (R.M.); (E.J.C.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
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7
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Is It Possible to Differentiate Pneumocystis jirovecii Pneumonia and Colonization in the Immunocompromised Patients with Pneumonia? J Fungi (Basel) 2021; 7:jof7121036. [PMID: 34947017 PMCID: PMC8707387 DOI: 10.3390/jof7121036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 11/18/2022] Open
Abstract
Respiratory sample staining is a standard tool used to diagnose Pneumocystis jirovecii pneumonia (PjP). Although molecular tests are more sensitive, their interpretation can be difficult due to the potential of colonization. We aimed to validate a Pneumocystis jirovecii (Pj) real-time PCR (qPCR) assay in bronchoscopic bronchoalveolar lavage (BAL) and oropharyngeal washes (OW). We included 158 immunosuppressed patients with pneumonia, 35 lung cancer patients who underwent BAL, and 20 healthy individuals. We used a SYBR green qPCR assay to look for a 103 bp fragment of the Pj mtLSU rRNA gene in BAL and OW. We calculated the qPCR cut-off as well as the analytical and diagnostic characteristics. The qPCR was positive in 67.8% of BAL samples from the immunocompromised patients. The established cut-off for discriminating between disease and colonization was Ct 24.53 for BAL samples. In the immunosuppressed group, qPCR detected all 25 microscopy-positive PjP cases, plus three additional cases. Pj colonization in the immunocompromised group was 66.2%, while in the cancer group, colonization rates were 48%. qPCR was ineffective at diagnosing PjP in the OW samples. This new qPCR allowed for reliable diagnosis of PjP, and differentiation between PjP disease and colonization in BAL of immunocompromised patients with pneumonia.
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8
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Irinyi L, Hu Y, Hoang MTV, Pasic L, Halliday C, Jayawardena M, Basu I, McKinney W, Morris AJ, Rathjen J, Stone E, Chen S, Sorrell TC, Schwessinger B, Meyer W. Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens: A paradigm shift in mycological diagnostics. Med Mycol 2021; 58:650-660. [PMID: 31758176 DOI: 10.1093/mmy/myz109] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/26/2019] [Accepted: 11/19/2019] [Indexed: 11/14/2022] Open
Abstract
The advent of next generation sequencing technologies has enabled the characterization of the genetic content of entire communities of organisms, including those in clinical specimens, without prior culturing. The MinION from Oxford Nanopore Technologies offers real-time, direct sequencing of long DNA fragments directly from clinical samples. The aim of this study was to assess the ability of unbiased, genome-wide, long-read, shotgun sequencing using MinION to identify Pneumocystis jirovecii directly from respiratory tract specimens and to characterize the associated mycobiome. Pneumocystis pneumonia (PCP) is a life-threatening fungal disease caused by P. jirovecii. Currently, the diagnosis of PCP relies on direct microscopic or real-time quantitative polymerase chain reaction (PCR) examination of respiratory tract specimens, as P. jirovecii cannot be cultured readily in vitro. P. jirovecii DNA was detected in bronchoalveolar lavage (BAL) and induced sputum (IS) samples from three patients with confirmed PCP. Other fungi present in the associated mycobiome included known human pathogens (Aspergillus, Cryptococcus, Pichia) as well as commensal species (Candida, Malassezia, Bipolaris). We have established optimized sample preparation conditions for the generation of high-quality data, curated databases, and data analysis tools, which are key to the application of long-read MinION sequencing leading to a fundamental new approach in fungal diagnostics.
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Affiliation(s)
- Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia
| | - Yiheng Hu
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Minh Thuy Vi Hoang
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia
| | - Lana Pasic
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia
| | - Catriona Halliday
- Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Menuk Jayawardena
- Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Indira Basu
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Wendy McKinney
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Arthur J Morris
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - John Rathjen
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Eric Stone
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,ANU-CSIRO Centre for Genomics, Metabolomics and Bioinformatics, Canberra, ACT, Australia
| | - Sharon Chen
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Tania C Sorrell
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia.,Westmead Hospital (Research and Education Network), Westmead, NSW, Australia
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9
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Chotiprasitsakul D, Pewloungsawat P, Setthaudom C, Santanirand P, Pornsuriyasak P. Performance of real-time PCR and immunofluorescence assay for diagnosis of Pneumocystis pneumonia in real-world clinical practice. PLoS One 2020; 15:e0244023. [PMID: 33347478 PMCID: PMC7751978 DOI: 10.1371/journal.pone.0244023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/01/2020] [Indexed: 11/21/2022] Open
Abstract
Background PCR is more sensitive than immunofluorescence assay (IFA) for detection of Pneumocystis jirovecii. However, PCR cannot always distinguish infection from colonization. This study aimed to compare the performance of real-time PCR and IFA for diagnosis of P. jirovecii pneumonia (PJP) in a real-world clinical setting. Methods A retrospective cohort study was conducted at a 1,300-bed hospital between April 2017 and December 2018. Patients whose respiratory sample (bronchoalveolar lavage or sputum) were tested by both Pneumocystis PCR and IFA were included. Diagnosis of PJP was classified based on multicomponent criteria. Sensitivity, specificity, 95% confidence intervals (CI), and Cohen's kappa coefficient were calculated. Results There were 222 eligible patients. The sensitivity and specificity of PCR was 91.9% (95% CI, 84.0%–96.7%) and 89.7% (95% CI, 83.3%–94.3%), respectively. The sensitivity and specificity of IFA was 7.0% (95% CI, 2.6%–14.6%) and 99.2% (95% CI, 95.6%–100.0%), respectively. The percent agreement between PCR and IFA was 56.7% (Cohen's kappa -0.02). Among discordant PCR-positive and IFA-negative samples, 78% were collected after PJP treatment. Clinical management would have changed in 14% of patients using diagnostic information, mainly based on PCR results. Conclusions PCR is highly sensitive compared with IFA for detection of PJP. Combining clinical, and radiological features with PCR is useful for diagnosis of PJP, particularly when respiratory specimens cannot be promptly collected before initiation of PJP treatment.
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Affiliation(s)
- Darunee Chotiprasitsakul
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pataraporn Pewloungsawat
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Chavachol Setthaudom
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pitak Santanirand
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Prapaporn Pornsuriyasak
- Division of Pulmonary and Critical Care, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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Calvo-Lozano O, Aviñó A, Friaza V, Medina-Escuela A, S. Huertas C, Calderón EJ, Eritja R, Lechuga LM. Fast and Accurate Pneumocystis Pneumonia Diagnosis in Human Samples Using a Label-Free Plasmonic Biosensor. NANOMATERIALS 2020; 10:nano10061246. [PMID: 32604931 PMCID: PMC7353103 DOI: 10.3390/nano10061246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 01/30/2023]
Abstract
Pneumocystis jirovecii is a fungus responsible for human Pneumocystis pneumonia, one of the most severe infections encountered in immunodepressed individuals. The diagnosis of Pneumocystis pneumonia continues to be challenging due to the absence of specific symptoms in infected patients. Moreover, the standard diagnostic method employed for its diagnosis involves mainly PCR-based techniques, which besides being highly specific and sensitive, require specialized personnel and equipment and are time-consuming. Our aim is to demonstrate an optical biosensor methodology based on surface plasmon resonance to perform such diagnostics in an efficient and decentralized scheme. The biosensor methodology employs poly-purine reverse-Hoogsteen hairpin probes for the detection of the mitochondrial large subunit ribosomal RNA (mtLSU rRNA) gene, related to P. jirovecii detection. The biosensor device performs a real-time and label-free identification of the mtLSU rRNA gene with excellent selectivity and reproducibility, achieving limits of detection of around 2.11 nM. A preliminary evaluation of clinical samples showed rapid, label-free and specific identification of P. jirovecii in human lung fluids such as bronchoalveolar lavages or nasopharyngeal aspirates. These results offer a door for the future deployment of a sensitive diagnostic tool for fast, direct and selective detection of Pneumocystis pneumonia disease.
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Affiliation(s)
- Olalla Calvo-Lozano
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, CIBER in Bioengineering, Biomaterials and Nanomedicine and BIST, Campus UAB Bellaterra, 08193 Barcelona, Spain; (O.C.-L.); (C.S.H.); (L.M.L.)
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, CIBER in Bioengineering, Biomaterials and Nanomedicine c/Jordi Girona 18–26, 08034 Barcelona, Spain;
- Correspondence:
| | - Vicente Friaza
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville and CIBER in Epidemiology and Public Health, 41013 Seville, Spain; (V.F.); (E.J.C.)
| | - Alfonso Medina-Escuela
- Institute for Applied Microelectronics (IUMA), University of Las Palmas de Gran Canaria, 35017 Las Palmas, Spain;
| | - César S. Huertas
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, CIBER in Bioengineering, Biomaterials and Nanomedicine and BIST, Campus UAB Bellaterra, 08193 Barcelona, Spain; (O.C.-L.); (C.S.H.); (L.M.L.)
- Integrated Photonics and Applications Centre, School of Engineering, RMIT University, Melbourne 3001, Australia
| | - Enrique J. Calderón
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville and CIBER in Epidemiology and Public Health, 41013 Seville, Spain; (V.F.); (E.J.C.)
- Department of Medicine, University of Seville, 41013 Seville, Spain
| | - Ramón Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, CIBER in Bioengineering, Biomaterials and Nanomedicine c/Jordi Girona 18–26, 08034 Barcelona, Spain;
| | - Laura M. Lechuga
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, CIBER in Bioengineering, Biomaterials and Nanomedicine and BIST, Campus UAB Bellaterra, 08193 Barcelona, Spain; (O.C.-L.); (C.S.H.); (L.M.L.)
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11
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Bavaro DF, Fiordelisi D, Angarano G, Monno L, Saracino A. Targeted therapies for autoimmune/idiopathic nonmalignant diseases: risk and management of opportunistic infections. Expert Opin Drug Saf 2020; 19:817-842. [PMID: 32394759 DOI: 10.1080/14740338.2020.1767585] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
INTRODUCTION The management of patients affected by autoimmune/idiopathic diseases has been revolutionized by the development of targeted therapies (TT). However, the use of TT is complicated by several adverse events, like opportunistic infections (OIs). The potential of TT to predispose to OIs mainly depends on the site of action; nevertheless, such associations are far from being deterministic, because many factors could increase the infection risk. AREAS COVERED The impact on the infective risk of different TT used for autoimmune/idiopathic diseases is far from being completely understood. Indeed, many post-marketing reports documented severe or unexpected infections in patients treated with TT that did not emerge during registrative trials. In this review, the authors attempt to provide an easy and practical update about the 'infectious' safety of TT and examine the management strategies of OIs and other infections more frequently observed in the course of treatment with TT. EXPERT OPINION The authors suggest to precisely schedule the clinical management of these subjects, both to prevent and eventually treat promptly the TT-related infectious complications. A coordinated approach should be implemented from different medical specialties to improve the overall understanding of safety of TT and, in general, the management of opportunistic infections in immune-compromised hosts.
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Affiliation(s)
- Davide Fiore Bavaro
- Department of Biomedical Sciences and Human Oncology, Clinic of Infectious Diseases, University of Bari "Aldo Moro" , Bari, Italy
| | - Deborah Fiordelisi
- Department of Biomedical Sciences and Human Oncology, Clinic of Infectious Diseases, University of Bari "Aldo Moro" , Bari, Italy
| | - Gioacchino Angarano
- Department of Biomedical Sciences and Human Oncology, Clinic of Infectious Diseases, University of Bari "Aldo Moro" , Bari, Italy
| | - Laura Monno
- Department of Biomedical Sciences and Human Oncology, Clinic of Infectious Diseases, University of Bari "Aldo Moro" , Bari, Italy
| | - Annalisa Saracino
- Department of Biomedical Sciences and Human Oncology, Clinic of Infectious Diseases, University of Bari "Aldo Moro" , Bari, Italy
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Panizo MM, Ferrara G, García N, Moreno X, Navas T, Calderón E. Diagnosis, Burden and Mortality of Pneumocystis jirovecii Pneumonia in Venezuela. CURRENT FUNGAL INFECTION REPORTS 2020. [DOI: 10.1007/s12281-020-00377-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Vera C, Aguilar YA, Vélez LA, Rueda ZV. High transient colonization by Pneumocystis jirovecii between mothers and newborn. Eur J Pediatr 2017; 176:1619-1627. [PMID: 28913714 DOI: 10.1007/s00431-017-3011-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/23/2017] [Accepted: 09/04/2017] [Indexed: 12/20/2022]
Abstract
UNLABELLED The aim of the study was to explore the frequency and dynamics of acquisition and colonization of Pneumocystis jirovecii among neonates, as well as the epidemiological and genotypic characteristics in mother-child binomial. In a prospective enrolled cohort of women in their third trimester of pregnancy, nasopharyngeal swabs (NPS) and clinical and epidemiological data were collected at four different times: 17 days, 2nd, 4th, and 6th month of life of the newborn. P. jirovecii was detected by nested-PCR for the mtLSU-rRNA gene in each NPS; the genotypes were determined amplifying four genes. Forty-three pairs and 301 NPS were included. During the third trimester, 16.3% of pregnant women were colonized. The rate of colonization in mothers at delivery was 16, 6, 16, and 5% and in their children 28, 43, 42, and 25%, respectively. Within pregnant women, 53% remained negative throughout follow-up, and among these, 91% of their children were positive in at least one of their samples. In both, mothers and children, the most frequent genotype of P. jirovecii was 1. CONCLUSION The frequency of colonization by P. jirovecii was higher in newborns than in their respective progenitors. Colonization of both mothers and children is transitory; however, the mother of the newborn is not necessarily the source of primary infection. What is Known: • We did not find studies comparing P. jirovecii colonization between mothers and children simultaneously, yet the frequency of colonization by serologic and molecular methods in pregnant women has been reported. What is New: • According to our findings, 3/4 of the children had transient colonization during the first 6 months of life, in only half in the mothers, without proof of mother-to-child transmission or vice versa.
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Affiliation(s)
- Cristian Vera
- Grupo investigador de Problemas en Enfermedades Infecciosas (GRIPE), Universidad de Antioquia, Medellín, Colombia.
- Facultad Nacional de Salud Pública, Universidad de Antioquia, Medellín, Colombia.
| | - Yudy A Aguilar
- Grupo investigador de Problemas en Enfermedades Infecciosas (GRIPE), Universidad de Antioquia, Medellín, Colombia
| | - Lázaro A Vélez
- Grupo investigador de Problemas en Enfermedades Infecciosas (GRIPE), Universidad de Antioquia, Medellín, Colombia
- Sección de Enfermedades Infecciosas, Hospital Universitario San Vicente Fundación, Medellín, Colombia
| | - Zulma Vanessa Rueda
- Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Colombia
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14
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Hoarau G, Le Gal S, Zunic P, Poubeau P, Antok E, Jaubert J, Nevez G, Picot S. Evaluation of quantitative FTD-Pneumocystis jirovecii kit for Pneumocystis infection diagnosis. Diagn Microbiol Infect Dis 2017; 89:212-217. [PMID: 28851493 DOI: 10.1016/j.diagmicrobio.2017.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 08/02/2017] [Accepted: 08/04/2017] [Indexed: 11/28/2022]
Abstract
We evaluated the Fast track Diagnostics (FTD) Pneumocystis PCR kit, targeting the mitochondrial large subunit ribosomal RNA gene (mtLSU rRNA) of Pneumocystis jirovecii (P. jirovecii). A hundred and thirty-three patients were prospectively enrolled. Respiratory specimens were examined using both microscopy and the PCR assay. Twenty-six patients led to P. jirovecii detection. Fourteen patients presented with Pneumocystis pneumonia (PCP) whereas 12 patients were considered to be colonized. The median copy numbers in bronchoalveolar lavage fluid were significantly different in the PCP and colonization groups (1.35×108/ml vs. 1.45×105/ml, P < 0.0001). Lower and upper cut-off values of 3.9×105 copies/ml and 3.2×106 copies/ml allowed differentiating PCP and colonization. The FTD P. jirovecii assay was secondarily compared to an in-house reference PCR assay targeting the mtLSUrRNA gene. A concordance rate of 97.5% was observed (Cohen's kappa coefficient κ=0.935). The FTD Pneumocystis PCR kit showed good performance and represents an alternative method to diagnose P. jirovecii infections.
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Affiliation(s)
- Gautier Hoarau
- Department of Microbiology, CHU La Reunion, St Pierre, France; UMR PIMIT « processus infectieux en milieu insulaire tropical », Inserm 1187, CNRS 9192, IRD 249, université de La Réunion, CYROI, 97490 Sainte-Clotilde, Reunion.
| | | | - Patricia Zunic
- Department of Hematology and Medical Oncology, CHU La Reunion, St Pierre, France
| | - Patrice Poubeau
- Department of Infectious Diseases, CHU La Reunion, St Pierre, France
| | | | - Julien Jaubert
- Department of Microbiology, CHU La Reunion, St Pierre, France
| | - Gilles Nevez
- University of Brest, GEIHP EA, 3142, Brest, France
| | - Sandrine Picot
- Department of Microbiology, CHU La Reunion, St Pierre, France
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Nevez G, Robert-Gangneux F, Pougnet L, Virmaux M, Belleguic C, Deneuville E, Rault G, Chevrier S, Ramel S, Le Bihan J, Guillaud-Saumur T, Calderon E, Le Govic Y, Gangneux JP, Le Gal S. Pneumocystis jirovecii and Cystic Fibrosis in Brittany, France. Mycopathologia 2017; 183:81-87. [DOI: 10.1007/s11046-017-0172-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 06/27/2017] [Indexed: 11/30/2022]
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16
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Comparison of quantitative real-time PCR and direct immunofluorescence for the detection of Pneumocystis jirovecii. PLoS One 2017; 12:e0180589. [PMID: 28683092 PMCID: PMC5500343 DOI: 10.1371/journal.pone.0180589] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 06/16/2017] [Indexed: 11/23/2022] Open
Abstract
Background Pneumocystis pneumonia (PCP) is a serious risk for HIV-positive patients. Asymptomatic infection or colonisation with P. jirovecii has been shown to occur frequently. PCR assays frequently identify such cases, due to their high sensitivity. Quantitative real-time PCR (qPCR) gene copy number cut-off values have been suggested to differentiate colonisation and infection; these need to be standardised for routine use. We compared the results of qPCR with an immunofluorescence assay (IFA) to determine a specific cut-off value. Methods From March 2005 through June 2009, induced sputum specimens were collected from adult patients who were clinically suspected of having PCP, at the Chris Hani Baragwanath Hospital in Gauteng, South Africa. Laboratory diagnosis of PCP was done by a conventional direct IFA and a qPCR assay. A receiver operating characteristic (ROC) analysis was performed to determine a suitable copy number cut-off value. Results P. jirovecii was identified in 51% (156/305) and 67% (204/305) of specimens using IFA and qPCR, respectively. The cut-off value for the qPCR that best predicted the IFA results was 78 copies/5 μl (area under ROC curve 0.92). The sensitivity and specificity of qPCR using this cut-off was 94.6% and 89.1%, respectively, compared with the IFA. Discussion The results of the ROC curve analysis indicate an excellent predictive value of the qPCR using the proposed cut-off. However, the IFA test is an imperfect gold standard and so this cut-off should not be used in isolation; clinical data should also contribute to the interpretation of the qPCR result.
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Santos CR, de Assis ÂM, Luz EA, Lyra L, Toro IF, Seabra JCC, Daldin DH, Marcalto TU, Galasso MT, Macedo RF, Schreiber AZ, Aoki FH. Detection of Pneumocystis jirovecii by nested PCR in HIV-negative patients with pulmonary disease. Rev Iberoam Micol 2017; 34:83-88. [DOI: 10.1016/j.riam.2015.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 11/08/2015] [Accepted: 12/01/2015] [Indexed: 11/27/2022] Open
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18
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Hviid CJ, Lund M, Sørensen A, Ellermann- Eriksen S, Jespersen B, Dam MY, Dahlerup JF, Benfield T, Jespersen S, Østergaard LJ, Laursen AL. Detection of Pneumocystis jirovecii in oral wash from immunosuppressed patients as a diagnostic tool. PLoS One 2017; 12:e0174012. [PMID: 28358900 PMCID: PMC5373571 DOI: 10.1371/journal.pone.0174012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 03/01/2017] [Indexed: 11/29/2022] Open
Abstract
Background Diagnosis of Pneumocystis jirovecii (PJ) pneumonia ordinarily requires invasive procedures that could be avoided by PCR methodologies, if these could be designed with adequate cut-off values for confounding background carriage. Methods We designed a novel quantitative real-time PCR assay to detect the mitochondrial large subunit rRNA gene of PJ in oral washes. To benchmark levels of PJ carriage versus infection, we tested asymptomatic immunosuppressed patients including Danish (n = 88) and West African HIV-infected (n = 142) patients, renal transplant recipients (n = 51), rheumatologic patients (n = 102), patients with inflammatory bowel diseases (n = 98), and healthy blood donors (controls, n = 50). The fungal burden in patients with PJ pneumonia (PCP, n = 7) was also investigated. Results Danish HIV-infected patients (with viremia/low CD4) and recent transplant recipients were at most risk of being carriers (prevalence of 23% and 16.7% respectively), whereas PJ was rarely detected among rheumatologic patients, patients with inflammatory bowel diseases, and untreated West African HIV patients. PJ was not detected among healthy controls. The fungal burden in patients with PCP fell rapidly on treatment. Conclusions The quantitative PCR method described could conceivably discriminate between carriage and disease, given suitable threshold values for the former, and predict treatment efficacy by measures of the fungal burden in daily oral washes.
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Affiliation(s)
- Cecilie Juul Hviid
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Marianne Lund
- Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark
| | - Allan Sørensen
- The Bissau HIV Cohort Study Group, Bandim Health Project, Bissau, Guinea Bissau
| | | | - Bente Jespersen
- Department of Nephrology, Aarhus University Hospital, Aarhus, Denmark
| | - Mette Yde Dam
- Department of Rheumatology, Aarhus University Hospital, Aarhus, Denmark
| | - Jens Frederik Dahlerup
- Department of Hepatology and Gastroenterology, Aarhus Aarhus University Hospital, Denmark
| | - Thomas Benfield
- Department of Infectious Diseases, Hvidovre Hospital, Hvidovre, Denmark
| | - Sanne Jespersen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- The Bissau HIV Cohort Study Group, Bandim Health Project, Bissau, Guinea Bissau
| | - Lars Jørgen Østergaard
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- * E-mail: (ALL); (LJØ)
| | - Alex Lund Laursen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- The Bissau HIV Cohort Study Group, Bandim Health Project, Bissau, Guinea Bissau
- * E-mail: (ALL); (LJØ)
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Unnewehr M, Friederichs H, Bartsch P, Schaaf B. High Diagnostic Value of a New Real-Time Pneumocystis PCR from Bronchoalveolar Lavage in a Real-Life Clinical Setting. Respiration 2016; 92:144-9. [PMID: 27595408 DOI: 10.1159/000448626] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/21/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND To diagnose Pneumocystis jirovecii pneumonia (PCP), PCR testing in bronchoalveolar lavage (BAL) fluid has recently become an alternative to immunofluorescence testing (IFT); however, its diagnostic accuracy is less clear. OBJECTIVE To analyze the diagnostic value of a new semiquantitative real-time PCR (RT-PCR) in BAL in a real-life clinical setting. METHODS Retrospective analysis of all RT-PCR results [semiquantitative: negative, weakly positive, and strongly positive; measured in cycle thresholds (Ct)] in BAL in the period between 2010 and 2014. The diagnosis of PCP was defined by clinical, radiological, and laboratory signs and by treatment initiation. Any positive PCR was compared with subsequent IFT. RESULTS Of 128 patient samples, 32 had PCP. There is a relevant correlation of high significance between positive PCR Ct and IFT (r = -0.7781, p < 0.001), which amounts to about 60% of the variance. Sensitivity, specificity, and positive predictive values (PPV) of any positive RT-PCR were 100, 80, and 63%, respectively. No patient with negative RT-PCR had PCP. Specificity and PPV are 100% in strongly positive RT-PCR, whereas they decrease to 80 and 21% in weakly positive RT-PCR. CONCLUSION A negative RT-PCR (Ct >45) rules out PCP. A strongly positive PCR (Ct <31.5) confirms PCP. In these cases, the diagnostic value of the new method is at least equal to the IFT. A weakly positive PCR probably represents pneumocystis colonization and can occur under PCP treatment.
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Affiliation(s)
- Markus Unnewehr
- Pneumologie, Infektiologie, Intensivmedizin, Medizinische Klinik Nord, Klinikum Dortmund gGmbH, Dortmund, Germany
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Shafiek H, Fiorentino F, Cosio BG, Kersul A, Thiberville L, Gómez C, Riera M, Martín ML, Martínez R, Noguera MA, Agustí A, Sauleda J. Usefulness of Bronchoscopic Probe-Based Confocal Laser Endomicroscopy in the Diagnosis of Pneumocystis jirovecii Pneumonia. Respiration 2016; 92:40-7. [DOI: 10.1159/000447431] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 06/06/2016] [Indexed: 11/19/2022] Open
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Detection of Pneumocystis jirovecii by Quantitative PCR To Differentiate Colonization and Pneumonia in Immunocompromised HIV-Positive and HIV-Negative Patients. J Clin Microbiol 2016; 54:1487-1495. [PMID: 27008872 DOI: 10.1128/jcm.03174-15] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/14/2016] [Indexed: 01/01/2023] Open
Abstract
Pneumocystis jirovecii pneumonia (PCP) is an acute and life-threatening lung disease caused by the fungus Pneumocystis jirovecii The presentation of PCP in HIV-positive patients is well-known and consists of a triad of dyspnea, fever, and cough, whereas the presentation of PCP in HIV-negative patients is atypical and consists of a sudden outbreak, O2 desaturation, and a rapid lethal outcome without therapy. Despite the availability of direct and indirect identification methods, the diagnosis of PCP remains difficult. The cycle threshold (CT) values obtained by quantitative PCR (qPCR) allow estimation of the fungal burden. The more elevated that the fungal burden is, the higher the probability that the diagnosis is pneumonia. The purposes of the present study were to evaluate the CT values to differentiate colonization and pneumonia in a population of immunocompromised patients overall and patients stratified on the basis of their HIV infection status. Testing of bronchoalveolar lavage (BAL) fluid samples from the whole population of qPCR-positive patients showed a mean CT value for patients with PCP of 28 (95% confidence interval [CI], 26 to 30) and a mean CT value for colonized patients of 35 (95% CI, 34 to 36) (P < 10(-3)). For the subgroup of HIV-positive patients, we demonstrated that a CT value below 27 excluded colonization and a CT value above 30 excluded PCP with a specificity of 100% and a sensitivity of 80%, respectively. In the subgroup of HIV-negative patients, we demonstrated that a CT value below 31 excluded colonization and a CT value above 35 excluded PCP with a specificity of 80% and a sensitivity of 80%, respectively. Thus, qPCR of BAL fluid samples is an important tool for the differentiation of colonization and pneumonia in P. jirovecii-infected immunocompromised patients and patients stratified on the basis of HIV infection status with different CT values.
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Evaluation of Loop-Mediated Isothermal Amplification Assay for the Detection of Pneumocystis jirovecii in Immunocompromised Patients. Mol Biol Int 2015; 2015:819091. [PMID: 26664746 PMCID: PMC4668309 DOI: 10.1155/2015/819091] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 09/06/2015] [Accepted: 10/20/2015] [Indexed: 12/04/2022] Open
Abstract
Pneumocystis pneumonia (PCP) is one of the common opportunistic infection among HIV and non-HIV immunocompromised patients. The lack of a rapid and specific diagnostic test necessitates a more reliable laboratory diagnostic test for PCP. In the present study, the loop-mediated isothermal amplification (LAMP) assay was evaluated for the detection of Pneumocystis jirovecii. 185 clinical respiratory samples, including both BALF and IS, were subjected to GMS staining, nested PCR, and LAMP assay. Of 185 respiratory samples, 12/185 (6.5%), 41/185 (22.2%), and 49/185 (26.5%) samples were positive by GMS staining, nested PCR, and LAMP assay, respectively. As compared to nested PCR, additional 8 samples were positive by LAMP assay and found to be statistically significant (p < 0.05) with the detection limit of 1 pg. Thus, the LAMP assay may serve as a better diagnostic tool for the detection of P. jirovecii with high sensitivity and specificity, less turn-around time, operational simplicity, single-step amplification, and immediate visual detection.
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Iriart X, Bouar ML, Kamar N, Berry A. Pneumocystis Pneumonia in Solid-Organ Transplant Recipients. J Fungi (Basel) 2015; 1:293-331. [PMID: 29376913 PMCID: PMC5753127 DOI: 10.3390/jof1030293] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 12/27/2022] Open
Abstract
Pneumocystis pneumonia (PCP) is well known and described in AIDS patients. Due to the increasing use of cytotoxic and immunosuppressive therapies, the incidence of this infection has dramatically increased in the last years in patients with other predisposing immunodeficiencies and remains an important cause of morbidity and mortality in solid-organ transplant (SOT) recipients. PCP in HIV-negative patients, such as SOT patients, harbors some specificity compared to AIDS patients, which could change the medical management of these patients. This article summarizes the current knowledge on the epidemiology, risk factors, clinical manifestations, diagnoses, prevention, and treatment of Pneumocystis pneumonia in solid-organ transplant recipients, with a particular focus on the changes caused by the use of post-transplantation prophylaxis.
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Affiliation(s)
- Xavier Iriart
- Department of Parasitology-Mycology, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, Institut Fédératif de biologie (IFB), 330 avenue de Grande Bretagne, TSA 40031, Toulouse 31059, France.
- INSERM U1043, Toulouse F-31300, France.
- CNRS UMR5282, Toulouse F-31300, France.
- Université de Toulouse, UPS, Centre de Physiopathiologie de Toulouse Purpan (CPTP), Toulouse F-31300, France.
| | - Marine Le Bouar
- Department of Parasitology-Mycology, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, Institut Fédératif de biologie (IFB), 330 avenue de Grande Bretagne, TSA 40031, Toulouse 31059, France.
- INSERM U1043, Toulouse F-31300, France.
- CNRS UMR5282, Toulouse F-31300, France.
- Université de Toulouse, UPS, Centre de Physiopathiologie de Toulouse Purpan (CPTP), Toulouse F-31300, France.
| | - Nassim Kamar
- INSERM U1043, Toulouse F-31300, France.
- Université de Toulouse, UPS, Centre de Physiopathiologie de Toulouse Purpan (CPTP), Toulouse F-31300, France.
- Department of Nephrology and Organ Transplantation, CHU Rangueil, TSA 50032, Toulouse 31059, France.
| | - Antoine Berry
- Department of Parasitology-Mycology, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, Institut Fédératif de biologie (IFB), 330 avenue de Grande Bretagne, TSA 40031, Toulouse 31059, France.
- INSERM U1043, Toulouse F-31300, France.
- CNRS UMR5282, Toulouse F-31300, France.
- Université de Toulouse, UPS, Centre de Physiopathiologie de Toulouse Purpan (CPTP), Toulouse F-31300, France.
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Cooley L, Dendle C, Wolf J, Teh BW, Chen SC, Boutlis C, Thursky KA. Consensus guidelines for diagnosis, prophylaxis and management of Pneumocystis jirovecii pneumonia in patients with haematological and solid malignancies, 2014. Intern Med J 2015; 44:1350-63. [PMID: 25482745 DOI: 10.1111/imj.12599] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Pneumocystis jirovecii infection (PJP) is a common cause of pneumonia in patients with cancer-related immunosuppression. There are well-defined patients who are at risk of PJP due to the status of their underlying malignancy, treatment-related immunosuppression and/or concomitant use of corticosteroids. Prophylaxis is highly effective and should be given to all patients at moderate to high risk of PJP. Trimethoprim-sulfamethoxazole is the drug of choice for prophylaxis and treatment, although several alternative agents are available.
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Affiliation(s)
- L Cooley
- Department of Microbiology and Infectious Diseases, Royal Hobart Hospital, Hobart, Tasmania
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Parian M, Fata A, Najafzadeh MJ, Rezaeitalab F. Molecular detection of Pneumocystis jirovecii using polymerase chain reaction in immunocompromised patients with pulmonary disorders in northeast of Iran. Curr Med Mycol 2015; 1:13-18. [PMID: 28680983 PMCID: PMC5490308 DOI: 10.18869/acadpub.cmm.1.2.13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Background and Purpose: Pneumocystis pneumonia, caused by Pneumocystis jirovecii, is a fatal disease threatening patients with AIDS or immunosuppression. Assessment of colonization in these patients is of great significance, since it can lead to severe pulmonary disorders. Considering the scarcity of published reports on Pneumocystis jirovecii isolates from patients in Mashhad, Iran, we aimed to evaluate pneumocystis colonization in individuals with different pulmonary disorders. Materials and Methods: We used nested polymerase chain reaction (PCR) method to amplify mitochondrial large subunit-ribosomal ribonucleic acid (mtLSU-rRNA) gene in 60 bronchoalveolar lavage (BAL) samples, obtained from patients, referring to the Department of Internal Medicine (Pulmonary Diseases Section) at Imam Reza Hospital, affiliated to Mashhad University of Medical Sciences, Mashhad, Iran. Results: DNA of Pneumocystis jirovecii was detected in 10 out of 60 BAL samples (16.66%) via nested PCR method. Conclusion: According to the present findings, the colonization rate of Pneumocystis jirovecii was similar to the rates reported in other similar studies in Iran.
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Affiliation(s)
- M Parian
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - A Fata
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Research Center for Skin Diseases & Cutaneous Leishmaniasis, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - M J Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - F Rezaeitalab
- Department of Internal Medicine, Imam Reza Hospital, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Diagnosis of Pneumocystis jirovecii pneumonia in immunocompromised patients by real-time PCR: a 4-year prospective study. J Clin Microbiol 2014; 52:3370-6. [PMID: 25009050 DOI: 10.1128/jcm.01480-14] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pneumocystis jirovecii pneumonia (PCP) is a life-threatening infection in immunocompromised patients. Quantitative real-time PCR (qPCR) is more sensitive than microscopic examination for the detection of P. jirovecii but also detects colonized patients. Hence, its positive predictive value (PPV) needs evaluation. In this 4-year prospective observational study, all immunocompromised patients with acute respiratory symptoms who were investigated for PCP were included, totaling 659 patients (814 bronchoalveolar lavage fluid samples). Patients with negative microscopy but positive qPCR were classified through medical chart review as having retained PCP, possible PCP, or colonization, and their clinical outcomes were compared to those of patients with microscopically proven PCP. Overall, 119 patients were included for analysis, of whom 35, 41, and 43 were classified as having retained PCP, possible PCP, and colonization, respectively. The 35 patients with retained PCP had clinical findings similar to those with microscopically proven PCP but lower fungal loads (P < 0.001) and were mainly non-HIV-infected patients (P < 0.05). Although the mean amplification threshold was higher in colonized patients, it was not possible to determine a discriminant qPCR cutoff. The PPV of qPCR in patients with negative microscopy were 29.4% and 63.8% when considering retained PCP and retained plus possible PCP, respectively. Patients with possible PCP had a higher mortality rate than patients with retained PCP or colonization (63% versus 3% and 16%, respectively); patients who died had not received co-trimoxazole. In conclusion, qPCR is a useful tool to diagnose PCP in non-HIV patients, and treatment might be better targeted through a multicomponent algorithm including both clinical/radiological parameters and qPCR results.
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Cytomegalovirus viral load kinetics in patients with HIV/AIDS admitted to a medical intensive care unit: a case for pre-emptive therapy. PLoS One 2014; 9:e93702. [PMID: 24699683 PMCID: PMC3974798 DOI: 10.1371/journal.pone.0093702] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 03/06/2014] [Indexed: 12/27/2022] Open
Abstract
Background Cytomegalovirus (CMV) infection is associated with severe diseases in immunosuppressed patients; however, there is a lack of data for pre-emptive therapy in patients with HIV/AIDS. Method This was a retrospective study, which enrolled patients diagnosed with HIV/AIDS (CD4<200 cells/μl), who had detectable CMV viral load (VL) during their stay in an adult medical intensive care unit between 2009–2012. Results After screening 82 patients’ records, 41 patients met the enrolment criteria. Their median age was 37 (interquartile range [IQR]: 31–46), and median CD4 count was 29 cells/μl (IQR: 5–55). Sixteen patients (39%) had serial measurements of CMV VL before treatment with ganciclovir. Patients whose baseline CMV VL values were between 1,000–3,000 copies/ml had significantly higher values (median of 14,650 copies/ml) on follow-up testing done 4–12 days later. Those with undetectable VLs at baseline testing had detectable VLs (median of 1,590 copies/ml) mostly within 20 days of follow-up testing. Patients who had VLs >1,000 copies/ml at baseline testing had significantly higher mortality compared to those who had <1,000 copies/ml {hazard ratio of 3.46, p = 0.003 [95% confidence interval (CI): 1.55–7.71]}. Analysis of the highest CMV VL per patient showed that patients who had VLs of >5,100 copies/ml and did not receive ganciclovir had 100% mortality compared to 58% mortality in those who received ganciclovir at VLs of >5,100 copies/ml, 50% mortality in those who were not treated and had low VLs of <5,100 copies/ml, and 44% mortality in those who had ganciclovir treatment at VLs of <5,100 copies/ml (p = 0.084, 0.046, 0.037, respectively). Conclusion This study showed a significantly increased mortality in patients with HIV/AIDS who had high CMV VLs, and suggests that a threshold value of 1,000 copies/ml may be appropriate for pre-emptive treatment in this group.
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Choe PG, Kang YM, Kim G, Park WB, Park SW, Kim HB, Oh MD, Kim EC, Kim NJ. Diagnostic value of direct fluorescence antibody staining for detecting Pneumocystis jirovecii in expectorated sputum from patients with HIV infection. Med Mycol 2014; 52:326-30. [PMID: 24667822 DOI: 10.1093/mmy/myu002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Direct fluorescent antibody (DFA) staining of induced sputum is frequently used to diagnose Pneumocystis pneumonia (PCP) in patients infected with human immunodeficiency virus, although induction can provoke nausea and bronchospasm. Since the diagnostic value of expectorated sputum examined with DFA stain has not been well evaluated, we reviewed the medical records of HIV-infected patients who were clinically diagnosed as having PCP between 1999 and 2011. Over this 13-year period, we found 76 patients whose records included the results of DFA staining of expectorated sputum and noted that 42 (55.3%) were positive. Polymerase chain reaction to detect Pneumocystis in the sputum of 65 of the patients resulted in the finding of 43 (66.2%) who were positive. Our findings suggest that DFA staining of expectorated sputum could be a useful initial diagnostic method in HIV-infected patients with PCP.
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Affiliation(s)
- Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
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Pneumocystis jirovecii Pneumonia in Systemic Lupus Erythematosus From Southern Taiwan. J Clin Rheumatol 2013; 19:252-8. [DOI: 10.1097/rhu.0b013e31829d5017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Barbosa J, Costa-de-Oliveira S, Silva AT, Rodrigues AG, Pina-Vaz C. Specific detection of Pneumocystis jirovecii in clinical samples by flow cytometry. Methods Mol Biol 2013; 968:203-11. [PMID: 23296897 DOI: 10.1007/978-1-62703-257-5_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Pneumocystis jirovecii is an opportunistic pathogen responsible for severe pneumonia in immunocompromised patients. Flow cytometry (FC) is a method widely used in different areas of clinical diagnosis like hematology and immunology. Recently it has started to be used in microbiology with a great potential for diagnosis of emergent microorganisms in clinical samples, especially when present in low numbers. The detection of Pneumocystis jirovecii in respiratory samples can be performed by FC, using specific monoclonal antibodies. Considering clinical diagnosis as a reference method, we previously showed FC to be 100% sensitive and specific when compared to immunofluorescence. Being an automated method, it is faster and less subject to human error than microscopic evaluation.
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Affiliation(s)
- Joana Barbosa
- Department of Microbiology, Faculty of Medicine, Cardiovascular Research Unit, University of Porto, Porto, Portugal.
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Development and evaluation of a real-time PCR assay for detection of Pneumocystis jirovecii on the fully automated BD MAX platform. J Clin Microbiol 2013; 51:2337-43. [PMID: 23678059 DOI: 10.1128/jcm.00616-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Pneumocystis jirovecii is an opportunistic pathogen in immunocompromised and AIDS patients. Detection by quantitative PCR is faster and more sensitive than microscopic diagnosis yet requires specific infrastructure. We adapted a real-time PCR amplifying the major surface glycoprotein (MSG) target from Pneumocystis jirovecii for use on the new BD MAX platform. The assay allowed fully automated DNA extraction and multiplex real-time PCR. The BD MAX assay was evaluated against manual DNA extraction and conventional real-time PCR. The BD MAX was used in the research mode running a multiplex PCR (MSG, internal control, and sample process control). The assay had a detection limit of 10 copies of an MSG-encoding plasmid per PCR that equated to 500 copies/ml in respiratory specimens. We observed accurate quantification of MSG targets over a 7- to 8-log range. Prealiquoting and sealing of the complete PCR reagents in conical tubes allowed easy and convenient handling of the BD MAX PCR. In a retrospective analysis of 54 positive samples, the BD MAX assay showed good quantitative correlation with the reference PCR method (R(2) = 0.82). Cross-contamination was not observed. Prospectively, 278 respiratory samples were analyzed by both molecular assays. The positivity rate overall was 18.3%. The BD MAX assay identified 46 positive samples, compared to 40 by the reference PCR. The BD MAX assay required liquefaction of highly viscous samples with dithiothreitol as the only manual step, thus offering advantages for timely availability of molecular-based detection assays.
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De Vos FY, Gijtenbeek JM, Bleeker-Rovers CP, van Herpen CM. Pneumocystis jirovecii pneumonia prophylaxis during temozolomide treatment for high-grade gliomas. Crit Rev Oncol Hematol 2013; 85:373-82. [DOI: 10.1016/j.critrevonc.2012.08.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 07/23/2012] [Accepted: 08/02/2012] [Indexed: 12/24/2022] Open
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Dimonte S, Berrilli F, D’Orazi C, D’Alfonso R, Placco F, Bordi E, Perno C, Di Cave D. Molecular analysis based on mtLSU-rRNA and DHPS sequences of Pneumocystis jirovecii from immunocompromised and immunocompetent patients in Italy. INFECTION GENETICS AND EVOLUTION 2013. [DOI: 10.1016/j.meegid.2012.11.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Riebold D, Mohr E, Sombetzki M, Fritzsche C, Loebermann M, Reisinger E. Pneumocystis species in Brown Leghorn laying hens—A hint for an extra-mammalian reservoir. Poult Sci 2012; 91:1813-8. [DOI: 10.3382/ps.2011-01930] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Muñoz C, Zuluaga A, Restrepo A, Tobón A, Cano LE, Gonzalez A. Molecular diagnosis and detection of Pneumocystis jirovecii DHPS and DHFR genotypes in respiratory specimens from Colombian patients. Diagn Microbiol Infect Dis 2012; 72:204-13. [PMID: 22321995 DOI: 10.1016/j.diagmicrobio.2011.11.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 11/17/2011] [Accepted: 11/19/2011] [Indexed: 11/16/2022]
Abstract
A total of 98 respiratory specimens from 88 patients suspected of having Pneumocystis jirovecii pneumonia (PcP) were evaluated using a previously reported nested polymerase chain reaction (PCR) assay for mitochondrial large subunit rRNA (mtLSUrRNA). In addition, samples from patients with other pulmonary infections and a sizeable DNA collection from other fungal pathogens were studied. A panfungal PCR assay amplifying the ITS1-ITS2 regions were also used to identify all fungal DNAs. All samples positive for mtLSUrRNA-PCR were evaluated to determine mutations in dihydropteroate synthase (DHPS) and dihydrofolate reductase (DHFR) genes. All PCR-amplified products were sequenced. Of the 98 clinical specimens, 13 (13.2%) were positive by GMS stain and mtLSUrRNA-PCR, while 32 (32.6%) that were GMS stain-negative gave positive results with mtLSUrRNA-PCR. All the sequences corresponding to the 45 products amplified by mtLSUrRNA-PCR showed 99% or greater identity with P. jirovecii. The mtLSUrRNA-PCR exhibited 86% sensitivity and 98% and 96.6% specificity when results were compared to those corresponding to negative controls and other proven clinical entities, respectively. We found mutations in the DHPS gene in 3 (7.7%) patients, 2 located at codon 55 and 1 at codon 57. One patient showed a synonymous substitution at nucleotide position 312 in the DHFR gene. These results suggest that mtLSUrRNA-PCR is a useful test for diagnosing PcP. In contrast to other studies, this study found a low prevalence of mutations in the DHPS and DHFR genes in Colombian patients.
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Affiliation(s)
- Cesar Muñoz
- Medical and Experimental Mycology Group, Corporación para Investigaciones Biológicas, Medellín, Colombia
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Tia T, Putaporntip C, Kosuwin R, Kongpolprom N, Kawkitinarong K, Jongwutiwes S. A highly sensitive novel PCR assay for detection of Pneumocystis jirovecii DNA in bronchoalveloar lavage specimens from immunocompromised patients. Clin Microbiol Infect 2012; 18:598-603. [DOI: 10.1111/j.1469-0691.2011.03656.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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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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Pneumocystis jirovecii pneumonia in non-HIV-infected patients: new risks and diagnostic tools. Curr Opin Infect Dis 2012; 24:534-44. [PMID: 21986616 DOI: 10.1097/qco.0b013e32834cac17] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
PURPOSE OF REVIEW Non-HIV-infected populations are increasingly identified as being at risk for developing Pneumocystis jirovecii pneumonia (PJP). These patients typically present with severe disease and poorly tolerate invasive diagnostic procedures. This review examines recently reported risks for PJP in non-HIV populations and summarizes new diagnostic techniques. RECENT FINDINGS PJP is associated with immunomodulatory drug therapies, including monoclonal antibody therapies such as tumour necrosis factor α antagonists, and calcineurin inhibitors. Underlying disease states include solid-organ transplantation, connective tissue and rheumatologic disorders, inflammatory bowel disease, haematological malignancies, and solid tumours. Modern diagnostic techniques [conventional PCR, quantitative PCR, (1→3)-β-D-glucan assays, and PET] are reviewed with respect to predictive value and clinical utility. In particular, current literature regarding validation and specificity of molecular diagnostic techniques is summarized, including application to minimally invasive specimens. SUMMARY HIV-negative populations at risk for PJP can be identified. Conventional PCR increases diagnostic sensitivity but may detect asymptomatic colonization. Quantitative PCR demonstrates potential for distinguishing colonization from infection, but clinical validation is required. Serum (1→3)-β-D-glucan may be elevated in PJP, although standardized cut-off values for clinical infection have not been determined. Further validation of serum markers and molecular diagnostic methods is necessary for early and accurate diagnosis in non-HIV populations.
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Pneumocystis jirovecii testing by real-time polymerase chain reaction and direct examination among immunocompetent and immunosuppressed patient groups and correlation to disease specificity. Diagn Microbiol Infect Dis 2011; 69:145-52. [PMID: 21251557 DOI: 10.1016/j.diagmicrobio.2010.10.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 10/20/2010] [Accepted: 10/22/2010] [Indexed: 01/13/2023]
Abstract
We used real-time polymerase chain reaction (PCR) targeting the cdc2 gene and direct fluorescent microscopy examination (DFME) to evaluate the prevalence of Pneumocystis jirovecii among immunocompetent patients without clinical pulmonary infection and immunosuppressed patients evaluated for opportunistic pulmonary infections. Among 102 bronchoalveolar lavage samples collected from immunocompetent patients without infection, none tested positive for P. jirovecii by either DFME or real-time PCR despite the presence of other comorbidities. Among patients with suspected pulmonary infection and tested with either assay, real-time PCR produced a higher number of positive results compared to DFME and increased P. jirovecii detection by 7% when added to DFME-negative samples. Real-time PCR may have increased sensitivity for P. jirovecii detection over DFME and decrease the risk of sample contamination compared to conventional and nested PCR. The use of single-copy gene targets (e.g., cdc2) may lower the rate of "colonization" detection and confer a high predictive value for Pneumocystis pneumonia.
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Murdoch DR, Jennings LC, Bhat N, Anderson TP. Emerging advances in rapid diagnostics of respiratory infections. Infect Dis Clin North Am 2010; 24:791-807. [PMID: 20674804 PMCID: PMC7134633 DOI: 10.1016/j.idc.2010.04.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent developments in rapid diagnostics for respiratory infections have mostly occurred in the areas of antigen and nucleic acid detection. Nucleic acid amplification tests have improved the ability to identify respiratory viruses in clinical specimens and have played pivotal roles in the rapid characterization of new viral pathogens. Antigen-detection assays in immunochromatographic or similar formats are most easily developed as near-patient tests, although they have been developed commercially only for a limited range of respiratory pathogens. New approaches for respiratory pathogen detection are needed, and breath analysis is an exciting area with enormous potential.
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Affiliation(s)
- David R Murdoch
- Department of Pathology, University of Otago Christchurch, Christchurch 8140, New Zealand.
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A new method for the detection of Pneumocystis jirovecii using flow cytometry. Eur J Clin Microbiol Infect Dis 2010; 29:1147-52. [PMID: 20552243 DOI: 10.1007/s10096-010-0980-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 05/22/2010] [Indexed: 10/19/2022]
Abstract
Pneumocystis jirovecii is an opportunistic pathogen responsible for severe pneumonia in immunocompromised patients. Its diagnosis has been based upon direct microscopy either by classic staining (Gomori Grocott) or by epifluorescence microscopy (immunofluorescence staining, IFS), both of which are time-consuming and low on sensitivity. Our aim was to develop a flow cytometric (FC) protocol for the detection of P. jirovecii on respiratory samples. In our study, 420 respiratory samples were analysed in parallel by IFS and FC, and compared from clinical diagnosis to its resolution upon specific anti-Pneumocystis therapy. The optimum specific antibody concentration for FC analysis was determined to be 10 microg/ml, without any cross-reactions to bacteria or fungi. All positive cases detected by IFS were positive by FC; however, FC classified eight samples to be positive which were classified as negative by routine technique. These samples were obtained from patients with respiratory symptoms who responded favourably to Pneumocystis-specific therapy and were subsequently considered to be true-positives. Using clinical diagnosis as a reference method, FC showed 100% sensitivity and specificity, whereas IFS showed 90.9% sensitivity and 100% specificity. According to our results, a new diagnostic approach is now available to detect P. jirovecii in respiratory samples.
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Mekinian A, Queyrel V, Durand-Joly I, Moranne O, Denis G, Delhaes L, Morell-Dubois S, Lambert M, Launay D, Hachulla E, Hatron PY. PCR Pneumocystis jirovecii positive chez les patients atteints de maladie auto-immune : Pneumocystose pulmonaire ou simple colonisation ? Rev Med Interne 2010; 31:194-9. [DOI: 10.1016/j.revmed.2009.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Revised: 10/06/2009] [Accepted: 11/15/2009] [Indexed: 11/24/2022]
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Evidence for high prevalence of Pneumocystis jirovecii exposure among Cameroonians. Acta Trop 2009; 112:219-24. [PMID: 19665440 DOI: 10.1016/j.actatropica.2009.07.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 07/29/2009] [Accepted: 07/30/2009] [Indexed: 11/24/2022]
Abstract
Cameroon lacks the capacity for routine Pneumocystis pneumonia (PcP) diagnosis, thus, the prevalence of Cameroonian exposure to this microbe is unknown. It is known that Pneumocystis infecting different mammalian host species represent diverse phylogenetic backgrounds and are now designated as separate species. The highly sensitive nature of ELISA and the specificity afforded by using human-derived P. jirovecii Msg peptides has been shown to be useful for serological analysis of human sera. Thus, sera from patients in Yaoundé, the capital city of Cameroon, were analyzed for anti-P. jirovecii antibodies by enzyme-linked immunosorbent assay (ELISA) using three recombinant major surface glycoprotein (Msg) peptide fragments, MsgA1, MsgB, and MsgC1. Based on serum recognition of one or more of the three fragments, 82% of the total samples analyzed was positive for antibodies to P. jirovecii Msg, indicating high prevalence of P. jirovecii infection or colonization among Cameroonians. Different Msg fragments appear to be recognized more frequently by sera from different geographic regions of the globe. Antibodies in the Cameroonian serum samples recognized MsgA1>MsgC1>MsgB, suggesting that different P. jirovecii strains exist in different parts of the world and/or human populations differ in their response to P. jirovecii. Also, HIV(+) patients diagnosed with respiratory infections (such as TB and pneumonia) and maintained on trimethoprim/sulfamethoxazol prophylaxis had relatively lower anti-Msg titers. Whether PcP prophylaxis has significant effects on the quality of life among HIV(+) patients in Cameroon warrants further investigation.
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Gupta R, Mirdha BR, Guleria R, Kumar L, Samantaray JC, Agarwal SK, Kabra SK, Luthra K. Diagnostic significance of nested polymerase chain reaction for sensitive detection of Pneumocystis jirovecii in respiratory clinical specimens. Diagn Microbiol Infect Dis 2009; 64:381-8. [PMID: 19631091 DOI: 10.1016/j.diagmicrobio.2009.04.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Revised: 04/07/2009] [Accepted: 04/11/2009] [Indexed: 11/16/2022]
Abstract
A total of 327 clinical specimens, including both invasive and noninvasive samples, obtained from 275 patients with various types of underlying immunocompromised conditions and a clinical suspicion of Pneumocystis pneumonia (PCP) were subjected to 2 different nested polymerase chain reaction (PCR) assays. The target genes used for nested PCR were mitochondrial large subunit ribosomal RNA (mtLSU rRNA) and internal transcribed spacer (ITS) region. The results were compared with a single-round PCR targeting major surface glycoprotein (MSG) gene. Amplification was successful in 16% of cases by mtLSU rRNA nested PCR, in 14.5% by ITS nested PCR, and in 10.9% by MSG PCR. The nested mtLSU rRNA PCR was found to be more sensitive (100% sensitive and 98.7% specific) and useful in detecting PCP for its use in routine diagnosis in our settings. Thus, this assay may be quite useful in the identification of patients who are in the early stage of Pneumocystis jirovecii infection with an organism load that could not be easily detected by the single-step PCR.
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Affiliation(s)
- Rashmi Gupta
- Department of Microbiology, All Indian Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
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Krajicek BJ, Thomas CF, Limper AH. Pneumocystis pneumonia: current concepts in pathogenesis, diagnosis, and treatment. Clin Chest Med 2009; 30:265-78, vi. [PMID: 19375633 DOI: 10.1016/j.ccm.2009.02.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pneumocystis pneumonia (PCP) is an infection of the lungs caused by the opportunistic fungal genus Pneumocystis. In humans, PCP is a serious and potentially life-threatening infection occurring in immunocompromised individuals, particularly those who have AIDS, or following immune suppression from malignancy, organ transplantation, or therapies for inflammatory diseases. Several recent studies have contributed to understanding of the biology and pathogenesis of the organism yielding new diagnostic approaches and therapeutic targets. Although trimethoprim-sulfamethoxazole remains the mainstay of prophylaxis and treatment, ongoing concerns for emerging Pneumocystis resistance supports the continuing investigation for novel therapeutic agents.
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Affiliation(s)
- Bryan J Krajicek
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN 55905, USA
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Pneumocystose au cours des maladies systémiques. Presse Med 2009; 38:251-9. [DOI: 10.1016/j.lpm.2008.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 10/28/2008] [Accepted: 11/03/2008] [Indexed: 11/18/2022] Open
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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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Abstract
PURPOSE OF REVIEW Pneumocystis pneumonia remains the most prevalent opportunistic infection in patients with AIDS. It is also a common devastating infection in patients with other causes of altered immunity. Though scientific study of this fungal pathogen is challenging given the inability to propagate the organism outside of the host lung, studies utilizing advanced molecular techniques and genomic analysis have broadened our understanding of the epidemiology and pathogenesis of Pneumocystis and will be described herein. RECENT FINDINGS Results from advanced molecular techniques suggest that Pneumocystis organisms not only cause infection in patients with impaired immunity but also colonize mammals with normal immune systems. Advanced technology has also identified acquired Pneumocystis genetic mutations that confer resistance to currently utilized therapeutics. Though not yet widely utilized in clinical medicine, advanced polymerase chain reaction techniques improve the diagnostic yield of respiratory specimen analysis. Preliminary results from serum beta-glucan testing suggest that a noninvasive marker of Pneumocystis pneumonia infection and response to therapy may be on the horizon. SUMMARY Recent scientific advances suggest opportunities for improving the diagnosis and treatment surveillance of Pneumocystis pneumonia. Further investigations are necessary to define the optimal characteristics of these laboratory tests and to develop therapeutics directed at novel Pneumocystis genomic targets.
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