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Watson AL, Woodford J, Britton S, Gupta R, Whiley D, McCarthy K. Determining Pneumocystis jirovecii Colonisation from Infection Using PCR-Based Diagnostics in HIV-Negative Individuals. Diagnostics (Basel) 2024; 14:114. [PMID: 38201422 PMCID: PMC10802892 DOI: 10.3390/diagnostics14010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Pneumocystis jirovecii pneumonia is increasingly diagnosed with highly sensitive PCR diagnostics in immunocompromised, HIV-negative individuals. We assessed the performance of our in-house quantitative PCR with the aim to optimise interpretation. METHODS Retrospective audit of all positive P. jirovecii qPCRs on induced sputum or BAL fluid at a single centre from 2012 to 2023. Medical and laboratory records were analysed and people with HIV were excluded. Cases were categorised as colonisation, high-probability PCP or uncertain PCP infection against a clinical gold standard incorporating clinico-radiological data. Quantitative PCR assay targeting the 5s gene was utilised throughout the time period. RESULTS Of the 82 positive qPCRs, 28 were categorised as high-probability PCP infection, 30 as uncertain PCP and 24 as colonisation. There was a significant difference in qPCR values stratified by clinical category but not respiratory sample type. Current assay performance with a cutoff of 2.5 × 105 copies/mL had a sensitivity of 50% (95% CI, 30.65-69.35%) and specificity of 83.33% (95% CI, 62.62-95.26%). Youden Index calculated at 6.5 × 104 copies/mL had a sensitivity of 75% (56.64-87.32%, 95% CI) and specificity of 66.67% (46.71-82.03%, 95% CI). High and low cutoffs were explored. Significant variables associated with infection were age > 70 years old, the presence of fever, hypoxia or ground glass changes. CONCLUSIONS A single qPCR cutoff cannot reliably determine P. jirovecii infection from colonisation. Low and high cutoffs are useful, however, a large "possible infection" cohort will remain where interpretation of clinic-radiological factors remains essential. Standardisation of assays with prospective validation in specific immunocompromised groups will allow greater generalisability and allow large-scale prospective assay validation to be performed.
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Affiliation(s)
- Anna Louise Watson
- Infectious Diseases, Royal Brisbane & Women’s Hospital, Metro North Health, Herston, QLD 4006, Australia
- Herston Infectious Diseases Institute, Herston, QLD 4006, Australia
| | - John Woodford
- Infectious Diseases, Ipswich Hospital, Ipswich, QLD 4305, Australia
| | - Sumudu Britton
- Infectious Diseases, Royal Brisbane & Women’s Hospital, Metro North Health, Herston, QLD 4006, Australia
| | - Rita Gupta
- Pathology Queensland, Herston, QLD 4006, Australia
| | - David Whiley
- Pathology Queensland, Herston, QLD 4006, Australia
- The University of Queensland, Herston, QLD 4006, Australia
| | - Kate McCarthy
- Infectious Diseases, Royal Brisbane & Women’s Hospital, Metro North Health, Herston, QLD 4006, Australia
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Oka S. AIDS at 40 th: The progress of HIV treatment in Japan. Glob Health Med 2022; 4:1-8. [PMID: 35291198 PMCID: PMC8884036 DOI: 10.35772/ghm.2021.01120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/26/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Forty years have passed since the first five AIDS cases in Los Angeles were reported in 1981. Looking back at the history, these 40 years could be divided into 3 phases. During the first 15 years, when there was little efficacious therapy against HIV, clinical research was directed to develop diagnosis and treatment for opportunistic infections, mainly Pneumocystis jirovecii pneumonia. When combination antiretroviral therapy (cART) became available in 1996, taking cART had been troublesome to most patients following 10 years because some of them had severe side effects, diet restrictions, high pill burdens, drug interactions, etc. It was not easy for patients to keep high adherence and, therefore, the virus easily obtained drug resistance. Although the prognosis has been dramatically improved, patients had been still living with hard times during the second phase. Along with advancement of anti-retroviral drugs that have allowed simple treatment possible, their life expectancy has further improved and is reaching almost nearly the general population in the following 15 years. However, some patients have recently faced an additional load to treat life-related comorbidities and non-AIDS defining malignancies. The problem is that these diseases start to occur in the 40s- or 50s-year-old generations and that means HIV-infected persons are suffering from pre-mature aging. AIDS no longer signifies death. However, we still have a lot to improve for their quality of life.
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Affiliation(s)
- Shinichi Oka
- Address correspondence to:Shinichi Oka, AIDS Clinical Center, National Center for Global Health and Medicine, 1-21-1, Toyama, Shinjuku-ku, Tokyo 162-8655, Japan. E-mail:
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Abstract
PURPOSE OF REVIEW Pneumocystis pneumonia (PCP) is a frequent opportunistic infection associated with a high mortality rate. PCP is of increasing importance in non-HIV immunocompromised patients, who present with severe respiratory distress with low fungal loads. Molecular detection of Pneumocystis in broncho-alveolar lavage (BAL) has become an important diagnostic tool, but quantitative PCR (qPCR) needs standardization. RECENT FINDINGS Despite a high negative predictive value, the positive predictive value of qPCR is moderate, as it also detects colonized patients. Attempts are made to set a cut-off value of qPCR to discriminate between PCP and colonization, or to use noninvasive samples or combined strategies to increase specificity. SUMMARY It is easy to set a qPCR cut-off for HIV-infected patients. In non-HIV IC patients, a gain in specificity could be obtained by combining strategies, that is, qPCR on BAL and a noninvasive sample, or qPCR and serum beta-1,3-D-glucan dosage.
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Acquired Immunodeficiency from Maternal Chemotherapy and Severe Primary Pneumocystis Infection in an Infant. Case Rep Pediatr 2020; 2020:5740304. [PMID: 32257491 PMCID: PMC7102488 DOI: 10.1155/2020/5740304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 02/12/2020] [Indexed: 12/12/2022] Open
Abstract
Pneumocystis jirovecii is recognized as an opportunistic pathogen in immunosuppressed patients. We report a case of severe Pneumocystis pneumonia (PCP) in an infant with acquired combined immunodeficiency secondary to maternal chemotherapy exposure during the second and third trimesters of pregnancy. The infant required cardiorespiratory support with veno-venous extracorporeal membrane oxygenation (VV-ECMO) for severe respiratory failure. This case highlights the potential for severe acquired immunodeficiency in this patient cohort and further postnatal surveillance is highly recommended.
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5
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Molecular Diagnosis of Pneumocystis jirovecii Pneumonia by Use of Oral Wash Samples in Immunocompromised Patients: Usefulness and Importance of the DNA Target. J Clin Microbiol 2019; 57:JCM.01287-19. [PMID: 31578265 DOI: 10.1128/jcm.01287-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/26/2019] [Indexed: 12/23/2022] Open
Abstract
Pneumocystis jirovecii pneumonia (PJP) is an important cause of pneumonia in the HIV-negative immunocompromised population, for whom the fungal load is low, the differential diagnosis is difficult, and a bronchoalveolar lavage (BAL) sample is often not readily available. Molecular techniques have improved the microbiological diagnosis in this scenario. The usefulness of two real-time PCR techniques targeting nuclear single-copy and mitochondrial multicopy genes, respectively, applied to oral wash specimens (OW) for PJP diagnosis was assessed, and its accuracy was compared to a BAL fluid-based diagnosis. Immunocompromised patients having PJP in the differential diagnosis of an acute respiratory episode, and from whom OW and BAL or lung biopsy specimens were obtained ≤48 h apart, were retrospectively included. PCRs targeting the dihydropteroate synthase gene (DHPS) and the mitochondrial small-subunit (mtSSU) rRNA gene were performed in paired OW-BAL specimens. Thirty-six patients were included (88.6% HIV negative). Fifteen patients (41.7%) were classified as PJP, and a further 8 were considered P. jirovecii colonized. Quantification of DHPS and mtSSU in BAL fluid showed an accuracy of 96.9% and 93.0%, respectively, for PJP diagnosis, whereas a qualitative approach performed better when applied to OW (accuracy, 91.7%) irrespective of the PCR target studied (kappa = 1). Qualitative molecular diagnosis applied to OW showed an excellent performance for PJP diagnosis regardless of the target studied, being easier to interpret than the quantitative approach needed for BAL fluid.
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6
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Fréalle E, Gantois N, Aliouat-Denis CM, Leroy S, Zawadzki C, Perkhofer S, Aliouat EM, Dei-Cas E. Comparison of different blood compartments for the detection of circulating DNA using a rat model of Pneumocystis pneumonia. Med Mycol 2015; 53:754-9. [PMID: 26162469 DOI: 10.1093/mmy/myv050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 05/31/2015] [Indexed: 12/28/2022] Open
Abstract
Pneumocystis is mostly found in the alveolar spaces, but circulation of viable organisms also occurs and suggests that the detection of DNA in blood could be used as a noninvasive procedure to improve the diagnosis of Pneumocystis pneumonia (PcP). In order to determine the optimal compartment for Pneumocystis DNA detection, we used a rat model of PcP and tested the presence of Pneumocystis with a quantitative mtLSU targeting real-time PCR in four blood compartments: whole blood, clot, serum and Platelet-Rich-Plasma (PRP). All samples from 4 Pneumocystis-free control rats were negative. Pneumocystis was detected in 79, 64, 57, and 57% of samples from 14 PcP rats, respectively, but DNA release was not related to pulmonary loads. These data confirm the potential usefulness of Pneumocystis DNA detection in the blood for PcP diagnosis and suggest that whole blood could be the most appropriate compartment for Pneumocystis detection.
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Affiliation(s)
- E Fréalle
- Centre d'Infection et d'Immunité de Lille (CIIL), Inserm U1019 - CNRS UMR 8204 - Université de Lille, IFR142, Institut Pasteur de Lille, France Laboratoire de Parasitologie-Mycologie, CHRU de Lille & Faculté de Médecine de Lille - Université de Lille, France
| | - N Gantois
- Centre d'Infection et d'Immunité de Lille (CIIL), Inserm U1019 - CNRS UMR 8204 - Université de Lille, IFR142, Institut Pasteur de Lille, France
| | - C M Aliouat-Denis
- Centre d'Infection et d'Immunité de Lille (CIIL), Inserm U1019 - CNRS UMR 8204 - Université de Lille, IFR142, Institut Pasteur de Lille, France Laboratoire de Parasitologie, Faculté de Pharmacie de Lille - Université de Lille, France
| | - S Leroy
- Laboratoire de Parasitologie-Mycologie, CHRU de Lille & Faculté de Médecine de Lille - Université de Lille, France
| | - C Zawadzki
- Laboratoire d'Hématologie & EA2693 Interface sang - vaisseaux et réparation cardiovasculaire, CHRU de Lille & Faculté de Médecine de Lille - Université de Lille, France
| | - S Perkhofer
- University of Applied Sciences Tyrol, Innsbruck, Austria
| | - E M Aliouat
- Centre d'Infection et d'Immunité de Lille (CIIL), Inserm U1019 - CNRS UMR 8204 - Université de Lille, IFR142, Institut Pasteur de Lille, France Laboratoire de Parasitologie, Faculté de Pharmacie de Lille - Université de Lille, France
| | - E Dei-Cas
- Centre d'Infection et d'Immunité de Lille (CIIL), Inserm U1019 - CNRS UMR 8204 - Université de Lille, IFR142, Institut Pasteur de Lille, France Laboratoire de Parasitologie-Mycologie, CHRU de Lille & Faculté de Médecine de Lille - Université de Lille, France
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Weissenbacher-Lang C, Nedorost N, Weissenböck H. Finding your way through Pneumocystis sequences in the NCBI gene database. J Eukaryot Microbiol 2014; 61:537-55. [PMID: 24966006 DOI: 10.1111/jeu.12132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/16/2014] [Accepted: 04/02/2014] [Indexed: 11/30/2022]
Abstract
Pneumocystis sequences can be downloaded from GenBank for purposes as primer/probe design or phylogenetic studies. Due to changes in nomenclature and assignment, available sequences are presented with a variety of inhomogeneous information, which renders practical utilization difficult. The aim of this study was the descriptive evaluation of different parameters of 532 Pneumocystis sequences of mitochondrial and ribosomal origin downloaded from GenBank with regard to completeness and information content. Pneumocystis sequences were characterized by up to four different names. Official changes in nomenclature have only been partly implemented and the usage of the "forma specialis", a special feature of Pneumocystis, has only been established fragmentary in the database. Hints for a mitochondrial or ribosomal genomic origin could be found, but can easily be overlooked, which renders the download of wrong reference material possible. The specification of the host was either not available or variable regarding the used language and the localization of this information in the title or several subtitles, which limits their applicability in phylogenetic studies. Declaration of products and geographic origin was incomplete. The print version of this manuscript is completed by an online database which contains detailed information to every accession number included in the meta-analysis.
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Affiliation(s)
- Christiane Weissenbacher-Lang
- Institute of Pathology and Forensic Veterinary Medicine, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
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8
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Iikuni N, Kitahama M, Ohta S, Okamoto H, Kamatani N, Nishinarita M. Evaluation ofPneumocystispneumonia infection risk factors in patients with connective tissue disease. Mod Rheumatol 2014. [DOI: 10.3109/s10165-006-0502-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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9
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KOBORI T, TAKAHASHI H. Expanding Possibilities of Rolling Circle Amplification as a Biosensing Platform. ANAL SCI 2014; 30:59-64. [DOI: 10.2116/analsci.30.59] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Toshiro KOBORI
- National Food Research Institute, National Agriculture and Food Research Organization
| | - Hirokazu TAKAHASHI
- National Food Research Institute, National Agriculture and Food Research Organization
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10
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Alli OAT, Ogbolu DO, Ademola O, Oyenike MA. Molecular detection of pneumocystis jirovecii in patients with respiratory tract infections. NORTH AMERICAN JOURNAL OF MEDICAL SCIENCES 2012; 4:479-85. [PMID: 23112970 PMCID: PMC3482780 DOI: 10.4103/1947-2714.101993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background: Pneumocystis jirovecii, formerly known as P. carinii, is an opportunistic fungus causing Pneumocystis carinii pneumonia especially in immunocompromised patients. Aim: The aim of this study was to detect P. jirovecii in sputum samples from patients suspected of having respiratory tract infections. Materials and Methods: In this study, 230 acid fast bacilli negative sputum samples from 230 patients presenting with respiratory tract infections submitted to three teaching hospitals’ medical microbiology laboratories in Osun and Oyo States, Nigeria for routine investigation were examined for P. jirovecii by microscopical and polymerase chain reaction methods. Results: P. jirovecii cysts were observed in 15 (6.5%) samples and polymerase chain reaction was positive for 29 (12.6%) samples out of 230 samples examined. It was observed that the detection of P. jirovecii was associated with age (P < 0.05) while there were no associations between diagnosis, sex, and prevalence of P. jirovecii (P > 0.05). Polymerase chain reaction was showed to be a better method for the detection of P. jirovecii based on the 51.7% sensitivity and 100% specificity of the microscopy. Conclusion: The study concluded that P. jirovecii is prevalent in patients with respiratory tract infections in hospitals from the southwestern part of Nigeria and should be included in diagnosis of these infections in this part of the world.
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Affiliation(s)
- Oyebode Armstrong Terry Alli
- Department of Biomedical Sciences, College of Health Sciences, Ladoke Akintola University of Technology, Osogbo, Nigeria
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11
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Döşkaya M, Caner A, Değirmenci A, Wengenack NL, Yolasığmaz A, Turgay N, Özensoy Töz S, Gürüz Y. Degree and frequency of inhibition in a routine real-time PCR detecting Pneumocystis jirovecii for the diagnosis of Pneumocystis pneumonia in Turkey. J Med Microbiol 2011; 60:937-944. [PMID: 21459903 DOI: 10.1099/jmm.0.030775-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Routine laboratory diagnosis of Pneumocystis jirovecii is currently achieved by PCR in almost all laboratories with sufficient equipment due to its high sensitivity and specificity compared to staining methods. A current issue that limits the reliability and sensitivity of PCR is the degree of inhibition caused by inhibitory substances in respiratory samples. The present study aimed to analyse the degree and frequency of inhibition in real-time PCR detecting P. jirovecii in respiratory specimens submitted to a Pneumocystis pneumonia (PcP) diagnosis laboratory in Ege University Medical School, Turkey. Between July 2009 and December 2010, 76 respiratory specimens [63 bronchoalveolar lavage (BAL) fluid, 10 sputum samples, two tracheal aspiration fluid and one thoracentesis fluid] obtained from 69 PcP-suspected patients were investigated for the presence of P. jirovecii using real-time PCR targeting the cdc2 gene. Of these samples, 42 of the specimens were stained and examined by microscopy according to the request of the clinicians. PCR was positive in 15 specimens in the initial run. Of the remaining 61 samples, 41 of them were negative with positive internal inhibition controls (i.e. true-negative group). The frequency of inhibition in the initial run was 26.31 % (20/76) as determined by spiked negative controls. All of the inhibited samples were resolved after 1 : 2, 1 : 5, 1 : 10 and 1 : 20 dilutions. P. jirovecii was detected by PCR in two inhibited specimens after retesting with diluted samples which were also positive by microscopy. The incidence of P. jirovecii in respiratory specimens was 22.36 % (17/76) as determined by real-time PCR and 7.14 % (3/42) by microscopy. Overall, the incidence of P. jirovecii in respiratory samples was 23.68 % (18/76) as detected by both methods. In conclusion, inclusion of spiked positive controls in each sample and retesting with diluted samples to resolve inhibition increased the reliability of the real-time PCR assay in terms of determining false-negative results and influencing the treatment of the patient. Furthermore, results of the present study determined for the first time the frequency and degree of inhibition in a real-time PCR detecting P. jirovecii in respiratory specimens during routine diagnosis of PcP.
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Affiliation(s)
- Mert Döşkaya
- Department of Parasitology, Ege University Medical School, Bornova/Izmir 35100, Turkey
| | - Ayşe Caner
- Department of Parasitology, Ege University Medical School, Bornova/Izmir 35100, Turkey
| | - Aysu Değirmenci
- Department of Parasitology, Ege University Medical School, Bornova/Izmir 35100, Turkey
| | - Nancy L Wengenack
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic and Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Ayşegül Yolasığmaz
- Department of Parasitology, Ege University Medical School, Bornova/Izmir 35100, Turkey
| | - Nevin Turgay
- Department of Parasitology, Ege University Medical School, Bornova/Izmir 35100, Turkey
| | - Seray Özensoy Töz
- Department of Parasitology, Ege University Medical School, Bornova/Izmir 35100, Turkey
| | - Yüksel Gürüz
- Department of Parasitology, Ege University Medical School, Bornova/Izmir 35100, Turkey
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12
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Takahashi H, Matsumoto A, Sugiyama S, Kobori T. Direct detection of green fluorescent protein messenger RNA expressed in Escherichia coli by rolling circle amplification. Anal Biochem 2010; 401:242-9. [DOI: 10.1016/j.ab.2010.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 03/10/2010] [Accepted: 03/10/2010] [Indexed: 10/19/2022]
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13
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14
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Robberts FJL, Liebowitz LD, Chalkley LJ. Polymerase chain reaction detection of Pneumocystis jiroveci: evaluation of 9 assays. Diagn Microbiol Infect Dis 2007; 58:385-92. [PMID: 17689766 DOI: 10.1016/j.diagmicrobio.2007.02.014] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Revised: 02/26/2007] [Accepted: 02/27/2007] [Indexed: 11/26/2022]
Abstract
Various polymerase chain reaction (PCR) amplification strategies have been described for detecting Pneumocystis jiroveci in clinical specimens. Different combinations of primer/target and platforms have been reported to yield varying PCR detection rates. PCR was evaluated on clinical specimens using internal transcribed spacer regions of the rRNA nested, dihydropteroate synthase single and nested, dihydrofolate reductase nested, major surface glycoprotein heminested, mitochondrial large subunit rRNA (mtLSUrRNA) single and nested, 18S rRNA 1-tube nested, and real-time 5S rRNA PCR. The most sensitive PCR was subsequently compared with routine diagnostic immunofluorescence (IF) microscopy. Discrepant PCR and IF results were resolved after review of clinical and histology/cytology records. Major discrepancies were observed among the methods investigated. mtLSUrRNA nested PCR was the most sensitive, produced less false-negative results, and displayed the highest degree of concordance with histology. Direct comparison of mtLSUrRNA nested PCR versus IF yielded low sensitivity and specificity, which were improved for PCR and lowered for IF on review of clinical and laboratory records.
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MESH Headings
- DNA, Fungal/genetics
- DNA, Mitochondrial/genetics
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/genetics
- Dihydropteroate Synthase/genetics
- False Negative Reactions
- Fungal Proteins/genetics
- Humans
- Membrane Glycoproteins/genetics
- Microscopy, Fluorescence
- Pneumocystis Infections/diagnosis
- Pneumocystis Infections/microbiology
- Pneumocystis Infections/pathology
- Pneumocystis carinii/genetics
- Pneumocystis carinii/isolation & purification
- Polymerase Chain Reaction/methods
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 5S/genetics
- Sensitivity and Specificity
- Tetrahydrofolate Dehydrogenase/genetics
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Affiliation(s)
- Frans J L Robberts
- Department of Medical Microbiology, The University of Stellenbosch, Tygerberg, South Africa.
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15
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Weisbroth SH. Pneumocystis: newer knowledge about the biology of this group of organisms in laboratory rats and mice. Lab Anim (NY) 2006; 35:55-61. [PMID: 17008910 DOI: 10.1038/laban1006-55] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2006] [Accepted: 08/28/2006] [Indexed: 11/08/2022]
Abstract
This review is an update on some of the remarkable advances that have led to greater understanding of Pneumocystis, an important group of rodent pathogens. The author outlines the life cycle of these pulmonic fungi, their taxonomic position, and their nomenclature. He discusses how infections begin and spread in laboratory rodent colonies, and how those infections are inadvertently maintained in barriered breeding colonies. He also addresses the diagnosis of Pneumocystis infection and provides suggestions for the establishment of Pneumocystis-free animal colonies.
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16
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Palladino S, Kay I, Fonte R, Flexman J. Use of real-time PCR and the LightCycler system for the rapid detection of Pneumocystis carinii in respiratory specimens. Diagn Microbiol Infect Dis 2001; 39:233-6. [PMID: 11404066 DOI: 10.1016/s0732-8893(01)00232-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Pneumocystis carinii pneumonia (PCP) remains a major cause of morbidity and mortality in immunocompromised patients, including those infected with human immunodeficiency virus (HIV). The advent of real-time PCR technology offers the potential for rapid PCR results for the detection of P. carinii. In this report we describe the modification and evaluation of an existing PCR-based method for the detection of P. carinii DNA, into a real-time PCR assay suitable for use with the LightCycler system. Twenty eight induced sputum and bronchial washing specimens from 28 patients were tested by both a conventional PCR assay and a real-time PCR assay. Twelve specimens (42.9%) were positive in both the conventional and real-time PCR assays and sixteen (57.1%) were negative in both assays. The melting points of the amplified P. carinii DNA product obtained by melting curve analysis by the LightCycler of all P. carinii positive specimens ranged from 81.5 degrees C to 83.9 degrees C. There were no discordant results between the two assays for any of the specimens tested and results were available within 2 h for the real-time PCR assay compared to up to 11 h for the conventional PCR assay.
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Affiliation(s)
- S Palladino
- Department of Microbiology, Royal Perth Hospital, Wellington Street, W. A. 6847, Perth, Australia.
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17
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Agostoni F, Atzori C, Angeli E, Mainini A, Micheli V, Cargnel A. Pneumocystis carinii diagnosis: an update. Int J Antimicrob Agents 2000; 16:549-57. [PMID: 11118878 DOI: 10.1016/s0924-8579(00)00292-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
From 1994 to date we have been using the internal transcribed spacers (ITSs) nested polymerase chain reaction (PCR) to investigate the possibility of diagnosing Pneumocystis carinii pneumonia on non-invasive samples collected from HIV-positive patients with pulmonary involvement. The objectives were: (1) to test the sensitivity, specificity and prognostic value of PCR in diagnosis and follow up of PCP; (2) to investigate the eventual occurrence and role of asymptomatic carriers of P. carinii; (3) to evaluate the prognostic significance of blood PCR positivity versus respiratory samples; (4) to verify the occurrence of exogenous infections or endogenous reactivations in cases of recurrent P. carinii pneumonia; and (5) to study the possible correlation between P. carinii genotype identified and capability of blood dissemination, prior prophylactic treatments, clinical parameters and outcome of the patients.
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Affiliation(s)
- F Agostoni
- II Department of Infectious Diseases, Luigi Sacco Hospital, Via G.B. Grassi, 20157 Milan, Italy
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18
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Yusa N, Watanabe K, Yoshida S, Shirafuji N, Shimomura S, Tani K, Asano S, Sato N. Transcription factor Sp3 activates the liver/bone/kidney‐type alkaline phosphatase promoter in hematopoietic cells. J Leukoc Biol 2000. [DOI: 10.1189/jlb.68.5.772] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Nozomi Yusa
- Department of Laboratory Medicine, The Institute of Medical Science, The University of Tokyo; The Institute of Bio‐Medical Research, Teijin Ltd., Tokyo; and Department of Oncology/Hematology, The Institute of Medical Science, The University of Tokyo, Japan
| | - Kunihito Watanabe
- Department of Laboratory Medicine, The Institute of Medical Science, The University of Tokyo; The Institute of Bio‐Medical Research, Teijin Ltd., Tokyo; and Department of Oncology/Hematology, The Institute of Medical Science, The University of Tokyo, Japan
| | - Satoru Yoshida
- Department of Laboratory Medicine, The Institute of Medical Science, The University of Tokyo; The Institute of Bio‐Medical Research, Teijin Ltd., Tokyo; and Department of Oncology/Hematology, The Institute of Medical Science, The University of Tokyo, Japan
| | - Naoki Shirafuji
- Department of Laboratory Medicine, The Institute of Medical Science, The University of Tokyo; The Institute of Bio‐Medical Research, Teijin Ltd., Tokyo; and Department of Oncology/Hematology, The Institute of Medical Science, The University of Tokyo, Japan
| | - Satoshi Shimomura
- Department of Laboratory Medicine, The Institute of Medical Science, The University of Tokyo; The Institute of Bio‐Medical Research, Teijin Ltd., Tokyo; and Department of Oncology/Hematology, The Institute of Medical Science, The University of Tokyo, Japan
| | - Kenzaburo Tani
- Department of Laboratory Medicine, The Institute of Medical Science, The University of Tokyo; The Institute of Bio‐Medical Research, Teijin Ltd., Tokyo; and Department of Oncology/Hematology, The Institute of Medical Science, The University of Tokyo, Japan
| | - Shigetaka Asano
- Department of Laboratory Medicine, The Institute of Medical Science, The University of Tokyo; The Institute of Bio‐Medical Research, Teijin Ltd., Tokyo; and Department of Oncology/Hematology, The Institute of Medical Science, The University of Tokyo, Japan
| | - Noriharu Sato
- Department of Laboratory Medicine, The Institute of Medical Science, The University of Tokyo; The Institute of Bio‐Medical Research, Teijin Ltd., Tokyo; and Department of Oncology/Hematology, The Institute of Medical Science, The University of Tokyo, Japan
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Abstract
Many pathogens have been reported to cause disease in the laboratory rat. This chapter concentrates on the pathology of the more common pathogens of the laboratory rat. Based on serologic surveys, parvo viruses are some of the most common viral pathogens in wild and laboratory rat. In general, there are three main serogroups, including Rat virus (RV), H-1 virus, and Ratparvovirus (RPV). Both RPV and RV are tropic for many of the same tissues and they both may result in a persistent infection. However, RPV is antigenically and genetically distinct from RV, and it apparently does not cause clinical signs or lesions in infant rats. M. pulmonis causes natural disease in rats and mice. The infection in young rats is usually clinically silent. In older rats, there are nonspecific clinical signs such as snuffling, chromodacryorrhea, and face and ear rubbing. Several bacteria of the genus Streptococcus can cause clinical disease in rats. All of the streptococci of concern in rats are Gram-positive cocci, and are catalase-negative, nonfermentative, and generally nonmotile. Cilia-associated respiratory bacillus has been identified in rats. In rats, infection is usually asymptomatic although nonspecific clinical signs, such as weight loss and dyspnea, may be observed.
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Atzori C, Angeli E, Agostoni F, Mainini A, Micheli V, Cargnel A. Biomolecular techniques to detect Pneumocystis carinii f. sp. hominis pneumonia in patients with acquired immunodeficiency syndrome. Int J Infect Dis 1999; 3:76-81. [PMID: 10225984 DOI: 10.1016/s1201-9712(99)90013-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES To verify the clinical value of two different polymerase chain reactions (PCRs) for noninvasive diagnosis and follow-up during Pneumocystis carinii f. sp. hominis pneumonia (PCP) and to analyze the P. carinii f. sp. hominis genotypes involved. METHODS Internal transcribed spacers (ITSs) nested PCR was applied to 630 samples (bronchoalveolar lavage, sera, peripheral blood mononuclear cells, and oropharyngeal samples) from 122 patients with acquired immunodeficiency syndrome and pneumonia and 40 control samples from 20 subjects seronegative for human immunodeficiency virus. One hundred and eighty samples also were examined by mt-rRNA PCR. Bronchoalveolar lavage samples and 33 sera were analyzed by type-specific oligonucleotide hybridization. RESULTS On bronchoalveolar lavage samples, the two PCRs consistently confirmed the morphologic diagnosis of PCP. The sensitivity of ITSs nested PCR versus mt-rRNA PCR was 57.3% versus 14.3% on sera, 32.3% versus 22. 8% on peripheral blood mononuclear cells, and 69.1% versus 48.6% on oropharyngeal samples (garglings). Both PCRs had 100% specificity. Type-specific oligonucleotide hybridization revealed in 72.2% of bronchoalveolar lavage samples a single P. carinii f. sp. hominis genotype, whereas in 27.8% co-infection with more than one strain was detected. CONCLUSION On noninvasive samples, ITSs nested PCR was more sensitive than mt-rRNA PCR, and it confirmed the diagnosis in all patients with PCP. For each patient with PCP at least one noninvasive sample was positive for P. carinii f. sp. hominis DNA.
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Affiliation(s)
- C Atzori
- II Department of Infectious Diseases, L. Sacco Hospital, Milan, Italy
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21
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Weisbroth SH, Geistfeld J, Weisbroth SP, Williams B, Feldman SH, Linke MJ, Orr S, Cushion MT. Latent Pneumocystis carinii infection in commercial rat colonies: comparison of inductive immunosuppressants plus histopathology, PCR, and serology as detection methods. J Clin Microbiol 1999; 37:1441-6. [PMID: 10203502 PMCID: PMC84796 DOI: 10.1128/jcm.37.5.1441-1446.1999] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/1998] [Accepted: 02/02/1999] [Indexed: 11/20/2022] Open
Abstract
Histopathologic evaluation combined with a period of immunosuppression has been the standard procedure for detection of Pneumocystis carinii in commercial rat colonies. Variation in induction regimens and in the sensitivity of detection methods may result in underreporting of the presence of P. carinii in breeding colonies or delay its detection. In the present study, methylprednisolone and cyclophosphamide were evaluated for the ability to induce P. carinii infection in rats from an enzootically infected commercial barrier colony. The presence of P. carinii was detected by histopathologic methods and by amplification of a targeted region of the P. carinii thymidylate synthase gene by PCR over the 8-week study period. Sera taken from rats prior to either induction regimen were evaluated for the presence of P. carinii-specific antibodies by the immunoblotting technique. Few significant differences in ability to induce organism burden or in histopathology were observed between the two immunosuppressive regimens. However, a dramatic loss of weight over the study period was observed in rats treated with methylprednisolone but not in rats treated with cyclophosphamide. Although histopathologic changes attributable to P. carinii did not appear before 2 weeks with either immunosuppressant, the presence of the organism in these animals was detected by immunoblotting and PCR. Cyst scores and the intensities of the histopathologic lesions increased during the study period, but the number of rats exhibiting evidence of P. carinii infection did not change after week 3. These results suggest that use of the PCR method on postmortem lung tissue of rats without prior induction regimens or identification of anti-P. carinii antibodies in antemortem serum samples is a sufficiently sensitive method for detection of the presence of a P. carinii carrier state in rodent breeding colonies.
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22
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Ruiz-González A, Falguera M, Nogués A, Rubio-Caballero M. Is Streptococcus pneumoniae the leading cause of pneumonia of unknown etiology? A microbiologic study of lung aspirates in consecutive patients with community-acquired pneumonia. Am J Med 1999; 106:385-90. [PMID: 10225239 DOI: 10.1016/s0002-9343(99)00050-9] [Citation(s) in RCA: 183] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
PURPOSE Although a wide variety of recognized pathogens can cause community-acquired pneumonia, in many patients the etiology remains unknown after routine diagnostic workup. The aim of this study was to identify the causal agent in these patients by obtaining lung aspirates with transthoracic needle aspiration. SUBJECTS AND METHODS During a 15-month period, all consecutive patients with community-acquired pneumonia who were eligible for transthoracic needle aspiration were enrolled in the study. In addition to conventional microbial methods (culture of blood and sputum, serologic studies), we performed cultures and genetic and antigen tests for common respiratory pathogens in lung aspirates. RESULTS The study group consisted of 109 patients. Conventional microbial studies identified an etiology in 54 patients (50%), including Mycoplasma pneumoniae in 19 patients, Chlamydia pneumoniae in 9 patients, and Streptococcus pneumoniae in 9 patients. Among the remaining 55 patients, study of the lung aspiration provided evidence of the causal agent in 36 (65%). In 4 additional patients with a single microbial diagnosis by conventional methods, the lung sample provided evidence of an additional microorganism. The new pathogens detected by lung aspiration were S. pneumoniae in 18 patients, Haemophilus influenzae in 6 patients, Pneumocystis carinii in 4 patients, and C. pneumoniae in 3 patients; other organisms were identified in 4 patients. CONCLUSIONS In our study, S. pneumoniae was the leading cause of community-acquired pneumonia, accounting for 25% of all cases, including about one-third of the cases the cause of which could not be ascertained with routine diagnostic methods.
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Affiliation(s)
- A Ruiz-González
- Department of Internal Medicine, Arnau de Vilanova University Hospital, Lleida, Spain
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23
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Rabodonirina M, Cotte L, Boibieux A, Kaiser K, Mayencon M, Raffenot D, Trepo C, Peyramond D, Picot S. Detection of Pneumocystis carinii DNA in blood specimens from human immunodeficiency virus-infected patients by nested PCR. J Clin Microbiol 1999; 37:127-31. [PMID: 9854076 PMCID: PMC84186 DOI: 10.1128/jcm.37.1.127-131.1999] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/1998] [Accepted: 10/06/1998] [Indexed: 11/20/2022] Open
Abstract
The detection of Pneumocystis carinii DNA in blood by PCR could be useful for studying the natural history of pneumocystosis and could also be a noninvasive diagnostic method. The results of previous studies are nevertheless conflicting. In our study, we compared three commercially available DNA extraction kits (GeneReleaser, QIAamp Tissue Kit, and ReadyAmp Genomic DNA Purification System) and proteinase K and proteinase K-phenol-chloroform treatments for the extraction of P. carinii DNA from dilutions of a P. carinii f. sp. hominis cyst suspension mixed with human whole blood. A rapid and simple nested PCR protocol which amplifies a portion of the mitochondrial large-subunit rRNA gene was applied to all the extraction products. The QIAmp Tissue Kit was the most effective kit for the isolation of amplification-ready P. carinii DNA and was used with nested PCR for the testing of whole-blood specimens from 35 immunocompetent control patients and 84 human immunodeficiency virus (HIV)-infected patients investigated for pulmonary disease and/or fever. In HIV-infected patients, P. carinii DNA was detected by nested PCR in blood samples from 3 of 14 patients with microscopically proven P. carinii pneumonia, 7 of 22 patients who were considered to be colonized with P. carinii, and 9 of 48 patients who were neither infected nor colonized with P. carinii. P. carinii DNA was not detected in blood specimens from the 35 immunocompetent patients. P. carinii DNA in blood might represent viable P. carinii organisms or DNA complexes released from pulmonary phagocytes. In conclusion, P. carinii DNA may be detected in whole blood from HIV-infected patients, but the nature and the meaning of the circulating form of P. carinii remain to be established.
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Affiliation(s)
- M Rabodonirina
- Departement de Parasitologie et de Mycologie, Universite Claude-Bernard, Lyon, France.
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24
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Gottfredsson M, Cox GM, Perfect JR. Molecular methods for epidemiological and diagnostic studies of fungal infections. Pathology 1998; 30:405-18. [PMID: 9839319 DOI: 10.1080/00313029800169726] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Over the past two decades there has been a remarkable increase in the incidence of invasive fungal infections. Molecular methods, such as karyotyping, restriction analysis and polymerase chain reaction (PCR), have now been applied to improve our current understanding of the epidemiology of these fungal infections. For example, investigations on nosocomial outbreaks of fungal infections have been greatly facilitated by molecular methods. In addition, the ability to diagnose and identify deep-seated mycoses may be enhanced by the use of molecular techniques. In the near future it is possible that PCR-based methods will supplement, or perhaps even replace, traditional methods for detection of Candida albicans blood stream infections, invasive aspergillosis and Pneumocystis carinii pneumonia. This review examines the progress of molecular biology into the clinical arena of fungal epidemiology, laboratory identification and diagnosis.
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Affiliation(s)
- M Gottfredsson
- Duke University Medical Center, Department of Medicine, Durham, North Carolina, United States of America
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25
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Nakamura Y, Wada M. Molecular pathobiology and antigenic variation of Pneumocystis carinii. ADVANCES IN PARASITOLOGY 1998; 41:63-107. [PMID: 9734292 DOI: 10.1016/s0065-308x(08)60422-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Y Nakamura
- Department of Tumor Biology, University of Tokyo, Japan
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26
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Tamburrini E, Mencarini P, Visconti E, Zolfo M, Marinaci S, Zinzi D, Margutti P, Ortona E, Siracusano A. Potential impact of Pneumocystis genetic diversity on the molecular detection of the parasite in human host. FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY 1998; 22:37-49. [PMID: 9792059 DOI: 10.1111/j.1574-695x.1998.tb01185.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Our aim was to evaluate if genetic diversity of Pneumocystis carinii could influence the detection by molecular techniques in bronchoalveolar lavage (BAL) fluids and in non-invasive specimens (induced sputum, oropharyngeal washing and serum/blood). P. carinii is morphologically similar in different hosts although several strains have been identified by biomolecular techniques. Variations of mt-LSU and ITSs sequences could determine a lack of hybridization of some clinical samples and could have diagnostic consequences with loss in sensitivity and specificity of available molecular tests, but at the moment no data support a significant impact of genetic diversity in these sequences on molecular detection of P. carinii for clinical purposes.
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Affiliation(s)
- E Tamburrini
- Clinic of Infectious Diseases, Catholic University, Rome, Italy
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27
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Lundgren B, Wakefield AE. PCR for detecting Pneumocystis carinii in clinical or environmental samples. FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY 1998; 22:97-101. [PMID: 9792067 DOI: 10.1111/j.1574-695x.1998.tb01193.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Since Pneumocystis carinii cannot be cultured in vitro, the introduction of polymerase chain reaction (PCR) has been an enormous advantage for research purposes. It is now possible to detect P. carinii in specimens containing low numbers of organisms where conventional detection methods using microscopic examination of histochemical stains has been insufficient. PCR has been used to detect P. carinii in bronchoalveolar lavage, induced sputum, spontaneous expectorates, oropharyngeal gargles, nasopharyngeal aspirates, serum, blood and in environmental samples. The use of PCR will enable the study of the epidemiology of P. carinii infection by detecting the organism in environmental samples, permitting molecular typing and thereby the study of the transmission of the organism. Furthermore PCR will facilitate studies on the response to therapy, studies monitoring for the emergence of drug resistant strains of P. carinii and in the diagnosis of P. carinii pneumonia in noninvasive specimens, in patients unable to undergo more invasive diagnostic procedures.
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Affiliation(s)
- B Lundgren
- Department of Clinical Microbiology, Statens Serum Institut, Copenhagen, Denmark
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28
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Latouche S, Rabodonirina M, Mazars E. Pneumocystis: the 'carrier state': epidemiology and transmission of human pneumocystosis. FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY 1998; 22:81-6. [PMID: 9792064 DOI: 10.1111/j.1574-695x.1998.tb01190.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S Latouche
- Laboratoire de Parasitologie-Mycologie CHU Saint-Antoine, Paris, France
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29
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Atzori C, Angeli E, Agostoni F, Mainini A, Filippini M, Micheli V, Cargnel A. Emerging aspects related to the application of biomolecular techniques to the diagnosis of Pneumocystis carinii pneumonia: our experience with ITSs primers. FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY 1998; 22:93-5. [PMID: 9792066 DOI: 10.1111/j.1574-695x.1998.tb01192.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- C Atzori
- Department of Infectious Diseases, Sacco Hospital, Milan, Italy
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30
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Hauser PM, Blanc DS, Bille J, Francioli P. Typing methods to approach Pneumocystis carinii genetic heterogeneity. FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY 1998; 22:27-35. [PMID: 9792058 DOI: 10.1111/j.1574-695x.1998.tb01184.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The study of the genetic heterogeneity of P. carinii is complicated by the lack of an in vitro culture system, as well as by the likely occurrence of co-infections with several special forms or types in a single host. Karyotyping and multilocus enzyme electrophoresis are useful for studies at the evolutionary level. However, these methods require a large number of cells, which prevents their use for the special form infecting humans. DNA sequence analysis of genomic regions is useful to study P. carinii diversity, both at the evolutionary and epidemiological levels. To type the special form specific to humans, several methods are currently used to detect polymorphism in PCR products of polymorphic regions of the genome: DNA sequencing, type-specific hybridisations, and single-strand conformation polymorphism. All these methods still need evaluation. The frequency of potential co-infections in humans determined by these various methods is different. The differences could be due to methodological problems or to real variations between patient populations, geographical locations and/or prophylaxis regimens. In the future, elucidating the population structure of P. carinii and the frequency of potential co-infections is going to be crucial for a better understanding of its epidemiology, and thus for a better prevention of P. carinii pneumonia in humans.
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Affiliation(s)
- P M Hauser
- Centre Hospitalier Universitaire Vaudois, Division Autonome de Médecine Préventive Hospitalière, Lausanne, Switzerland.
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31
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Atzori C, Agostoni F, Angeli E, Mainini A, Orlando G, Cargnel A. Combined use of blood and oropharyngeal samples for noninvasive diagnosis of Pneumocystis carinii pneumonia using the polymerase chain reaction. Eur J Clin Microbiol Infect Dis 1998; 17:241-6. [PMID: 9707306 DOI: 10.1007/bf01699980] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
To evaluate the clinical use of a polymerase chain reaction (PCR) assay for diagnosis of Pneumocystis carinii pneumonia (PCP) using samples collected noninvasively, the Internal Transcribed Spacers (ITSs) nested PCR was performed on 148 samples from 40 subjects. Bronchoalveolar lavage (BAL) fluid sera, gargled oropharyngeal washes, and peripheral blood mononuclear cells (PBMC) from 14 AIDS patients (mean age, 35.6 years; mean CD4+ cell count, 49.2 cells/mm3) with proven PCP and from 13 HIV-seropositive controls (mean age, 34.6 years; mean CD4+ cell count, 107.3 cells/mm3) with other AIDS-related opportunistic infections were evaluated. Sera and oropharyngeal samples were also collected from 13 HIV-seronegative health care personnel working in an infectious disease ward for use as negative controls. The ITSs nested PCR confirmed the morphological diagnosis of PCP in all patients when BAL fluid was tested (100% sensitivity). This technique also detected Pneumocystis carinii DNA in oropharyngeal samples from 78.6% of patients, in sera from 71.4% of patients, in PBMC from 35.7% of patients. When all results obtained after ITSs nested PCR were considered together for the same patient, the sensitivity for PCP diagnosis was 100% for blood and oropharyngeal samples (gargled saline), as confirmed by subsequent BAL. All samples collected noninvasively from 26 of 26 controls were negative using ITSs nested PCR (100% specificity).
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Affiliation(s)
- C Atzori
- II Department of Infectious Diseases, Sacco Hospital, Milan, Italy
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32
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Miyawaki H, Fujita J, Yamadori I, Hojo S, Obayashi Y, Nakamura H, Yamaji Y, Suemitsu I, Harada M, Suguri S, Takahara J. Detection of Pneumocystis carinii Sequences in Serum by Polymerase Chain Reaction: Clinical Application in Two Patients with P. carinii Pneumonia. J Infect Chemother 1998. [DOI: 10.1007/bf02490065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Molecular typing methods have enabled infection control personnel to investigate outbreaks and endemic nosocomial infections more quickly and thoroughly than they could have with basic epidemiologic and microbiologic methods. This article reviews molecular typing methods that have been used successfully in the practice of hospital epidemiology. Included is an explanation of the basic principles of these methods and a description of their strengths and weaknesses.
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Affiliation(s)
- S Weber
- Department of Internal Medicine, University of Iowa College of Medicine, University of Iowa Hospitals and Clinics, Iowa City, USA
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34
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Tang X, Bartlett MS, Smith JW, Lee CH. A single-tube nested PCR for Pneumocystis carinii f. sp. hominis. J Clin Microbiol 1997; 35:1597-9. [PMID: 9163492 PMCID: PMC229797 DOI: 10.1128/jcm.35.6.1597-1599.1997] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A single-tube nested PCR which amplifies the internal transcribed spacer (ITS) regions of the rRNA genes of human Pneumocystis carinii was developed. The outer primers for the first PCR, which anneal to the 18S and the 26S rRNA genes of P. carinii, were made to have a midpoint temperature (Tm) of 74 degrees C. The inner primers for the second PCR have a Tm of 56 to 58 degrees C and are specific for human P. carinii; they anneal to an area close to the beginning of ITS1 and the junction of ITS2 and the 26S rRNA genes. The reaction mixture contained 2.5 pmol of the first-PCR primers and 25 pmol of the second-PCR primers. The first PCR was performed at an annealing temperature of 68 degrees C, which did not allow the second-PCR primers to function. Since very small amounts (2.5 pmol) of the first-PCR primers were used, they were exhausted when the first PCR was completed. The single-tube nested PCR did not amplify P. carinii isolated from rats, mice, or ferrets. All 10 bronchoalveolar lavage (BAL) specimens from patients with P. carinii pneumonia were positive, whereas all 10 BAL specimens from patients with other diseases or patients infected with several commonly found fungi were negative by PCR.
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Affiliation(s)
- X Tang
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis 46202, USA
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35
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Graves DC, Chary-Reddy S, Becker-Hapak M. Detection of Pneumocystis carinii in induced sputa from immunocompromised patients using a repetitive DNA probe. Mol Cell Probes 1997; 11:1-9. [PMID: 9076709 DOI: 10.1006/mcpr.1996.0070] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A hybridization assay for the detection of Pneumocystis carinii was developed using a repetitive DNA fragment of P.c. hominis. The assay was specific as different micro-organisms typically found in the respiratory tract, normal human lung DNA (A 549 cell line) and normal rat lung DNA did not react with the repetitive probe. In a slot blot (SB) hybridization assay, the repetitive probe was able to detect as few as 100 P.c. hominis organisms with no false-positives. The results of the SB hybridization assay were compared with an immunofluorescence (IFA) assay for the detection of P.c. hominis in 84 induced sputum (IS) samples obtained from 52 human immunodeficiency virus (HIV)-seropositive patients, 22 HIV-seronegative patients and 10 healthy individuals. Samples from 24 patients clinically diagnosed with P. carinii pneumonia (PCP) were positive for P.c. hominis by both assays. In addition, the SB assay detected P.c. hominis in 14 patients (10 HIV-positive and four HIV-negative) who were negative by IFA. All 14 samples showed a positive PCR signal for the P.c. hominis dihydrofolate reductase gene, further confirming the presence of P.c. hominis in these specimens. Twelve of these patients had a clinical course highly suggestive of PCP and were either on P. carinii prophylaxis or P. carinii chemotherapy. The other two samples were from HIV-positive patients who had respiratory illness due to causes other than P.c. hominis (disseminated histoplasmosis and fatal Bordetella pneumonia). Detection of P.c. hominis in these samples suggests that these patients may have subclinical colonization by P.c. hominis. Furthermore, P.c. hominis was detected in all 12 sequential IS samples from six AIDS patients who had primary episodes of PCR using the SB assay, while P.c. hominis was detected only in eight samples by IFA (66.6%). All six patients developed recurrent PCP within 6 months from the time the assays were performed, further illustrating the potential of the SB hybridization assay in monitoring PCP recurrence. Thus, the ability of the SB hybridization assay to detect a low parasite load suggests that this assay may become an important supplemental tool, along with current cytological methods, for detecting P.c. hominis in patient populations with lower burdens of the organism and in identifying asymptomatic carriers of the parasite in healthy and immunosuppressed individuals.
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Affiliation(s)
- D C Graves
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City 73190, USA
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Latouche S, Ortona E, Mazars E, Margutti P, Tamburrini E, Siracusano A, Guyot K, Nigou M, Roux P. Biodiversity of Pneumocystis carinii hominis: typing with different DNA regions. J Clin Microbiol 1997; 35:383-7. [PMID: 9003601 PMCID: PMC229585 DOI: 10.1128/jcm.35.2.383-387.1997] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The purpose of this study was to identify the most useful gene for the detection of biodiversity of Pneumocystis carinii hominis isolates and to compare samples from French and Italian subjects. We studied 20 bronchoalveolar lavage fluid specimens from 20 human immunodeficiency virus-infected patients (10 French and 10 Italian patients) with Pneumocystis carinii pneumonia by DNA sequencing of the thymidylate synthase (TS), 5S rRNA, large-subunit mitochondrial rRNA (mt LSU rRNA), and internal transcribed spacer (ITS1 and ITS2) genes. Thirteen of the 20 sequenced samples had the prototype TS gene sequence. Fourteen of the 20 samples showed the prototype sequence of the 5S rRNA gene, and 6 had variant sequences of the 5S rRNA gene. The mt LSU rRNA gene was sequenced for 18 of the 20 samples; all sequences were different from the prototype sequence and were classified into four groups. Thirteen of the 20 ITS1 and ITS2 sequences were analyzed, and all the sequences were found to be different from the prototype sequence and were classified into 10 groups. The internal transcribed spacer regions thus appear to be the most discriminatory region of DNA for analysis of the biodiversity of P. carinii hominis isolates.
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Affiliation(s)
- S Latouche
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalier Universitaire Saint-Antoine, Paris, France
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Wagner D, Königer J, Kern WV, Kern P. Serum PCR of Pneumocystis carinii DNA in immunocompromised patients. SCANDINAVIAN JOURNAL OF INFECTIOUS DISEASES 1997; 29:159-64. [PMID: 9181652 DOI: 10.3109/00365549709035877] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The detection of Pneumocystis carinii DNA in serum, a potentially useful and attractive tool for the diagnosis of P. carinii infection and for monitoring the success of therapeutic interventions, remains a controversial issue. In a prospective study of 29 immunocompromised patients, including 16 with HIV infection undergoing bronchoscopy and bronchoalveolar lavage, we examined 32 bronchoalveolar lavage fluids and multiple serum samples for the presence of P. carinii DNA by using mitochondrial rRNA gene fragments pAZ102-E as pAZ102-H as primers. Samples from 7 immunocompetent patients were analysed as a control. 13/32 bronchoalveolar lavage fluids of immunocompromised patients (41%), but none of the controls, had both microscopic evidence of P. carinii cysts as well as P. carinii DNA detection. In none of these patients were serum samples obtained before therapy positive for P. carinii DNA, while in 1 patient (8%), P. carinii DNA was detected in 2/5 serum samples obtained during therapy. Interestingly, PCR detected P. carinii DNA in sera of 3/15 immunocompromised patients without detection of P. carinii DNA or organisms in BAL. Two of these 3 patients were taking secondary prophylactics for P. carinii pneumonia. In conclusion, PCR for P. carinii DNA in serum, at least in certain circumstances, may be of little value for the diagnosis of P. carinii pneumonia.
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Affiliation(s)
- D Wagner
- Department for Gastroenterology and Infectious Diseases, University Hospital and Medical Center, Tübingen, Germany
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38
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Kobayashi M, Urata T, Ikezoe T, Hakoda E, Uemura Y, Sonobe H, Ohtsuki Y, Manabe T, Miyagi S, Miyoshi I. Simple detection of the 5S ribosomal RNA of Pneumocystis carinii using in situ hybridisation. J Clin Pathol 1996; 49:712-6. [PMID: 9038753 PMCID: PMC500718 DOI: 10.1136/jcp.49.9.712] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
AIMS To investigate the effectiveness of digoxigenin incorporated double stranded DNA probes produced by the polymerase chain reaction (PCR), for the detection of Pneumocystis carinii, using in situ hybridisation (ISH). METHODS Formalin fixed, paraffin wax embedded sections of 26 human lung samples from 11 patients with P carinii pneumonia (PCP), and 15 with various types of fungal and viral pneumonia, were obtained during necropsy or transbronchial lung biopsy. Three additional PCP induced rat lung samples were also tested. PCR probes were prepared using the digoxigenin labelling mixture, and they were amplified from the DNA of a PCP induced rat lung after administration of dexamethasone, on the basis that 5S ribosomal RNA sequences are identical in human and rat P carinii. ISH was performed using this probe, and visualised using the digoxigenin nucleic acid detection kit. An immunohistochemical study using anti-human Pneumocystis monoclonal antibody was also carried out in parallel. RESULTS ISH positively stained eight (of eight) lung necropsy specimens from patients with PCP, three (of three) transbronchial lung biopsy specimens from patients with PCP, and none of the three PCP induced rat lung specimens. In contrast, none of the specimens from patients with pneumonia caused by Aspergillus sp (n = 5), Candida sp (n = 4), Cryptococcus sp (n = 2), mucormycosis (n = 2), or cytomegalovirus (n = 2) were positive on ISH or immunohistochemistry. CONCLUSIONS Using a digoxigenin labelled PCR probe for the entire 5S rRNA sequence in conjunction with conventional staining, ISH is highly reactive and specific for the diagnosis of PCP.
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Affiliation(s)
- M Kobayashi
- Department of Internal Medicine, Kochi Medical School, Japan
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39
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Latouche S, Ortona E, Mazars E, Margutti P, Siracusano A, Tamburrini E, Guyot K, Nigou M, Roux P. Biodiversity of French and Italian human Pneumocystis carinii. J Eukaryot Microbiol 1996; 43:54S-55S. [PMID: 8822856 DOI: 10.1111/j.1550-7408.1996.tb04989.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- S Latouche
- Lab. of Parasitol-Myco, CHU Saint-Antoine, Paris
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40
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Hong ST. PCR in diagnosis of pneumocystosis of rats. THE KOREAN JOURNAL OF PARASITOLOGY 1996; 34:191-6. [PMID: 8843695 DOI: 10.3347/kjp.1996.34.3.191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Polymerase chain reaction (PCR) is a powerful technique to detect scanty amount of DNA from living organisms. The present study intended to develop specific primers for PCR diagnosis of pneumocystosis and to evaluate diagnostic efficacy by preparation of template DNAs from invasive BAL fluid and also to screen serum or blood as a non-invasive specimen. Albino rats of Wistar or Fischer strains were experimentally infected by Pneumocystis carinii. Extracted DNAs or cell lysates of their blood, bronchoalveolar lavage fluid, and lung homogenate were used as the template DNA. Primers were synthetic oligonucleotides among 16s rDNA sequences. All of the primer combinations gave PCR products, but the primer pair of #24 and #27 gave best quality product of 666 bp. The sensitivity of PCR with lysates of BAL fluid was 57.7% but it increased to 84.6% with extracted DNAs. None of BAL lysate or DNA was positive among 13 microscopically negatives. The serum DNAs were positive only in 2 cases out of 20 morphologically positive rats. DNAs of human, rat, other parasites, yeast, and microorganisms were negative. The findings suggest that the present primers are specific but simple lysate of BAL fluid is not sensitive. PCR may be used as a routine diagnostic method of pneumocystosis if simple and rapid preparation of non-invasive clinical specimens are available.
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Affiliation(s)
- S T Hong
- Department of Parasitology, Seoul National University College of Medicine, Korea
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41
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Schönian G, Tietz HJ, Thanos M, Gräser Y. [Application of molecular biological methods for diagnosis and epidemiology of human fungal infections]. Mycoses 1996; 39 Suppl 1:73-80. [PMID: 8767275 DOI: 10.1111/j.1439-0507.1996.tb00509.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
For mycological diagnosis molecular methods can be applied to detect the pathogen directly without prior cultivation and to identify species and subspecies. For the detection of infecting agents specific DNA probes and/or the polymerase chain reaction (PCR) are widely used, whereas normally only PCR can provide sufficient sensitivity for the direct detection of pathogens in clinical material. Prospects and limitations of PCR approaches for the detection of pathogenic fungi reported in the literature will be discussed. DNA polymorphisms which are useful for species identification and epidemiological strain typing of medically relevant fungi can be detected by such methods as the analysis of restriction fragment length polymorphisms (RFLP), and Southern hybridization with appropriate DNA probes, and as karyotyping by pulsed field gel electrophoresis (PFGE). These techniques which could be applied successfully to different epidemiological studies are, however, laborious and time consuming. By using a PCR-fingerprinting method which can be performed much simpler polymorphic DNA regions are amplified with different non-specific primers. Distinctive and reproducible sets of amplification products were observed for 26 different Candida and 8 other fungal species. The number and size of the amplification products obtained were characteristic for each species. By comparing species-specific PCR-fingerprints of clinical isolates with those of reference strains, clinical isolates could be identified to the species level even if they could not be identified by conventional typing methods. With all primers, PCR-fingerprints also displayed intraspecies variability. Therefore, PCR-fingerprinting can also be applied for epidemiological strain characterization among medically relevant fungi.
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Affiliation(s)
- G Schönian
- Institut für Mikrobiologie und Hygiene, Universitätsklinikum Charité, Humboldt-Universität, Berlin, BR Deutschland
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42
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Miyawaki H, Fujita J, Hojo S, Harada M, Yamaji Y, Suguri S, Takahara J. Detection of Pneumocystis carinii sequences in serum by polymerase chain reaction. Respir Med 1996; 90:153-7. [PMID: 8736207 DOI: 10.1016/s0954-6111(96)90157-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The clinical significance of the detection of Pneumocystis carinii DNA was evaluated, as well as the detection of circulating P. carinii antigen from serum using previously collected samples. Fourteen serum samples from 13 patients were diagnosed positively for P. carinii DNA by polymerase chain reaction (PCR). Ten of 14 episodes (71.4%) of pulmonary complications were compatible with P. carinii pneumonia. Two patients were definitely diagnosed as having had P. carinii pneumonia at autopsy. All patients positive for circulating antigens were also positive for P. carinii DNA, suggesting that the detection of P. carinii DNA by PCR is more sensitive compared to the detection of circulating antigens by the Ouchterlony method. It is concluded that the detection of P. carinii DNA in serum by PCR provides useful information for identifying P. carinii pneumonia.
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Affiliation(s)
- H Miyawaki
- First Department of Internal Medicine, Kagawa Medical School, Japan
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43
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Yasuoka A, Tachikawa N, Shimada K, Kimura S, Oka S. (1-->3) beta-D-glucan as a quantitative serological marker for Pneumocystis carinii pneumonia. CLINICAL AND DIAGNOSTIC LABORATORY IMMUNOLOGY 1996; 3:197-9. [PMID: 8991635 PMCID: PMC170276 DOI: 10.1128/cdli.3.2.197-199.1996] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We detected (1 --> 3) beta-D-glucan (beta-glucan), which is one of the major components of the cyst wall of Pneumocystis carinii, in sera obtained from patients with P. carinii pneumonia (PCP). We confirmed that beta-glucan was detectable by a beta-glucan detection kit (G test; Seikagaku Corporation) in bronchoalveolar lavage fluids (BALFs). The mean concentration of beta-glucan in BALFs obtained from specific-pathogen-free nude mice infected with P. carinii (n = 7; mean, 2,631 [range, 1,031 to 9,095] pg/ml) was significantly higher (P < 0.001) than that in uninfected, specific-pathogen-free mice (n = 7; 6.5 [range, 4.0 to 8.3] pg/ml). The mean level of beta-glucan in BALFs from PCP patients was significantly higher (P < 0.05) than that in BALFs from patients with other lung diseases (7,268 [range, 1,355 to 15,500] pg/ml [n = 4] versus 242.5 [17 to 615] pg/ml [n = 4]). In sera from six of seven patients with PCP, significant levels of beta-glucan (494.1 [8.5 to 1,135] pg/ml) were detected, while it was undetectable in patients with other lung diseases and in a control group. In five patients at follow-up, the level of beta-glucan decreased with clinical improvement. These results suggest that beta-glucan is detectable in sera from patients with PCP and it is a practical serological marker for monitoring of the disease during treatment.
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Affiliation(s)
- A Yasuoka
- Department of Infectious Diseases, University of Tokyo, Japan.
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44
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Shah JS, Pieciak W, Liu J, Buharin A, Lane DJ. Diversity of host species and strains of Pneumocystis carinii is based on rRNA sequences. CLINICAL AND DIAGNOSTIC LABORATORY IMMUNOLOGY 1996; 3:119-27. [PMID: 8770515 PMCID: PMC170258 DOI: 10.1128/cdli.3.1.119-127.1996] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have amplified by PCR Pneumocystis carinii cytoplasmic small-subunit rRNA (variously referred to as 16S-like or 18S-like rRNA) genes from DNA extracted from bronchoalveolar lavage and induced sputum specimens from patients positive for P. carinii and from infected ferret lung tissue. The amplification products were cloned into pUC18, and individual clones were sequenced. Comparison of the determined sequences with each other and with published rat and partial human P.carinii small-subunit rRNA gene sequences reveals that, although all P. carinii small-subunit rRNAs are closely related (approximately 96% identity), small-subunit rRNA genes isolated from different host species (human, rat, and ferret) exhibit distinctive patterns of sequence variation. Two types of sequences were isolated from the infected ferret lung tissue, one as a predominant species and the other as a minor species. There was 96% identity between the two types. In situ hybridization of the infected ferret lung tissue with oligonucleotide probes specific for each type revealed that there were two distinct strains of P. carinii present in the ferret lung tissue. Unlike the ferret P. carinii isolates, the small-subunit rRNA gene sequences from different human P. carinii isolates have greater than 99% identity and are distinct from all rat and ferret sequences so far inspected or reported in the literature. Southern blot hybridization analysis of PCR amplification products from several additional bronchoalveolar lavage or induced sputum specimens from P. carinii-infected patients, using a 32P-labeled oligonucleotide probe specific for human P. carinii, also suggests that all of the human P. carinii isolates are identical. These findings indicate that human P. carinii isolates may represent a distinct species of P. carinii distinguishable from rat and ferret P. carinii on the basis of characterization of small-subunit rRNA gene sequences.
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MESH Headings
- Animals
- Base Sequence
- DNA Primers/genetics
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/genetics
- DNA, Ribosomal/isolation & purification
- Ferrets
- Genetic Variation
- Humans
- In Situ Hybridization, Fluorescence
- Lung/microbiology
- Molecular Sequence Data
- Pneumocystis/classification
- Pneumocystis/genetics
- Pneumocystis/isolation & purification
- Pneumonia, Pneumocystis/microbiology
- Polymerase Chain Reaction
- RNA, Fungal/genetics
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 18S/genetics
- Rats
- Sequence Homology, Nucleic Acid
- Species Specificity
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Affiliation(s)
- J S Shah
- VYSIS, Inc., Framingham, Massachusetts 01701, USA
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45
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Leibovitz E, Pollack H, Moore T, Papellas J, Gallo L, Krasinski K, Borkowsky W. Comparison of PCR and standard cytological staining for detection of Pneumocystis carinii from respiratory specimens from patients with or at high risk for infection by human immunodeficiency virus. J Clin Microbiol 1995; 33:3004-7. [PMID: 8576362 PMCID: PMC228623 DOI: 10.1128/jcm.33.11.3004-3007.1995] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The detection of Pneumocystis carinii DNA by PCR was compared with routine cytologic staining techniques (CYT). A total of 284 clinical respiratory specimens, including 137 bronchoalveolar lavage (BAL), 63 bronchoalveolar washing, 63 sputum, and 21 induced sputum samples, obtained from patients with or at high risk for human immunodeficiency virus infection were evaluated. Eighty specimens were positive by PCR, and 69 were positive by CYT. PCR was able to detect P. carinii in more bronchoalveolar washing specimens (15 versus 11) and in comparable BAL specimens (53 versus 54) compared with CYT. PCR was particularly more sensitive than CYT in detecting P. carinii in expectorated sputum (12 versus 4 samples). Of the 19 patients whose respiratory specimens were positive for P. carinii by PCR but negative by CYT, 5 had P. carinii pneumonia (PCP) confirmed by subsequent BAL and transbronchial or mediastinal lymph node biopsy and 9 had a clinical course highly suggestive of acute PCP. Eleven (58%) of the 19 patients with discordant PCR and CYT results had received prior anti-PCP prophylaxis. In this clinical setting in particular and in the evaluation of sputum specimens, the ability of PCR to detect a low parasitic load suggests that this technique may become an important additional tool, along with current cytological methods, for the detection of P. carinii.
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Affiliation(s)
- E Leibovitz
- Department of Pediatrics, New York University Medical Center, New York 10016, USA
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46
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Lu JJ, Chen CH, Bartlett MS, Smith JW, Lee CH. Comparison of six different PCR methods for detection of Pneumocystis carinii. J Clin Microbiol 1995; 33:2785-8. [PMID: 8567928 PMCID: PMC228578 DOI: 10.1128/jcm.33.10.2785-2788.1995] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have recently developed a nested PCR method which amplifies internal transcribed spacers (ITS) of the ribosomal RNA genes of Pneumocystis carinii. To determine whether this PCR method can be used to diagnose P. carinii infections, we examined 30 bronchoalveolar lavage (BAL) specimens that were shown microscopically to contain P. carinii organisms by the P. carinii ITS PCR (Pc-ITS-PCR) and five other PCR methods that have been described for detecting P. carinii in clinical specimens. The targets of these PCR methods are portions of 18S rRNA, mitochondrial (mt) rRNA, 5S rRNA, thymidylate synthase (TS), and dihydrofolate reductase (DHFR). We also examined five different fungi, including Saccharomyces cerevisiae, Candida albicans, Histoplasma capsulatum, Cryptococcus neoformans, and Aspergillus fumigatus to determine the specificity of these six PCR methods for P. carinii. All 30 BAL specimens were positive by both the Pc-ITS-PCR and the 18S rRNA gene PCR, whereas only 26 (87%), 18 (60%), 10 (33%), and 7 (23%) of 30 BAL specimens were positive by mt rRNA gene PCR, TS gene PCR, 5S rRNA gene PCR, and DHFR gene PCR, respectively. Although the 18S rRNA gene PCR had the same sensitivity as the Pc-ITS-PCR, it nonspecifically amplified S. cerevisiae and C. albicans. The TS gene PCR also produced false-positive PCR results with C. albicans and C. neoformans. None of the other PCR methods (Pc-ITS-PCR, mt rRNA gene, 5S rRNA gene, and DHFR gene PCR) amplified the control fungal DNA. Considering both sensitivity and specificity, we conclude that Pc-ITS-PCR is the most effective of the six PCR methods evaluated in this study for the detection of P. carinii in BAL specimens.
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Affiliation(s)
- J J Lu
- Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan, Republic of China
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47
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De Luca A, Tamburrini E, Ortona E, Mencarini P, Margutti P, Antinori A, Visconti E, Siracusano A. Variable efficiency of three primer pairs for the diagnosis of Pneumocystis carinii pneumonia by the polymerase chain reaction. Mol Cell Probes 1995; 9:333-40. [PMID: 8569774 DOI: 10.1016/s0890-8508(95)91636-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The efficiency of three different primer pairs, complementary to different Pneumocystis carinii DNA regions, was compared in the polymerase chain reaction (PCR) for the diagnosis of Pneumocystis carinii pneumonia (PCP) on bronchoalveolar fluid (BALF) from patients with AIDS. PCR coupled with dot-blot hybridization (BLOT) using primers and probe from the mitochondrial 23SrDNA region showed the highest sensitivity, with a lower detection limit of 0.5-1 organisms microliter-1. When testing 47 BALF, PCR plus BLOT of the mitochondrial 23SrDNA region showed also the best diagnostic efficiency (97% sensitivity, 100% specificity). Sensitivity was significantly higher than with PCR and BLOT of the 5SrDNA region (81.5% sensitivity; P = 0.025, McNemar test); and of the dehydrofolate reductase (DHFR) gene region (75.6% sensitivity; P = 0.019). Sensitivity was also significantly higher than indirect immunofluorescence (75.8% sensitivity; P = 0.008). Using DHFR primers and probe, specificity was also reduced. The diagnostic sensitivity in clinical specimens paralleled the detection limit in the standard dilutions. The use of repeated DNA sequences of proven specificity as target of PCR amplification favourably influences sensitivity and specificity. This comparative study demonstrates that primer selection plays a significant role in the diagnosis of PCP by PCR.
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Affiliation(s)
- A De Luca
- Institute of Clinical Infectious Diseases, Catholic University, Rome, Italy
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48
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Yasuoka A, Oka S, Komuro K, Shimizu H, Kitada K, Nakamura Y, Shibahara S, Takeuchi T, Kondo S, Shimada K. Successful treatment of Pneumocystis carinii Pneumonia in mice with benanomicin A (ME1451). Antimicrob Agents Chemother 1995; 39:720-4. [PMID: 7793879 PMCID: PMC162611 DOI: 10.1128/aac.39.3.720] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Benanomicin A (BNM-A) has antimycotic activities via binding to mannan in the cell walls of fungi. Anti-Pneumocystis carinii activity of the agent was examined in the P. carinii-infected BALB/c nu/nu female mouse model because P. carinii also possesses mannan in the membranes. The infected mice were treated with intraperitoneal injections of six doses of BNM-A (1, 2.5, 5, 10, 30, and 100 mg/kg of body weight), 4 mg of pentamidine isethionate per kg, 100 mg of sulfamethoxazole per kg combined with 20 mg of trimethoprim per kg (co-trimoxazole), or saline for 21 days. Each dosage group consisted of 10 mice. During treatment, five mice in the control group (saline) died, whereas 8 to 10 mice in all treatment groups survived. Almost the same efficacies were obtained for the groups treated with 5 mg or more and 10 mg or more of BNM-A per kg regarding the weight and number, respectively, of cysts found in the lungs as were obtained for the groups treated with pentamidine isethionate and co-trimoxazole. Overall, a dose of 10 mg of BNM-A per kg was effective against P. carinii pneumonia infection in the mice. Thus, BNM-A is a good candidate for a novel treatment for P. carinii pneumonia as a compound with a new mechanism of action against P. carinii.
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Affiliation(s)
- A Yasuoka
- Department of Infectious Diseases, University of Tokyo, Japan
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49
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O'Leary TJ, Tsai MM, Wright CF, Cushion MT. Use of semiquantitative PCR to assess onset and treatment of Pneumocystis carinii infection in rat model. J Clin Microbiol 1995; 33:718-24. [PMID: 7751383 PMCID: PMC228020 DOI: 10.1128/jcm.33.3.718-724.1995] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The use of semiquantitative PCR (SQPCR) to assess Pneumocystis carinii pneumonia (PCP) infection and its response to treatment was studied with rats. Groups of eight rats were immunosuppressed with steroids for 3 to 12 weeks. Untreated controls were maintained for the same periods. Three groups of rats were treated with pentamidine, three groups were treated with trimethoprim-sulfamethoxazole, and three groups of rats were tapered from steroids. At various times during suppression, rats from the different groups were sacrificed. At necropsy, lungs were lavaged to obtain bronchoalveolar fluids and then homogenized. Bronchoalveolar fluids and homogenates were assayed by cyst counting and SQPCR. An increase in the SQPCR signal was seen throughout immunosuppression, with a slow decrease upon the withdrawal of steroids and a faster decrease with drug treatment. SQPCR results with lung homogenates and bronchoalveolar fluids strongly correlated with each other and with cyst counts. These results warrant investigation of SQPCR for assessing treatment results of human P. carinii pneumonia infection.
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Affiliation(s)
- T J O'Leary
- Department of Cellular Pathology, Armed Forces Institute of Pathology, Washington, D.C. 20306-6000, USA
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50
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Mazars E, Odberg-Ferragut C, Dei-Cas E, Fourmaux MN, Aliouat EM, Brun-Pascaud M, Mougeot G, Camus D. Polymorphism of the thymidylate synthase gene of Pneumocystis carinii from different host species. J Eukaryot Microbiol 1995; 42:26-32. [PMID: 7728138 DOI: 10.1111/j.1550-7408.1995.tb01536.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Pneumocystis carinii is an opportunistic agent found in the lung of various mammals which often causes severe pneumonia in immunocompromised humans, especially in AIDS patients. In the past several years significant additions have been made to the collection of knowledge we have concerning the genetic diversity of P. carinii. These additions provide new understanding of Pneumocystis transmission and the effect of possible reservoirs of Pneumocystis in the various species. In this study, a 400-bp fragment of the thymidylate synthase (TS) gene of P. carinii has been amplified by PCR from 43 parasite isolates obtained from 4 mammalian host species: rat, mouse, rabbit and human. A probe selected from the TS gene sequence of rat-derived P. carinii was hybridized with the amplified products from rat- and mouse-derived P. carinii, but not with rabbit or human P. carinii DNA. Restriction profiles were performed on amplified fragments from all isolates, and the 4 nucleotide sequences of the TS gene fragment amplified from rat, mouse, rabbit and human P. carinii were determined. Differences were detected in the gene fragment in P. carinii isolates from the 4 host species; however no difference was revealed in P. carinii isolates within a single host species, whatever the host strain or its geographic origin. Thus, the sequence differences of the P. carinii TS gene appeared as host-species specific. A specific probe which recognized all human P. carinii isolates was defined.
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Affiliation(s)
- E Mazars
- INSERM (U. 42), Villeneuve d'Ascq, France
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