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Chen F, Chen Y, Chi Y, Gao T, Zhao Y, Shao H. Diagnosis of invasive pulmonary fungal infections by a real-time panfungal PCR assay in non-neutropenic patients. Medicine (Baltimore) 2023; 102:e36385. [PMID: 38134111 PMCID: PMC10735100 DOI: 10.1097/md.0000000000036385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/09/2023] [Indexed: 12/24/2023] Open
Abstract
This study explored the utility of quantitative real-time panfungal PCR assay in diagnosing invasive pulmonary fungal diseases (IPFD) in non-neutropenic patients. Panfungal PCR assay was performed on respiratory tract specimens from patients whose clinical signs could not exclude fungal infection. At the same time, the samples were subjected to bacterial and fungal culture, microscopic examination and galactomannan antigen (GM) test in order to find the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the 4 diagnostic methods in proven and probable cases. 518 specimens were collected while 63 respiratory tract specimens tested by PCR had positive results. According to diagnostic criteria, 40 patients were diagnosed with IPFD, with 12 proven, 20 probable and 8 possible cases. Among these, 33 patients of PCR results were positive, most of which were from BALF samples (44.12%). 23 cases were caused by Aspergillus species, with Aspergillus fumigatus was the major cause. Other Aspergillus species, including Aspergillus flavus, Aspergillus terreus and Aspergillus nidulans were found in 1 sample respectively. Candida species were found in 5 samples, Pneumocystis jeroveci pneumonia (PJP) in 4 samples and Mucormycosis in 1 sample. An analysis of proven/probable diagnosis showed a sensitivity of 78.13%, specificity of 92.18%, PPV of 39.68% and NPV of 98.46% for PCR and 50%, 85.27%, 35.7%, 95.65% for GM test respectively. The Ct value difference between proven/probable and possible cases had no statistical significance (P = .824). Fungal culture showed a sensitivity of 17.5% while microscopic examination sensitivity of 32.5%. Through stratified analysis, no apparent correlation was found between the Ct value of the PCR assay and GM value (r: 0.223, P = .294). But a conjunction of the 2 tests raised the PPV of Aspergillus to 90%. As shown in this study, the panfungal RT-PCR assay has high sensitivity and consistency with serological test and culture. Its high PPV in the detection of Aspergillus and PJP were also evident.
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Affiliation(s)
- Feifei Chen
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yubao Chen
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yin Chi
- NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, China
| | - Tianyi Gao
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Youcai Zhao
- Department of Pathology Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Hongtao Shao
- Department of Gerontology Medicine, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
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Grønseth S, Rogne T, Heggelund L, Åsvold BO, Afset JE, Damås JK. Role of fungal burden in risk stratification of HIV-negative patients with Pneumocystis pneumonia: A 12-year, retrospective, observational, multicenter cohort. Int J Infect Dis 2023; 134:177-186. [PMID: 37339716 DOI: 10.1016/j.ijid.2023.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/22/2023] Open
Abstract
OBJECTIVES This study aimed to explore the role of fungal burden in risk stratification of patients without HIV-negative patients with Pneumocystis pneumonia (PCP). METHODS This was a retrospective analysis of the characteristics associated with 30-day mortality in patients who were positive for P. jirovecii using polymerase chain reaction in bronchoalveolar lavage fluid between 2006 and 2017 in a multicenter cohort from Central Norway. The fungal burden was indicated by the cycle threshold (CT) values from semiquantitative real-time polymerase chain reaction targeting the β-tubulin gene. RESULTS We included 170 patients with proven or probable PCP. The all-cause 30-day mortality was 18.2%. After adjusting for host characteristics and premorbid corticosteroid use, a higher fungal burden was associated with a higher risk of dying: adjusted odds ratio 1.42 (95% confidence interval 0.48-4.25) for a CT value 31-36, increasing to odds ratio 5.43 (95% confidence interval 1.48-19.9) for a CT value ≤30 compared with patients with a CT value ≥37. The Charlson comorbidity index (CCI) improved the risk stratification: patients with a CT value ≥37 and CCI ≤2 had a 9% mortality risk compared with 70% among those with a CT value ≤30 and CCI ≥6. Comorbid cardiovascular disease, solid tumors, immunological disorders, premorbid corticosteroids, hypoxemia, abnormal leukocyte counts, low serum albumin, and C-reactive protein ≥100 were also independently associated with 30-day mortality. The sensitivity analyses did not suggest selection bias. CONCLUSION Fungal burden may improve the risk stratification of patients without HIV-negative patients with PCP.
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Affiliation(s)
- Stine Grønseth
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
| | - Tormod Rogne
- Department of Circulation and Medical Imaging, NTNU, Trondheim, Norway; Department of Chronic Disease Epidemiology and Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, USA
| | - Lars Heggelund
- Department of Internal Medicine, Vestre Viken Hospital Trust, Drammen, Norway; Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Bjørn Olav Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Trondheim, Norway; HUNT Research Center, Department of Public Health and Nursing, The Trøndelag Health Study, NTNU, Levanger, Norway; Department of Endocrinology, St. Olavs hospital, Clinic of Medicine, Trondheim University Hospital, Trondheim, Norway
| | - Jan Egil Afset
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Department of Medical Microbiology, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jan Kristian Damås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Department of Infectious Diseases, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway; Centre of Molecular Inflammation Research, NTNU, Trondheim, Norway
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Grønseth S, Rogne T, Hannula R, Åsvold BO, Afset JE, Damås JK. Semiquantitative Real-Time PCR to Distinguish Pneumocystis Pneumonia from Colonization in a Heterogeneous Population of HIV-Negative Immunocompromised Patients. Microbiol Spectr 2021; 9:e0002621. [PMID: 34346746 PMCID: PMC8552647 DOI: 10.1128/spectrum.00026-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/14/2021] [Indexed: 11/20/2022] Open
Abstract
Pneumocystis jirovecii is a threat to iatrogenically immunosuppressed individuals, a heterogeneous population at rapid growth. We assessed the ability of an in-house semiquantitative real-time PCR assay to discriminate Pneumocystis pneumonia (PCP) from colonization and identified risk factors for infection in these patients. Retrospectively, 242 PCR-positive patients were compared according to PCP status, including strata by immunosuppressive conditions, human immunodeficiency virus (HIV) infection excluded. Associations between host characteristics and cycle threshold (CT) values, semiquantitative real-time PCR correlates of fungal loads in lower respiratory tract specimens, were investigated. CT values differed significantly according to PCP status. Overall, a CT value of 36 allowed differentiation between PCP and colonization with sensitivity and specificity of 71.3% and 77.1%, respectively. A CT value of less than 31 confirmed PCP, whereas no CT value permitted exclusion. A considerable diversity was uncovered; solid organ transplant (SOT) recipients had significantly higher fungal loads than patients with hematological malignancies. In SOT recipients, a CT cutoff value of 36 resulted in sensitivity and specificity of 95.0% and 83.3%, respectively. In patients with hematological malignancies, a higher CT cutoff value of 37 improved sensitivity to 88.5% but reduced specificity to 66.7%. For other conditions, assay validity appeared inferior. Corticosteroid usage was an independent predictor of PCP in a multivariable analysis and was associated with higher fungal loads at PCP expression. Semiquantitative real-time PCR improves differentiation between PCP and colonization in immunocompromised HIV-negative individuals with acute respiratory syndromes. However, heterogeneity in disease evolution requires separate cutoff values across intrinsic and iatrogenic predisposition for predicting non-HIV PCP. IMPORTANCE Pneumocystis jirovecii is potentially life threatening to an increasing number of individuals with compromised immune systems. This microorganism can cause severe pneumonia in susceptible hosts, including patients with cancer and autoimmune diseases and people undergoing solid organ transplantation. Together, these patients constitute an ever-diverse population. In this paper, we demonstrate that the heterogeneity herein has important implications for how we diagnose and assess the risk of Pneumocystis pneumonia (PCP). Specifically, low loads of microorganisms are sufficient to cause infection in patients with blood cancer compared to those in solid organ recipients. With this new insight into host versus P. jirovecii biology, clinicians can manage patients at risk of PCP more accurately. As a result, we take a significant step toward offering precision medicine to a vulnerable patient population. One the one hand, these patients have propensity for adverse effects from antimicrobial treatment. On the other hand, this population is susceptible to life-threatening infections, including PCP.
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Affiliation(s)
- Stine Grønseth
- Department of Clinical and Molecular Medicine, NTNU, Trondheim, Norway
| | - Tormod Rogne
- Department of Circulation and Medical Imaging, NTNU, Trondheim, Norway
- Department of Chronic Disease Epidemiology, Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
| | - Raisa Hannula
- Department of Infectious Diseases, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Bjørn Olav Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Trondheim, Norway
- HUNT Research Center, Department of Public Health and Nursing, NTNU, Levanger, Norway
- Department of Endocrinology, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jan Egil Afset
- Department of Clinical and Molecular Medicine, NTNU, Trondheim, Norway
- Department of Medical Microbiology, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jan Kristian Damås
- Department of Clinical and Molecular Medicine, NTNU, Trondheim, Norway
- Department of Infectious Diseases, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
- Centre of Molecular Inflammation Research, NTNU, Trondheim, Norway
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Grønseth S, Rogne T, Hannula R, Åsvold BO, Afset JE, Damås JK. Epidemiological and clinical characteristics of immunocompromised patients infected with Pneumocystis jirovecii in a twelve-year retrospective study from Norway. BMC Infect Dis 2021; 21:659. [PMID: 34233631 PMCID: PMC8262122 DOI: 10.1186/s12879-021-06144-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/08/2021] [Indexed: 01/10/2023] Open
Abstract
Background Pneumocystis pneumonia (PCP) severely menaces modern chemotherapy and immunosuppression. Detailed description of the epidemiology of Pneumocystis jirovecii today is needed to identify candidates for PCP-prophylaxis. Methods We performed a 12-year retrospective study of patients with P. jirovecii detected by polymerase chain reaction in Central Norway. In total, 297 patients were included. Comprehensive biological, clinical and epidemiological data were abstracted from patients’ medical records. Regional incidence rates and testing trends were also assessed. Results From 2007 to 2017 we found a 3.3-fold increase in testing for P. jirovecii accompanied by a 1.8-fold increase in positive results. Simultaneously, regional incidence rates doubled from 5.0 cases per 100,000 person years to 10.8. A majority of the study population had predisposing conditions other than human immunodeficiency virus (HIV). Hematological (36.0%) and solid cancers (25.3%) dominated. Preceding corticosteroids were a common denominator for 72.1%. Most patients (74.4%) presented with at least two cardinal symptoms; cough, dyspnea or fever. Main clinical findings were hypoxia, cytopenias and radiological features consistent with PCP. A total of 88 (29.6%) patients required intensive care and 121 (40.7%) suffered at least one complication. In-hospital mortality was 21.5%. Three patients (1.0%) had received prophylaxis. Conclusions P. jirovecii is re-emerging; likely due to increasing immunosuppressants use. This opportunistic pathogen threatens the life of heterogenous non-HIV immunosuppressed populations currently at growth. Corticosteroids seem to be a major risk factor. A strategy to increase prophylaxis is called for. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06144-1.
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Affiliation(s)
- Stine Grønseth
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, NO-7491, Trondheim, Norway.
| | - Tormod Rogne
- Department of Circulation and Medical Imaging, NTNU, Trondheim, Norway
| | - Raisa Hannula
- Department of Infectious Diseases, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Bjørn Olav Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Trondheim, Norway.,HUNT Research Center, Department of Public Health and Nursing, NTNU, Levanger, Norway.,Department of Endocrinology, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jan Egil Afset
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, NO-7491, Trondheim, Norway.,Department of Medical Microbiology, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jan Kristian Damås
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, NO-7491, Trondheim, Norway.,Department of Infectious Diseases, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway.,Centre of Molecular Inflammation Research, NTNU, Trondheim, Norway
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Irinyi L, Hu Y, Hoang MTV, Pasic L, Halliday C, Jayawardena M, Basu I, McKinney W, Morris AJ, Rathjen J, Stone E, Chen S, Sorrell TC, Schwessinger B, Meyer W. Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens: A paradigm shift in mycological diagnostics. Med Mycol 2021; 58:650-660. [PMID: 31758176 DOI: 10.1093/mmy/myz109] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/26/2019] [Accepted: 11/19/2019] [Indexed: 11/14/2022] Open
Abstract
The advent of next generation sequencing technologies has enabled the characterization of the genetic content of entire communities of organisms, including those in clinical specimens, without prior culturing. The MinION from Oxford Nanopore Technologies offers real-time, direct sequencing of long DNA fragments directly from clinical samples. The aim of this study was to assess the ability of unbiased, genome-wide, long-read, shotgun sequencing using MinION to identify Pneumocystis jirovecii directly from respiratory tract specimens and to characterize the associated mycobiome. Pneumocystis pneumonia (PCP) is a life-threatening fungal disease caused by P. jirovecii. Currently, the diagnosis of PCP relies on direct microscopic or real-time quantitative polymerase chain reaction (PCR) examination of respiratory tract specimens, as P. jirovecii cannot be cultured readily in vitro. P. jirovecii DNA was detected in bronchoalveolar lavage (BAL) and induced sputum (IS) samples from three patients with confirmed PCP. Other fungi present in the associated mycobiome included known human pathogens (Aspergillus, Cryptococcus, Pichia) as well as commensal species (Candida, Malassezia, Bipolaris). We have established optimized sample preparation conditions for the generation of high-quality data, curated databases, and data analysis tools, which are key to the application of long-read MinION sequencing leading to a fundamental new approach in fungal diagnostics.
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Affiliation(s)
- Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia
| | - Yiheng Hu
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Minh Thuy Vi Hoang
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia
| | - Lana Pasic
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia
| | - Catriona Halliday
- Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Menuk Jayawardena
- Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Indira Basu
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Wendy McKinney
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Arthur J Morris
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - John Rathjen
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Eric Stone
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,ANU-CSIRO Centre for Genomics, Metabolomics and Bioinformatics, Canberra, ACT, Australia
| | - Sharon Chen
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Tania C Sorrell
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia.,Westmead Hospital (Research and Education Network), Westmead, NSW, Australia
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Evaluation of the Amplex eazyplex Loop-Mediated Isothermal Amplification Assay for Rapid Diagnosis of Pneumocystis jirovecii Pneumonia. J Clin Microbiol 2020; 58:JCM.01739-20. [PMID: 32938732 DOI: 10.1128/jcm.01739-20] [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: 07/12/2020] [Accepted: 09/08/2020] [Indexed: 11/20/2022] Open
Abstract
Quantitative PCR (qPCR) assays are the gold standard for diagnosis of Pneumocystis jirovecii pneumonia (PCP). However, they are laborious and require skilled personnel. Therefore, execution outside regular working hours of the molecular biology laboratory is limited. The eazyplex P. jirovecii assay (PJA) uses loop-mediated isothermal amplification for detection of P. jirovecii It is performed directly with respiratory specimens, without the need for special skills, and delivers a result within 3 to 25 min. The goal of our study was to compare the performance of the eazyplex PJA with that of established P. jirovecii qPCR assays. All archived bronchoalveolar lavage fluid (BALF) samples that had previously tested positive for P. jirovecii by qPCR assay and 50 control samples (retrospective part), as well as all BALF samples received for P. jirovecii analysis over a period of 4 months (prospective part), were tested. Forty-nine patients with proven PCP and 126 patients without PCP were included. The sensitivity and specificity of the eazyplex PJA (95.7% and 96.5%, respectively) were comparable to those for three different P. jirovecii qPCR assays. The detection limit of the eazyplex PJA was analogous to 103 copies of the major surface glycoprotein gene per 25 μl of BALF, corresponding to 10 to 20 P. jirovecii cells. The eazyplex PJA reliably discriminated patients with PCP from patients with P. jirovecii colonization. It delivered a positive result within a mean of 9 min 38 s and required a hands-on time of 2 min 45 s. In summary, the eazyplex PJA showed identical performance for the diagnosis of PCP, compared to qPCR assays. However, in terms of time to result, practicability, and robustness, the eazyplex PJA is clearly superior and allows for around-the-clock molecular testing.
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Consensus Multilocus Sequence Typing Scheme for Pneumocystis jirovecii. J Fungi (Basel) 2020; 6:jof6040259. [PMID: 33143112 PMCID: PMC7711988 DOI: 10.3390/jof6040259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/10/2020] [Accepted: 10/18/2020] [Indexed: 12/26/2022] Open
Abstract
Pneumocystis jirovecii is an opportunistic human pathogenic fungus causing severe pneumonia mainly in immunocompromised hosts. Multilocus sequence typing (MLST) remains the gold standard for genotyping of this unculturable fungus. However, the lack of a consensus scheme impedes a global comparison, large scale population studies and the development of a global MLST database. To overcome this problem this study compared all genetic regions (19 loci) currently used in 31 different published Pneumocystis MLST schemes. The most diverse/commonly used eight loci, β-TUB, CYB, DHPS, ITS1, ITS1/2, mt26S and SOD, were further assess for their ability to be successfully amplified and sequenced, and for their discriminatory power. The most successful loci were tested to identify genetically related and unrelated cases. A new consensus MLST scheme consisting of four genetically independent loci: β-TUB, CYB, mt26S and SOD, is herein proposed for standardised P. jirovecii typing, successfully amplifying low and high fungal burden specimens, showing adequate discriminatory power, and correctly identifying suspected related and unrelated isolates. The new consensus MLST scheme, if accepted, will for the first time provide a powerful tool to investigate outbreak settings and undertake global epidemiological studies shedding light on the spread of this important human fungal pathogen.
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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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Calvo-Lozano O, Aviñó A, Friaza V, Medina-Escuela A, S. Huertas C, Calderón EJ, Eritja R, Lechuga LM. Fast and Accurate Pneumocystis Pneumonia Diagnosis in Human Samples Using a Label-Free Plasmonic Biosensor. NANOMATERIALS 2020; 10:nano10061246. [PMID: 32604931 PMCID: PMC7353103 DOI: 10.3390/nano10061246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 01/30/2023]
Abstract
Pneumocystis jirovecii is a fungus responsible for human Pneumocystis pneumonia, one of the most severe infections encountered in immunodepressed individuals. The diagnosis of Pneumocystis pneumonia continues to be challenging due to the absence of specific symptoms in infected patients. Moreover, the standard diagnostic method employed for its diagnosis involves mainly PCR-based techniques, which besides being highly specific and sensitive, require specialized personnel and equipment and are time-consuming. Our aim is to demonstrate an optical biosensor methodology based on surface plasmon resonance to perform such diagnostics in an efficient and decentralized scheme. The biosensor methodology employs poly-purine reverse-Hoogsteen hairpin probes for the detection of the mitochondrial large subunit ribosomal RNA (mtLSU rRNA) gene, related to P. jirovecii detection. The biosensor device performs a real-time and label-free identification of the mtLSU rRNA gene with excellent selectivity and reproducibility, achieving limits of detection of around 2.11 nM. A preliminary evaluation of clinical samples showed rapid, label-free and specific identification of P. jirovecii in human lung fluids such as bronchoalveolar lavages or nasopharyngeal aspirates. These results offer a door for the future deployment of a sensitive diagnostic tool for fast, direct and selective detection of Pneumocystis pneumonia disease.
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Affiliation(s)
- Olalla Calvo-Lozano
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, CIBER in Bioengineering, Biomaterials and Nanomedicine and BIST, Campus UAB Bellaterra, 08193 Barcelona, Spain; (O.C.-L.); (C.S.H.); (L.M.L.)
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, CIBER in Bioengineering, Biomaterials and Nanomedicine c/Jordi Girona 18–26, 08034 Barcelona, Spain;
- Correspondence:
| | - Vicente Friaza
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville and CIBER in Epidemiology and Public Health, 41013 Seville, Spain; (V.F.); (E.J.C.)
| | - Alfonso Medina-Escuela
- Institute for Applied Microelectronics (IUMA), University of Las Palmas de Gran Canaria, 35017 Las Palmas, Spain;
| | - César S. Huertas
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, CIBER in Bioengineering, Biomaterials and Nanomedicine and BIST, Campus UAB Bellaterra, 08193 Barcelona, Spain; (O.C.-L.); (C.S.H.); (L.M.L.)
- Integrated Photonics and Applications Centre, School of Engineering, RMIT University, Melbourne 3001, Australia
| | - Enrique J. Calderón
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville and CIBER in Epidemiology and Public Health, 41013 Seville, Spain; (V.F.); (E.J.C.)
- Department of Medicine, University of Seville, 41013 Seville, Spain
| | - Ramón Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, CIBER in Bioengineering, Biomaterials and Nanomedicine c/Jordi Girona 18–26, 08034 Barcelona, Spain;
| | - Laura M. Lechuga
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, CIBER in Bioengineering, Biomaterials and Nanomedicine and BIST, Campus UAB Bellaterra, 08193 Barcelona, Spain; (O.C.-L.); (C.S.H.); (L.M.L.)
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Carrillo JD, Mayorquin JS, Stajich JE, Eskalen A. Probe-Based Multiplex Real-Time PCR as a Diagnostic Tool to Distinguish Distinct Fungal Symbionts Associated With Euwallacea kuroshio and Euwallacea whitfordiodendrus in California. PLANT DISEASE 2020; 104:227-238. [PMID: 31647694 DOI: 10.1094/pdis-01-19-0201-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
California has been invaded by two distinct Euwallacea spp. that vector unique plant pathogenic symbiotic fungi on multiple hosts and cause Fusarium dieback. The objective of this study was to develop multiplex real-time quantitative PCR assays using hydrolysis probes targeting the β-tubulin gene to detect, distinguish, and quantify fungi associated with the polyphagous shot hole borer (PSHB; Euwallacea whitfordiodendrus, Fusarium euwallaceae, Graphium euwallaceae, and Paracremonium pembeum) as well as the Kuroshio shot hole borer (KSHB; Euwallacea kuroshio, Fusarium kuroshium, and Graphium kuroshium) from various sample types. Absolute quantification reaction efficiencies ranged from 88.2 to 104.3%, with a coefficient of determination >0.992 and a limit of detection of 100 copies µl-1 for all targets across both assays. Qualitative detection using the real-time assays on artificially inoculated avocado shoot extracts showed more sensitivity compared with conventional fungal isolation from wood. All symbiotic fungi, except P. pembeum, from PSHB and KSHB female heads were detectable and quantified. Field samples from symptomatic Platanus racemosa, Populus spp., and Salix spp. across 17 of 26 city parks were positively identified as PSHB and KSHB through detection of their symbiotic fungi, and both were found occurring together on five trees from three different park locations. The molecular assays presented here can be utilized to accurately identify fungi associated with these invasive pests in California.
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Affiliation(s)
- Joseph D Carrillo
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521
| | - Joey S Mayorquin
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521
| | - Akif Eskalen
- Department of Plant Pathology, University of California, Davis, CA 95616
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Yang SL, Wen YH, Wu YS, Wang MC, Chang PY, Yang S, Lu JJ. Diagnosis of Pneumocystis pneumonia by real-time PCR in patients with various underlying diseases. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2019; 53:785-790. [PMID: 31635929 DOI: 10.1016/j.jmii.2019.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/16/2019] [Accepted: 08/22/2019] [Indexed: 11/19/2022]
Abstract
BACKGROUND Pneumocystis pneumonia (PCP) is a disease caused by the opportunistic infection of the fungus Pneumocystis jirovecii. Several PCR methods have been developed to aid in the diagnosis of PCP. In this study, we evaluated the performance of a real-time PCR in the diagnosis of PCP, in patients with various underlying diseases. METHODS Ninety-seven BAL samples and 94 sputum samples from 191 patients were used in the study. Patients were classified as PCP (121 patients) or non-PCP (70 patients) based on their clinical and radiological presentations. RESULTS Real time PCR amplified the P. jirovecii mitochondrial large-subunit rRNA gene with a detection limit of 68 copies of DNA per reaction. Non-PCP pathogens including 32 different fungi and bacteria were also evaluated. Overall, 71.9% of the samples from PCP patients and 14.5% of those from non-PCP patients were positive for the PCR test with a CT value of the real-time PCR below 45. The main underlying diseases of the patients were hematological or solid malignancies (47.1%) and HIV infection (8.9%). The CT values of the test were significantly lower in BAL samples from PCP patients than those from non-PCP patients (p = 0.024). No non-PCP patient had a CT value below 30, whereas samples from 24.8% of PCP patients with underlying diseases had a CT value below 30. CONCLUSION Since false positive PCR results were obtained, perhaps due to colonization, we suggest that the diagnosis of PCP should be based on a combination of clinical symptoms, underlying diseases, and PCR results.
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Affiliation(s)
- Shu-Li Yang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Ying-Hao Wen
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Yu-Shan Wu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Mei-Chia Wang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Pi-Yueh Chang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan; Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Shuan Yang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan; Department of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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Danesi P, Ravagnan S, Johnson LR, Furlanello T, Milani A, Martin P, Boyd S, Best M, Galgut B, Irwin P, Canfield PJ, Krockenberger MB, Halliday C, Meyer W, Malik R. Molecular diagnosis of Pneumocystis pneumonia in dogs. Med Mycol 2018; 55:828-842. [PMID: 28339756 DOI: 10.1093/mmy/myx007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 01/20/2017] [Indexed: 11/12/2022] Open
Abstract
Pneumocystis pneumonia (PCP) is a life-threatening fungal disease that can occur in dogs. The aim of this study was to provide a preliminary genetic characterisation of Pneumocystis carinii f.sp.'canis' (P. canis) in dogs and thereby develop a reliable molecular protocol to definitively diagnose canine PCP. We investigated P. canis in a variety of lung specimens from dogs with confirmed or strongly suspected PCP (Group 1, n = 16), dogs with non-PCP lower respiratory tract problems (Group 2, n = 65) and dogs not suspected of having PCP or other lower respiratory diseases (Group 3, n = 11). Presence of Pneumocystis DNA was determined by nested PCR of the large and small mitochondrial subunit rRNA loci and by a real-time quantitative polymerase chain reaction (qPCR) assay developed using a new set of primers. Molecular results were correlated with the presence of Pneumocystis morphotypes detected in cytological/histological preparations. Pneumocystis DNA was amplified from 13/16 PCP-suspected dogs (Group 1) and from 4/76 dogs of control Groups 2 and 3 (combined). The latter four dogs were thought to have been colonized by P. canis. Comparison of CT values in 'infected' versus 'colonized' dogs was consistent with this notion, with a distinct difference in molecular burden between groups (CT ≤ 26 versus CT range (26 <CT < 35), respectively). Phylogenetic analyses showed that P. canis is specifically 'canine' associated, being separated from other mammalian Pneumocystis species, thereby confirming the accuracy of qPCR amplicon for Pneumocystis in dogs. Using qPCR, Pneumocystis DNA can be detected in specimens from the respiratory tract and a CT value can be interpreted to distinguish infection versus colonization.
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Affiliation(s)
- Patrizia Danesi
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Silvia Ravagnan
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Lynelle R Johnson
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | | | - Adelaide Milani
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Patricia Martin
- Veterinary Pathology Diagnostic Services, Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Susan Boyd
- QML Vetnostics, Riverview Place, Metroplex on Gateway, Murrarie, QLD Australia
| | - Matthew Best
- Brisbane Veterinary Specialist Centre, Corner Keong & Old Northern Roads, Albany Creek, QLD Australia
| | - Bradley Galgut
- Australian Specialised Animal Pathology (ASAP) Laboratories, Victoria, Australia
| | - Peter Irwin
- School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
| | - Paul J Canfield
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Mark B Krockenberger
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Catriona Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, Westmead Hospital, Sydney, New South Wales, Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity, University of Sydney, Westmead Institute for Medical Research, Sydney, Australia
| | - Richard Malik
- Centre for Veterinary Education, B22, University of Sydney, Sydney, New South Wales, Australia
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Alanio A, Hauser PM, Lagrou K, Melchers WJG, Helweg-Larsen J, Matos O, Cesaro S, Maschmeyer G, Einsele H, Donnelly JP, Cordonnier C, Maertens J, Bretagne S. ECIL guidelines for the diagnosis of Pneumocystis jirovecii pneumonia in patients with haematological malignancies and stem cell transplant recipients. J Antimicrob Chemother 2016; 71:2386-96. [PMID: 27550991 DOI: 10.1093/jac/dkw156] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The Fifth European Conference on Infections in Leukaemia (ECIL-5) convened a meeting to establish evidence-based recommendations for using tests to diagnose Pneumocystis jirovecii pneumonia (PCP) in adult patients with haematological malignancies. Immunofluorescence assays are recommended as the most sensitive microscopic method (recommendation A-II: ). Real-time PCR is recommended for the routine diagnosis of PCP ( A-II: ). Bronchoalveolar lavage (BAL) fluid is recommended as the best specimen as it yields good negative predictive value ( A-II: ). Non-invasive specimens can be suitable alternatives ( B-II: ), acknowledging that PCP cannot be ruled out in case of a negative PCR result ( A-II: ). Detecting β-d-glucan in serum can contribute to the diagnosis but not the follow-up of PCP ( A-II: ). A negative serum β-d-glucan result can exclude PCP in a patient at risk ( A-II: ), whereas a positive test result may indicate other fungal infections. Genotyping using multilocus sequence markers can be used to investigate suspected outbreaks ( A-II: ). The routine detection of dihydropteroate synthase mutations in cases of treatment failure is not recommended ( B-II: ) since these mutations do not affect response to high-dose co-trimoxazole. The clinical utility of these diagnostic tests for the early management of PCP should be further assessed in prospective, randomized interventional studies.
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Affiliation(s)
- Alexandre Alanio
- Parasitology-Mycology Laboratory, Groupe Hospitalier Lariboisière Saint-Louis Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Diderot, Sorbonne Paris Cité, and Institut Pasteur, Unité de Mycologie Moléculaire, CNRS URA3012, Centre National de Référence Mycoses Invasives et Antifongiques, Paris, France
| | - Philippe M Hauser
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Katrien Lagrou
- Department of Microbiology and Immunology, Catholic University Leuven, Leuven, Belgium and National Reference Center for Mycosis, Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jannik Helweg-Larsen
- Department of Infectious Diseases, Rigshospitalet-Copenhagen University Hospital, Copenhagen, Denmark
| | - Olga Matos
- Medical Parasitology Unit, Group of Opportunistic Protozoa/HIV and Other Protozoa, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal Universidade Nova de Lisboa, Lisboa, Portugal
| | - Simone Cesaro
- Hematology Department, Oncoematologia Pediatrica, Policlinico G. B. Rossi, Verona, Italy
| | - Georg Maschmeyer
- Department of Hematology, Oncology and Palliative Care, Ernst-von-Bergmann Klinikum, Potsdam, Germany
| | - Hermann Einsele
- Medizinische Klinik und Poliklinik II, Julius Maximilians Universitaet, Würzburg, Germany
| | - J Peter Donnelly
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Catherine Cordonnier
- Hematology Department, Henri Mondor Hospital, APHP and Université Paris-Est-Créteil, Créteil, France
| | - Johan Maertens
- Hematology Department, University Hospital Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Stéphane Bretagne
- Parasitology-Mycology Laboratory, Groupe Hospitalier Lariboisière Saint-Louis Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Diderot, Sorbonne Paris Cité, and Institut Pasteur, Unité de Mycologie Moléculaire, CNRS URA3012, Centre National de Référence Mycoses Invasives et Antifongiques, Paris, France
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Comparison of 2 real-time PCR assays for diagnosis of Pneumocystis jirovecii pneumonia in human immunodeficiency virus (HIV) and non-HIV immunocompromised patients. Diagn Microbiol Infect Dis 2015; 82:143-7. [PMID: 25801778 DOI: 10.1016/j.diagmicrobio.2015.03.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 12/11/2022]
Abstract
A total of 120 bronchoalveolar lavage specimens from HIV and non-HIV immunocompromised patients, positive for Pneumocystis jirovecii by an "in house" real-time polymerase chain reaction (PCR), were evaluated by the Bio-Evolution Pneumocystis real-time PCR, a commercial quantitative assay. Patients were classified in 2 categories based on clinical and radiological findings: definite and unlikely Pneumocystis pneumonia (PCP). For the "in house" PCR, cycle threshold 34 was established as cut-off value to discriminate definite PCP from unlikely PCP with 65% and 85% of sensitivity and specificity, respectively. For the Bio-Evolution quantitative PCR, a cut-off value of 2.8×10(5)copies/mL was defined with 72% and 82% of sensitivity and specificity, respectively. Overlapped zones of results for definite and unlikely PCP were observed. Quantitative PCR is probably a useful tool for PCP diagnosis. However, for optimal management of PCP in non-HIV immunocompromised patients, operational thresholds should be assessed according to underlying diseases and other clinical and radiological parameters.
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Diagnosis of Pneumocystis jirovecii Pneumonia: Role of β-D-Glucan Detection and PCR. CURRENT FUNGAL INFECTION REPORTS 2014. [DOI: 10.1007/s12281-014-0198-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Gustot T, Maillart E, Bocci M, Surin R, Trépo E, Degré D, Lucidi V, Taccone FS, Delforge ML, Vincent JL, Donckier V, Jacobs F, Moreno C. Invasive aspergillosis in patients with severe alcoholic hepatitis. J Hepatol 2014; 60:267-74. [PMID: 24055548 DOI: 10.1016/j.jhep.2013.09.011] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 08/07/2013] [Accepted: 09/09/2013] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Severe alcoholic hepatitis (AH) has a poor short-term prognosis. Although infections are frequent complications of AH, the incidence of invasive aspergillosis (IA) and its impact on outcome remain unknown. METHODS We prospectively followed 94 biopsy-proven severe AH episodes for 3 months. We retrospectively reviewed our diagnosis of IA based on EORTC/MSG and AspICU criteria, except for host factors. RESULTS Fifteen IA (6 proven, 8 probable, and 1 possible) were diagnosed after a median delay of 26 days following diagnosis of AH. The sites of infection were the lungs (n=11) and central nervous system (n=2), while IA was disseminated in 2 cases. Baseline MELD score ≥24 and ICU admission were independent risk factors for IA. Thirteen IA occurred in the context of corticosteroids, and 2 had received no specific treatment for AH. Non-response to corticosteroids at day 7 was not a risk factor for IA, but IA was associated with absence of liver improvement at day 28. Despite antifungal treatment, 3-month transplant-free survival of patients with IA was 0% compared to 53% in those without IA. IA, Lille score ≥0.45, and overt encephalopathy were independent predictors of transplant-free mortality. CONCLUSIONS IA is a frequent complication of severe AH and carries a very high risk of mortality. Systematic screening for IA should be recommended in these patients. Further studies are needed to identify high-risk populations requiring antifungal prophylactic treatment.
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Affiliation(s)
- Thierry Gustot
- Department of Gastroenterology and Hepato-Pancreatology, Erasme Hospital, Brussels, Belgium; Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium; INSERM, U773, Centre de Recherche Biomédicale Bichat-Beaujon CRB3, Paris, France.
| | - Evelyne Maillart
- Department of Infectious Diseases, Erasme Hospital, Brussels, Belgium
| | - Massimo Bocci
- Department of Gastroenterology and Hepato-Pancreatology, Erasme Hospital, Brussels, Belgium
| | - Rudy Surin
- Department of Infectious Diseases, Erasme Hospital, Brussels, Belgium
| | - Eric Trépo
- Department of Gastroenterology and Hepato-Pancreatology, Erasme Hospital, Brussels, Belgium; Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium
| | - Delphine Degré
- Department of Gastroenterology and Hepato-Pancreatology, Erasme Hospital, Brussels, Belgium; Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium
| | - Valerio Lucidi
- Department of Digestive Surgery, Erasme Hospital, Brussels, Belgium
| | | | | | | | - Vincent Donckier
- Department of Digestive Surgery, Erasme Hospital, Brussels, Belgium
| | - Frédérique Jacobs
- Department of Infectious Diseases, Erasme Hospital, Brussels, Belgium
| | - Christophe Moreno
- Department of Gastroenterology and Hepato-Pancreatology, Erasme Hospital, Brussels, Belgium; Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium
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Development and evaluation of a real-time PCR assay for detection of Pneumocystis jirovecii on the fully automated BD MAX platform. J Clin Microbiol 2013; 51:2337-43. [PMID: 23678059 DOI: 10.1128/jcm.00616-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Pneumocystis jirovecii is an opportunistic pathogen in immunocompromised and AIDS patients. Detection by quantitative PCR is faster and more sensitive than microscopic diagnosis yet requires specific infrastructure. We adapted a real-time PCR amplifying the major surface glycoprotein (MSG) target from Pneumocystis jirovecii for use on the new BD MAX platform. The assay allowed fully automated DNA extraction and multiplex real-time PCR. The BD MAX assay was evaluated against manual DNA extraction and conventional real-time PCR. The BD MAX was used in the research mode running a multiplex PCR (MSG, internal control, and sample process control). The assay had a detection limit of 10 copies of an MSG-encoding plasmid per PCR that equated to 500 copies/ml in respiratory specimens. We observed accurate quantification of MSG targets over a 7- to 8-log range. Prealiquoting and sealing of the complete PCR reagents in conical tubes allowed easy and convenient handling of the BD MAX PCR. In a retrospective analysis of 54 positive samples, the BD MAX assay showed good quantitative correlation with the reference PCR method (R(2) = 0.82). Cross-contamination was not observed. Prospectively, 278 respiratory samples were analyzed by both molecular assays. The positivity rate overall was 18.3%. The BD MAX assay identified 46 positive samples, compared to 40 by the reference PCR. The BD MAX assay required liquefaction of highly viscous samples with dithiothreitol as the only manual step, thus offering advantages for timely availability of molecular-based detection assays.
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Martin SI, Fishman JA. Pneumocystis pneumonia in solid organ transplantation. Am J Transplant 2013; 13 Suppl 4:272-9. [PMID: 23465020 DOI: 10.1111/ajt.12119] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- S I Martin
- Division of Infectious Diseases and Comprehensive Transplant Center at The Ohio State University, Wexner Medical Center, Columbus, OH, USA.
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Rising incidence of Pneumocystis jirovecii pneumonia suggests iatrogenic exposure of immune-compromised patients may be becoming a significant problem. J Med Microbiol 2012; 61:1009-1015. [DOI: 10.1099/jmm.0.043984-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Nosocomial Pneumocystis jirovecii Pneumonia: Lessons From a Cluster in Kidney Transplant Recipients. Transplantation 2011; 92:1327-34. [DOI: 10.1097/tp.0b013e3182384b57] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Clinical significance of quantifying Pneumocystis jirovecii DNA by using real-time PCR in bronchoalveolar lavage fluid from immunocompromised patients. J Clin Microbiol 2011; 50:227-31. [PMID: 22162560 DOI: 10.1128/jcm.06036-11] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Quantitative PCR (qPCR) is more sensitive than microscopy for detecting Pneumocystis jirovecii in bronchoalveolar lavage (BAL) fluid. We therefore developed a qPCR assay and compared the results with those of a routine immunofluorescence assay (IFA) and clinical data. The assay included automated DNA extraction, amplification of the mitochondrial large-subunit rRNA gene and an internal control, and quantification of copy numbers with the help of a plasmid clone. We studied 353 consecutive BAL fluids obtained for investigation of unexplained fever and/or pneumonia in 287 immunocompromised patients. No qPCR inhibition was observed. Seventeen (5%) samples were both IFA and qPCR positive, 63 (18%) were IFA negative and qPCR positive, and 273 (77%) were both IFA and qPCR negative. The copy number was significantly higher for IFA-positive/qPCR-positive samples than for IFA-negative/qPCR-positive samples (4.2 ± 1.2 versus 1.1 ± 1.1 log(10) copies/μl; P < 10(-4)). With IFA as the standard, the qPCR assay sensitivity was 100% for ≥2.6 log(10) copies/μl and the specificity was 100% for ≥4 log(10) copies/μl. Since qPCR results were not available at the time of decision-making, these findings did not trigger cotrimoxazole therapy. Patients with systemic inflammatory diseases and IFA-negative/qPCR-positive BAL fluid had a worse 1-year survival rate than those with IFA-negative/qPCR-negative results (P < 10(-3)), in contrast with solid-organ transplant recipients (P = 0.88) and patients with hematological malignancy (P = 0.26). Quantifying P. jirovecii DNA in BAL fluids independently of IFA positivity should be incorporated into the investigation of pneumonia in immunocompromised patients. The relevant threshold remains to be determined and may vary according to the underlying disease.
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Samuel CM, Whitelaw A, Corcoran C, Morrow B, Hsiao NY, Zampoli M, Zar HJ. Improved detection of Pneumocystis jirovecii in upper and lower respiratory tract specimens from children with suspected pneumocystis pneumonia using real-time PCR: a prospective study. BMC Infect Dis 2011; 11:329. [PMID: 22123076 PMCID: PMC3254081 DOI: 10.1186/1471-2334-11-329] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 11/28/2011] [Indexed: 12/02/2022] Open
Abstract
Background Pneumocystis pneumonia (PCP) is a major cause of hospitalization and mortality in HIV-infected African children. Microbiologic diagnosis relies predominantly on silver or immunofluorescent staining of a lower respiratory tract (LRT) specimens which are difficult to obtain in children. Diagnosis on upper respiratory tract (URT) specimens using PCR has been reported useful in adults, but data in children are limited. The main objectives of the study was (1) to compare the diagnostic yield of PCR with immunofluorescence (IF) and (2) to investigate the usefulness of upper compared to lower respiratory tract samples for diagnosing PCP in children. Methods Children hospitalised at an academic hospital with suspected PCP were prospectively enrolled. An upper respiratory sample (nasopharyngeal aspirate, NPA) and a lower respiratory sample (induced sputum, IS or bronchoalveolar lavage, BAL) were submitted for real-time PCR and direct IF for the detection of Pneumocystis jirovecii. A control group of children with viral lower respiratory tract infections were investigated with PCR for PCP. Results 202 children (median age 3.3 [inter-quartile range, IQR 2.2 - 4.6] months) were enrolled. The overall detection rate by PCR was higher than by IF [180/349 (52%) vs. 26/349 (7%) respectively; p < 0.0001]. PCR detected more infections compared to IF in lower respiratory tract samples [93/166 (56%) vs. 22/166 (13%); p < 0.0001] and in NPAs [87/183 (48%) vs. 4/183 (2%); p < 0.0001]. Detection rates by PCR on upper (87/183; 48%) compared with lower respiratory tract samples (93/166; 56%) were similar (OR, 0.71; 95% CI, 0.46 - 1.11). Only 2/30 (6.6%) controls were PCR positive. Conclusion Real-time PCR is more sensitive than IF for the detection of P. jirovecii in children with PCP. NPA samples may be used for diagnostic purposes when PCR is utilised. Wider implementation of PCR on NPA samples is warranted for diagnosing PCP in children.
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Affiliation(s)
- Catherine M Samuel
- Division of Medical Microbiology, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa.
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Harris JR, Marston BJ, Sangrujee N, DuPlessis D, Park B. Cost-effectiveness analysis of diagnostic options for pneumocystis pneumonia (PCP). PLoS One 2011; 6:e23158. [PMID: 21858013 PMCID: PMC3156114 DOI: 10.1371/journal.pone.0023158] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 07/07/2011] [Indexed: 12/16/2022] Open
Abstract
Background Diagnosis of Pneumocystis jirovecii pneumonia (PCP) is challenging, particularly in developing countries. Highly sensitive diagnostic methods are costly, while less expensive methods often lack sensitivity or specificity. Cost-effectiveness comparisons of the various diagnostic options have not been presented. Methods and Findings We compared cost-effectiveness, as measured by cost per life-years gained and proportion of patients successfully diagnosed and treated, of 33 PCP diagnostic options, involving combinations of specimen collection methods [oral washes, induced and expectorated sputum, and bronchoalveolar lavage (BAL)] and laboratory diagnostic procedures [various staining procedures or polymerase chain reactions (PCR)], or clinical diagnosis with chest x-ray alone. Our analyses were conducted from the perspective of the government payer among ambulatory, HIV-infected patients with symptoms of pneumonia presenting to HIV clinics and hospitals in South Africa. Costing data were obtained from the National Institutes of Communicable Diseases in South Africa. At 50% disease prevalence, diagnostic procedures involving expectorated sputum with any PCR method, or induced sputum with nested or real-time PCR, were all highly cost-effective, successfully treating 77–90% of patients at $26–51 per life-year gained. Procedures using BAL specimens were significantly more expensive without added benefit, successfully treating 68–90% of patients at costs of $189–232 per life-year gained. A relatively cost-effective diagnostic procedure that did not require PCR was Toluidine Blue O staining of induced sputum ($25 per life-year gained, successfully treating 68% of patients). Diagnosis using chest x-rays alone resulted in successful treatment of 77% of patients, though cost-effectiveness was reduced ($109 per life-year gained) compared with several molecular diagnostic options. Conclusions For diagnosis of PCP, use of PCR technologies, when combined with less-invasive patient specimens such as expectorated or induced sputum, represent more cost-effective options than any diagnostic procedure using BAL, or chest x-ray alone.
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Affiliation(s)
- Julie R Harris
- Mycotic Diseases Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.
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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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Chumpitazi BFF, Flori P, Kern JB, Brenier-Pinchart MP, Hincky-Vitrat V, Brion JP, Thiebaut-Bertrand A, Minet C, Maubon D, Pelloux H. Characteristics and clinical relevance of the quantitative touch-down major surface glycoprotein polymerase chain reaction in the diagnosis of Pneumocystis pneumonia. Med Mycol 2011; 49:704-13. [PMID: 21417683 DOI: 10.3109/13693786.2011.566894] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The evaluation of quantitative polymerase chain reaction (PCR) characteristics can increase the accuracy of the laboratory diagnosis of Pneumocystis pneumonia (PCP). Between July 2008 and September 2009, 66 non-sequential prospective bronchoalveolar lavage (BAL) samples, obtained from five HIV-infected and 49 non HIV-infected patients were investigated, using a quantitative-touch-down-PCR to determine the number of copies of major surface glycoprotein (MSG) genes of Pneumocystis jirovecii (q-TD-MSG-PCR). PCP was confirmed by microscopic observation of Pneumocystis, radio-clinical and therapeutic data in 18/54 patients. For PCP, the cut-off was 54.3 MSG copies per ml of BAL fluid. The PCR was positive in these same 18 cases and it was the only positive assay in two cases and the earliest diagnosis test in one case of PCP relapse. The likelihood positive ratio, sensitivity and specificity of the q-TD-MSG-PCR were 44, 100% and 97.7%, respectively. The Predictive Negative Value was 100% and the Predictive Positive Value of 95.5%, the intra- and inter-assay variability values were 2.7% (at more than 30 MSG copies) and 11.7% (at 10,000 MSG copies), respectively. Quantitative PCR can help diagnose PCP even in cases of low Pneumocystis load and might decrease morbidity in association with very early specific treatments.
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Affiliation(s)
- Bernabé F F Chumpitazi
- Laboratory of Parasitology and Mycology, Grenoble University Hospital, Joseph Fourier University (Grenoble 1), France.
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27
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28
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Detection of Pneumocystis jirovecii by Two Staining Methods and Two Quantitative PCR Assays. Infection 2008; 37:261-5. [DOI: 10.1007/s15010-008-8027-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Accepted: 06/24/2008] [Indexed: 11/26/2022]
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[Pnemocystis jiroveci pneumonia: Comparison between conventional PCR and staining techniques]. ACTA ACUST UNITED AC 2008; 57:373-7. [PMID: 19038508 DOI: 10.1016/j.patbio.2008.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Accepted: 09/30/2008] [Indexed: 11/21/2022]
Abstract
Diagnosis of pneumocystis pneumonia is usually based on clinical features and X-rays photography and confirmed in the laboratory by visualisation of Pneumocystis organisms in stained preparations of respiratory specimens using several techniques (Gomori-Grocott, May-Grünwald Giemsa, bleu de toluidine O). Actually, PCR has considerably increased sensitivity of detection of Pneumocystis. The aim of this study is to compare conventional PCR results to those of staining techniques (Gomori-Grocott, May-Grünwald Giemsa) in addition to the X-ray and clinical findings in order to evaluate the contribution of each method. Sixty-four respiratory specimens were collected from 54 immuno-compromised patients with clinical symptoms of pulmonary infection. We diagnosed pneumocystis pneumonia in 16 patients according to staining techniques and/or typical clinical and radiological findings and/or response to treatment. Of the 15 patients, 14 were positive by PCR and only five were positive by direct examination, yielding a sensitivity and specificity of 93.3 and 87.1% for PCR and 33.3 and 100% for staining techniques. Conventional PCR provides a sensitive and objective method for the detection Pneumocystis jiroveci from less invasive sample.
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30
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31
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Uemura N, Makimura K, Onozaki M, Otsuka Y, Shibuya Y, Yazaki H, Kikuchi Y, Abe S, Kudoh S. Development of a loop-mediated isothermal amplification method for diagnosing Pneumocystis pneumonia. J Med Microbiol 2008; 57:50-57. [PMID: 18065667 DOI: 10.1099/jmm.0.47216-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a novel, rapid nucleic acid amplification method with high specificity and sensitivity under isothermal conditions. In this study a LAMP assay for diagnosing Pneumocystis pneumonia (PCP) was developed. Oligonucleotide primers specific for Pneumocystis species were designed corresponding to 18S rRNA gene sequences. The assay, performed for 30 min at 61 degrees C, was capable of detecting 50 copies per tube (2 x 10(3) copies ml(-1)) in 30 min and did not show cross-reactivity to other species of fungi, including the genera Candida, Aspergillus and Cryptococcus. A total of 21 of 24 clinical specimens (sputum and bronchoalveolar lavage fluid) from patients with suspected PCP tested positive using the LAMP assay by real-time fluorescence detection. The results of the LAMP reaction were also observed by real-time turbidity detection and end-point visual turbidity or fluorescence detection. With real-time fluorescence detection, melting curves of the products were effective at distinguishing specific amplification from non-specific amplification or self-amplification. Visual detection was also possible as a rapid and easy assay using only a heat block and a black light.
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Affiliation(s)
- Natsu Uemura
- Department of Pulmonary Medicine/Infection and Oncology, Nippon Medical School, Tokyo, Japan.,Teikyo University Institute of Medical Mycology, 539 Otsuka, Hachioji, Tokyo 192-0395, Japan
| | - Koichi Makimura
- Teikyo University Institute of Medical Mycology, 539 Otsuka, Hachioji, Tokyo 192-0395, Japan
| | | | | | | | - Hirohisa Yazaki
- AIDS Clinical Center, International Medical Center of Japan, Tokyo, Japan
| | - Yoshimi Kikuchi
- AIDS Clinical Center, International Medical Center of Japan, Tokyo, Japan
| | - Shigeru Abe
- Teikyo University Institute of Medical Mycology, 539 Otsuka, Hachioji, Tokyo 192-0395, Japan
| | - Shoji Kudoh
- Department of Pulmonary Medicine/Infection and Oncology, Nippon Medical School, Tokyo, Japan
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32
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Environmental detection of Penicillium marneffei and growth in soil microcosms in competition with Talaromyces stipitatus. FUNGAL ECOL 2008. [DOI: 10.1016/j.funeco.2008.02.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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33
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Haque AK, Adegboyega PA. Pneumocystis jiroveci Pneumonia. DAIL AND HAMMAR’S PULMONARY PATHOLOGY 2008. [PMCID: PMC7121032 DOI: 10.1007/978-0-387-68792-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Pneumocystis pneumonia (PCP) is one of the most common pulmonary infections in persons with impaired cell-mediated immunity, and particularly those infected with human immunodeficiency virus (HIV).1–7 Pneumocystis was first described in the lungs of guinea pigs, during experiments on American trypanosomiasis by Carlos Chagas8 in 1909 and by Antonio Carinii9 in 1910. Both considered the cysts of Pneumocystis as part of the trypanosome’s life cycle. Shortly afterward the Delanoes10 found identical forms in the lungs of rats that had not been infected with trypanosomes and recognized the organism as a separate species. The name Pneumocystis carinii, was given to this organism as a generic name (Greek:pneumon, “lung”; kystis, “cyst”), honoring Carinii.11
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Abstract
CONTEXT Pulmonary infections are common and often life-threatening in solid organ and stem cell transplant recipients. Understanding their pathology is critical to making improvements in care and survival as well as in surgical techniques, immunosuppression management, prophylaxis, and treatment. Pulmonary infections are particularly common and serious in the susceptible population of lung transplant recipients. OBJECTIVE To summarize recent updates in the field for opportunistic infections and some common pathogens, and to consider the role of the diagnostic pulmonary histopathologist as well as advances in molecular diagnosis. DATA SOURCES This work is based on a selected review of the relevant medical and scientific literature, with emphasis on lung transplantation experience gained during 2 decades of practice. CONCLUSIONS Pulmonary infections in transplant recipients present a diagnostic challenge and are a continuing source of mortality and morbidity despite improvement in prophylaxis and treatment. Accurate diagnosis requires multidisciplinary input from clinicians, radiologists, and pathology disciplines as well as complementary molecular methods.
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Affiliation(s)
- Susan Stewart
- Department of Histopathology, Papworth Hospital, Papworth Everard, Cambridge CB3 8RE, United Kingdom.
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35
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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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36
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Francois P, Hernandez D, Schrenzel J. Genome content determination in methicillin-resistant Staphylococcus aureus. Future Microbiol 2007; 2:187-98. [PMID: 17661655 DOI: 10.2217/17460913.2.2.187] [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] [Indexed: 11/21/2022] Open
Abstract
Staphylococcus aureus is a major pathogen responsible for both nosocomial and community-acquired infections. While the first S. aureus isolates displaying resistance to methicillin were reported in the early 1960s, endemic strains of methicillin-resistant S. aureus (MRSA) carrying multiple resistance determinants only became a worldwide nosocomial problem in the early 1980s, carrying a threefold attributable cost and a threefold excess length of hospital stay when compared with methicillin-susceptible S. aureus bacteremia. Recent efforts in the field of high-throughput sequencing resulted in the release of several MRSA genome sequences enabling the development of massively parallel tools to study clinical isolates of MRSA at the organism scale. Microarrays covering whole genomes and high-throughput sequencing devices are the two main techniques currently utilizable for whole-genome characterization. These tools not only provide information for the development of genotyping assays but also allow evaluation of potential virulence of the strains, by enumerating genetic-encoded resistance markers and toxin content. This appears particularly attractive for understanding the epidemiology of MRSA and the relationship between genome content on one side and virulence potential or epidemicity on the other side. In addition, sequence information is mandatory for the development of molecular tests allowing the rapid identification, genotyping and characterization of clinical isolates.
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Affiliation(s)
- Patrice Francois
- Service of Infectious Diseases, Genomic Research Laboratory, Department of Internal Medicine, Geneva 14, Switzerland.
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Alvarez-Martínez MJ, Miró JM, Valls ME, Moreno A, Rivas PV, Solé M, Benito N, Domingo P, Muñoz C, Rivera E, Zar HJ, Wissmann G, Diehl ARS, Prolla JC, de Anta MTJ, Gatell JM, Wilson PE, Meshnick SR. Sensitivity and specificity of nested and real-time PCR for the detection of Pneumocystis jiroveci in clinical specimens. Diagn Microbiol Infect Dis 2006; 56:153-60. [PMID: 16678378 DOI: 10.1016/j.diagmicrobio.2006.03.010] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2005] [Revised: 02/23/2006] [Accepted: 03/08/2006] [Indexed: 02/08/2023]
Abstract
A polymerase chain reaction (PCR)-based test for Pneumocystis jiroveci (formerly Pneumocystis carinii f. sp. hominis) might be an alternative to histologic diagnoses of P. jiroveci pneumonia (PCP). However, previously developed nested PCR methods tend to have low specificities (high false-positive rates). In this study, nested and quantitative real-time PCR methods for the amplification of the P. jiroveci DHPS (dihydropteroate synthase) gene were evaluated in a variety of stored clinical samples from Spain, South Africa, and Brazil. The sensitivities of both assays were high, ranging from 62.5% to 100% depending on the type of specimen. In a subset of 71 microscopically confirmed PCP cases and 70 negative cases, the sensitivities and specificities were 94% and 81% for nested PCR and 94% and 96% for real-time PCR, respectively. Real-time PCR has a statistically significantly better specificity than nested PCR (P = .015) and is likely to generate fewer false positives.
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Li W, Hartung JS, Levy L. Quantitative real-time PCR for detection and identification of Candidatus Liberibacter species associated with citrus huanglongbing. J Microbiol Methods 2006; 66:104-15. [PMID: 16414133 DOI: 10.1016/j.mimet.2005.10.018] [Citation(s) in RCA: 423] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2005] [Revised: 10/25/2005] [Accepted: 10/26/2005] [Indexed: 10/25/2022]
Abstract
Citrus huanglongbing (HLB, ex greening) is one of the most serious diseases of citrus. Different forms of the disease are caused by different Candidatus Liberobacter species, Candidatus Liberibacter asiaticus (Las), Ca. L. africanus (Laf) and Ca. L. americanus (Lam). The pathogen is transmitted by psyllid insects and by budding with contaminated plant materials. The vector psyllid Diaphorina citri can transmit both Las and Lam. Establishment of this vector into Florida, reports of Lam and Las in Brazil in 2004, and recent confirmation of HLB in Florida in September 2005 is of great concern to the citrus industry. Research on HLB has been hampered by the unculturable nature of the causal bacterium in artificial media. It has also been difficult to detect and identify the pathogens, possibly because of low concentration and uneven distribution in host plants and vector psyllids. In this study, we developed quantitative TaqMan PCR using 16S rDNA-based TaqMan primer-probe sets specific to the different Ca. Liberobacter spp. An additional primer-probe set based on plant cytochrome oxidase (COX) was used as a positive internal control to assess the quality of the DNA extracts. The assays do not cross-react with other pathogens or endophytes commonly resident in citrus plants, and are very sensitive. HLB pathogen DNA was successfully amplified from the equivalent of 20 ng of midrib tissue from symptomatic leaves. The consistent results of the assays with DNA extracted from plants infected by various Ca. Liberibacter species grown in greenhouses and in the field demonstrated a degree of reproducibility for these TaqMan assays. Inhibitors of the PCR that are frequently present in plant extracts did not affect the assay results. The population of the pathogens was estimated to be 5 x 10(7) and 2 x 10(6) cells/g of fresh midribs of symptomatic sweet orange leaves infected by Las and Lam, respectively. The ratio of pathogen DNA to host plant DNA was estimated by to be 1:13,000 (w/w) and 1:1000 (c/c: target copy/target copy) in DNA extracts obtained by a standard CTAB method. Our rapid, sensitive and specific TaqMan PCR assay for the detection, identification and quantification of Ca. Liberibacter species has been successfully used in the confirmation of HLB caused by Las in Florida, and will be very useful for a broad range of research programs as well as the regulatory response and management of HLB disease.
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Affiliation(s)
- Wenbin Li
- National Plant Germplasm and Biotechnology Laboratory, USDA-APHIS-PPQ-CPHST, Beltsville, MD 20705, USA
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