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McCracken GR, Gaston D, Pettipas J, Loder A, Majer A, Grudeski E, Labbé G, Joy BK, Patriquin G, LeBlanc JJ. Neglected SARS-CoV-2 variants and potential concerns for molecular diagnostics: a framework for nucleic acid amplification test target site quality assurance. Microbiol Spectr 2023; 11:e0076123. [PMID: 37815347 PMCID: PMC10715164 DOI: 10.1128/spectrum.00761-23] [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: 02/21/2023] [Accepted: 06/02/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE Molecular tests like polymerase chain reaction were widely used during the COVID-19 pandemic but as the pandemic evolved, so did SARS-CoV-2. This virus acquired mutations, prompting concerns that mutations could compromise molecular test results and be falsely negative. While some manufacturers may have in-house programs for monitoring mutations that could impact their assay performance, it is important to promptly report mutations in circulating viral strains that could adversely impact a diagnostic test result. However, commercial test target sites are proprietary, making independent monitoring difficult. In this study, SARS-CoV-2 test target sites were sequenced to monitor and assess mutations impact, and 29 novel mutations impacting SARS-CoV-2 detection were identified. This framework for molecular test target site quality assurance could be adapted to any molecular test, ensuring accurate diagnostic test results and disease diagnoses.
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Affiliation(s)
- Gregory R. McCracken
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health (NSH), Halifax, Nova Scotia, Canada
| | - Daniel Gaston
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, Nova Scotia Health (NSH), Halifax, Nova Scotia, Canada
| | - Janice Pettipas
- Nova Scotia Provincial Public Health Laboratory Network (PPHLN), Halifax, Nova Scotia, Canada
| | - Allana Loder
- National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Anna Majer
- National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Elsie Grudeski
- National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Geneviève Labbé
- National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Bryn K. Joy
- Medical Sciences Program, Faculty of Sciences, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Glenn Patriquin
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health (NSH), Halifax, Nova Scotia, Canada
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jason J. LeBlanc
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health (NSH), Halifax, Nova Scotia, Canada
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Medicine (Infectious Diseases), Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
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2
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Usefulness of ß-d-Glucan Assay for the First-Line Diagnosis of Pneumocystis Pneumonia and for Discriminating between Pneumocystis Colonization and Pneumocystis Pneumonia. J Fungi (Basel) 2022; 8:jof8070663. [PMID: 35887420 PMCID: PMC9318034 DOI: 10.3390/jof8070663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/16/2022] [Accepted: 06/23/2022] [Indexed: 11/17/2022] Open
Abstract
According to the immunodepression status, the diagnosis of Pneumocystis jirovecii pneumonia (PjP) may be difficult. Molecular methods appear very sensitive, but they lack specificity because Pj DNA can be detected in Pneumocystis-colonized patients. The aim of this study was to evaluate the value of a serum ß-d-Glucan (BDG) assay for the diagnosis of PjP in a large cohort of HIV-negative and HIV-positive patients, either as a first-line diagnostic test for PjP or as a tool to distinguish between colonization and PjP in cases of low fungal load. Data of Pj qPCR performed on bronchopulmonary specimens over a 3-year period were retrieved retrospectively. For each result, we searched for a BDG serum assay performed within ±5 days. Among the 69 episodes that occurred in HIV-positive patients and the 609 episodes that occurred in immunocompromised HIV-negative patients, we find an equivalent sensitivity of BDG assays compared with molecular methods to diagnose probable/proven PjP, in a first-line strategy. Furthermore, BDG assay can be used confidently to distinguish between infected and colonized patients using a 80 pg/mL cut-off. Finally, it is necessary to search for causes of false positivity to increase BDG assay performance. BDG assay represents a valuable adjunctive tool to distinguish between colonization and infection.
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Khudhair YI, Saleh ZF, Ayyez HN. First study on microscopic and molecular evidences of two bovine hemoplasma species in cattle herds in Al-Qadisiyah Province, Iraq. Vet World 2022; 15:1323-1327. [PMID: 35765475 PMCID: PMC9210837 DOI: 10.14202/vetworld.2022.1323-1327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/25/2022] [Indexed: 11/18/2022] Open
Abstract
Background and Aim: Hemotropic Mycoplasmas are small epierythrocytic bacteria that cause infectious anemia in several livestock species and in humans. Several reports have been made on hemoplasma infections in the south and north of Iraq, but there have been no studies in the middle Euphrates of Iraq. This study aimed to evaluate the presence of hemoplasma species in cattle in Al-Qadisiyah Province, Iraq. Materials and Methods: Two hundred blood samples were collected from cattle with pale mucous membrane from regions with heavy tick endemicity. The samples were analyzed for the presence of Rickettsia pathogens using thin blood smears and the Diff-Quik stains. All the samples were also examined using polymerase chain reaction (PCR) to amplify the 16S ribosomal ribonucleic acid (rRNA) gene to confirm the presence of the smear-identified microorganisms. Ten PCR positive samples were subjected to 16S rRNA partial gene sequencing to identify the species. Results: The findings uncovered positivity in 68 (34%) blood smears. PCR revealed positive confirmation in 18 (9%) of the 200 blood samples. Mycoplasma wenyonii and Candidatus mycoplasma hemobos were identified from 10 PCR positive samples. The nucleotide sequences of the isolates were closely related to isolates from cattle, buffalo, and dogs in Vietnam, Cuba, India, and Germany. Conclusion: Bovine hemoplasma infections are prevalent in cattle in the Al-Qadisiyah Province in Iraq. Our results may have significance for the development of control programs.
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Affiliation(s)
- Yahia Ismail Khudhair
- Department of Internal and Preventive Medicine, College of Veterinary Medicine, University of Al-Qadisiyah, Al Diwaniyah, Iraq
| | - Zeena Fouad Saleh
- Unit of Zoonotic Disease Research, College of Veterinary Medicine, Al-Qadisiyah University, Al Diwaniyah, Iraq
| | - Hayder N. Ayyez
- Unit of Zoonotic Disease Research, College of Veterinary Medicine, Al-Qadisiyah University, Al Diwaniyah, Iraq
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4
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Hoffmann CV, Nevez G, Moal MC, Quinio D, Le Nan N, Papon N, Bouchara JP, Le Meur Y, Le Gal S. Selection of Pneumocystis jirovecii Inosine 5'-Monophosphate Dehydrogenase Mutants in Solid Organ Transplant Recipients: Implication of Mycophenolic Acid. J Fungi (Basel) 2021; 7:jof7100849. [PMID: 34682270 PMCID: PMC8537117 DOI: 10.3390/jof7100849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
Mycophenolic acid (MPA) targets the inosine 5'-monophosphate dehydrogenase (IMPDH) of human lymphocytes. It is widely used as an immunosuppressant to prevent rejection in solid organ transplant (SOT) recipients who, incidentally, are at risk for Pneumocystis pneumonia (PCP). We hypothesized that MPA exerts selective pressure on P. jirovecii microorganisms considering its in vitro antifungal activity on other fungi. Thus, we analysed impdh gene in P. jirovecii isolates from SOT recipients. P. jirovecii specimens from 26 patients diagnosed with PCP from 2010 to 2020 were retrospectively examined: 10 SOT recipients treated with MPA and 16 non-SOT patients without prior exposure to MPA. The P. jirovecii impdh gene was amplified and sequenced. Nucleotide sequences were aligned with the reference sequences retrieved from available P. jirovecii whole genomes. The deduced IMPDH protein sequences were aligned with available IMPDH proteins from Pneumocystis spp. and other fungal species known to be in vitro sensitive or resistant to MPA. A total of nine SNPs was identified. One SNP (G1020A) that results in an Ala261Thr substitution was identified in all SOT recipients and in none of the non-SOT patients. Considering that IMPDHs of other fungi, resistant to MPA, harbour Thr (or Ser) at the analogous position, the Ala261Thr mutation observed in MPA-treated patients was considered to represent the signature of P. jirovecii exposure to MPA. These results suggest that MPA may be involved in the selection of specific P. jirovecii strains that circulate in the SOT recipient population.
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Affiliation(s)
- Claire V. Hoffmann
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, 29609 Brest, France; (C.V.H.); (D.Q.)
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université d’Angers, Université de Brest, 29238 Brest, France;
| | - Gilles Nevez
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, 29609 Brest, France; (C.V.H.); (D.Q.)
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université d’Angers, Université de Brest, 29238 Brest, France;
- Correspondence: (G.N.); (S.L.G.); Tel.: +33-(0)-2-98-14-51-02 (G.N. & S.L.G.); Fax: +33-(0)-2-98-14-51-49 (G.N. & S.L.G.)
| | - Marie-Christine Moal
- Département de Néphrologie, CHU de Brest, 29609 Brest, France; (M.-C.M.); (Y.L.M.)
| | - Dorothée Quinio
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, 29609 Brest, France; (C.V.H.); (D.Q.)
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université d’Angers, Université de Brest, 29238 Brest, France;
| | - Nathan Le Nan
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université d’Angers, Université de Brest, 29238 Brest, France;
| | - Nicolas Papon
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université de Brest, Université d’Angers, 49035 Angers, France; (N.P.); (J.-P.B.)
| | - Jean-Philippe Bouchara
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université de Brest, Université d’Angers, 49035 Angers, France; (N.P.); (J.-P.B.)
| | - Yannick Le Meur
- Département de Néphrologie, CHU de Brest, 29609 Brest, France; (M.-C.M.); (Y.L.M.)
- UMR1227, Lymphocytes B et Autoimmunité, Université de Brest, Inserm, Labex IGO, 20609 Brest, France
| | - Solène Le Gal
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, 29609 Brest, France; (C.V.H.); (D.Q.)
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université d’Angers, Université de Brest, 29238 Brest, France;
- Correspondence: (G.N.); (S.L.G.); Tel.: +33-(0)-2-98-14-51-02 (G.N. & S.L.G.); Fax: +33-(0)-2-98-14-51-49 (G.N. & S.L.G.)
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5
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Gits-Muselli M, White PL, Mengoli C, Chen S, Crowley B, Dingemans G, Fréalle E, L Gorton R, Guiver M, Hagen F, Halliday C, Johnson G, Lagrou K, Lengerova M, Melchers WJG, Novak-Frazer L, Rautemaa-Richardson R, Scherer E, Steinmann J, Cruciani M, Barnes R, Donnelly JP, Loeffler J, Bretagne S, Alanio A. The Fungal PCR Initiative's evaluation of in-house and commercial Pneumocystis jirovecii qPCR assays: Toward a standard for a diagnostics assay. Med Mycol 2021; 58:779-788. [PMID: 31758173 DOI: 10.1093/mmy/myz115] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 10/22/2019] [Accepted: 10/31/2019] [Indexed: 01/04/2023] Open
Abstract
Quantitative real-time PCR (qPCR) is increasingly used to detect Pneumocystis jirovecii for the diagnosis of Pneumocystis pneumonia (PCP), but there are differences in the nucleic acids targeted, DNA only versus whole nucleic acid (WNA), and also the target genes for amplification. Through the Fungal PCR Initiative, a working group of the International Society for Human and Animal Mycology, a multicenter and monocenter evaluation of PCP qPCR assays was performed. For the multicenter study, 16 reference laboratories from eight different countries, performing 20 assays analyzed a panel consisting of two negative and three PCP positive samples. Aliquots were prepared by pooling residual material from 20 negative or positive- P. jirovecii bronchoalveolar lavage fluids (BALFs). The positive pool was diluted to obtain three concentrations (pure 1:1; 1:100; and 1:1000 to mimic high, medium, and low fungal loads, respectively). The monocenter study compared five in-house and five commercial qPCR assays testing 19 individual BALFs on the same amplification platform. Across both evaluations and for all fungal loads, targeting WNA and the mitochondrial small sub-unit (mtSSU) provided the earliest Cq values, compared to only targeting DNA and the mitochondrial large subunit, the major surface glycoprotein or the beta-tubulin genes. Thus, reverse transcriptase-qPCR targeting the mtSSU gene could serve as a basis for standardizing the P. jirovecii load, which is essential if qPCR is to be incorporated into clinical care pathways as the reference method, accepting that additional parameters such as amplification platforms still need evaluation.
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Affiliation(s)
- Maud Gits-Muselli
- Institut Pasteur, Molecular Mycology Unit, CNRS UMR2000, Paris, France.,Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Université de Paris, Paris, France
| | - P Lewis White
- Public Health Wales, Microbiology Cardiff, UHW, Heath Park, Cardiff, UK
| | | | - Sharon Chen
- Clinical Mycology reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, and the University of Sydney, Australia
| | - Brendan Crowley
- Department of Virology, St James's Hospital, Dublin, Ireland
| | | | - Emilie Fréalle
- CHU Lille, Laboratoire de Parasitologie-Mycologie, F-59000 Lille, France & Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL-Centre for Infection and Immunity of Lille, F-59000 Lille, France
| | - Rebecca L Gorton
- Regional UK Clinical Mycology Network (UK CMN) Laboratory, Dept. Infection Sciences, Health Services Laboratories (HSL) LLP, London, UK
| | - Malcom Guiver
- Public Health Laboratory, National Infection Service Public Health England, Manchester University NHS Foundation Trust, Manchester, UK
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands.,Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
| | - Catriona Halliday
- Clinical Mycology reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, and the University of Sydney, Australia
| | | | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, KU Leuven, and Department of Laboratory Medicine and National Reference Centre for Mycosis, Excellence Centre for Medical Mycology (ECMM), University Hospitals Leuven, Leuven, Belgium
| | - Martina Lengerova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Willem J G Melchers
- Radboud University Medical Centre, Department of Medical Microbiology, Nijmegen, The Netherlands
| | - Lily Novak-Frazer
- Mycology Reference Centre Manchester, Manchester University NHS Foundation Trust; and Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Riina Rautemaa-Richardson
- Department of Infectious Diseases and the Mycology Reference Centre Manchester, Manchester University NHS Foundation Trust; and Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Emeline Scherer
- Department of Parasitology-Mycology, University Hospital of Besançon, Besançon, France
| | - Joerg Steinmann
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Klinikum Nürnberg, Paracelsus Medical University, Nuremberg, Germany.,Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Mario Cruciani
- Infectious Diseases Unit, San Bonifacio Hospital, Verona, Italy
| | | | | | - Juergen Loeffler
- University Hospital Wuerzburg, Medical Hospital II, C11, Wuerzburg, Germany
| | - Stéphane Bretagne
- Institut Pasteur, Molecular Mycology Unit, CNRS UMR2000, Paris, France.,Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Université de Paris, Paris, France
| | - Alexandre Alanio
- Institut Pasteur, Molecular Mycology Unit, CNRS UMR2000, Paris, France.,Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Université de Paris, Paris, France
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6
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Dellière S, Hamane S, Aissaoui N, Gits-Muselli M, Bretagne S, Alanio A. Increased sensitivity of a new commercial reverse transcriptase-quantitative PCR for the detection of Pneumocystis jirovecii in respiratory specimens. Med Mycol 2021; 59:845-848. [PMID: 33983431 DOI: 10.1093/mmy/myab029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/21/2021] [Accepted: 05/10/2021] [Indexed: 12/22/2022] Open
Abstract
Optimal sensitivity to detect low Pneumocystis loads is of importance to take individual and collective measures to avoid evolution towards Pneumocystis pneumonia and outbreaks in immunocompromised patients. This study compares two qPCR procedures, a new automated RTqPCR using the GeneLEAD VIII extractor/thermocycler (GLVIII; ∼2.2 h workflow) and a previously validated in-house qPCR assays (IH; ∼5 h workflow) both targeting mtSSU and mtLSU for detecting P. jirovecii in 213 respiratory samples. GLVIII was found to be more sensitive than IH, detecting eight more specimens. Bland-Altman analysis between the two procedures showed a Cq bias of 1.17 ± 0.07 in favor of GLVIII. LAY SUMMARY The fungus Pneumocystis needs to be detected early in respiratory samples to prevent pneumonia in immunocompromised hosts. We evaluated a new commercial RTqPCR on 213 respiratory samples to detect Pneumocystis and found it more sensitive and faster than our routine sensitive in-house qPCR assay.
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Affiliation(s)
- Sarah Dellière
- Université de Paris, Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), 75010, Paris, France.,Institut Pasteur, Molecular Mycology Unit, CNRS UMR2000, 75015, Paris, France
| | - Samia Hamane
- Université de Paris, Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), 75010, Paris, France
| | - Nesrine Aissaoui
- Université de Paris, Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), 75010, Paris, France
| | - Maud Gits-Muselli
- Université de Paris, Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), 75010, Paris, France.,Institut Pasteur, Molecular Mycology Unit, CNRS UMR2000, 75015, Paris, France
| | - Stéphane Bretagne
- Université de Paris, Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), 75010, Paris, France.,Institut Pasteur, Molecular Mycology Unit, CNRS UMR2000, 75015, Paris, France.,National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Institut Pasteur, 75015, Paris, France
| | - Alexandre Alanio
- Université de Paris, Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), 75010, Paris, France.,Institut Pasteur, Molecular Mycology Unit, CNRS UMR2000, 75015, Paris, France.,National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Institut Pasteur, 75015, Paris, France
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7
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Le Gal S, Bonnet P, Huguenin A, Chapelle C, Boulic P, Tonnelier JM, Moal MC, Gut-Gobert C, Barnier A, Nevez G. The shift from pulmonary colonization to Pneumocystis pneumonia. Med Mycol 2020; 59:510-513. [PMID: 33369642 DOI: 10.1093/mmy/myaa107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/24/2020] [Accepted: 12/04/2020] [Indexed: 11/13/2022] Open
Abstract
Pulmonary specimen pairs from five patients who presented with pulmonary colonization and later developed Pneumocystis Pneumonia (PcP) were retrospectively examined for P. jirovecii genotyping. A match of genotypes in pulmonary specimen pairs of three patients was observed, whereas a partial match and a mismatch were observed in the fourth and fifth patients, respectively. The genotyping results suggest that the colonization state can differ from PcP but can also represent the incubation period of PcP. Clinicians should not systematically rule out the treatment of putative colonized patients and should at least discuss the initiation of prophylaxis on a case-by-case basis.
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Affiliation(s)
- Solène Le Gal
- Université de Brest, Université d'Angers, GEIHP, Brest, France.,Laboratory of Parasitology and Mycology, Brest University Hospital, Brest, France
| | - Pierre Bonnet
- Université de Brest, Université d'Angers, GEIHP, Brest, France.,Laboratory of Parasitology and Mycology, Brest University Hospital, Brest, France
| | - Antoine Huguenin
- EA 7510, ESCAPE, Laboratory of Parasitology and Mycology, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51092 Reims CEDEX, France
| | - Célia Chapelle
- Université de Brest, Université d'Angers, GEIHP, Brest, France
| | - Pierrick Boulic
- Université de Brest, Université d'Angers, GEIHP, Brest, France
| | | | | | | | - Aude Barnier
- Pneumology and Internal Medicine, Brest University Hospital, Brest, France
| | - Gilles Nevez
- Université de Brest, Université d'Angers, GEIHP, Brest, France.,Laboratory of Parasitology and Mycology, Brest University Hospital, Brest, France
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8
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Mantadakis E. Pneumocystis jirovecii Pneumonia in Children with Hematological Malignancies: Diagnosis and Approaches to Management. J Fungi (Basel) 2020; 6:jof6040331. [PMID: 33276699 PMCID: PMC7761543 DOI: 10.3390/jof6040331] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/01/2020] [Accepted: 12/01/2020] [Indexed: 12/21/2022] Open
Abstract
Pneumocystis jirovecii pneumonia (PJP) is an opportunistic infection that mostly affects children with suppressed cellular immunity. PJP was the most common cause of infectious death in children with acute lymphoblastic leukemia prior to the inclusion of cotrimoxazole prophylaxis as part of the standard medical care in the late 1980s. Children with acute leukemia, lymphomas, and those undergoing hematopoietic stem cell transplantation, especially allogeneic transplantation, are also at high risk of PJP. Persistent lymphopenia, graft versus host disease, poor immune reconstitution, and lengthy use of corticosteroids are significant risk factors for PJP. Active infection may be due to reactivation of latent infection or recent acquisition from environmental exposure. Intense hypoxemia and impaired diffusing capacity of the lungs are hallmarks of PJP, while computerized tomography of the lungs is the diagnostic technique of choice. Immunofluorescence testing with monoclonal antibodies followed by fluorescent microscopy and polymerase chain reaction testing of respiratory specimens have emerged as the best diagnostic methods. Measurement of (1-3)-β-D-glucan in the serum has a high negative predictive value in ruling out PJP. Oral cotrimoxazole is effective for prophylaxis, but in intolerant patients, intravenous and aerosolized pentamidine, dapsone, and atovaquone are effective alternatives. Ιntravenous cotrimoxazole is the treatment of choice, but PJP has a high mortality even with appropriate therapy.
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Affiliation(s)
- Elpis Mantadakis
- Department of Pediatrics, Hematology/Oncology Unit, University General Hospital of Alexandroupolis, Democritus University of Thrace, 68 100 Alexandroupolis, Thrace, Greece
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9
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Liu B, Totten M, Nematollahi S, Datta K, Memon W, Marimuthu S, Wolf LA, Carroll KC, Zhang SX. Development and Evaluation of a Fully Automated Molecular Assay Targeting the Mitochondrial Small Subunit rRNA Gene for the Detection of Pneumocystis jirovecii in Bronchoalveolar Lavage Fluid Specimens. J Mol Diagn 2020; 22:1482-1493. [PMID: 33069878 DOI: 10.1016/j.jmoldx.2020.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/10/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022] Open
Abstract
The fungal pathogen Pneumocystis jirovecii causes Pneumocystis pneumonia. Although the mitochondrial large subunit rRNA gene (mtLSU) is commonly used as a PCR target, a mitochondrial small subunit rRNA gene (mtSSU)-targeted MultiCode PCR assay was developed on the fully automated ARIES platform for detection of P. jirovecii in bronchoalveolar lavage fluid specimens in 2.5 hours. The assay showed a limit of detection of 800 copies/mL (approximately equal to 22 organisms/mL), with no cross-reactivity with other respiratory pathogens. Compared with the reference Pneumocystis-specific direct fluorescent antibody assay (DFA) and mtLSU-targeted PCR assay, the new assay demonstrated sensitivity of 96.9% (31/32) and specificity of 94.6% (139/147) in detecting P. jirovecii in 180 clinical bronchoalveolar lavage fluid specimens. This assay was concordant with all DFA-positive samples and all but one mtLSU PCR-positive sample, and detected eight positive samples that were negative by DFA and mtLSU PCR. Receiver operating characteristic curve analysis revealed an area under the curve of 0.98 and a threshold cycle (CT) cutoff of 39.1 with sensitivity of 90.9% and specificity of 99.3%. The detection of 39.1 <CT < 40.0 indicates the presence of a low load of the organism and needs further determination of either colonization or probable/possible Pneumocystis pneumonia. Overall, the new assay demonstrates excellent analytical and clinical performance and may be more sensitive than mtLSU PCR target for the detection of P. jirovecii.
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Affiliation(s)
- Baoming Liu
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marissa Totten
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Saman Nematollahi
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kausik Datta
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Warda Memon
- Microbiology Laboratory, Johns Hopkins Hospital, Baltimore, Maryland
| | - Subathra Marimuthu
- Division of Infectious Diseases, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky
| | - Leslie A Wolf
- Division of Infectious Diseases, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Microbiology Laboratory, Johns Hopkins Hospital, Baltimore, Maryland
| | - Sean X Zhang
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Microbiology Laboratory, Johns Hopkins Hospital, Baltimore, Maryland.
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10
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Nevez G, Guillaud-Saumur T, Cros P, Papon N, Vallet S, Quinio D, Minoui-Tran A, Pilorgé L, de Parscau L, Sizun J, Ochoa TJ, Bustamante B, Ponce C, Vargas SL, Le Gal S. Pneumocystis primary infection in infancy: Additional French data and review of the literature. Med Mycol 2020; 58:163-171. [PMID: 31127850 PMCID: PMC7107579 DOI: 10.1093/mmy/myz040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 11/12/2022] Open
Abstract
Data on features of Pneumocystis primary infection in infancy are still fragmented. To study Pneumocystis primary infection, 192 infants who were monitored for acute pulmonary disease or fever over a 40-month period were retrospectively investigated. P. jirovecii detection on archival nasopharyngeal aspirates was performed using a qPCR assay. Factors associated with P. jirovecii were assessed using univariate and multivariate analyses. P. jirovecii genotypes in infants and a control group of adults contemporaneously diagnosed with Pneumocystis pneumonia were identified using unilocus, bilocus, and multilocus sequence typing (MLST). P. jirovecii was detected in 35 infants (18.2%). The univariate analysis pointed out four factors: viral infection (P = .035, OR [IC 95], 2.2 [1.1–4.7]), lower respiratory tract infection (P = .032, OR [IC 95], 2.5 [1.1–5.9]), absence of hospital discharge after birth (P = .003, OR (IC 95), 0.1 (0.02–0.5]), and the 63–189-day group (P < .001, OR [IC 95], 42.2 [5.4–332]). The multivariate analysis confirmed these two latter factors (P = .02, OR [IC 95], 0.1 [0.02–0.72]; P = .005, OR [IC 95], 11.5 [2.1–63.5]). Thus, P. jirovecii acquisition mostly takes place in the community. A comparison of these data with those of previously published studies showed that median and interquartile range of positive-infant ages were close to those observed in Chile, Denmark, and Peru, highlighting similar characteristics. Common unilocus or bilocus genotypes were identified in infants and adults, whereas no MLST genotypes were shared. Therefore, a common reservoir made up of infected infants and adults is still hypothetical. Finally, primary infection is a worldwide phenomenon occurring at the same time in childhood regardless of geographical location, rather than an incidental event.
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Affiliation(s)
- Gilles Nevez
- Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP) EA 3142, Angers-Brest, Université de Bretagne-Loire, France.,Laboratoire de Mycologie et Parasitologie, CHRU de Brest, Brest, France
| | - Thibaud Guillaud-Saumur
- Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP) EA 3142, Angers-Brest, Université de Bretagne-Loire, France.,Laboratoire de Mycologie et Parasitologie, CHRU de Brest, Brest, France
| | - Pierrick Cros
- Département de Pédiatrie, CHRU de Brest, Brest, France
| | - Nicolas Papon
- Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP) EA 3142, Angers-Brest, Université de Bretagne-Loire, France
| | - Sophie Vallet
- Laboratoire de Virologie, CHRU de Brest, Brest, France.,UMR INSERM U 1078, Université de Bretagne-Loire, Brest, France
| | - Dorothée Quinio
- Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP) EA 3142, Angers-Brest, Université de Bretagne-Loire, France.,Laboratoire de Mycologie et Parasitologie, CHRU de Brest, Brest, France
| | | | - Léa Pilorgé
- Laboratoire de Virologie, CHRU de Brest, Brest, France
| | | | - Jacques Sizun
- Département de Pédiatrie, CHRU de Brest, Brest, France
| | - Theresa J Ochoa
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Beatriz Bustamante
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Carolina Ponce
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago
| | - Sergio L Vargas
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago
| | - Solène Le Gal
- Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP) EA 3142, Angers-Brest, Université de Bretagne-Loire, France.,Laboratoire de Mycologie et Parasitologie, CHRU de Brest, Brest, France
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11
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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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12
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Le Gal S, Hoarau G, Bertolotti A, Negri S, Le Nan N, Bouchara JP, Papon N, Blanchet D, Demar M, Nevez G. Pneumocystis jirovecii Diversity in Réunion, an Overseas French Island in Indian Ocean. Front Microbiol 2020; 11:127. [PMID: 32117149 PMCID: PMC7019000 DOI: 10.3389/fmicb.2020.00127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/20/2020] [Indexed: 12/17/2022] Open
Abstract
Data on Pneumocystis jirovecii characteristics from the overseas French territories are still scarce whereas numerous data on P. jirovecii genotypes are available for metropolitan France. The main objective of the present study was to identify P. jirovecii multilocus genotypes in patients living in Réunion and to compare them with those identified using the same method in metropolitan France and in French Guiana. Archival P. jirovecii specimens from immunosuppressed patients, 16 living in Réunion (a French island of the Indian ocean), six living in French Guiana (a South-American French territory), and 24 living in Brest (Brittany, metropolitan France) were examined at the large subunit rRNA (mtLSUrRNA) genes, cytochrome b (CYB), and superoxide dismutase (SOD) genes using PCR assays and direct sequencing. A total of 23 multi-locus genotypes (MLG) were identified combining mtLSUrRNA, CYB, and SOD alleles, i.e., six in Reunionese patients, three in Guianese patients, and 15 in Brest patients. Only one MLG (mtLSU1-CYB1-SOD2) was shared by Reunionese and Guianese patients (one patient from each region) whereas none of the 22 remaining MLG were shared by the 3 patient groups. A total of eight MLG were newly identified, three in Réunion and five in Brest. These results that were obtained through a retrospective investigation of a relatively low number of P. jirovecii specimens, provides original and first data on genetic diversity of P. jirovecii in Réunion island. The results suggest that P. jirovecii organisms from Réunion present specific characteristics compared to other P. jirovecii organisms from metropolitan France and French Guiana.
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Affiliation(s)
- Solène Le Gal
- Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP) EA 3142, Université d'Angers-Université de Brest, Angers, France.,Laboratory of Mycology and Parasitology, CHRU de Brest, Brest, France
| | - Gautier Hoarau
- Department of Microbiology, CHU La Réunion, Saint Pierre, France
| | | | - Steven Negri
- Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP) EA 3142, Université d'Angers-Université de Brest, Angers, France
| | - Nathan Le Nan
- Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP) EA 3142, Université d'Angers-Université de Brest, Angers, France
| | - Jean-Philippe Bouchara
- Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP) EA 3142, Université d'Angers-Université de Brest, Angers, France
| | - Nicolas Papon
- Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP) EA 3142, Université d'Angers-Université de Brest, Angers, France
| | - Denis Blanchet
- Laboratory of Mycology and Parasitology, Andrée Rosemon Hospital, Cayenne, French Guiana.,Equipe EA3593 - Ecosystèmes Amazoniens et Pathologie Tropicale, Université de Guyane, Cayenne, French Guiana
| | - Magalie Demar
- Laboratory of Mycology and Parasitology, Andrée Rosemon Hospital, Cayenne, French Guiana.,Equipe EA3593 - Ecosystèmes Amazoniens et Pathologie Tropicale, Université de Guyane, Cayenne, French Guiana
| | - Gilles Nevez
- Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP) EA 3142, Université d'Angers-Université de Brest, Angers, France.,Laboratory of Mycology and Parasitology, CHRU de Brest, Brest, France
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13
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Danesi P, Falcaro C, Ravagnan S, Da Rold G, Porcellato E, Corrò M, Iatta R, Cafarchia C, Frangipane di Regalbono A, Meyer W, Capelli G. Real-time PCR assay for screening Pneumocystis in free-living wild squirrels and river rats in Italy. J Vet Diagn Invest 2018; 30:862-867. [PMID: 30204066 DOI: 10.1177/1040638718797379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We used a real-time PCR (rtPCR) targeting a 150-bp amplicon of the mitochondrial small subunit of ribosomal RNA (mtSSU rRNA) to screen for Pneumocystis DNA in lungs of wild squirrels ( Callosciurus finlaysonii, n = 85) and river rats ( Myocastor coypus, n = 43) in Italy. The rtPCR revealed Pneumocystis DNA in 20 of 85 (24%) squirrels and in 35 of 43 (81%) river rats, and was more sensitive than a nested PCR that targets a portion of the mtSSU rRNA and the mitochondrial large subunit of rRNA (mtLSU rRNA). Phylogenetic analysis based on mtSSU rRNA and mtLSU rRNA sequences showed distinct Pneumocystis sequence types in these rodents. The rtPCR assay should be reliable for screening large populations for this potential pathogen, thereby allowing cost-effective monitoring of the disease in wild animals.
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Affiliation(s)
- Patrizia Danesi
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Christian Falcaro
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Silvia Ravagnan
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Graziana Da Rold
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Elena Porcellato
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Michela Corrò
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Roberta Iatta
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Claudia Cafarchia
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Antonio Frangipane di Regalbono
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Wieland Meyer
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Gioia Capelli
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
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14
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Otašević S, Momčilović S, Stojanović NM, Skvarč M, Rajković K, Arsić-Arsenijević V. Non-culture based assays for the detection of fungal pathogens. J Mycol Med 2018; 28:236-248. [PMID: 29605542 PMCID: PMC7110445 DOI: 10.1016/j.mycmed.2018.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 01/05/2023]
Abstract
Traditional, culture based methods for the diagnosis of fungal infections are still considered as gold standard, but they are time consuming and low sensitive. Therefore, in order to overcome the limitations, many researchers have focused on the development of new immunological and molecular based rapid assays that could enable early diagnosis of infection and accurate identification of fungal pathogens causing superficial and invasive infection. In this brief review, we highlighted the advantages and disadvantages of conventional diagnostic methods and possibility of non-culture based assays in diagnosis of superficial fungal infections and presented the overview on currently available immunochromatographic assays as well as availability of biomarkers detection by immunodiagnostic procedures in prompt and accurate diagnosis of invasive fungal infections. In addition, we presented diagnostic efficiency of currently available molecular panels and researches in this area.
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Affiliation(s)
- S Otašević
- Center of Microbiology and Parasitology, Public Health Institute Niš, Serbia, boulevard Zorana Djindjica 50, 18000 Niš, Serbia; Department of Microbiology and Immunology, Faculty of Medicine, University of Niš, Serbia, boulevard Zorana Djindjica 81, 18000 Niš, Serbia.
| | - S Momčilović
- Department of Microbiology and Immunology, Faculty of Medicine, University of Niš, Serbia, boulevard Zorana Djindjica 81, 18000 Niš, Serbia
| | - N M Stojanović
- Faculty of Medicine, University of Niš, Serbia, boulevard Zorana Djindjica 81, 18000 Niš, Serbia
| | - M Skvarč
- University of Ljubljana, Faculty of Medicine, Institute of Microbiology and Immunology, Zaloska 4, Ljubljana, Slovenia
| | - K Rajković
- High Chemical and Technological School for Professional Studies, Kosančićeva 36, 37000 Kruševac, Serbia
| | - V Arsić-Arsenijević
- Department for Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Serbia, Dr Subotića 1, 11000 Belgrade, Serbia
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15
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Rudramurthy SM, Sharma M, Sharma M, Rawat P, Ghosh A, Venkatesan L, Aggarwal R, Singh M, Chakrabarti A. Reliable differentiation of Pneumocystis pneumonia from Pneumocystis colonisation by quantification of Major Surface Glycoprotein gene using real-time polymerase chain reaction. Mycoses 2017; 61:96-103. [DOI: 10.1111/myc.12708] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 09/21/2017] [Accepted: 09/21/2017] [Indexed: 12/01/2022]
Affiliation(s)
- Shivaprakash M. Rudramurthy
- Department of Medical Microbiology; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Megha Sharma
- Department of Medical Microbiology; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Madhubala Sharma
- Department of Medical Microbiology; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Pankaj Rawat
- Department of Medical Microbiology; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Anup Ghosh
- Department of Medical Microbiology; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Lakshmishree Venkatesan
- Department of Medical Microbiology; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Ritesh Aggarwal
- Department of Pulmonary Medicine; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Meenu Singh
- Department of Pediatrics; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology; Postgraduate Institute of Medical Education and Research; Chandigarh India
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16
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Hoarau G, Le Gal S, Zunic P, Poubeau P, Antok E, Jaubert J, Nevez G, Picot S. Evaluation of quantitative FTD-Pneumocystis jirovecii kit for Pneumocystis infection diagnosis. Diagn Microbiol Infect Dis 2017; 89:212-217. [PMID: 28851493 DOI: 10.1016/j.diagmicrobio.2017.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 08/02/2017] [Accepted: 08/04/2017] [Indexed: 11/28/2022]
Abstract
We evaluated the Fast track Diagnostics (FTD) Pneumocystis PCR kit, targeting the mitochondrial large subunit ribosomal RNA gene (mtLSU rRNA) of Pneumocystis jirovecii (P. jirovecii). A hundred and thirty-three patients were prospectively enrolled. Respiratory specimens were examined using both microscopy and the PCR assay. Twenty-six patients led to P. jirovecii detection. Fourteen patients presented with Pneumocystis pneumonia (PCP) whereas 12 patients were considered to be colonized. The median copy numbers in bronchoalveolar lavage fluid were significantly different in the PCP and colonization groups (1.35×108/ml vs. 1.45×105/ml, P < 0.0001). Lower and upper cut-off values of 3.9×105 copies/ml and 3.2×106 copies/ml allowed differentiating PCP and colonization. The FTD P. jirovecii assay was secondarily compared to an in-house reference PCR assay targeting the mtLSUrRNA gene. A concordance rate of 97.5% was observed (Cohen's kappa coefficient κ=0.935). The FTD Pneumocystis PCR kit showed good performance and represents an alternative method to diagnose P. jirovecii infections.
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Affiliation(s)
- Gautier Hoarau
- Department of Microbiology, CHU La Reunion, St Pierre, France; UMR PIMIT « processus infectieux en milieu insulaire tropical », Inserm 1187, CNRS 9192, IRD 249, université de La Réunion, CYROI, 97490 Sainte-Clotilde, Reunion.
| | | | - Patricia Zunic
- Department of Hematology and Medical Oncology, CHU La Reunion, St Pierre, France
| | - Patrice Poubeau
- Department of Infectious Diseases, CHU La Reunion, St Pierre, France
| | | | - Julien Jaubert
- Department of Microbiology, CHU La Reunion, St Pierre, France
| | - Gilles Nevez
- University of Brest, GEIHP EA, 3142, Brest, France
| | - Sandrine Picot
- Department of Microbiology, CHU La Reunion, St Pierre, France
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17
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Nevez G, Robert-Gangneux F, Pougnet L, Virmaux M, Belleguic C, Deneuville E, Rault G, Chevrier S, Ramel S, Le Bihan J, Guillaud-Saumur T, Calderon E, Le Govic Y, Gangneux JP, Le Gal S. Pneumocystis jirovecii and Cystic Fibrosis in Brittany, France. Mycopathologia 2017; 183:81-87. [DOI: 10.1007/s11046-017-0172-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 06/27/2017] [Indexed: 11/30/2022]
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