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Douglas AP, Stewart AG, Halliday CL, Chen SCA. Outbreaks of Fungal Infections in Hospitals: Epidemiology, Detection, and Management. J Fungi (Basel) 2023; 9:1059. [PMID: 37998865 PMCID: PMC10672668 DOI: 10.3390/jof9111059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
Nosocomial clusters of fungal infections, whilst uncommon, cannot be predicted and are associated with significant morbidity and mortality. Here, we review reports of nosocomial outbreaks of invasive fungal disease to glean insight into their epidemiology, risks for infection, methods employed in outbreak detection including genomic testing to confirm the outbreak, and approaches to clinical and infection control management. Both yeasts and filamentous fungi cause outbreaks, with each having general and specific risks. The early detection and confirmation of the outbreak are essential for diagnosis, treatment of affected patients, and termination of the outbreak. Environmental sampling, including the air in mould outbreaks, for the pathogen may be indicated. The genetic analysis of epidemiologically linked isolates is strongly recommended through a sufficiently discriminatory approach such as whole genome sequencing or a method that is acceptably discriminatory for that pathogen. An analysis of both linked isolates and epidemiologically unrelated strains is required to enable genetic similarity comparisons. The management of the outbreak encompasses input from a multi-disciplinary team with epidemiological investigation and infection control measures, including screening for additional cases, patient cohorting, and strict hygiene and cleaning procedures. Automated methods for fungal infection surveillance would greatly aid earlier outbreak detection and should be a focus of research.
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Affiliation(s)
- Abby P. Douglas
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia
| | - Adam G. Stewart
- Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women’s Hospital Campus, The University of Queensland, Herston, QLD 4006, Australia;
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (C.L.H.); (S.C.-A.C.)
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia; (C.L.H.); (S.C.-A.C.)
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
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2
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Xue T, Kong X, Ma L. Trends in the Epidemiology of Pneumocystis Pneumonia in Immunocompromised Patients without HIV Infection. J Fungi (Basel) 2023; 9:812. [PMID: 37623583 PMCID: PMC10455156 DOI: 10.3390/jof9080812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/19/2023] [Accepted: 07/19/2023] [Indexed: 08/26/2023] Open
Abstract
The increasing morbidity and mortality of life-threatening Pneumocystis pneumonia (PCP) in immunocompromised people poses a global concern, prompting the World Health Organization to list it as one of the 19 priority invasive fungal diseases, calling for increased research and public health action. In response to this initiative, we provide this review on the epidemiology of PCP in non-HIV patients with various immunodeficient conditions, including the use of immunosuppressive agents, cancer therapies, solid organ and stem cell transplantation, autoimmune and inflammatory diseases, inherited or primary immunodeficiencies, and COVID-19. Special attention is given to the molecular epidemiology of PCP outbreaks in solid organ transplant recipients; the risk of PCP associated with the increasing use of immunodepleting monoclonal antibodies and a wide range of genetic defects causing primary immunodeficiency; the trend of concurrent infection of PCP in COVID-19; the prevalence of colonization; and the rising evidence supporting de novo infection rather than reactivation of latent infection in the pathogenesis of PCP. Additionally, we provide a concise discussion of the varying effects of different immunodeficient conditions on distinct components of the immune system. The objective of this review is to increase awareness and knowledge of PCP in non-HIV patients, thereby improving the early identification and treatment of patients susceptible to PCP.
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Affiliation(s)
- Ting Xue
- NHC Key Laboratory of Pneumoconiosis, Key Laboratory of Prophylaxis and Treatment and Basic Research of Respiratory Diseases of Shanxi Province, Shanxi Province Key Laboratory of Respiratory, Department of Respiratory and Critical Care Medicine, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Xiaomei Kong
- NHC Key Laboratory of Pneumoconiosis, Key Laboratory of Prophylaxis and Treatment and Basic Research of Respiratory Diseases of Shanxi Province, Shanxi Province Key Laboratory of Respiratory, Department of Respiratory and Critical Care Medicine, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, MD 20892, USA
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3
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Friaza V, de Armas Y, Capó V, Morilla R, Plascencia-Hernández A, Pérez-Gómez HR, Iglesias E, Fonte L, de la Horra C, Calderón EJ. Multilocus Genotyping of Pneumocystis jirovecii from Deceased Cuban AIDS Patients Using Formalin-Fixed and Paraffin-Embedded Tissues. J Fungi (Basel) 2021; 7:jof7121042. [PMID: 34947024 PMCID: PMC8706017 DOI: 10.3390/jof7121042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022] Open
Abstract
The results of the genotypic characterization of Pneumocystis jirovecii are described in lung tissue samples from 41 Cubans who died of AIDS with pneumocystosis between 1995 and 2008. Histological sections of the lung preserved as formalin-fixed and paraffin-embedded tissue were examined. PCR amplification and nucleotide sequencing of the two mitochondrial genes (large and small) of the pathogen allowed verification of a predominance of genotype 3 (85T/248C) of the large mitochondrial gene and genotype 3 (160A/196T) of the small mitochondrial gene over a period of 14 years (1995–2008). These results suggest that the 85T/248C//160A/196T genotype circulates with the highest frequency (81.3%) among AIDS patients in Cuba. Multilocus analysis indicates a limited circulation of pathogen genotypes on the island with the existence of a clonal genotype with an epidemic structure. Furthermore, it appears that circulating strains of P. jirovecii have not developed mutations related to sulfonamide resistance. Taken together, the data in this study revealed important elements about pneumocystosis in Cuban patients dying of AIDS and the usefulness of formalin-fixed and paraffin-embedded samples to carry out molecular epidemiology studies of P. jirovecii.
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Affiliation(s)
- Vicente Friaza
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (V.F.); (R.M.); (E.J.C.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
| | - Yaxsier de Armas
- Department of Clinical Microbiology Diagnostic, Hospital Center of Institute of Tropical Medicine “Pedro Kourí”, 11400 Havana, Cuba;
- Pathology Department, Hospital Center of Institute of Tropical Medicine “Pedro Kourí”, 11400 Havana, Cuba;
| | - Virginia Capó
- Pathology Department, Hospital Center of Institute of Tropical Medicine “Pedro Kourí”, 11400 Havana, Cuba;
| | - Rubén Morilla
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (V.F.); (R.M.); (E.J.C.)
| | - Arturo Plascencia-Hernández
- Centro Universitario de Ciencias para la Salud, Universidad de Guadalajara, 44100 Guadalajara, Mexico; (A.P.-H.); (H.R.P.-G.)
| | - Héctor R. Pérez-Gómez
- Centro Universitario de Ciencias para la Salud, Universidad de Guadalajara, 44100 Guadalajara, Mexico; (A.P.-H.); (H.R.P.-G.)
| | - Enrique Iglesias
- Centro de Ingeniería Genética y Biotecnología, Departamento de Vacunas, 10600 Havana, Cuba;
| | - Luis Fonte
- Parasitology Department, Institute of Tropical Medicine “Pedro Kourí”, 11400 Havana, Cuba;
| | - Carmen de la Horra
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (V.F.); (R.M.); (E.J.C.)
- Correspondence:
| | - Enrique J. Calderón
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (V.F.); (R.M.); (E.J.C.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
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4
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Goterris L, Pasic L, Murillo MG, Kan A, Anton A, Company JA, Ruiz-Camps I, Meyer W, Martin-Gomez MT. Pneumocystis jirovecii genetic diversity in a Spanish tertiary hospital. Med Mycol 2021; 60:6410670. [PMID: 34698858 DOI: 10.1093/mmy/myab065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/29/2021] [Accepted: 10/21/2021] [Indexed: 12/19/2022] Open
Abstract
Pneumocystis jirovecii is associated with non-noxious colonization or severe pneumonia in immunocompromised hosts. Epidemiological investigations have been hampered by the lack of a standardized typing scheme. Thus, only partial molecular data on Spanish P. jirovecii cases are available. Recently a new ISHAM consensus multilocus sequence typing scheme (MLST) targeting β-TUB, mt26S, CYB, and SOD with a publicly accessible database has been launched to overcome this problem.The molecular epidemiology of P. jirovecii from immunocompromised patients either colonized (n = 50) or having pneumonia (n = 36) seen between 2014 and 2018 at a single center in Barcelona, Spain, was studied. The new ISHAM consensus MSLT scheme was used to investigate the local epidemiology and identify possible unnoticed outbreaks. Mutations in the DHPS gene, not included in the scheme but giving information about potential sulpha treatment failure, were also studied. The study assigned 32 sequence types (ST) to 72.2% pneumonia and 56% colonization cases. The most frequent STs were ST21 (18.5%), ST22 (14.8%), and ST37(14.8%). For non-unique STs, ST3, ST30 and ST31 were found only in pneumonia cases, whereas ST27 was associated exclusively to colonization's. Despite 38 patients sharing similar STs, only two were involved in a potential cross transmission event. No DHPS mutations were identified. The new consensus typing scheme was useful to ascertain the molecular epidemiology of P. jirovecii in our center revealing a high genetic diversity and the potential association of specific STs to colonization and pneumonia cases. LAY SUMMARY A newly described MLST scheme aims at providing a standardized tool to study and compare Pneumocystis jirovecii epidemiology. A high diversity amongst P. jirovecii isolates from patients in Barcelona, Spain, and a potential association between specific STs and infection/colonization were identified.
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Affiliation(s)
- Lidia Goterris
- Microbiology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Genetics and Microbiology Department, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Lana Pasic
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.,Westmead Institute for Medical Research, Westmead, Australia
| | | | - Alex Kan
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.,Westmead Institute for Medical Research, Westmead, Australia
| | - Andres Anton
- Microbiology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Genetics and Microbiology Department, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Juan Aguilar Company
- Infectious Diseases Department, Vall d'Hebron Hospital Universitari, Barcelona, Spain.,Oncology Department, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Isabel Ruiz-Camps
- Infectious Diseases Department, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.,Westmead Institute for Medical Research, Westmead, Australia.,Westmead Hospital (Research and Education Network), Westmead, Australia
| | - María Teresa Martin-Gomez
- Microbiology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Genetics and Microbiology Department, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Nyuykonge B, Eadie K, Zandijk WHA, Ahmed SA, Desnos-Ollivier M, Fahal AH, de Hoog S, Verbon A, van de Sande WWJ, Klaassen CHW. A Short-Tandem-Repeat Assay ( MmySTR) for Studying Genetic Variation in Madurella mycetomatis. J Clin Microbiol 2021; 59:e02331-20. [PMID: 33298608 DOI: 10.1128/JCM.02331-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/01/2020] [Indexed: 12/27/2022] Open
Abstract
Madurella mycetomatis is the major causative agent of eumycetoma, a neglected tropical infection characterized by painless subcutaneous lesions, inflammation, and grains draining from multiple sinuses. To study the epidemiology of mycetoma, a robust discriminatory typing technique is needed. We describe the use of a short-tandem-repeat assay (MmySTR) for genotyping of M. mycetomatis isolates predominantly from Sudan. Eleven microsatellite markers (3 dinucleotides, 4 trinucleotide repeats, and 4 tetranucleotide repeats) were selected from the M. mycetomatis MM55 genome using the Tandem Repeats Finder software. PCR amplification primers were designed for each microsatellite marker using primer3 software and amplified in a multicolor multiplex PCR approach. To establish the extent of genetic variation within the population, a collection of 120 clinical isolates from different regions was genotyped with this assay. The 11 selected MmySTR markers showed a large genotypic heterogeneity. From a collection of 120 isolates, 108 different genotypes were obtained. Simpson's diversity index (D) value for individual markers ranged from 0.081 to 0.881, and the combined panel displayed an overall D value of 0.997. The MmySTR assay demonstrated high stability, reproducibility, and specificity. The MmySTR assay is a promising new typing technique that can be used to genotype isolates of M. mycetomatis Apart from the possible contribution of host factors, the genetic diversity observed among this group of isolates might contribute to the different clinical manifestations of mycetoma. We recommend that the MmySTR assay be used to establish a global reference database for future study of M. mycetomatis isolates.
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Gits-Muselli M, Campagne P, Desnos-Ollivier M, Le Pape P, Bretagne S, Morio F, Alanio A. Comparison of MultiLocus Sequence Typing (MLST) and Microsatellite Length Polymorphism (MLP) for Pneumocystis jirovecii genotyping. Comput Struct Biotechnol J 2020; 18:2890-2896. [PMID: 33163149 PMCID: PMC7593342 DOI: 10.1016/j.csbj.2020.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/28/2020] [Accepted: 10/02/2020] [Indexed: 01/02/2023] Open
Abstract
Pneumocystis jirovecii is an atypical fungus responsible for severe respiratory infections, often reported as local outbreaks in immunocompromised patients. Epidemiology of this infection, and transmission risk emphasises the need for developing genotyping techniques. Currently, two methods have emerged: Multilocus Sequence typing (MLST) and microsatellite length polymorphism (MLP). Here we compare an MLST strategy, including 2 nuclear loci and 2 mitochondrial loci, with an MLP strategy including 6 nuclear markers using 37 clinical PCR-positive respiratory samples from two French hospitals. Pneumocystis jirovecii MLST and MLP provided 30 and 35 different genotypes respectively. A higher number of mixed infections was detected using MLP (48.6% vs. 13.5% respectively; p = 0.002). Only one MLP marker (STR279) was statistically associated with the geographical origin of samples. Haplotype network inferred using the available genotypes yielded expanded network for MLP, characterized by more mutational steps as compared to MLST, suggesting that the MLP approach is more resolutive to separate genotypes. The correlation between genetic distances calculated based on MLST and MLP was modest with a R2 value = 0.32 (p < 0.001). Finally, both genotyping methods fulfilled important criteria: (i) a discriminatory power from 97.5% to 99.5% and (ii) being quick and convenient genotyping tools. While MLP appeared highly resolutive regarding genotypes mixture within samples, using one genotyping method rather than the other may also depend on the context (i.e., MLST for investigation of suspected clonal outbreaks versus MLP for population structure study) as well as local facilities.
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Affiliation(s)
- Maud Gits-Muselli
- Laboratoire de Parasitologie-Mycologie; AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France.,Institut Pasteur, CNRS, unité de Mycologie Moléculaire, Centre National de référence Mycoses invasives et Antifongiques (CNRMA), UMR2000, Paris, France
| | - Pascal Campagne
- Hub of Bioinformatics and Biostatistics - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Marie Desnos-Ollivier
- Institut Pasteur, CNRS, unité de Mycologie Moléculaire, Centre National de référence Mycoses invasives et Antifongiques (CNRMA), UMR2000, Paris, France
| | - Patrice Le Pape
- Laboratoire de Parasitologie-Mycologie, Institut de Biologie, CHU Nantes, Nantes, France.,Département de Parasitologie et Mycologie Médicale, EA1155 IICiMed, Institut de Recherche en Santé 2, Université de Nantes, Nantes Atlantique Universités, Nantes, France
| | - Stéphane Bretagne
- Laboratoire de Parasitologie-Mycologie; AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France.,Institut Pasteur, CNRS, unité de Mycologie Moléculaire, Centre National de référence Mycoses invasives et Antifongiques (CNRMA), UMR2000, Paris, France
| | - Florent Morio
- Laboratoire de Parasitologie-Mycologie, Institut de Biologie, CHU Nantes, Nantes, France.,Département de Parasitologie et Mycologie Médicale, EA1155 IICiMed, Institut de Recherche en Santé 2, Université de Nantes, Nantes Atlantique Universités, Nantes, France
| | - Alexandre Alanio
- Laboratoire de Parasitologie-Mycologie; AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France.,Institut Pasteur, CNRS, unité de Mycologie Moléculaire, Centre National de référence Mycoses invasives et Antifongiques (CNRMA), UMR2000, Paris, France
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8
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Chen J, He T, Li X, Wang X, Peng L, Ma L. Metagenomic Next-Generation Sequencing in Diagnosis of a Case of Pneumocystis jirovecii Pneumonia in a Kidney Transplant Recipient and Literature Review. Infect Drug Resist 2020; 13:2829-2836. [PMID: 32884306 PMCID: PMC7431457 DOI: 10.2147/idr.s257587] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/21/2020] [Indexed: 12/16/2022] Open
Abstract
Background Despite the increasing incidences of Pneumocystis jirovecii pneumonia (PCP) in renal transplant recipients, diagnosis of PCP remains challenging due to its nonspecific clinical presentation and the inadequate performance of conventional diagnostic methods. There is a need for novel diagnostic methods. Case Presentation A 27-year-old woman developed acute pneumonia 4 months after renal transplantation. Blood tests revealed a low CD4 count, a normal 1,3-beta-D-glucan level and other changes typical of inflammatory responses. Chest imaging showed bilateral diffuse infiltrates. Microscopic examination of stained sputum and bronchoalveolar lavage fluid (BALF) smear specimens did not find Pneumocystis organisms. There was also no evidence for other pathogens known to cause pneumonia in various antibody and culture tests. Direct metagenomic next-generation sequencing (mNGS) analysis of a BALF specimen identified a large number of P. jirovecii reads, allowing to confirm the diagnosis of PCP. Following treatment with trimethoprim-sulfamethoxazole for two weeks, the patient was cured and discharged. Conclusion This case report supports the value of mNGS in diagnosing PCP, highlights the inadequate sensitivity of conventional diagnostic methods for PCP, and calls for the need to add PCP prophylaxis to the current Diagnosis and Treatment Guideline of Invasive Fungal Infections in Solid Organ Transplant Recipients in China.
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Affiliation(s)
- Jie Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Ting He
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Xiujun Li
- Department of Pathology, College of Basic Medicine, Chongqing Medical University, Chongqing, People's Republic of China
| | - Xue Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Li Peng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, MD, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Dellière S, Gits-Muselli M, White PL, Mengoli C, Bretagne S, Alanio A. Quantification of Pneumocystis jirovecii: Cross-Platform Comparison of One qPCR Assay with Leading Platforms and Six Master Mixes. J Fungi (Basel) 2019; 6:jof6010009. [PMID: 31888050 PMCID: PMC7151141 DOI: 10.3390/jof6010009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 12/23/2019] [Accepted: 12/23/2019] [Indexed: 12/17/2022] Open
Abstract
Diagnosis of Pneumocystis jirovecii pneumonia relies on nucleic acid quantification in respiratory samples. Lack of standardization among molecular assays results in significant differences among assays/centers. To further promote standardization, we compared four thermocyclers and six master mixes for the detection of P. jirovecii. Whole nucleic acid (WNA) was extracted from broncho-alveolar lavages. Positive and negative sample extracts were pooled to get enough homogeneous materials. Three master mixes were tested to detect DNA by qPCR (D1, D2, and D3), and three to detect WNA by reverse transcriptase qPCR (W1, W2, and W3) manufactured by Roche, Eurogentec, Applied Biosystem, Invitrogen and Thermofischer Scientific. Experiments were performed on four thermocyclers (Roche LightCycler 480, Qiagen Rotor-Gene Q, Applied Biosystem ABI7500, and QuantStudio). Comparison of quantitative cycle (Cq) values between the methods targeting WNA versus DNA showed lower Cq values for WNA, independently of thermocycler and master mix. For high and low fungal loads, ∆Cq values between DNA and WNA amplification were 6.97 (±2.95) and 5.81 (±3.30), respectively (p < 0.0001). Regarding DNA detection, lower Cqs were obtained with D1 compared to D2 and D3, with median ∆Cq values of 2.6 (p = 0.015) and 2.9 (p = 0.039) respectively. Regarding WNA detection, no mix was superior to the others. PCR efficiency was not significantly different according to the qPCR platform (p = 0.14). This study confirmed the superiority of WNA over DNA detection. A calibration method (e.g., an international standard) for accurate comparative assessment of fungal load seems necessary.
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Affiliation(s)
- Sarah Dellière
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, 75475 Paris, France; (S.D.); (M.G.-M.); (S.B.)
- Molecular Mycology Unit, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR2000), Institut Pasteur, CEDEX 15, 75724 Paris, France
- National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Institut Pasteur, CEDEX 15, 75724 Paris, France
| | - Maud Gits-Muselli
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, 75475 Paris, France; (S.D.); (M.G.-M.); (S.B.)
- Molecular Mycology Unit, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR2000), Institut Pasteur, CEDEX 15, 75724 Paris, France
| | - P. Lewis White
- Public Health Wales, Microbiology Cardiff, Heath Park, University Hospital of Wales (UHW), Cardiff CF14 4XW, UK;
| | - Carlo Mengoli
- Department of Molecular Medicine, University of Padua, 35122 Padua, Italy;
| | - Stéphane Bretagne
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, 75475 Paris, France; (S.D.); (M.G.-M.); (S.B.)
- Molecular Mycology Unit, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR2000), Institut Pasteur, CEDEX 15, 75724 Paris, France
- National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Institut Pasteur, CEDEX 15, 75724 Paris, France
| | - Alexandre Alanio
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, 75475 Paris, France; (S.D.); (M.G.-M.); (S.B.)
- Molecular Mycology Unit, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR2000), Institut Pasteur, CEDEX 15, 75724 Paris, France
- National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Institut Pasteur, CEDEX 15, 75724 Paris, France
- Correspondence: ; Tel.: +33-1406-13255; Fax: +33-1456-88420
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Abstract
Pneumocystis jirovecii pneumonia (PCP) is an important cause of morbidity in immunocompromised patients, with a higher mortality in non-HIV than in HIV patients. P. jirovecii is one of the rare transmissible pathogenic fungi and the only one that depends fully on the host to survive and proliferate. Transmissibility among humans is one of the main specificities of P. jirovecii. Hence, the description of multiple outbreaks raises questions regarding preventive care management of the disease, especially in the non-HIV population. Indeed, chemoprophylaxis is well codified in HIV patients but there is a trend for modifications of the recommendations in the non-HIV population. In this review, we aim to discuss the mode of transmission of P. jirovecii, identify published outbreaks of PCP and describe molecular tools available to study these outbreaks. Finally, we discuss public health and infection control implications of PCP outbreaks in hospital setting for in- and outpatients.
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Affiliation(s)
- Sarah Dellière
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
- Molecular Mycology Unit, CNRS UMR2000, Institut Pasteur, 25 rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Maud Gits-Muselli
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
- Molecular Mycology Unit, CNRS UMR2000, Institut Pasteur, 25 rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Stéphane Bretagne
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
- Molecular Mycology Unit, CNRS UMR2000, Institut Pasteur, 25 rue du Dr Roux, 75724, Paris Cedex 15, France
- National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Institut Pasteur, Paris, France
| | - Alexandre Alanio
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France.
- Molecular Mycology Unit, CNRS UMR2000, Institut Pasteur, 25 rue du Dr Roux, 75724, Paris Cedex 15, France.
- National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Institut Pasteur, Paris, France.
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13
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Brunet K, Alanio A, Lortholary O, Rammaert B. Reactivation of dormant/latent fungal infection. J Infect 2018; 77:463-468. [DOI: 10.1016/j.jinf.2018.06.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/23/2018] [Accepted: 06/25/2018] [Indexed: 12/18/2022]
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White PL, Price JS, Backx M. Therapy and Management of Pneumocystis jirovecii Infection. J Fungi (Basel) 2018; 4:E127. [PMID: 30469526 DOI: 10.3390/jof4040127] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/08/2018] [Accepted: 11/11/2018] [Indexed: 12/21/2022] Open
Abstract
The rates of Pneumocystis pneumonia (PcP) are increasing in the HIV-negative susceptible population. Guidance for the prophylaxis and treatment of PcP in HIV, haematology, and solid-organ transplant (SOT) recipients is available, although for many other populations (e.g., auto-immune disorders) there remains an urgent need for recommendations. The main drug for both prophylaxis and treatment of PcP is trimethoprim/sulfamethoxazole, but resistance to this therapy is emerging, placing further emphasis on the need to make a mycological diagnosis using molecular based methods. Outbreaks in SOT recipients, particularly renal transplants, are increasingly described, and likely caused by human-to-human spread, highlighting the need for efficient infection control policies and sensitive diagnostic assays. Widespread prophylaxis is the best measure to gain control of outbreak situations. This review will summarize diagnostic options, cover prophylactic and therapeutic management in the main at risk populations, while also covering aspects of managing resistant disease, outbreak situations, and paediatric PcP.
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Abstract
Pneumocystis, a unique atypical fungus with an elusive lifestyle, has had an important medical history. It came to prominence as an opportunistic pathogen that not only can cause life-threatening pneumonia in patients with HIV infection and other immunodeficiencies but also can colonize the lungs of healthy individuals from a very early age. The genus Pneumocystis includes a group of closely related but heterogeneous organisms that have a worldwide distribution, have been detected in multiple mammalian species, are highly host species specific, inhabit the lungs almost exclusively, and have never convincingly been cultured in vitro, making Pneumocystis a fascinating but difficult-to-study organism. Improved molecular biologic methodologies have opened a new window into the biology and epidemiology of Pneumocystis. Advances include an improved taxonomic classification, identification of an extremely reduced genome and concomitant inability to metabolize and grow independent of the host lungs, insights into its transmission mode, recognition of its widespread colonization in both immunocompetent and immunodeficient hosts, and utilization of strain variation to study drug resistance, epidemiology, and outbreaks of infection among transplant patients. This review summarizes these advances and also identifies some major questions and challenges that need to be addressed to better understand Pneumocystis biology and its relevance to clinical care.
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Affiliation(s)
- Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, Maryland, USA
| | - Ousmane H Cissé
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, Maryland, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, Maryland, USA
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Charpentier E, Garnaud C, Wintenberger C, Bailly S, Murat JB, Rendu J, Pavese P, Drouet T, Augier C, Malvezzi P, Thiébaut-Bertrand A, Mallaret MR, Epaulard O, Cornet M, Larrat S, Maubon D. Added Value of Next-Generation Sequencing for Multilocus Sequence Typing Analysis of a Pneumocystis jirovecii Pneumonia Outbreak1. Emerg Infect Dis 2018; 23:1237-1245. [PMID: 28726611 PMCID: PMC5547796 DOI: 10.3201/eid2308.161295] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Pneumocystis jirovecii is a major threat for immunocompromised patients, and clusters of pneumocystis pneumonia (PCP) have been increasingly described in transplant units during the past decade. Exploring an outbreak transmission network requires complementary spatiotemporal and strain-typing approaches. We analyzed a PCP outbreak and demonstrated the added value of next-generation sequencing (NGS) for the multilocus sequence typing (MLST) study of P. jirovecii strains. Thirty-two PCP patients were included. Among the 12 solid organ transplant patients, 5 shared a major and unique genotype that was also found as a minor strain in a sixth patient. A transmission map analysis strengthened the suspicion of nosocomial acquisition of this strain for the 6 patients. NGS-MLST enables accurate determination of subpopulation, which allowed excluding other patients from the transmission network. NGS-MLST genotyping approach was essential to deciphering this outbreak. This innovative approach brings new insights for future epidemiologic studies on this uncultivable opportunistic fungus.
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Cordonnier C, Alanio A, Cesaro S, Maschmeyer G, Einsele H, Donnelly JP, Hauser PM, Lagrou K, Melchers WJG, Helweg-Larsen J, Matos O, Bretagne S, Maertens J. Pneumocystis jirovecii pneumonia: still a concern in patients with haematological malignancies and stem cell transplant recipients-authors' response. J Antimicrob Chemother 2018; 72:1266-1268. [PMID: 28122911 DOI: 10.1093/jac/dkw580] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Catherine Cordonnier
- Department of Haematology, Henri Mondor Teaching Hospital, Assistance Publique-hôpitaux de Paris, and Université Paris-Est-Créteil, Créteil, France
| | - 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
| | - Simone Cesaro
- Department of Haematology, Oncoematologia Pediatrica, Policlinico G. B. Rossi, Verona, Italy
| | - Georg Maschmeyer
- Department of Haematology, Oncology and Palliative Care, Ernst-von-Bergmann Klinikum, Potsdam, Germany
| | - Hermann Einsele
- Department of Internal Medicine II, Julius Maximilians University, Würzburg, Germany
| | - J Peter Donnelly
- Department of Haematology Radboud University Medical Center, Nijmegen, The Netherlands
| | - Philippe M Hauser
- Institute of Microbiology, Lausanne University Hospital and University, Lausanne, Switzerland
| | - Katrien Lagrou
- Department of Microbiology and Immunology, KU Leuven?-?University of 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, Lisboa, Portugal
| | - 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
| | - Johan Maertens
- Department of Haematology, Acute Leukaemia and Stem Cell Transplantation Unit, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium
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Alanio A, Desnos-Ollivier M, Garcia-Hermoso D, Bretagne S. Investigating Clinical Issues by Genotyping of Medically Important Fungi: Why and How? Clin Microbiol Rev 2017; 30:671-707. [PMID: 28490578 DOI: 10.1128/CMR.00043-16] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genotyping studies of medically important fungi have addressed elucidation of outbreaks, nosocomial transmissions, infection routes, and genotype-phenotype correlations, of which secondary resistance has been most intensively investigated. Two methods have emerged because of their high discriminatory power and reproducibility: multilocus sequence typing (MLST) and microsatellite length polymorphism (MLP) using short tandem repeat (STR) markers. MLST relies on single-nucleotide polymorphisms within the coding regions of housekeeping genes. STR polymorphisms are based on the number of repeats of short DNA fragments, mostly outside coding regions, and thus are expected to be more polymorphic and more rapidly evolving than MLST markers. There is no consensus on a universal typing system. Either one or both of these approaches are now available for Candida spp., Aspergillus spp., Fusarium spp., Scedosporium spp., Cryptococcus neoformans, Pneumocystis jirovecii, and endemic mycoses. The choice of the method and the number of loci to be tested depend on the clinical question being addressed. Next-generation sequencing is becoming the most appropriate method for fungi with no MLP or MLST typing available. Whatever the molecular tool used, collection of clinical data (e.g., time of hospitalization and sharing of similar rooms) is mandatory for investigating outbreaks and nosocomial transmission.
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Alanio A, Gits-Muselli M, Guigue N, Desnos-Ollivier M, Calderon EJ, Di Cave D, Dupont D, Hamprecht A, Hauser PM, Helweg-Larsen J, Kicia M, Lagrou K, Lengerova M, Matos O, Melchers WJG, Morio F, Nevez G, Totet A, White LP, Bretagne S. Diversity of Pneumocystis jirovecii Across Europe: A Multicentre Observational Study. EBioMedicine 2017; 22:155-63. [PMID: 28705464 DOI: 10.1016/j.ebiom.2017.06.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/13/2017] [Accepted: 06/28/2017] [Indexed: 12/30/2022] Open
Abstract
Pneumocystis jirovecii is an airborne human-specific ascomycetous fungus responsible for Pneumocystis pneumonia (PCP) in immunocompromised patients, affecting > 500,000 patients per year (www.gaffi.org). The understanding of its epidemiology is limited by the lack of standardised culture. Recent genotyping data suggests a limited genetic diversity of P. jirovecii. The objective of the study was to assess the diversity of P. jirovecii across European hospitals and analyse P. jirovecii diversity in respect to clinical data obtained from the patients. Genotyping was performed using six already validated short tandem repeat (STR) markers on 249 samples (median: 17 per centre interquartile range [11 − 20]) from PCP patients of 16 European centres. Mixtures of STR markers (i.e., ≥ 2 alleles for ≥ 1 locus) were detected in 67.6% (interquartile range [61.4; 76.5]) of the samples. Mixture was significantly associated with the underlying disease of the patient, with an increased proportion in HIV patients (78.3%) and a decreased proportion in renal transplant recipients (33.3%) (p < 0.001). The distribution of the alleles was significantly different (p < 0.001) according to the centres in three out of six markers. In analysable samples, 201 combinations were observed corresponding to 137 genotypes: 116 genotypes were country-specific; 12 in two; six in three; and two in four and one in five countries. Nine genotypes were recorded more than once in a given country. Genotype 123 (Gt123) was significantly associated with France (14/15, p < 0.001) and Gt16 with Belgium (5/5, p < 0.001). More specifically, Gt123 was observed mainly in France (14/15/16 patients) and in renal transplant patient (13/15). Our study showed the wide population diversity across Europe, with evidence of local clusters of patients harbouring a given genotype. These data suggest a specific association between genotype and underlying disease, with evidence of a different natural history of PCP in HIV patients and renal transplant recipients. Limited number of P. jirovecii genetic complexes across Europe but high number of genotypes uncovered. Association between mixture of genotype and HIV patients. Specific relationship between renal transplant recipients and specific P. jirovecii genotypes with the description of multiple local transmissions. Potential geographical and temporal dissemination of a given genotype within an area of 600 km.
Pneumocystis jirovecii is an airborne opportunistic fungal organism. As it is not culturable, genotyping and population genetics is difficult. We implemented recently a method allowing us to genotype the largest cohort of P. jirovecii isolates (n = 249) across Europe. We evidenced that HIV patients were more prone to harbour mixtures of genotypes compared to other underlying diseases, that local transmission of a given genotype was frequent in renal transplant recipients with potential dissemination within a timescale of several years and an area of 600 km. This work advances our understanding of the population structure and the transmission of P. jirovecii in humans.
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Abstract
Pneumocystis jirovecii is an unusual ascomycetous fungus that can be detected in the lungs of healthy individuals. Transmission from human to human is one of its main characteristics in comparison with other fungi responsible for invasive infections.
P. jirovecii is transmitted through the air between healthy individuals, who are considered to be the natural reservoir, at least transiently. In immunocompromised patients,
P. jirovecii multiplies, leading to subacute infections and acute life-threatening pneumonia, called Pneumocystis pneumonia [PCP]. PCP is caused by genotypically distinct mixtures of organisms in more than 90% of cases, reinforcing the hypothesis that there is constant inhalation of
P. jirovecii from different contacts over time, although reactivation of latent organisms from previous exposures may be possible. Detection of
P. jirovecii DNA without any symptoms or related radiological signs has been called “colonization”. This situation could be considered as the result of recent exposure to
P. jirovecii that could evolve towards PCP, raising the issue of cotrimoxazole prophylaxis for at-risk quantitative polymerase chain reaction (qPCR)-positive immunocompromised patients. The more accurate way to diagnose PCP is the use of real-time quantitative PCR, which prevents amplicon contamination and allows determination of the fungal load that is mandatory to interpret the qPCR results and manage the patient appropriately. The detection of
P. jirovecii in respiratory samples of immunocompromised patients should be considered for potential risk of developing PCP. Many challenges still need to be addressed, including a better description of transmission, characterization of organisms present at low level, and prevention of environmental exposure during immunodepression.
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Affiliation(s)
- Alexandre Alanio
- Parasitology-Mycology Laboratory, Lariboisière Saint-Louis Fernand Widal Hospitals, Assistance Publique-Hôpitaux de Paris, Paris, France.,Paris-Diderot, Sorbonne Paris Cité University, Paris, France.,Molecular Mycology Unit, CNRS, Institut Pasteur, URA 3012, Paris, France
| | - Stéphane Bretagne
- Parasitology-Mycology Laboratory, Lariboisière Saint-Louis Fernand Widal Hospitals, Assistance Publique-Hôpitaux de Paris, Paris, France.,Paris-Diderot, Sorbonne Paris Cité University, Paris, France.,Molecular Mycology Unit, CNRS, Institut Pasteur, URA 3012, Paris, France
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Robin C, Alanio A, Gits-Muselli M, la Martire G, Schlemmer F, Botterel F, Angebault C, Leclerc M, Beckerich F, Redjoul R, Pautas C, Toma A, Maury S, Bretagne S, Cordonnier C. Molecular Demonstration of a Pneumocystis Outbreak in Stem Cell Transplant Patients: Evidence for Transmission in the Daycare Center. Front Microbiol 2017; 8:700. [PMID: 28484441 PMCID: PMC5401873 DOI: 10.3389/fmicb.2017.00700] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/05/2017] [Indexed: 12/24/2022] Open
Abstract
Pneumocystis jirovecii pneumonia (PCP) is a life-threatening infection in hematology. Although occasionally reported, the role of interhuman transmission of P. jirovecii in PCP, compared to that of reactivation, remains an unresolved question; the recommendation to isolate PCP patients in the hematology ward are not well evidence-based. Following an unexpected increase in the number of febrile pneumonia patients with P. jirovecii DNA detected in respiratory samples in our hematology ward, we explored 12 consecutive patients from November 2015 to May 2016. Genotyping of P jirovecii was performed using microsatellite markers. The frequency of simultaneous occupancy of these 12 patients in the same unit on the same day from 4 months prior to the first diagnosis was recorded. In three patients, the P. jirovecii genotype could not be determined because DNA was insufficient. One rare single genotype (Gt2) was found in four of the other nine, all allogeneic stem cell transplant recipients. The transmission map showed that these 4 patients had multiple opportunities to meet on the same day (median, 6.5; range, 4–10) at the daycare center. It was much less among the eight non-Gt2 patients (median, 1; range, 0–9; P = 0.048). This study, based on modern molecular technics, strongly suggests that interhuman transmission of P. jirovecii between allogeneic stem cell transplant recipients is possible. P. jirovecii DNA detected in respiratory specimens supports that isolation and respiratory precautions be recommended in such cases in the hematology ward.
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Affiliation(s)
- Christine Robin
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Henri Mondor Teaching HospitalCréteil, France.,Paris-Est Créteil UniversityCréteil, France
| | - Alexandre Alanio
- Parasitology-Mycology Laboratory, Assistance Publique-Hôpitaux de Paris, Lariboisière Saint-Louis Fernand Widal HospitalParis, France.,Paris-Diderot, Sorbonne Paris Cité UniversityParis, France.,Molecular Mycology Unit, National Reference Center of Invasive Mycosis and Antifungals, Centre National de la Recherche Scientifique, Institut Pasteur, URA3012Paris, France
| | - Maud Gits-Muselli
- Parasitology-Mycology Laboratory, Assistance Publique-Hôpitaux de Paris, Lariboisière Saint-Louis Fernand Widal HospitalParis, France.,Paris-Diderot, Sorbonne Paris Cité UniversityParis, France
| | - Giulia la Martire
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Henri Mondor Teaching HospitalCréteil, France
| | - Frédéric Schlemmer
- Paris-Est Créteil UniversityCréteil, France.,Unit of Pneumology, Intensive Care Department, Assistance Publique-Hôpitaux de Paris, Henri Mondor Teaching Hospital, DHU A-TVBCréteil, France
| | - Françoise Botterel
- Paris-Est Créteil UniversityCréteil, France.,Parasitology-Mycology Laboratory, Assistance Publique-Hôpitaux de Paris, Henri Mondor Teaching HospitalCréteil, France
| | - Cécile Angebault
- Paris-Est Créteil UniversityCréteil, France.,Parasitology-Mycology Laboratory, Assistance Publique-Hôpitaux de Paris, Henri Mondor Teaching HospitalCréteil, France
| | - Mathieu Leclerc
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Henri Mondor Teaching HospitalCréteil, France.,Paris-Est Créteil UniversityCréteil, France
| | - Florence Beckerich
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Henri Mondor Teaching HospitalCréteil, France.,Paris-Est Créteil UniversityCréteil, France
| | - Rabah Redjoul
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Henri Mondor Teaching HospitalCréteil, France.,Paris-Est Créteil UniversityCréteil, France
| | - Cécile Pautas
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Henri Mondor Teaching HospitalCréteil, France
| | - Andrea Toma
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Henri Mondor Teaching HospitalCréteil, France
| | - Sébastien Maury
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Henri Mondor Teaching HospitalCréteil, France.,Paris-Est Créteil UniversityCréteil, France
| | - Stéphane Bretagne
- Parasitology-Mycology Laboratory, Assistance Publique-Hôpitaux de Paris, Lariboisière Saint-Louis Fernand Widal HospitalParis, France.,Paris-Diderot, Sorbonne Paris Cité UniversityParis, France.,Molecular Mycology Unit, National Reference Center of Invasive Mycosis and Antifungals, Centre National de la Recherche Scientifique, Institut Pasteur, URA3012Paris, France
| | - Catherine Cordonnier
- Department of Hematology, Assistance Publique-Hôpitaux de Paris, Henri Mondor Teaching HospitalCréteil, France.,Paris-Est Créteil UniversityCréteil, France
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Wintenberger C, Maubon D, Charpentier E, Rendu J, Pavese P, Augier C, Malvezzi P, Camara B, Mallaret MR, Bouillet L, Epaulard O. Grouped Cases of Pulmonary Pneumocystosis After Solid Organ Transplantation: Advantages of Coordination by an Infectious Diseases Unit for Overall Management and Epidemiological Monitoring. Infect Control Hosp Epidemiol 2017; 38:179-85. [PMID: 27890037 DOI: 10.1017/ice.2016.274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
OBJECTIVE To determine the origin of grouped cases of Pneumocystis pneumonia in solid-organ transplant recipients at our institution. DESIGN A case series with clinical examinations, genotyping, and an epidemiological survey. SETTING A university hospital in France. PATIENTS We report 12 solid-organ transplant recipients with successive cases of Pneumocystis pneumonia that occurred over 3 years; 10 of these cases occurred in a single year. METHODS We used molecular typing of P. jirovecii strains by multilocus sequence typing and clinical epidemiological survey to determine potential dates and places of transmission. RESULTS Between May 2014 and March 2015, 10 solid-organ transplant recipients (5 kidney transplants, 4 heart transplants, and 1 lung transplant) presented with Pneumocystis pneumonia. Molecular genotyping revealed the same P. jirovecii strain in at least 6 patients. This Pneumocystis strain was not identified in control patients (ie, nontransplant patients presenting with pulmonary pneumocystosis) during this period. The epidemiological survey guided by sequencing results provided information on the probable or possible dates and places of contamination for 5 of these patients. The mobile infectious diseases unit played a coordination role in the clinical management (adaptation of the local guidelines) and epidemiological survey. CONCLUSION Our cardiac and kidney transplant units experienced grouped cases of pulmonary pneumocystosis. Genotyping and epidemiological surveying results suggested interhuman contamination, which was quickly eliminated thanks to multidisciplinary coordination. Infect Control Hosp Epidemiol 2017;38:179-185.
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Antinori S, Binda F, van den Bogaart L, Rech R, Castelli A, Galli M, Milazzo L, Corbellino M, Ridolfo AL. Comment on:Pneumocystis jiroveciipneumonia: still a concern in patients with haematological malignancies and stem cell transplant recipients. J Antimicrob Chemother 2016; 72:1264-1266. [DOI: 10.1093/jac/dkw460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Le Gal S, Robert-Gangneux F, Pépino Y, Belaz S, Damiani C, Guéguen P, Pitous M, Virmaux M, Lissillour E, Pougnet L, Guillaud-Saumur T, Toubas D, Valot S, Hennequin C, Morio F, Hasseine L, Bouchara JP, Totet A, Nevez G. A misleading false-negative result of Pneumocystis real-time PCR assay due to a rare punctual mutation: A French multicenter study. Med Mycol 2016; 55:180-184. [PMID: 27489302 DOI: 10.1093/mmy/myw051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 02/05/2016] [Accepted: 06/18/2016] [Indexed: 11/13/2022] Open
Abstract
This article describes a previously unreported mutation at position 210 (C210T) of the mitochondrial large subunit ribosomal RNA (mtLSUrRNA) gene of Pneumocystis jirovecii, which led to a false-negative result of a real-time polymerase chain reaction (PCR) assay. Since the aforementioned real-time PCR assay is widely used in France, a French multicenter study was conducted to estimate the mutation frequency and its potential impact on the routine diagnosis of Pneumocystis pneumonia (PCP). Through analysis of data obtained from eight centers, the mutation frequency was estimated at 0.28%. This low frequency should not call into question the routine use of this PCR assay. Nonetheless, the occurrence of the false-negative PCR result provides arguments for maintaining microscopic techniques combined to PCR assays to achieve PCP diagnosis.
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Affiliation(s)
- Solène Le Gal
- University of Brest, GEIHP EA 3142, Brest, France .,Laboratory of Parasitology and Mycology, Brest University Hospital, Brest, France
| | - Florence Robert-Gangneux
- University of Rennes 1, INSERM U1085, Rennes, France.,Laboratory of Parasitology and Mycology, Rennes University Hospital, Rennes, France
| | - Yann Pépino
- University of Brest, GEIHP EA 3142, Brest, France
| | - Sorya Belaz
- University of Rennes 1, INSERM U1085, Rennes, France.,Laboratory of Parasitology and Mycology, Rennes University Hospital, Rennes, France
| | - Céline Damiani
- University of Picardy-Jules Verne, EA 4285 UMR-I 01 INERIS, Amiens, France.,Department of Parasitology and Mycology, Amiens University Hospital, Amiens, France
| | - Paul Guéguen
- Laboratory of Molecular Genetics and Histocompatibility, Brest University Hospital, Brest, France.,University of Brest, INSERM 1078, Molecular Genetics and Epidemiological Genetics, SFR 148, Brest, France
| | | | | | | | | | | | - Dominique Toubas
- Parasitology and Mycology laboratory, Reims University Hospital, Reims, France
| | - Stéphane Valot
- Parasitology and Mycology laboratory, Dijon University Hospital, Dijon, France
| | - Christophe Hennequin
- Parasitology and Mycology laboratory, Saint Antoine Hospital, Assistance Publique-Hôpitaux de Paris, France
| | - Florent Morio
- Parasitology and Mycology laboratory, Nantes University Hospital, Nantes, France
| | - Lilia Hasseine
- Parasitology and Mycology laboratory, Nice University Hospital, Nice, France
| | | | - Anne Totet
- University of Picardy-Jules Verne, EA 4285 UMR-I 01 INERIS, Amiens, France.,Department of Parasitology and Mycology, Amiens University Hospital, Amiens, France
| | - Gilles Nevez
- University of Brest, GEIHP EA 3142, Brest, France .,Laboratory of Parasitology and Mycology, Brest University Hospital, Brest, France
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Alanio A, Gits-Muselli M, Calderon E, Di Cave D, Dupont D, Hamprecht A, Hauser P, Helweg-Larsen J, Kicia M, Lagrou K, Lengerova M, Matos O, Melchers W. European study on Pneumocystis jirovecii short tandem repeats genotyping reveals wide population diversity with geographic specificities. J Mycol Med 2016. [DOI: 10.1016/j.mycmed.2016.04.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Alanio A, Gits-Muselli M, Mercier-Delarue S, Dromer F, Bretagne S. Diversity of Pneumocystis jirovecii during Infection Revealed by Ultra-Deep Pyrosequencing. Front Microbiol 2016; 7:733. [PMID: 27252684 PMCID: PMC4877386 DOI: 10.3389/fmicb.2016.00733] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/02/2016] [Indexed: 01/05/2023] Open
Abstract
Pneumocystis jirovecii is an uncultivable fungal pathogen responsible for Pneumocystis pneumonia (PCP) in immunocompromised patients, the physiopathology of which is only partially understood. The diversity of the Pneumocystis strains associated with acute infection has mainly been studied by Sanger sequencing techniques precluding any identification of rare genetic events (< 20% frequency). We used next-generation sequencing to detect minority variants causing infection, and analyzed the complexity of the genomes of infection-causing P. jirovecii. Ultra-deep pyrosequencing (UDPS) of PCR amplicons of two nuclear target region [internal transcribed spacer 2 (ITS2) and dihydrofolate reductase (DHFR)] and one mitochondrial DNA target region [the mitochondrial ribosomal RNA large subunit gene (mtLSU)] was performed on 31 samples from 25 patients. UDPS revealed that almost all patients (n = 23/25, 92%) were infected with mixtures of strains. An analysis of repeated samples from six patients showed that the proportion of each variant change significantly (by up to 30%) over time on treatment in three of these patients. A comparison of mitochondrial and nuclear UDPS data revealed heteroplasmy in P. jirovecii. The recognition site for the homing endonuclease I-SceI was recovered from the mtLSU gene, whereas its two conserved motifs of the enzyme were not. This suggests that heteroplasmy may result from recombination induced by unidentified homing endonucleases. This study sheds new light on the biology of P. jirovecii during infection. PCP results from infection not with a single microorganism, but with a complex mixture of different genotypes, the proportions of which change over time due to intricate selection and reinfection mechanisms that may differ between patients, treatments, and predisposing diseases.
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Affiliation(s)
- Alexandre Alanio
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique Hôpitaux de Paris, Hôpital Saint-LouisParis, France; Université Paris Diderot, Sorbonne Paris CitéParis, France; Unité de Mycologie Moléculaire, Département de Mycologie, Centre National de Référence Mycoses Invasives et Antifongiques, Institut PasteurParis, France; Centre National de la Recherche Scientifique CNRS URA3012Paris, France
| | - Maud Gits-Muselli
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique Hôpitaux de Paris, Hôpital Saint-LouisParis, France; Université Paris Diderot, Sorbonne Paris CitéParis, France
| | - Séverine Mercier-Delarue
- Laboratoire de Microbiologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique Hôpitaux de Paris, Hôpital Saint-Louis Paris, France
| | - Françoise Dromer
- Unité de Mycologie Moléculaire, Département de Mycologie, Centre National de Référence Mycoses Invasives et Antifongiques, Institut PasteurParis, France; Centre National de la Recherche Scientifique CNRS URA3012Paris, France
| | - Stéphane Bretagne
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique Hôpitaux de Paris, Hôpital Saint-LouisParis, France; Université Paris Diderot, Sorbonne Paris CitéParis, France; Unité de Mycologie Moléculaire, Département de Mycologie, Centre National de Référence Mycoses Invasives et Antifongiques, Institut PasteurParis, France; Centre National de la Recherche Scientifique CNRS URA3012Paris, France
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27
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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: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Yiannakis E, Boswell T. Systematic review of outbreaks of Pneumocystis jirovecii pneumonia: evidence that P. jirovecii is a transmissible organism and the implications for healthcare infection control. J Hosp Infect 2016; 93:1-8. [DOI: 10.1016/j.jhin.2016.01.018] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/18/2016] [Indexed: 11/28/2022]
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Goto N, Futamura K, Okada M, Yamamoto T, Tsujita M, Hiramitsu T, Narumi S, Watarai Y. Management of Pneumocystis jirovecii Pneumonia in Kidney Transplantation to Prevent Further Outbreak. Clin Med Insights Circ Respir Pulm Med 2015; 9:81-90. [PMID: 26609250 PMCID: PMC4648609 DOI: 10.4137/ccrpm.s23317] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/11/2015] [Accepted: 08/12/2015] [Indexed: 12/19/2022]
Abstract
The outbreak of Pneumocystis jirovecii pneumonia (PJP) among kidney transplant recipients is emerging worldwide. It is important to control nosocomial PJP infection. A delay in diagnosis and treatment increases the number of reservoir patients and the number of cases of respiratory failure and death. Owing to the large number of kidney transplant recipients compared to other types of organ transplantation, there are greater opportunities for them to share the same time and space. Although the use of trimethoprim-sulfamethoxazole (TMP-SMX) as first choice in PJP prophylaxis is valuable for PJP that develops from infections by trophic forms, it cannot prevent or clear colonization, in which cysts are dominant. Colonization of P. jirovecii is cleared by macrophages. While recent immunosuppressive therapies have decreased the rate of rejection, over-suppressed macrophages caused by the higher levels of immunosuppression may decrease the eradication rate of colonization. Once a PJP cluster enters these populations, which are gathered in one place and uniformly undergoing immunosuppressive therapy for kidney transplantation, an outbreak can occur easily. Quick actions for PJP patients, other recipients, and medical staff of transplant centers are required. In future, lifelong prophylaxis may be required even in kidney transplant recipients.
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Affiliation(s)
- Norihiko Goto
- Department of Transplant Surgery, Nagoya Daini Red Cross Hospital, Nagoya, Japan
| | - Kenta Futamura
- Department of Transplant Surgery, Nagoya Daini Red Cross Hospital, Nagoya, Japan
| | - Manabu Okada
- Department of Transplant Surgery, Nagoya Daini Red Cross Hospital, Nagoya, Japan
| | - Takayuki Yamamoto
- Department of Transplant Surgery, Nagoya Daini Red Cross Hospital, Nagoya, Japan
| | - Makoto Tsujita
- Department of Transplant Surgery, Nagoya Daini Red Cross Hospital, Nagoya, Japan
| | - Takahisa Hiramitsu
- Department of Transplant Surgery, Nagoya Daini Red Cross Hospital, Nagoya, Japan
| | - Shunji Narumi
- Department of Transplant Surgery, Nagoya Daini Red Cross Hospital, Nagoya, Japan
| | - Yoshihiko Watarai
- Department of Transplant Surgery, Nagoya Daini Red Cross Hospital, Nagoya, Japan
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Wang DD, Zheng MQ, Zhang N, An CL. Investigation of Pneumocystis jirovecii colonization in patients with chronic pulmonary diseases in the People's Republic of China. Int J Chron Obstruct Pulmon Dis 2015; 10:2079-85. [PMID: 26491278 PMCID: PMC4598221 DOI: 10.2147/copd.s89666] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The detection of Pneumocystis jirovecii DNA in respiratory specimen from individuals who do not have signs or symptoms of pneumonia has been defined as colonization. The role of P. jirovecii colonization in the development or progression of various lung diseases has been reported, but little information about P. jirovecii colonization in patients is available in the People's Republic of China. OBJECTIVE To determine the prevalence of P. jirovecii colonization in patients with various pulmonary diseases, including the acute and stable stage of COPD, interstitial lung diseases, cystic fibrosis, and chronic bronchiectasis. MATERIALS AND METHODS A loop-mediated isothermal amplification (LAMP) and a conventional polymerase chain reaction (PCR) method for detecting P. jirovecii were developed. Ninety-eight HIV-negative patients who were followed-up and who had undergone bronchoscopy for diagnosis of various underlying respiratory diseases were included in the study. Sputa of these patients were analyzed with LAMP amplification of P. jirovecii gene. In addition, conventional PCR, Giemsa and Gomori's methenamine silver nitrate staining assays were applied to all specimens. RESULTS The sensitivity and specificity test showed that there was no cross-reaction with other fungi or bacteria in detecting the specific gene of P. jirovecii by LAMP, and the minimum detection limits by LAMP was 50 copies/mL. P. jirovecii DNA was detected in 62 of 98 (63.3%) sputa specimens by LAMP assay and 22.45% (22/98) by conventional PCR. However, no P. jirovecii cysts were found by Giemsa and Gomori's methenamine silver nitrate in all of gene-positive specimens. CONCLUSION The results of our study showed that prevalence of P. jirovecii colonization is particularly high in patients with chronic pulmonary diseases in the People's Republic of China, and the LAMP method is better for evaluation of the colonization of P. jirovecii in sputum specimen than conventional PCR.
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Affiliation(s)
- Dong-Dong Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Ming-Quan Zheng
- Department of Microbiology and Parasitology, College of Basic Medical Science, China Medical University, Shenyang, People's Republic of China ; Richard King Mellon Foundation Institute for Pediatric Research, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Nan Zhang
- Department of Microbiology and Parasitology, College of Basic Medical Science, China Medical University, Shenyang, People's Republic of China
| | - Chun-Li An
- Department of Microbiology and Parasitology, College of Basic Medical Science, China Medical University, Shenyang, People's Republic of China
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Mori S, Sugimoto M. Pneumocystis jirovecii Pneumonia in Rheumatoid Arthritis Patients: Risks and Prophylaxis Recommendations. Clin Med Insights Circ Respir Pulm Med 2015; 9:29-40. [PMID: 26396551 PMCID: PMC4562607 DOI: 10.4137/ccrpm.s23286] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 08/03/2015] [Accepted: 08/06/2015] [Indexed: 01/05/2023]
Abstract
Pneumocystis jirovecii infection causes fulminant interstitial pneumonia (Pneumocystis pneumonia, PCP) in patients with rheumatoid arthritis (RA) who are receiving biological and/or nonbiological antirheumatic drugs. Recently, we encountered a PCP outbreak among RA outpatients at our institution. Hospital-acquired, person-to-person transmission appears to be the most likely mode of this cluster of P. jirovecii infection. Carriage of P. jirovecii seems a time-limited phenomenon in immunocompetent hosts, but in RA patients receiving antirheumatic therapy, clearance of this organism from the lungs is delayed. Carriers among RA patients can serve as sources and reservoirs of P. jirovecii infection for other susceptible patients in outpatient facilities. Development of PCP is a matter of time in such carriers. Considering the poor survival rates of PCP cases, prophylactic antibiotics should be considered for RA patients who are scheduled to receive antirheumatic therapy. Once a new case of PCP occurs, we should take prompt action not only to treat the PCP patient but also to prevent other patients from becoming new carriers of P. jirovecii. Short-term prophylaxis with trimethoprim-sulfamethoxazole is effective in controlling P. jirovecii infection and preventing future outbreaks of PCP among RA patients.
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Affiliation(s)
- Shunsuke Mori
- Department of Rheumatology, Clinical Research Center for Rheumatic Diseases, NHO Kumamoto Saishunsou National Hospital, Kumamoto, Japan
| | - Mineharu Sugimoto
- Division of Respiratory Medicine, Department of Medicine, Social Insurance Omuta Tenryo Hospital, Fukuoka, Japan
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