1
|
Cissé OH, Ma L, Kovacs JA. Retracing the evolution of Pneumocystis species, with a focus on the human pathogen Pneumocystis jirovecii. Microbiol Mol Biol Rev 2024:e0020222. [PMID: 38587383 DOI: 10.1128/mmbr.00202-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
SUMMARYEvery human being is presumed to be infected by the fungus Pneumocystis jirovecii at least once in his or her lifetime. This fungus belongs to a large group of species that appear to exclusively infect mammals, with P. jirovecii being the only one known to cause disease in humans. The mystery of P. jirovecii origin and speciation is just beginning to unravel. Here, we provide a review of the major steps of P. jirovecii evolution. The Pneumocystis genus likely originated from soil or plant-associated organisms during the period of Cretaceous ~165 million years ago and successfully shifted to mammals. The transition coincided with a substantial loss of genes, many of which are related to the synthesis of nutrients that can be scavenged from hosts or cell wall components that could be targeted by the mammalian immune system. Following the transition, the Pneumocystis genus cospeciated with mammals. Each species specialized at infecting its own host. Host specialization is presumably built at least partially upon surface glycoproteins, whose protogene was acquired prior to the genus formation. P. jirovecii appeared at ~65 million years ago, overlapping with the emergence of the first primates. P. jirovecii and its sister species P. macacae, which infects macaques nowadays, may have had overlapping host ranges in the distant past. Clues from molecular clocks suggest that P. jirovecii did not cospeciate with humans. Molecular evidence suggests that Pneumocystis speciation involved chromosomal rearrangements and the mounting of genetic barriers that inhibit gene flow among species.
Collapse
Affiliation(s)
- Ousmane H Cissé
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Liang Ma
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
2
|
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] [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.
Collapse
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
| |
Collapse
|
3
|
Hänsel L, Schumacher J, Denis B, Hamane S, Cornely OA, Koehler P. How to diagnose and treat a non-HIV patient with Pneumocystis jirovecii pneumonia (PCP)? Clin Microbiol Infect 2023:S1198-743X(23)00186-6. [PMID: 37086781 DOI: 10.1016/j.cmi.2023.04.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/24/2023]
Abstract
BACKGROUND Pneumocystis jirovecii Pneumonia (PCP) incidence is increasing in non-HIV infected patients. In contrast to PCP in patients infected with HIV, diagnosis is often delayed, and illness is associated with an increased mortality. OBJECTIVE To provide a comprehensive review of clinical presentation, risk factors, diagnostic strategies, and treatment options of PCP in non-HIV-infected patients. SOURCES Web-based literature review on PCP for trials, meta-analyses and systematic reviews using PubMed. Restriction to English language was applied. CONTENT Common underlying conditions in non-HIV-infected patients with PCP are haematological malignancies, autoimmune and inflammatory diseases, solid organ or haematopoietic stem cell transplant and prior exposure to corticosteroids. New risk groups include patients receiving monoclonal antibodies and immunomodulating therapies. Non-HIV-infected patients with PCP present with rapid onset and progression of pneumonia, increased duration of hospitalization and a significantly higher mortality rate than patients infected with HIV. PCP is diagnosed by a combination of clinical symptoms, radiological and mycological features. Immunofluorescence microscopy from bronchoalveolar lavage (BAL) or PCR testing CT imaging and evaluation of the clinical presentation are required. The established treatment regime consists of trimethoprim and sulfamethoxazole. IMPLICATIONS While the number of patients immunosuppressed for other causes than HIV is increasing, a simultaneous rise in PCP incidence is observed. In the group of non-HIV-infected patients, a rapid onset of symptoms, a more complex course, and a higher mortality rate are recorded. Therefore, time to diagnosis must be as short as possible to initiate effective therapy promptly. This review aims to raise awareness of PCP in an increasingly affected at-risk group and provide clinicians with a practical guide for efficient diagnosis and targeted therapy. Furthermore, it intends to display current inadequacies in research on the topic of PCP.
Collapse
Affiliation(s)
- Luise Hänsel
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Cologne, Germany
| | - Jana Schumacher
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Cologne, Germany
| | - Blandine Denis
- Department of infectious diseases, Saint Louis and Lariboisière Hospitals, APHP, Paris, France, Excellence Centre for Medical Mycology (ECMM), Paris, France
| | - Samia Hamane
- Department of infectious diseases, Saint Louis and Lariboisière Hospitals, APHP, Paris, France, Excellence Centre for Medical Mycology (ECMM), Paris, France
| | - Oliver A Cornely
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Clinical Trials Centre Cologne (ZKS Köln), Cologne, Germany
| | - Philipp Koehler
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Cologne, Germany.
| |
Collapse
|
4
|
Analysis of Pneumocystis Transcription Factor Evolution and Implications for Biology and Lifestyle. mBio 2023; 14:e0271122. [PMID: 36651897 PMCID: PMC9973273 DOI: 10.1128/mbio.02711-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Pneumocystis jirovecii kills hundreds of thousands of immunocompromised patients each year. Yet many aspects of the biology of this obligate pathogen remain obscure because it is not possible to culture the fungus in vitro independently of its host. Consequently, our understanding of Pneumocystis pathobiology is heavily reliant upon bioinformatic inferences. We have exploited a powerful combination of genomic and phylogenetic approaches to examine the evolution of transcription factors in Pneumocystis species. We selected protein families (Pfam families) that correspond to transcriptional regulators and used bioinformatic approaches to compare these families in the seven Pneumocystis species that have been sequenced to date with those from other yeasts, other human and plant pathogens, and other obligate parasites. Some Pfam families of transcription factors have undergone significant reduction during their evolution in the Pneumocystis genus, and other Pfam families have been lost or appear to be in the process of being lost. Meanwhile, other transcription factor families have been retained in Pneumocystis species, and some even appear to have undergone expansion. On this basis, Pneumocystis species seem to have retained transcriptional regulators that control chromosome maintenance, ribosomal gene regulation, RNA processing and modification, and respiration. Meanwhile, regulators that promote the assimilation of alternative carbon sources, amino acid, lipid, and sterol biosynthesis, and iron sensing and homeostasis appear to have been lost. Our analyses of transcription factor retention, loss, and gain provide important insights into the biology and lifestyle of Pneumocystis. IMPORTANCE Pneumocystis jirovecii is a major fungal pathogen of humans that infects healthy individuals, colonizing the lungs of infants. In immunocompromised and transplant patients, this fungus causes life-threatening pneumonia, and these Pneumocystis infections remain among the most common and serious infections in HIV/AIDS patients. Yet we remain remarkably ignorant about the biology and epidemiology of Pneumocystis due to the inability to culture this fungus in vitro. Our analyses of transcription factor retentions, losses, and gains in sequenced Pneumocystis species provide valuable new views of their specialized biology, suggesting the retention of many metabolic and stress regulators and the loss of others that are essential in free-living fungi. Given the lack of in vitro culture methods for Pneumocystis, this powerful bioinformatic approach has advanced our understanding of the lifestyle of P. jirovecii and the nature of its dependence on the host for survival.
Collapse
|
5
|
Alsayed AR, Al-Dulaimi A, Alkhatib M, Al Maqbali M, Al-Najjar MAA, Al-Rshaidat MMD. A comprehensive clinical guide for Pneumocystis jirovecii pneumonia: a missing therapeutic target in HIV-uninfected patients. Expert Rev Respir Med 2022; 16:1167-1190. [PMID: 36440485 DOI: 10.1080/17476348.2022.2152332] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Pneumocystis jirovecii is an opportunistic, human-specific fungus that causes Pneumocystis pneumonia (PCP). PCP symptoms are nonspecific. A patient with P. jirovecii and another lung infection faces a diagnostic challenge. It may be difficult to determine which of these agents is responsible for the clinical symptoms, preventing effective treatment. Diagnostic and treatment efforts have been made more difficult by the rising frequency with which coronavirus 2019 (COVID-19) and PCP co-occur. AREAS COVERED Herein, we provide a comprehensive review of clinical and pharmacological recommendations along with a literature review of PCP in immunocompromised patients focusing on HIV-uninfected patients. EXPERT OPINION PCP may be masked by identifying co-existing pathogens that are not necessarily responsible for the observed infection. Patients with severe form COVID-19 should be examined for underlying immunodeficiency, and co-infections must be considered as co-infection with P. jirovecii may worsen COVID-19's severity and fatality. PCP should be investigated in patients with PCP risk factors who come with pneumonia and suggestive radiographic symptoms but have not previously received PCP prophylaxis. PCP prophylaxis should be explored in individuals with various conditions that impair the immune system, depending on their PCP risk.
Collapse
Affiliation(s)
- Ahmad R Alsayed
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman, Jordan
| | - Abdullah Al-Dulaimi
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman, Jordan
| | - Mohammad Alkhatib
- Department of Experimental Medicine, University of Rome "Tor Vergata", Roma, Italy
| | - Mohammed Al Maqbali
- Department of Nursing Midwifery and Health, Northumbria University, Newcastle-Upon-Tyne, UK
| | - Mohammad A A Al-Najjar
- Department of Pharmaceutical Sciences and Pharmaceutics, Applied Science Private University, Amman, Kingdom of Jordan
| | - Mamoon M D Al-Rshaidat
- Laboratory for Molecular and Microbial Ecology (LaMME), Department of Biological Sciences, School of Sciences, The University of Jordan, Amman, Jordan
| |
Collapse
|
6
|
Babb-Biernacki SJ, Esselstyn JA, Doyle VP. Predicting Species Boundaries and Assessing Undescribed Diversity in Pneumocystis, an Obligate Lung Symbiont. J Fungi (Basel) 2022; 8:jof8080799. [PMID: 36012788 PMCID: PMC9409666 DOI: 10.3390/jof8080799] [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: 05/23/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
Far more biodiversity exists in Fungi than has been described, or could be described in several lifetimes, given current rates of species discovery. Although this problem is widespread taxonomically, our knowledge of animal-associated fungi is especially lacking. Fungi in the genus Pneumocystis are obligate inhabitants of mammal lungs, and they have been detected in a phylogenetically diverse array of species representing many major mammal lineages. The hypothesis that Pneumocystis cospeciate with their mammalian hosts suggests that thousands of Pneumocystis species may exist, potentially equal to the number of mammal species. However, only six species have been described, and the true correspondence of Pneumocystis diversity to host species boundaries is unclear. Here, we use molecular species delimitation to estimate the boundaries of Pneumocystis species sampled from 55 mammal species representing eight orders. Our results suggest that Pneumocystis species often colonize several closely related mammals, especially those in the same genus. Using the newly estimated ratio of fungal to host diversity, we estimate ≈4600 to 6250 Pneumocystis species inhabit the 6495 currently recognized extant mammal species. Additionally, we review the literature and find that only 240 (~3.7%) mammal species have been screened for Pneumocystis, and many detected Pneumocystis lineages are not represented by any genetic data. Although crude, our findings challenge the dominant perspective of strict specificity of Pneumocystis to their mammal hosts and highlight an abundance of undescribed diversity.
Collapse
Affiliation(s)
- Spenser J. Babb-Biernacki
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
- Correspondence:
| | - Jacob A. Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Vinson P. Doyle
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA 70809, USA;
| |
Collapse
|
7
|
Evaluation of Metagenomic and Targeted Next-Generation Sequencing Workflows for Detection of Respiratory Pathogens from Bronchoalveolar Lavage Fluid Specimens. J Clin Microbiol 2022; 60:e0052622. [PMID: 35695488 PMCID: PMC9297812 DOI: 10.1128/jcm.00526-22] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS) workflows applied to bronchoalveolar lavage (BAL) fluid specimens could enhance the detection of respiratory pathogens, although optimal approaches are not defined. This study evaluated the performance of the Respiratory Pathogen ID/AMR (RPIP) kit (Illumina, Inc.) with automated Explify bioinformatic analysis (IDbyDNA, Inc.), a targeted NGS workflow enriching specific pathogen sequences and antimicrobial resistance (AMR) markers, and a complementary untargeted metagenomic workflow with in-house bioinformatic analysis. Compared to a composite clinical standard consisting of provider-ordered microbiology testing, chart review, and orthogonal testing, both workflows demonstrated similar performances. The overall agreement for the RPIP targeted workflow was 65.6% (95% confidence interval, 59.2 to 71.5%), with a positive percent agreement (PPA) of 45.9% (36.8 to 55.2%) and a negative percent agreement (NPA) of 85.7% (78.1 to 91.5%). The overall accuracy for the metagenomic workflow was 67.1% (60.9 to 72.9%), with a PPA of 56.6% (47.3 to 65.5%) and an NPA of 77.2% (68.9 to 84.1%). The approaches revealed pathogens undetected by provider-ordered testing (Ureaplasma parvum, Tropheryma whipplei, severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2], rhinovirus, and cytomegalovirus [CMV]), although not all pathogens detected by provider-ordered testing were identified by the NGS workflows. The RPIP targeted workflow required more time and reagents for library preparation but streamlined bioinformatic analysis, whereas the metagenomic assay was less demanding technically but required complex bioinformatic analysis. The results from both workflows were interpreted utilizing standardized criteria, which is necessary to avoid reporting nonpathogenic organisms. The RPIP targeted workflow identified AMR markers associated with phenotypic resistance in some bacteria but incorrectly identified blaOXA genes in Pseudomonas aeruginosa as being associated with carbapenem resistance. These workflows could serve as adjunctive testing with, but not as a replacement for, standard microbiology techniques.
Collapse
|
8
|
Vera C, Rueda ZV. Transmission and Colonization of Pneumocystis jirovecii. J Fungi (Basel) 2021; 7:jof7110979. [PMID: 34829266 PMCID: PMC8622989 DOI: 10.3390/jof7110979] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 11/17/2022] Open
Abstract
Pneumocystis spp. was discovered in 1909 and was classified as a fungus in 1988. The species that infects humans is called P. jirovecii and important characteristics of its genome have recently been discovered. Important advances have been made to understand P. jirovecii, including aspects of its biology, evolution, lifecycle, and pathogenesis; it is now considered that the main route of transmission is airborne and that the infectious form is the asci (cyst), but it is unclear whether there is transmission by direct contact or droplet spread. On the other hand, P. jirovecii has been detected in respiratory secretions of hosts without causing disease, which has been termed asymptomatic carrier status or colonization (frequency in immunocompetent patients: 0–65%, pregnancy: 15.5%, children: 0–100%, HIV-positive patients: 20–69%, cystic fibrosis: 1–22%, and COPD: 16–55%). This article briefly describes the history of its discovery and the nomenclature of Pneumocystis spp., recently uncovered characteristics of its genome, and what research has been done on the transmission and colonization of P. jirovecii. Based on the literature, the authors of this review propose a hypothetical natural history of P. jirovecii infection in humans.
Collapse
Affiliation(s)
- Cristian Vera
- Grupo de Investigación en Salud Pública, Research Department, Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín 050031, Colombia
- Correspondence:
| | - Zulma Vanessa Rueda
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg RT3, Colombia;
| |
Collapse
|
9
|
Cushion MT, Ashbaugh A. The Long-Acting Echinocandin, Rezafungin, Prevents Pneumocystis Pneumonia and Eliminates Pneumocystis from the Lungs in Prophylaxis and Murine Treatment Models. J Fungi (Basel) 2021; 7:jof7090747. [PMID: 34575785 PMCID: PMC8468546 DOI: 10.3390/jof7090747] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 01/20/2023] Open
Abstract
Rezafungin is a novel echinocandin in Phase 3 development for prevention of invasive fungal disease caused by Candida spp., Aspergillus spp. and Pneumocystis jirovecii in blood and marrow transplantation patients. For such patients, standard antifungal prophylaxis currently comprises an azole for Candida and Aspergillus plus trimethoprim-sulfamethoxazole (TMP-SMX) for Pneumocystis pneumonia (PCP) despite drug-drug-interactions and intolerability that may limit their use, thus, alternatives are desirable. Rezafungin demonstrates a favorable safety profile and pharmacokinetic properties that allow for once-weekly dosing in addition, to antifungal activity against these predominant pathogens. Herein, the in vivo effects of rezafungin against Pneumocystis murina pneumonia were evaluated in immunosuppressed mouse models of prophylaxis and treatment using microscopy and qPCR assessments. In the prophylaxis model, immunosuppressed mice inoculated with P. murina were administered TMP-SMX (50/250 mg/kg 1×/week or 3×/week), caspofungin (5 mg/kg 3×/week), rezafungin (20 mg/kg, 1×/week or 3×/week; 5 mg/kg, 3×/week) intraperitoneally for 2, 4, 6 and 8 weeks, then immunosuppressed for an additional 6 weeks. Rezafungin administered for 4 weeks prevented P. murina from developing infection after rezafungin was discontinued. In the treatment model, immunosuppressed mice with P. murina pneumonia were treated with rezafungin 20 mg/kg 3×/week intraperitoneally for 2, 4, 6 and 8 weeks. Treatment with rezafungin for 8 weeks resulted in elimination of P. murina. Collectively, these studies showed that rezafungin could both prevent infection and eliminate P. murina from the lungs of mice. These findings support the obligate role of sexual reproduction for survival and growth of Pneumocystis spp. and warrant further investigation for treatment of P. jirovecii pneumonia in humans.
Collapse
Affiliation(s)
- Melanie T. Cushion
- Department of Internal Medicine, Division of Infectious Diseases, College of Medicine, University of Cincinnati, Cincinnati, OH 45221, USA;
- Cincinnati VAMC, Medical Research Service, Cincinnati, OH 45220, USA
- Correspondence:
| | - Alan Ashbaugh
- Department of Internal Medicine, Division of Infectious Diseases, College of Medicine, University of Cincinnati, Cincinnati, OH 45221, USA;
- Cincinnati VAMC, Medical Research Service, Cincinnati, OH 45220, USA
| |
Collapse
|
10
|
Schmid-Siegert E, Richard S, Luraschi A, Mühlethaler K, Pagni M, Hauser PM. Expression Pattern of the Pneumocystis jirovecii Major Surface Glycoprotein Superfamily in Patients with Pneumonia. J Infect Dis 2021; 223:310-318. [PMID: 32561915 DOI: 10.1093/infdis/jiaa342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/11/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The human pathogen Pneumocystis jirovecii harbors 6 families of major surface glycoproteins (MSGs) encoded by a single gene superfamily. MSGs are presumably responsible for antigenic variation and adhesion to host cells. The genomic organization suggests that a single member of family I is expressed at a given time per cell, whereas members of the other families are simultaneously expressed. METHODS We analyzed RNA sequences expressed in several clinical samples, using specific weighted profiles for sorting of reads and calling of single-nucleotide variants to estimate the diversity of the expressed genes. RESULTS A number of different isoforms of at least 4 MSG families were expressed simultaneously, including isoforms of family I, for which confirmation was obtained in the wet laboratory. CONCLUSION These observations suggest that every single P. jirovecii population is made of individual cells with distinct surface properties. Our results enhance our understanding of the unique antigenic variation system and cell surface structure of P. jirovecii.
Collapse
Affiliation(s)
| | - Sophie Richard
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Amanda Luraschi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Konrad Mühlethaler
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Marco Pagni
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Philippe M Hauser
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
11
|
Cushion MT, Tisdale-Macioce N, Sayson SG, Porollo A. The Persistent Challenge of Pneumocystis Growth Outside the Mammalian Lung: Past and Future Approaches. Front Microbiol 2021; 12:681474. [PMID: 34093506 PMCID: PMC8174303 DOI: 10.3389/fmicb.2021.681474] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022] Open
Abstract
The pathogenic fungi in the genus, Pneumocystis, have eluded attempts to continuously grow them in an ex vivo cultivation system. New data from transcriptomic and genomic sequencing studies have identified a myriad of absent metabolic pathways, helping to define their host obligate nature. These nutrients, factors, and co-factors are acquired from their mammalian host and provide clues to further supplementation of existing media formulations. Likewise, a new appreciation of the pivotal role for the sexual cycle in the survival and dissemination of the infection suggests that Pneumocystis species are obligated to undergo mating and sexual reproduction in their life cycle with a questionable role for an asexual cycle. The lack of ascus formation in any previous cultivation attempts may explain the failure to identify a sustainable system. Many characteristics of these ascomycetes suggest a biotrophic existence within the lungs of the mammalian hosts. In the present review, previous attempts at growing these fungi ex vivo are summarized. The significance of their life cycle is considered, and a list of potential supplements based on the genomic and transcriptomic studies is presented. State of the art technologies such as metabolomics, organoids, lung-on-a chip, and air lift cultures are discussed as potential growth systems.
Collapse
Affiliation(s)
- Melanie T Cushion
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Medical Research Service, Cincinnati Veterans Affairs Medical Center, Cincinnati, OH, United States
| | - Nikeya Tisdale-Macioce
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Medical Research Service, Cincinnati Veterans Affairs Medical Center, Cincinnati, OH, United States
| | - Steven G Sayson
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Medical Research Service, Cincinnati Veterans Affairs Medical Center, Cincinnati, OH, United States
| | - Aleksey Porollo
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| |
Collapse
|
12
|
Nevez G, Totet A, Matos O, Calderon EJ, Miller RF, Le Gal S. It is still PCP that can stand for Pneumocystis pneumonia: Appeal for generalized use of only one acronym. Med Mycol 2021; 59:842-844. [PMID: 34003930 DOI: 10.1093/mmy/myab024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/08/2021] [Accepted: 04/12/2021] [Indexed: 11/14/2022] Open
Abstract
Twenty-years ago, considering the host specificity of Pneumocystis species, the human-derived Pneumocystis, Pneumocystis carinii formae specialis hominis, was renamed Pneumocystis jirovecii. Pneumocystis carinii formae specialis carinii was finally renamed Pneumocystis carinii and kept for the species derived from Rattus norvegicus. P. jirovecii is now widely used by most authors. The PCP acronym that initially referred to "Pneumocystis cariniipneumonia" was contemporaneously redefined to stand for Pneumocystispneumonia in order to avoid changing the acronym of the name of the disease that clinicians have used for several decades. Using analysis of multidata bases on PubMed, we have noted a recent acceleration in the use of PJP for Pneumocystis jiroveciipneumonia, which may be grammatically correct but not in accordance with retaining PCP, which was proposed in the early 2000s. Through this reminder, in order to standardize the literature on P. jirovecii, we plead for the use of only one acronym, PCP. LAY SUMMARY Through this reminder on Pneumocystis nomenclature, we plead for the use of only one acronym, PCP, the retention of which was proposed in the early 2000s, and which currently stands for Pneumocystispneumonia.
Collapse
Affiliation(s)
- Gilles Nevez
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, Brest, France.,Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP), Université d'Angers, Université de Brest, France
| | - Anne Totet
- Parasitologie et Mycologie, CHU Amiens-Picardie, Amiens, France.,Agents Infectieux, Résistance et chimiothérapie (Laboratoire AGIR, UR 4294), Université de Picardie Jules Verne, Amiens, France
| | - 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.,Instituto de Saúde Ambiental, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Enrique J Calderon
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, and Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Hospital Universitario Virgen del Rocío, Seville, Spain
| | - Robert F Miller
- Institute for Global Health, University College London, London, UK.,Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Solène Le Gal
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, Brest, France.,Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP), Université d'Angers, Université de Brest, France
| |
Collapse
|
13
|
Sürgeç E, Can H, Döşkaya M, Karakavuk M, Atalay Şahar E, Değirmenci Döşkaya A, Pullukçu H, Taşbakan M, Sezai Taşbakan M, Akyol D, Yargucu Zihni F, Ün C, Yüksel Gürüz A, Demir S. Genotyping of Pneumocystis jirovecii isolates obtained from clinical samples by multilocus sequencing: a molecular epidemiology study conducted in Turkey. Arch Microbiol 2020; 202:1647-1652. [PMID: 32274557 DOI: 10.1007/s00203-020-01874-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/20/2020] [Accepted: 04/01/2020] [Indexed: 12/12/2022]
Abstract
Pneumocystis jirovecii is an opportunistic respiratory pathogen causing Pneumocystis pneumonia (PcP) in immunocompromised patients. The aim of this study was to investigate the genetic diversity of P. jirovecii isolates (n: 84) obtained from PcP patients using multilocus sequencing method based on mt26S, SOD, and CYB loci. Among the 84 clinical samples that were positive for P. jirovecii DNA, 31 (36.90%) of them were genotyped using at least one locus. Of the 31 clinical samples, 26 of them were successfully genotyped using all loci whereas three samples were genotyped using either mt26S/CYB loci or mt26S/SOD loci. Additionally, there were two more clinical samples that were genotyped using CYB or SOD locus. Using mt26S locus, genotypes 2, 3, 7, and 8 were detected. Frequencies of genotype 7 and 8 were higher and both of them were found in 11 (n: 29; 37.93%) clinical samples. Using SOD locus, SOD 1, 2, and 4 genotypes were detected. SOD 1 was the predominant genotype (20/28; 71.42%). During the analyses of CYB locus, CYB 1, 2, 5, 6, and 7 as well as a new CYB genotype were detected. CYB 1 (16/29; 55.17%) and 2 (10/29; 34.48%) were the predominant genotypes. Overall, according to the multilocus sequencing results E, F, M, N, P, and V multilocus genotypes were detected among the PcP patients. In addition, SOD 1 was the predominant genotype and CYB had a more polymorphic locus.
Collapse
Affiliation(s)
- Ecem Sürgeç
- Faculty of Science, Department of Biology, Zoology Section, Ege University, Izmir, Turkey
| | - Hüseyin Can
- Faculty of Science, Department of Biology, Molecular Biology Section, Ege University, Izmir, Turkey
| | - Mert Döşkaya
- Faculty of Medicine, Department of Parasitology, Ege University, Izmir, Turkey
| | | | - Esra Atalay Şahar
- Faculty of Engineering, Department of Biotechnology, Ege University, Izmir, Turkey
| | - Aysu Değirmenci Döşkaya
- Faculty of Medicine, Department of Parasitology, Ege University, Izmir, Turkey.,Faculty of Medicine, Blood Bank, Ege University, Izmir, Turkey
| | - Hüsnü Pullukçu
- Faculty of Medicine, Department of Infectious Diseases, Ege University, Izmir, Turkey
| | - Meltem Taşbakan
- Faculty of Medicine, Department of Infectious Diseases, Ege University, Izmir, Turkey
| | | | - Deniz Akyol
- Faculty of Medicine, Department of Infectious Diseases, Ege University, Izmir, Turkey
| | - Figen Yargucu Zihni
- Faculty of Medicine, Department of Rheumatology, Ege University, Izmir, Turkey
| | - Cemal Ün
- Faculty of Science, Department of Biology, Molecular Biology Section, Ege University, Izmir, Turkey
| | - Adnan Yüksel Gürüz
- Faculty of Medicine, Department of Parasitology, Ege University, Izmir, Turkey
| | - Samiye Demir
- Faculty of Science, Department of Biology, Zoology Section, Ege University, Izmir, Turkey.
| |
Collapse
|
14
|
Govender I, Maphasha OM, Rangiah S, Steyn C. An overview of Pneumocystis jirovecii pneumonia for the African generalist practitioner. Afr Health Sci 2019; 19:3200-3207. [PMID: 32127897 PMCID: PMC7040323 DOI: 10.4314/ahs.v19i4.43] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Introduction Pneumocystis jirovecii is the causative organism of Pneumocystis pneumonia (PCP) in humans, which is more common among immunocompromised patients. Classically patients present with fever, non-productive cough, and dyspnoea. In the HIV-infected individuals the symptoms may be subtle at first, but gradually progress over several weeks. In the HIV-uninfected patient, however, the duration of symptoms is shorter and more severe, mainly due to the increased inflammatory response of the HIV-uninfected patient. Methods This article focuses on the diagnostic methods and then the management and prophylaxis principles of PCP by reviewing the best current practices and guidelines in Africa. Conclusion This overview is presented by clinicians who have experience with PCP and is directed mainly at first-line healthcare providers.
Collapse
Affiliation(s)
- I Govender
- Department of Family Medicine, Sefako Makgatho Health Sciences University. P.O. BOX 222, MEDUNSA 0204
| | - OM Maphasha
- Department of Family Medicine, Sefako Makgatho Health Sciences University. P.O. BOX 222, MEDUNSA 0204
| | - S Rangiah
- Department of Family Medicine, University of Kwa Zulu Natal
| | - C Steyn
- Department of Family Medicine, Sefako Makgatho Health Sciences University. P.O. BOX 222, MEDUNSA 0204
| |
Collapse
|
15
|
Ma L, Cissé OH, Kovacs JA. A Molecular Window into the Biology and Epidemiology of Pneumocystis spp. Clin Microbiol Rev 2018; 31:e00009-18. [PMID: 29899010 PMCID: PMC6056843 DOI: 10.1128/cmr.00009-18] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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.
Collapse
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
| |
Collapse
|
16
|
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
| |
Collapse
|
17
|
Lee N, Lawrence D, Patel B, Ledot S. HIV-related Pneumocystis jirovecii pneumonia managed with caspofungin and veno-venous extracorporeal membrane oxygenation rescue therapy. BMJ Case Rep 2017; 2017:bcr-2017-221214. [PMID: 28978595 PMCID: PMC5652506 DOI: 10.1136/bcr-2017-221214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Patients with pneumocystis pneumonia have a risk of progressing to acute respiratory failure necessitating admission to intensive care. The case described is of a patient with a newly diagnosed HIV infection presenting with pneumocystis pneumonia. Despite initiating the appropriate pharmacological treatment the patient’s clinical condition deteriorated, and required both rescue pharmacological therapy with echinocandins as well as respiratory support with extracorporeal membrane oxygenation therapy. The patient recovered well on ventilator and circulatory support despite a long weaning process complicated by sequelae common to pneumocystis pneumonia. Following initialisation of antiretroviral therapy and step-down from an intensive care setting, the patient required further prolonged hospital stay for rehabilitation and mental health support before being discharged. This case reviews the novel pharmacological therapies and respiratory support strategies used in cases of pneumocystis pneumonia, including the clinical and psychological sequelae that may follow.
Collapse
Affiliation(s)
- Nathaniel Lee
- Adult Intensive Care Unit, Royal Brompton and Harefield NHS Foundation Trust, Anaesthesia and Critical Care, London, UK
| | - David Lawrence
- The Lawson Unit, Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
| | - Brijesh Patel
- Adult Intensive Care Unit, Royal Brompton and Harefield NHS Foundation Trust, Anaesthesia and Critical Care, London, UK.,Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Stephane Ledot
- Adult Intensive Care Unit, Royal Brompton and Harefield NHS Foundation Trust, Anaesthesia and Critical Care, London, UK
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Sugiyama J, Hosaka K, Suh SO. Early diverging Ascomycota: phylogenetic divergence and related evolutionary enigmas. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832628] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Junta Sugiyama
- Tokyo Office, TechnoSuruga Co. Ltd., Ogawamachi Kita Building 4F, Kanda Ogawamachi 1-8-3, Chiyoda-ku, Tokyo 101-0052, Japan
| | - Kentaro Hosaka
- Department of Botany, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605-2496
| | - Sung-Oui Suh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| |
Collapse
|
20
|
Development and validation of a Pneumocystis jirovecii real-time polymerase chain reaction assay for diagnosis of Pneumocystis pneumonia. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2015; 26:263-7. [PMID: 26600815 PMCID: PMC4644010 DOI: 10.1155/2015/138787] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BACKGROUND Pneumocystis jirovecii (PJ), a pathogenic fungus, causes severe interstitial Pneumocystis pneumonia (PCP) among immunocompromised patients. A laboratory-developed real-time polyermase chain reaction (PCR) assay was validated for PJ detection to improve diagnosis of PCP. METHODS Forty stored bronchoalveolar lavage (BAL) samples (20 known PJ positive [PJ+] and 20 known PJ negative [PJ-]) were initially tested using the molecular assay. Ninety-two sequentially collected BAL samples were then analyzed using an immunofluorescence assay (IFA) and secondarily tested using the PJ real-time PCR assay. Discrepant results were resolved by retesting BAL samples using another real-time PCR assay with a different target. PJ real-time PCR assay performance was compared with the existing gold standard (ie, IFA) and a modified gold standard, in which a true positive was defined as a sample that tested positive in two of three methods in a patient suspected to have PCP. RESULTS Ninety of 132 (68%) BAL fluid samples were collected from immunocompromised patients. Thirteen of 92 (14%) BALs collected were PJ+ when tested using IFA. A total of 40 BAL samples were PJ+ in the present study including: all IFA positive samples (n=13); all referred PJ+ BAL samples (n=20); and seven additional BAL samples that were IFA negative, but positive using the modified gold standard. Compared with IFA, the PJ real-time PCR had sensitivity, specificity, and positive and negative predictive values of 100%, 91%, 65% and 100%, respectively. Compared with the modified gold standard, PJ real-time PCR had a sensitivity, specificity, and positive and negative predictive values of 100%. CONCLUSION PJ real-time PCR improved detection of PJ in immunocompromised patients.
Collapse
|
21
|
Cissé OH, Pagni M, Hauser PM. Comparative genomics suggests that the human pathogenic fungus Pneumocystis jirovecii acquired obligate biotrophy through gene loss. Genome Biol Evol 2014; 6:1938-48. [PMID: 25062922 PMCID: PMC4159005 DOI: 10.1093/gbe/evu155] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Pneumocystis jirovecii is a fungal parasite that colonizes specifically humans and turns into an opportunistic pathogen in immunodeficient individuals. The fungus is able to reproduce extracellularly in host lungs without eliciting massive cellular death. The molecular mechanisms that govern this process are poorly understood, in part because of the lack of an in vitro culture system for Pneumocystis spp. In this study, we explored the origin and evolution of the putative biotrophy of P. jirovecii through comparative genomics and reconstruction of ancestral gene repertoires. We used the maximum parsimony method and genomes of related fungi of the Taphrinomycotina subphylum. Our results suggest that the last common ancestor of Pneumocystis spp. lost 2,324 genes in relation to the acquisition of obligate biotrophy. These losses may result from neutral drift and affect the biosyntheses of amino acids and thiamine, the assimilation of inorganic nitrogen and sulfur, and the catabolism of purines. In addition, P. jirovecii shows a reduced panel of lytic proteases and has lost the RNA interference machinery, which might contribute to its genome plasticity. Together with other characteristics, that is, a sex life cycle within the host, the absence of massive destruction of host cells, difficult culturing, and the lack of virulence factors, these gene losses constitute a unique combination of characteristics which are hallmarks of both obligate biotrophs and animal parasites. These findings suggest that Pneumocystis spp. should be considered as the first described obligate biotrophs of animals, whose evolution has been marked by gene losses.
Collapse
Affiliation(s)
- Ousmane H Cissé
- Institute of Microbiology, Centre Hospitalier Universitaire Vaudois and University of Lausanne, SwitzerlandVital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, SwitzerlandPresent address: Department of Plant Pathology & Microbiology and Institute for Integrative Genome Biology, University of California, Riverside, CA
| | - Marco Pagni
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Philippe M Hauser
- Institute of Microbiology, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Switzerland
| |
Collapse
|
22
|
Walzer PD. The ecology of pneumocystis: perspectives, personal recollections, and future research opportunities. J Eukaryot Microbiol 2013; 60:634-45. [PMID: 24001365 DOI: 10.1111/jeu.12072] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 07/17/2013] [Accepted: 07/17/2013] [Indexed: 11/28/2022]
Abstract
I am honored to receive the second Lifetime Achievement Award by International Workshops on Opportunistic Protists and to give this lecture. My research involves Pneumocystis, an opportunistic pulmonary fungus that is a major cause of pneumonia ("PcP") in the immunocompromised host. I decided to focus on Pneumocystis ecology here because it has not attracted much interest. Pneumocystis infection is acquired by inhalation, and the cyst stage appears to be the infective form. Several fungal lung infections, such as coccidiomycosis, are not communicable, but occur by inhaling < 5 μm spores from environmental sources (buildings, parks), and can be affected by environmental factors. PcP risk factors include environmental constituents (temperature, humidity, SO2 , CO) and outdoor activities (camping). Clusters of PcP have occurred, but no environmental source has been found. Pneumocystis is communicable and outbreaks of PcP, especially in renal transplant patients, are an ongoing problem. Recent evidence suggests that most viable Pneumocystis organisms detected in the air are confined to a patient's room. Further efforts are needed to define the risk of Pneumocystis transmission in health care facilities; to develop more robust preventive measures; and to characterize the effects of climatological and air pollutant factors on Pneumocystis transmission in animal models similar to those used for respiratory viruses.
Collapse
Affiliation(s)
- Peter D Walzer
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267-0560; Research Service, Veterans Affairs Medical Center, Cincinnati, Ohio, 45220
| |
Collapse
|
23
|
Le Gal S, Rouille A, Gueguen P, Virmaux M, Berthou C, Guillerm G, Couturaud F, Le Meur Y, Damiani C, Totet A, Nevez G. Pneumocystis jirovecii haplotypes at the internal transcribed spacers of the rRNA operon in French HIV-negative patients with diverse clinical presentations of Pneumocystis infections. Med Mycol 2013; 51:851-62. [PMID: 23964829 DOI: 10.3109/13693786.2013.824123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pneumocystis jirovecii, a transmissible fungus, is the causative agent of pulmonary infections. Its genomic diversity has appeared in reports from around the world but data on P. jirovecii genotypes in France are still limited. This study describes the typing of P. jirovecii isolates from 81 HIV-negative patients monitored at Brest University Hospital, Brittany, France, 40 of whom developed Pneumocystis pneumonia (PcP), and remaining 41 patients were colonized by the fungus. The isolates were assayed at the internal transcribed spacer (ITS)1 and ITS2 under improved amplification conditions to avoid in vitro ITS recombination. P. jirovecii ITS haplotypes were identified in 56/81 patients (31 PcP patients and 25 patients who were colonized) which revealed a high diversity in that 27 different haplotypes were identified. Eg was the most frequent haplotype (31/56, 55.3%), followed by Ec and Ai (5/56, 8.9% each). In contrast, Ne, usually the second most frequent haplotype in Europe and the USA, was observed in only 2/56 patients (3.6%). Mixed infections were detected in 18/56 patients (32.1%; 12 PcP patients and six who were colonized). No significant differences were observed in haplotype diversity, frequency of peculiar haplotypes, and mixed infection occurrence, between the two patient populations. The study, conducted with the largest HIV-negative patient population investigated so far, shows that ITS typing remains an efficient method for characterizing P. jirovecii among human populations, whatever their clinical presentation of Pneumocystis infections.
Collapse
|
24
|
Lobo ML, Esteves F, de Sousa B, Cardoso F, Cushion MT, Antunes F, Matos O. Therapeutic potential of caspofungin combined with trimethoprim-sulfamethoxazole for pneumocystis pneumonia: a pilot study in mice. PLoS One 2013; 8:e70619. [PMID: 23940606 PMCID: PMC3734247 DOI: 10.1371/journal.pone.0070619] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 06/20/2013] [Indexed: 11/18/2022] Open
Abstract
Pneumocystis pneumonia (PcP) is a major cause of mortality and morbidity in immunocompromised patients. There are limited alternative therapeutic choices to trimethoprim-sulfamethoxazole (TMP-SMX) which is the standard first line therapy/prophylaxis for PcP. The efficacy of low doses of caspofungin and caspofungin in association with TMP-SMX standard-prophylactic dose was evaluated in an experimental model of Pneumocystis. Susceptibility of Pneumocystis spp. to low doses of caspofungin and caspofungin/TMP-SMX was evaluated in Balb/c immunosuppressed mice, infected intranasally with P. murina. Caspofungin was administered once daily at 0.1 mg/kg, 0.05 mg/kg, and 0.001 mg/kg and TMP-SMX was administered by oral gavage (12.25 mg/62.5 mg/day), for 21 days. Efficacy was calculated based on the reduction in organism burden determined through quantitative fluorescent-based real-time PCR (qPCR). Serum β-1,3-D-glucan was measured as an additional marker of infection. The present data showed that caspofungin demonstrated anti-Pneumomocystis effect. However, the doses administrated were too low to achieve Pneumocystis eradication, which suggests that echinocandin treatment should not be administrated as mono-therapy. After 21 days of treatment, P. murina was not detected in the lungs of mice with either TMP-SMX or caspofungin/TMP-SMX. The results showed that, even at the lowest concentrations tested, the efficacy of caspofungin in association with TMP-SMX was higher than the efficacy of either drug used alone. The administration of caspofungin/TMP-SMX was at least 1.4 times more effective against P. murina infection than TMP-SMX used alone. The most promising result was achieved with the combination of caspofungin 0.05 mg/kg/day with TMP-SMX 12.5 mg–62.5 mg/day, which reduced the parasite burden to undetectable levels immediately at the 14th day of treatment, showing a highly marked anti-Pneumomocystis effect. These data suggest that the administration of low doses of caspofungin in combination with low doses of TMP-SMX may provide an improved treatment protocol for Pneumocystis infection clearance.
Collapse
Affiliation(s)
- Maria Luísa Lobo
- Unidade de Parasitologia Médica, Grupo de Protozoários Oportunistas/VIH e Outros Protozoários, CMDT, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Francisco Esteves
- Unidade de Parasitologia Médica, Grupo de Protozoários Oportunistas/VIH e Outros Protozoários, CMDT, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Bruno de Sousa
- Faculdade de Psicologia e Ciências da Educação, Universidade de Coimbra, CMDT, Coimbra, Portugal
| | - Fernando Cardoso
- Unidade de Parasitologia Médica, Grupo de Protozoários Oportunistas/VIH e Outros Protozoários, CMDT, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Melanie T. Cushion
- University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Francisco Antunes
- Faculdade de Medicina, Hospital de Santa Maria, Universidade de Lisboa, Lisboa, Portugal
| | - Olga Matos
- Unidade de Parasitologia Médica, Grupo de Protozoários Oportunistas/VIH e Outros Protozoários, CMDT, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
- * E-mail:
| |
Collapse
|
25
|
Ma L, Huang DW, Cuomo CA, Sykes S, Fantoni G, Das B, Sherman BT, Yang J, Huber C, Xia Y, Davey E, Kutty G, Bishop L, Sassi M, Lempicki RA, Kovacs JA. Sequencing and characterization of the complete mitochondrial genomes of three Pneumocystis species provide new insights into divergence between human and rodent Pneumocystis. FASEB J 2013; 27:1962-72. [PMID: 23392351 DOI: 10.1096/fj.12-224444] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Pneumocystis jirovecii is an important opportunistic pathogen associated with AIDS and other immunodeficient conditions. Currently, very little is known about its nuclear and mitochondrial genomes. In this study, we sequenced the complete mitochondrial genome (mtDNA) of this organism and its closely related species Pneumocystis carinii and Pneumocystis murina by a combination of sequencing technologies. Our study shows that P. carinii and P. murina mtDNA share a nearly identical number and order of genes in a linear configuration, whereas P. jirovecii has a circular mtDNA containing nearly the same set of genes but in a different order. Detailed studies of the mtDNA terminal structures of P. murina and P. carinii suggest a unique replication mechanism for linear mtDNA. Phylogenetic analysis supports a close association of Pneumocystis species with Taphrina, Saitoella, and Schizosaccharomyces, and divergence within Pneumocystis species, with P. murina and P. carinii being more closely related to each other than either is to P. jirovecii. Comparative analysis of four complete P. jirovecii mtDNA sequences in this study and previously reported mtDNA sequences for diagnosing and genotyping suggests that the current diagnostic and typing methods can be improved using the complete mtDNA data. The availability of the complete P. jirovecii mtDNA also opens the possibility of identifying new therapeutic targets.
Collapse
Affiliation(s)
- Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, 10 Center Dr., Bethesda, MD 20892, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Esteves F, Gaspar J, de Sousa B, Antunes F, Mansinho K, Matos O. Pneumocystis jirovecii multilocus genotyping in pooled DNA samples: a new approach for clinical and epidemiological studies. Clin Microbiol Infect 2012; 18:E177-84. [DOI: 10.1111/j.1469-0691.2012.03828.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
27
|
In silico ligand-based pharmacophore model generation for the identification of novel Pneumocystis carinii DHFR inhibitors. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0082-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
28
|
Hof H. Pneumocystis jirovecii: a peculiar fungus posing particular problems for therapy and prophylaxis. Mycoses 2012. [DOI: 10.1111/j.1439-0507.2011.02159.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
29
|
Henderson KS, Dole V, Parker NJ, Momtsios P, Banu L, Brouillette R, Simon MA, Albers TM, Pritchett-Corning KR, Clifford CB, Shek WR. Pneumocystis carinii causes a distinctive interstitial pneumonia in immunocompetent laboratory rats that had been attributed to "rat respiratory virus". Vet Pathol 2012; 49:440-52. [PMID: 22308234 DOI: 10.1177/0300985811432351] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A prevalent and distinctive infectious interstitial pneumonia (IIP) of immunocompetent laboratory rats was suspected to be caused by a putative virus, termed rat respiratory virus, but this was never substantiated. To study this disease, 2 isolators were independently populated with rats from colonies with endemic disease, which was perpetuated by the regular addition of naive rats. After Pneumocystis was demonstrated by histopathology and polymerase chain reaction (PCR) in the lungs of rats from both isolators and an earlier bedding transmission study, the relationship between Pneumocystis and IIP was explored further by analyzing specimens from 3 contact transmission experiments, diagnostic submissions, and barrier room breeding colonies, including 1 with and 49 without IIP. Quantitative (q) PCR and immunofluorescence assay only detected Pneumocystis infection and serum antibodies in rats from experiments or colonies in which IIP was diagnosed by histopathology. In immunocompetent hosts, the Pneumocystis concentration in lungs corresponded to the severity and prevalence of IIP; seroconversion occurred when IIP developed and was followed by the concurrent clearance of Pneumocystis from lungs and resolution of disease. Experimentally infected immunodeficient RNU rats, by contrast, did not seroconvert to Pneumocystis or recover from infection. qPCR found Pneumocystis at significantly higher concentrations and much more often in lungs than in bronchial and nasal washes and failed to detect Pneumocystis in oral swabs. The sequences of a mitochondrial ribosomal large-subunit gene region for Pneumocystis from 11 distinct IIP sources were all identical to that of P. carinii. These data provide substantial evidence that P. carinii causes IIP in immunocompetent rats.
Collapse
Affiliation(s)
- K S Henderson
- Research Models and Services, Charles River, 251 Ballardvale St, Wilmington, MA 01887, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Spieler P, Rössle M. Respiratory Tract and Mediastinum. ESSENTIALS OF DIAGNOSTIC PATHOLOGY 2012. [PMCID: PMC7122295 DOI: 10.1007/978-3-642-24719-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Normal cytology, abnormal and atypical cells, non-cellular components, and infectious cell changes are largely described together with benign, malignant, and neuroendocrine lesions regarding exfoliative and aspiration cytology of the lung. A separate section broadly addresses diagnostic findings and differential diagnoses in bronchoalveolar washings. The section ‘Fine needle aspiration biopsy of mediastinal disorders’ covers in particular biopsy techniques, accuracy of liquid-based cytology, and the complex lesions of the thymus gland. Cytodiagnostic algorithms of the major benign and malignant pulmonary and mediastinal lesions and their respective differential diagnoses are additionally presented in synoptic setups.
Collapse
Affiliation(s)
- Peter Spieler
- Institut für Pathologie, Kantonsspital St. Gallen, Rorschacherstraße 95, 9007 St. Gallen, Switzerland
| | - Matthias Rössle
- Institut für Klinische Pathologie, UniversitätsSpital Zürich, Schmelzbergstraße 12, 8091 Zürich, Switzerland
| |
Collapse
|
31
|
Calderón EJ, Friaza V, Dapena FJ, de La Horra C. Pneumocystis jirovecii and cystic fibrosis. Med Mycol 2011; 48 Suppl 1:S17-21. [PMID: 21067325 DOI: 10.3109/13693786.2010.505205] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Pneumocystis jirovecii is an atypical opportunistic fungus with lung tropism and worldwide distribution that causes pneumonia in immunosuppressed individuals. The development of sensitive molecular techniques has led to the recognition of a colonization or carrier state of P. jirovecii, in which low levels of the organism are detected in persons who do not have pneumonia. Pneumocystis colonization has been described in individuals with various lung diseases, and accumulating evidence suggests that it may be a relevant issue with potential clinical impact. Only a few published studies carried out in Europe have evaluated the prevalence of Pneumocystis colonization in patients with cystic fibrosis, reporting ranges from 1.3-21.6%. The evolution of P. jirovecii colonization in cystic fibrosis patients is largely unknown. In a longitudinal study, none of the colonized patients developed pneumonia during a 1-year follow-up. Since patients with cystic fibrosis could act as major reservoirs and sources of infection for susceptible individuals further research is thus warranted to assess the true scope of the problem and to design rational preventive strategies if necessary. Moreover, it's necessary to elucidate the role of P. jirovecii infection in the natural history of cystic fibrosis in order to improve the clinical management of this disease.
Collapse
Affiliation(s)
- Enrique J Calderón
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, CIBER de Epidemiología y Salud Pública, Seville, Spain.
| | | | | | | |
Collapse
|
32
|
Herrag M, Elfassy Fihry MT, Alaoui Yazidi A. [Pneumocystis jirovecii: what does this mean?]. REVUE DE PNEUMOLOGIE CLINIQUE 2010; 66:342-346. [PMID: 21167441 DOI: 10.1016/j.pneumo.2009.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 09/13/2009] [Indexed: 05/30/2023]
Abstract
Pneumocystis was discovered nearly a century ago. It causes fatal pneumonia in immunocompromised individuals, especially in AIDS patients. Knowledge of the different species remained rudimentary until the mid-eighties when DNA analysis revealed its extensive diversity. In fact, it is no longer considered as a zoonosis. Pneumocystis organisms derived from different hosts have very different DNA sequences, indicating multiple species. Due to the genetic and functional disparities, the organism that causes human PCP is now named Pneumocystis jirovecii/Frenkel, 1999. We continue to call Pneumocystis carinii the species found in rats. This will allow for a single international language and avoid confusion. Changing the organism's name does not preclude the use of the well-known acronym PCP because it can also be read "PneumoCystis Pneumonia." The DNA sequences and genotypage have shown that variations exist among samples of P. jiroveci. Molecular biology is helpful in the study of the mechanisms of transmission, which can only occur in the same host and the different resistances as well as providing a better understanding of the relationship between host and pathogen. P. jirovecii pneumonia in immunosuppressed patients was previously thought to result from the reactivation of a latent infection acquired in early childhood. However, today, it is believed to result from a new infection from an exogenous source.
Collapse
Affiliation(s)
- M Herrag
- Service de pneumologie, hôpital Ibn Nafis, CHU Mohammed VI, faculté de médecine et de pharmacie, université Cadi Ayyad, Marrakech, Maroc.
| | | | | |
Collapse
|
33
|
Feng X, Wei C, Adam RD, Li Z, Lu S. Phylogenetic status of Pneumocystis from corticosteroid-treated gerbils. SCIENCE CHINA-LIFE SCIENCES 2010; 53:1239-46. [PMID: 20953947 DOI: 10.1007/s11427-010-4074-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 07/29/2010] [Indexed: 11/25/2022]
Abstract
Pneumocystis spp. infect the lungs of multiple mammalian species and cause disease in immunosuppressed individuals. The Pneumocystis isolates that have been studied to date fall into two major clades, those from primates and those from rodents. Within each of these clades, different species have been described on the basis of host specificity and differences in sequence and morphology. Here, we demonstrate that dexamethasone immunosuppression consistently results in histologically apparent lung infection in gerbils (28/35 animals). Sequence analysis of the 18S, 5.8S and internal transcribed spacer regions of the rDNA and a portion of the mitochondrial large subunit rDNA demonstrated that this gerbil Pneumocystis is grouped with other rodent Pneumocystis spp., but is distinct from them. Our results suggest that gerbil Pneumocystis differs sufficiently from Pneumocystis species found in other rodents to be considered a separate species.
Collapse
Affiliation(s)
- XianMin Feng
- Department of Parasitology, Jilin Medical College, Jilin, China
| | | | | | | | | |
Collapse
|
34
|
Tyler KL, Selvaggi SM, Stewart J. Pneumocystis jirovecii in a bronchoalveolar lavage specimen on ThinPrep® cytology. Diagn Cytopathol 2010; 39:675-6. [PMID: 20949463 DOI: 10.1002/dc.21496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 06/10/2010] [Indexed: 11/07/2022]
Affiliation(s)
- Kevin L Tyler
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | | | | |
Collapse
|
35
|
Cushion MT, Stringer JR. Stealth and Opportunism: Alternative Lifestyles of Species in the Fungal GenusPneumocystis. Annu Rev Microbiol 2010; 64:431-52. [DOI: 10.1146/annurev.micro.112408.134335] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Melanie T. Cushion
- University of Cincinnati College of Medicine, Department of Internal Medicine, Division of Infectious Diseases, Cincinnati, Ohio 45267-0560
- Veterans Affairs Medical Center, Cincinnati, Ohio 45220;
| | - James R. Stringer
- Department of Molecular Genetics, Biochemistry, and Microbiology, Cincinnati, Ohio 45267-0560; ,
| |
Collapse
|
36
|
Are members of the fungal genus pneumocystis (a) commensals; (b) opportunists; (c) pathogens; or (d) all of the above? PLoS Pathog 2010; 6:e1001009. [PMID: 20885786 PMCID: PMC2944789 DOI: 10.1371/journal.ppat.1001009] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
37
|
Finkelman MA. Pneumocystis jiroveciiinfection: Cell wall (1→3)-β-D-glucan biology and diagnostic utility. Crit Rev Microbiol 2010; 36:271-81. [DOI: 10.3109/1040841x.2010.484001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
38
|
Matos O, Esteves F. Pneumocystis jirovecii multilocus gene sequencing: findings and implications. Future Microbiol 2010; 5:1257-67. [DOI: 10.2217/fmb.10.75] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Pneumocystis jirovecii pneumonia (PcP) remains a major cause of respiratory illness among immunocompromised patients, especially patients infected with HIV, but it has also been isolated from immunocompetent persons. This article discusses the application of multilocus genotyping analysis to the study of the genetic diversity of P. jirovecii and its epidemiological and clinical parameters, and the important concepts achieved to date with these approaches. The multilocus typing studies performed until now have shown that there is an important genetic diversity of stable and ubiquitous P. jirovecii genotypes; infection with P. jirovecii is not necessarily clonal, recombination between some P. jirovecii multilocus genotypes has been suggested. P. jirovecii-specific multilocus genotypes can be associated with severity of PcP. Patients infected with P. jirovecii, regardless of the form of infection they present with, are part of a common human reservoir for future infections. The CYB, DHFR, DHPS, mtLSU rRNA, SOD and the ITS loci are suitable genetic targets to be used in further epidemiological studies focused on the identification and characterization of P. jirovecii haplotypes correlated with drug resistance and PcP outcome.
Collapse
Affiliation(s)
| | - Francisco Esteves
- Unidade de Protozoários Oportunistas/VIH e Outras Protozooses, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| |
Collapse
|
39
|
Esteves F, Gaspar J, Marques T, Leite R, Antunes F, Mansinho K, Matos O. Identification of relevant single-nucleotide polymorphisms in Pneumocystis jirovecii: relationship with clinical data. Clin Microbiol Infect 2010; 16:878-84. [DOI: 10.1111/j.1469-0691.2009.03030.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
40
|
Abstract
The incidence of invasive mycoses is increasing, especially among patients who are immunocompromised or hospitalized with serious underlying diseases. Such infections may be broken into two broad categories: opportunistic and endemic. The most important agents of the opportunistic mycoses are Candida spp., Cryptococcus neoformans, Pneumocystis jirovecii, and Aspergillus spp. (although the list of potential pathogens is ever expanding); while the most commonly encountered endemic mycoses are due to Histoplasma capsulatum, Coccidioides immitis/posadasii, and Blastomyces dermatitidis. This review discusses the epidemiologic profiles of these invasive mycoses in North America, as well as risk factors for infection, and the pathogens' antifungal susceptibility.
Collapse
|
41
|
Catherinot E, Lanternier F, Bougnoux ME, Lecuit M, Couderc LJ, Lortholary O. Pneumocystis jirovecii Pneumonia. Infect Dis Clin North Am 2010; 24:107-38. [PMID: 20171548 DOI: 10.1016/j.idc.2009.10.010] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Pneumocystis jirovecii has gained attention during the last decade in the context of the AIDS epidemic and the increasing use of cytotoxic and immunosuppressive therapies. This article summarizes current knowledge on biology, pathophysiology, epidemiology, diagnosis, prevention, and treatment of pulmonary P jirovecii infection, with a particular focus on the evolving pathophysiology and epidemiology. Pneumocystis pneumonia still remains a severe opportunistic infection, associated with a high mortality rate.
Collapse
Affiliation(s)
- Emilie Catherinot
- Université Paris Descartes, Service de Maladies Infectieuses et Tropicales, 149 Rue de Sèvres, Centre d'Infectiologie Necker-Pasteur, Hôpital Necker-Enfants Malades, Paris 75015, France
| | | | | | | | | | | |
Collapse
|
42
|
Abstract
Pneumocystis jirovecii is the opportunistic fungal organism that causes Pneumocystis pneumonia (PCP) in humans. Similar to other opportunistic pathogens, Pneumocystis causes disease in individuals who are immunocompromised, particularly those infected with HIV. PCP remains the most common opportunistic infection in patients with AIDS. Incidence has decreased greatly with the advent of HAART. However, an increase in the non-HIV immunocompromised population, noncompliance with current treatments, emergence of drug-resistant strains and rise in HIV(+) cases in developing countries makes Pneumocystis a pathogen of continued interest and a public health threat. A great deal of research interest has addressed therapeutic interventions to boost waning immunity in the host to prevent or treat PCP. This article focuses on research conducted during the previous 5 years regarding the host immune response to Pneumocystis, including innate, cell-mediated and humoral immunity, and associated immunotherapies tested against PCP.
Collapse
Affiliation(s)
- Michelle N Kelly
- Section of Pulmonary/Critical Care Medicine, LSU Health Sciences Center, Medical Education Building 3205, 1901 Perdido Street, New Orleans, LA 70112, USA.
| | | |
Collapse
|
43
|
Matos J, Vale N, Collins MS, Gut J, Rosenthal PJ, Cushion MT, Moreira R, Gomes P. PRIMACENES: novel non-cytotoxic primaquine-ferrocene conjugates with anti-Pneumocystis carinii activity. MEDCHEMCOMM 2010. [DOI: 10.1039/c0md00082e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
44
|
Vale N, Prudêncio M, Marques CA, Collins MS, Gut J, Nogueira F, Matos J, Rosenthal PJ, Cushion MT, do Rosário VE, Mota MM, Moreira R, Gomes P. Imidazoquines as antimalarial and antipneumocystis agents. J Med Chem 2009; 52:7800-7. [PMID: 19799426 PMCID: PMC2788672 DOI: 10.1021/jm900738c] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptidomimetic imidazolidin-4-one derivatives of primaquine (imidazoquines) recently displayed in vitro activity against blood schizonts of a chloroquine-resistant strain of Plasmodium falciparum. Preliminary studies with a subset of such imidazoquines showed them to both block transmission of P. berghei malaria from mouse to mosquito and be highly stable toward hydrolysis at physiological conditions. This prompted us to have deeper insight into the activity of imidazoquines against both Plasmodia and Pneumocystis carinii, on which primaquine is also active. Full assessment of the in vivo transmission-blocking activity of imidazoquines, in vitro tissue-schizontocidal activity on P. berghei-infected hepatocytes, and in vitro anti-P. carinii activity is now reported. All compounds were active in these biological assays, with generally lower activity than the parent drug. However, imidazoquines' stability against both oxidative deamination and proteolytic degradation suggest that they will probably have higher oral bioavailability and lower hematotoxicity than primaquine, which might translate into higher therapeutic indexes.
Collapse
Affiliation(s)
- Nuno Vale
- CIQUP – Centro de Investigação em Química da Universidade do Porto, Departamento de Química, Faculdade de Ciências, Universidade do Porto, P-4169-007 Porto, Portugal
| | - Miguel Prudêncio
- Unidade de Malária, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, P-1649-028 Lisboa, Portugal
| | - Catarina A. Marques
- Unidade de Malária, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, P-1649-028 Lisboa, Portugal
| | - Margaret S. Collins
- Research Services, Veterans Affairs Medical Center, Cincinnati, OH 45220, USA
- Division of Infectious Diseases, Department of Internal Medicine, University of Cincinnati, OH 45267-0560, USA
| | - Jiri Gut
- Department of Medicine, San Francisco General Hospital, University of California, CA 94143-0811, USA
| | - Fátima Nogueira
- Centro de Malária e Outras Doenças Tropicais, IHMT - Universidade Nova de Lisboa, P-1349-008 Lisboa, Portugal
| | - Joana Matos
- CIQUP – Centro de Investigação em Química da Universidade do Porto, Departamento de Química, Faculdade de Ciências, Universidade do Porto, P-4169-007 Porto, Portugal
| | - Philip J. Rosenthal
- Department of Medicine, San Francisco General Hospital, University of California, CA 94143-0811, USA
| | - Melanie T. Cushion
- Research Services, Veterans Affairs Medical Center, Cincinnati, OH 45220, USA
- Division of Infectious Diseases, Department of Internal Medicine, University of Cincinnati, OH 45267-0560, USA
| | - Virgílio E. do Rosário
- Centro de Malária e Outras Doenças Tropicais, IHMT - Universidade Nova de Lisboa, P-1349-008 Lisboa, Portugal
| | - Maria M. Mota
- Unidade de Malária, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, P-1649-028 Lisboa, Portugal
| | - Rui Moreira
- iMed.UL, CECF, Faculdade de Farmácia, Universidade de Lisboa, P-1600-083 Lisboa, Portugal
| | - Paula Gomes
- CIQUP – Centro de Investigação em Química da Universidade do Porto, Departamento de Química, Faculdade de Ciências, Universidade do Porto, P-4169-007 Porto, Portugal
| |
Collapse
|
45
|
Brubaker R, Redhead SA, Stringer JR, Keely SP, Cushion MT. Misinformation about Pneumocystis. Clin Exp Dermatol 2009; 34:e426-7. [DOI: 10.1111/j.1365-2230.2009.03411.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
46
|
Complexity of the MSG gene family of Pneumocystis carinii. BMC Genomics 2009; 10:367. [PMID: 19664205 PMCID: PMC2743713 DOI: 10.1186/1471-2164-10-367] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 08/07/2009] [Indexed: 11/17/2022] Open
Abstract
Background The relationship between the parasitic fungus Pneumocystis carinii and its host, the laboratory rat, presumably involves features that allow the fungus to circumvent attacks by the immune system. It is hypothesized that the major surface glycoprotein (MSG) gene family endows Pneumocystis with the capacity to vary its surface. This gene family is comprised of approximately 80 genes, which each are approximately 3 kb long. Expression of the MSG gene family is regulated by a cis-dependent mechanism that involves a unique telomeric site in the genome called the expression site. Only the MSG gene adjacent to the expression site is represented by messenger RNA. Several P. carinii MSG genes have been sequenced, which showed that genes in the family can encode distinct isoforms of MSG. The vast majority of family members have not been characterized at the sequence level. Results The first 300 basepairs of MSG genes were subjected to analysis herein. Analysis of 581 MSG sequence reads from P. carinii genomic DNA yielded 281 different sequences. However, many of the sequence reads differed from others at only one site, a degree of variation consistent with that expected to be caused by error. Accounting for error reduced the number of truly distinct sequences observed to 158, roughly twice the number expected if the gene family contains 80 members. The size of the gene family was verified by PCR. The excess of distinct sequences appeared to be due to allelic variation. Discounting alleles, there were 73 different MSG genes observed. The 73 genes differed by 19% on average. Variable regions were rich in nucleotide differences that changed the encoded protein. The genes shared three regions in which at least 16 consecutive basepairs were invariant. There were numerous cases where two different genes were identical within a region that was variable among family members as a whole, suggesting recombination among family members. Conclusion A set of sequences that represents most if not all of the members of the P. carinii MSG gene family was obtained. The protein-changing nature of the variation among these sequences suggests that the family has been shaped by selection for protein variation, which is consistent with the hypothesis that the MSG gene family functions to enhance phenotypic variation among the members of a population of P. carinii.
Collapse
|
47
|
|
48
|
Linke MJ, Ashbaugh AA, Koch JV, Levin L, Tanaka R, Walzer PD. Effects of surfactant protein-A on the interaction of Pneumocystis murina with its host at different stages of the infection in mice. J Eukaryot Microbiol 2009; 56:58-65. [PMID: 19335775 DOI: 10.1111/j.1550-7408.2008.00363.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We examined the effects of surfactant protein A (SP-A), a collectin, on the interaction of Pneumocystis murina with its host at the beginning, early to middle, and late stages of infection. Pneumocystis murina from SP-A wild-type (WT) mice inoculated intractracheally into WT mice (WT(S)-WT(R)) adhered well to alveolar macrophages, whereas organisms from SP-A knockout (KO) mice inoculated into KO mice (KO(S)-KO(R)) did not. Substitution of WT mice as the source of organisms (WT(S)-KO(R)) or recipient host macrophages (KO(S)-WT(R)) restored adherence to that found with WT(S)-WT(R) mice. In contrast, when immunosuppressed KO and WT mice were inoculated with P. murina from a homologous source (KO(S)-KO(R), WT(S)-WT(R)) or heterologous source (WT(S)-KO(R), KO(S)-WT(R)) and followed sequentially, WT(S)-KO(R) mice had the highest levels of infection at weeks 3 and 4; these mice also had the highest levels of the chemokine macrophage inflammatory protein-2 and neutrophils in lavage fluid at week 3. Surfactant protein-A administered to immunosuppressed KO(S)-KO(R) mice with Pneumocystis pneumonia for 8 wk as a therapeutic agent failed to lower the organism burden. We conclude that SP-A can correct the host immune defect in the beginning of P. murina infection, but not in the middle or late stages of the infection.
Collapse
Affiliation(s)
- Michael J Linke
- Research Service, Department of Veterans Affairs Medical Center, Cincinnati, Ohio 45220, USA
| | | | | | | | | | | |
Collapse
|
49
|
Aliouat-Denis CM, Martinez A, Aliouat EM, Pottier M, Gantois N, Dei-Cas E. The Pneumocystis life cycle. Mem Inst Oswaldo Cruz 2009; 104:419-26. [DOI: 10.1590/s0074-02762009000300004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Accepted: 03/10/2009] [Indexed: 11/21/2022] Open
Affiliation(s)
| | - Anna Martinez
- University of Lille Nord de France, France; Pasteur Institute of Lille, France
| | - El Moukhtar Aliouat
- University of Lille Nord de France, France; Pasteur Institute of Lille, France
| | | | | | - Eduardo Dei-Cas
- Pasteur Institute of Lille, France; University Hospital Center
| |
Collapse
|
50
|
Sparagano O, Foggett S. Diagnosis of clinically relevant fungi in medicine and veterinary sciences. ADVANCES IN APPLIED MICROBIOLOGY 2009; 66:29-52. [PMID: 19203647 DOI: 10.1016/s0065-2164(08)00802-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This review focuses on the most economically and epidemiologically important fungi affecting humans and animals. This paper will also summarize the different techniques, either molecular, based on nucleic acid and antibody analysis, or nonmolecular such as microscopy, culture, UV Wood's lamp, radiology, and spectroscopy used to identify species or group of fungi assisting clinicians to take the best control approach to clear such infections. On the molecular side, the paper will review results on genome sequencing which can help colleagues to identify their own DNA/RNA tests if they are interested in the diagnostic of fungi in medicine and veterinary medicine.
Collapse
Affiliation(s)
- Olivier Sparagano
- School of Agriculture, Food and Rural Development, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | | |
Collapse
|