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Brown L, Rautemaa-Richardson R, Mengoli C, Alanio A, Barnes RA, Bretagne S, Chen SCA, Cordonnier C, Donnelly JP, Heinz WJ, Jones B, Klingspor L, Loeffler J, Rogers TR, Rowbotham E, White PL, Cruciani M. Polymerase Chain Reaction on Respiratory Tract Specimens of Immunocompromised Patients to Diagnose Pneumocystis Pneumonia: A Systematic Review and Meta-analysis. Clin Infect Dis 2024:ciae239. [PMID: 38860786 DOI: 10.1093/cid/ciae239] [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: 11/06/2023] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND This meta-analysis examines the comparative diagnostic performance of polymerase chain reaction (PCR) for the diagnosis of Pneumocystis pneumonia (PCP) on different respiratory tract samples, in both human immunodeficiency virus (HIV) and non-HIV populations. METHODS A total of 55 articles met inclusion criteria, including 11 434 PCR assays on respiratory specimens from 7835 patients at risk of PCP. QUADAS-2 tool indicated low risk of bias across all studies. Using a bivariate and random-effects meta-regression analysis, the diagnostic performance of PCR against the European Organisation for Research and Treatment of Cancer-Mycoses Study Group definition of proven PCP was examined. RESULTS Quantitative PCR (qPCR) on bronchoalveolar lavage fluid provided the highest pooled sensitivity of 98.7% (95% confidence interval [CI], 96.8%-99.5%), adequate specificity of 89.3% (95% CI, 84.4%-92.7%), negative likelihood ratio (LR-) of 0.014, and positive likelihood ratio (LR+) of 9.19. qPCR on induced sputum provided similarly high sensitivity of 99.0% (95% CI, 94.4%-99.3%) but a reduced specificity of 81.5% (95% CI, 72.1%-88.3%), LR- of 0.024, and LR+ of 5.30. qPCR on upper respiratory tract samples provided lower sensitivity of 89.2% (95% CI, 71.0%-96.5%), high specificity of 90.5% (95% CI, 80.9%-95.5%), LR- of 0.120, and LR+ of 9.34. There was no significant difference in sensitivity and specificity of PCR according to HIV status of patients. CONCLUSIONS On deeper respiratory tract specimens, PCR negativity can be used to confidently exclude PCP, but PCR positivity will likely require clinical interpretation to distinguish between colonization and active infection, partially dependent on the strength of the PCR signal (indicative of fungal burden), the specimen type, and patient population tested.
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Affiliation(s)
- Lottie Brown
- Institute of Infection and Immunity, St George's University and St Georges University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Riina Rautemaa-Richardson
- Mycology Reference Centre Manchester and Department of Infectious Diseases, Manchester Academic Health Science Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust and Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - Carlo Mengoli
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Instituto Superiore Di Sanita, Rome, Italy
| | | | - Rosemary A Barnes
- Department of Infection, Immunity and Biochemistry and School of Medicine, University of Cardiff, United Kingdom
| | - Stéphane Bretagne
- Université Paris Cité, Parasitology-Mycology Laboratory, Hôpital Saint-Louis, APHP, Paris, France
| | - Sharon C A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, Australia
| | - Catherine Cordonnier
- Haematology and Stem Cell Transplant Department, Henri Mondor Hospital, and University Paris-Est-Créteil, Créteil, France
| | - J Peter Donnelly
- Fungal PCR Initiative, a working group of the International Society of Human and Animal Mycology, Verona, Italy
| | - Werner J Heinz
- Med. Clinic II, Caritas Hospital Bad Mergentheim, Germany
| | - Brian Jones
- Institute of Infection, Immunity and Inflammation, University of Glasgow, United Kingdom
| | - Lena Klingspor
- Karolinska Institutet, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Juergen Loeffler
- Medizinische Klinik II, Labor WÜ4i, Universitätsklinikum Würzburg, Germany
| | - Thomas R Rogers
- Discipline of Clinical Microbiology, Trinity College Dublin, St James's Hospital Campus, Dublin, Ireland
| | - Eleanor Rowbotham
- Mycology Reference Centre Manchester and Department of Infectious Diseases, Manchester University, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester
| | - P Lewis White
- Public Health Wales Mycology Reference Laboratory, Public Health Wales Microbiology Cardiff, University Hospital of Wales, and Centre for Trials Research/Division of Infection and Immunity, Cardiff University, United Kingdom
| | - Mario Cruciani
- Fungal PCR Initiative, a working group of the International Society of Human and Animal Mycology, Verona, Italy
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Kamel T, Janssen-Langenstein R, Quelven Q, Chelly J, Valette X, Le MP, Bourenne J, Garot D, Fillatre P, Labruyere M, Heming N, Lambiotte F, Lascarrou JB, Lesieur O, Bachoumas K, Ferre A, Maury E, Chalumeau-Lemoine L, Bougon D, Roux D, Guisset O, Coudroy R, Boulain T. Pneumocystis pneumonia in intensive care: clinical spectrum, prophylaxis patterns, antibiotic treatment delay impact, and role of corticosteroids. A French multicentre prospective cohort study. Intensive Care Med 2024:10.1007/s00134-024-07489-2. [PMID: 38829531 DOI: 10.1007/s00134-024-07489-2] [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: 02/29/2024] [Accepted: 05/10/2024] [Indexed: 06/05/2024]
Abstract
PURPOSE Severe Pneumocystis jirovecii pneumonia (PJP) requiring intensive care has been the subject of few prospective studies. It is unclear whether delayed curative antibiotic therapy may impact survival in these severe forms of PJP. The impact of corticosteroid therapy combined with antibiotics is also unclear. METHODS This multicentre, prospective observational study involving 49 adult intensive care units (ICUs) in France was designed to evaluate the severity, the clinical spectrum, and outcomes of patients with severe PJP, and to assess the association between delayed curative antibiotic treatment and adjunctive corticosteroid therapy with mortality. RESULTS We included 158 patients with PJP from September 2020 to August 2022. Their main reason for admission was acute respiratory failure (n = 150, 94.9%). 12% of them received antibiotic prophylaxis for PJP before ICU admission. The ICU, hospital, and 6-month mortality were 31.6%, 35.4%, and 40.5%, respectively. Using time-to-event analysis with a propensity score-based inverse probability of treatment weighting, the initiation of curative antibiotic treatment after 96 h of ICU admission was associated with faster occurrence of death [time ratio: 6.75; 95% confidence interval (95% CI): 1.48-30.82; P = 0.014]. The use of corticosteroids for PJP was associated with faster occurrence of death (time ratio: 2.48; 95% CI 1.01-6.08; P = 0.048). CONCLUSION This study showed that few patients with PJP admitted to intensive care received prophylactic antibiotic therapy, that delay in curative antibiotic treatment was common and that both delay in curative antibiotic treatment and adjunctive corticosteroids for PJP were associated with accelerated mortality.
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Affiliation(s)
- Toufik Kamel
- Service de Médecine Intensive-Réanimation, Centre Hospitalier Universitaire d'Orléans, 14 Avenue de l'Hôpital CS 86709, 45067, Orleans Cedex 2, France
| | - Ralf Janssen-Langenstein
- Médecine Intensive-Réanimation, Hôpital de Hautepierre, Centre Hospitalier Universitaire de Strasbourg, Avenue Molière, 67200, Strasbourg, France
| | - Quentin Quelven
- Médecine Intensive-Réanimation, Centre Hospitalier Universitaire Rennes, Pontchaillou, 2, Rue Henri Le Guilloux, 35000, Rennes, France
| | - Jonathan Chelly
- Réanimation Polyvalente, Centre Hospitalier Intercommunal Toulon La Seyne Sur Mer, 54 Rue Henri Sainte Claire Deville, 83100, Toulon, France
| | - Xavier Valette
- Médecine Intensive-Réanimation, Centre Hospitalier Universitaire de Caen Normandie, 14000, Caen, France
| | - Minh-Pierre Le
- Médecine Intensive-Réanimation, Hôpital Cochin, 27 Rue du Faubourg Saint-Jacques, 75014, Paris, France
| | - Jeremy Bourenne
- Réanimation des Urgences et Dechocage Hôpital de La Timone, 264 Rue Saint-Pierre, 13005, Marseille, France
| | - Denis Garot
- Médecine Intensive-Réanimation, Centre Hospitalier Régional Universitaire Bretonneau, Tours, 37044, Tours, France
| | - Pierre Fillatre
- Réanimation Polyvalente, Centre Hospitalier Yves-Le Foll, 10, Rue Marcel Proust, 22000, Saint Brieuc, France
| | - Marie Labruyere
- Médecine Intensive-Réanimation, Centre Hospitalier Universitaire de Dijon, 14 Rue Gaffarel, BP 77908, 21079, Dijon Cedex, France
| | - Nicholas Heming
- Médecine Intensive-Réanimation, Hôpital Raymond-Poincaré, 104, Boulevard Raymond-Poincaré, 92380, Garches, France
| | - Fabien Lambiotte
- Médecine Intensive-Réanimation, Centre Hospitalier de Valenciennes-CHV, Avenue Désandrouin CS 50479, 59322, Valenciennes Cedex, France
| | - Jean-Baptiste Lascarrou
- Médecine Intensive-Réanimation, Centre Hospitalier Universitaire de Nantes, Hôtel-Dieu-HME, 1 Place Alexis Ricordeau, 44093, Nantes, France
| | - Olivier Lesieur
- Médecine Intensive-Réanimation, Hôpital Saint-Louis, Rue Du Dr Schweitzer, 17019, La Rochelle, France
| | - Konstantinos Bachoumas
- Médecine Intensive-Réanimation, Centre Hospitalier Départemental Vendée, Boulevard Stéphane Moreau, 85000, La Roche-Sur-Yon, France
| | - Alexis Ferre
- Intensive Care Unit, Versailles Hospital, 177 Rue De Versailles, 78157, Le Chesnay, France
| | - Eric Maury
- Médecine Intensive-Réanimation, Hôpital Saint-Antoine, 184 Rue du Faubourg Saint-Antoine, 75012, Paris, France
| | - Ludivine Chalumeau-Lemoine
- Service de Réanimation Médico-Chirurgicale, Hôpital Privé Claude Galien, 20 Route de Boussy, 91480, Quincy-Sous-Sénart, France
| | - David Bougon
- Médecine Intensive-Réanimation, CH Annecy-Genevois, Site Annecy, 1 Avenue De L'Hôpital, 74370, Annecy, France
| | - Damien Roux
- Université Paris Cité, AP-HP, Hôpital Louis Mourier, DMU ESPRIT, Service de Médecine Intensive Réanimation, Colombes, France
| | - Olivier Guisset
- Médecine Intensive-Réanimation, Centre Hospitalier Universitaire-SAINT-ANDRE, Bordeaux, 1 Rue Jean Burguet, 33075, Bordeaux, France
| | - Remi Coudroy
- Médecine Intensive Réanimation, CHU de Poitiers, Poitiers, France
- INSERM CIC 1402, IS-ALIVE Research Group, Université de Poitiers, Poitiers, France
| | - Thierry Boulain
- Service de Médecine Intensive-Réanimation, Centre Hospitalier Universitaire d'Orléans, 14 Avenue de l'Hôpital CS 86709, 45067, Orleans Cedex 2, France.
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Kamel T, Boulain T. Pneumocystis pneumonia in French intensive care units in 2013-2019: mortality and immunocompromised conditions. Ann Intensive Care 2024; 14:80. [PMID: 38776012 PMCID: PMC11111439 DOI: 10.1186/s13613-024-01309-y] [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: 02/05/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
PURPOSE The recent epidemiology of Pneumocystis pneumonia (PCP) requiring intensive care unit (ICU) admission and the associated spectrum of immunocompromising conditions are poorly described. METHODS We analyzed all adult PCP cases admitted to French ICUs via the French medical database system (PMSI), over the period from 2013 to 2019. RESULTS French ICUs admitted a total of 4055 adult patients with PCP. Among all hospitalized PCP cases, the proportion requiring ICU admission increased from 17.8 in 2014 to 21.3% in 2019 (P < 0.001). The incidence of severe PCP rose from 0.85 in 2013 to 1.32/100,000 adult inhabitants in 2019 (P < 0.0001), primarily due to the proportion of HIV-negative patients that increased from 60.6% to 74.4% (P < 0.0001). Meanwhile, the annual number of severe PCP cases among patients with HIV infection remained stable over the years. In-hospital mortality of severe PCP cases was 28.5% in patients with HIV infection and 49.7% in patients without. Multivariable logistic analysis showed that patients with HIV infection had a lower adjusted risk of death than patients without HIV infection (Odds Ratio [OR]: 0.30, 95% confidence interval [95CI]: 0.17-0.55). Comorbidities or conditions strongly associated with hospital mortality included the patient's age, Simplified Acute Physiologic Score II, congestive heart failure, coagulopathy, solid organ cancer, and cirrhosis. A vast array of autoimmune inflammatory diseases affected 19.9% of HIV-negative patients. CONCLUSIONS The number of PCP cases requiring ICU admission in France has risen sharply. While the yearly count of severe PCP cases in HIV-infected patients has remained steady, this rise predominantly affects cancer patients, with a recent surge observed in patients with autoimmune inflammatory diseases, affecting one in five individuals.
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Affiliation(s)
- Toufik Kamel
- Service de Médecine Intensive Réanimation, Centre Hospitalier Universitaire d'Orléans, 14 Avenue de L'Hôpital CS 86709, 45067, Orleans Cedex 2, France
| | - Thierry Boulain
- Service de Médecine Intensive Réanimation, Centre Hospitalier Universitaire d'Orléans, 14 Avenue de L'Hôpital CS 86709, 45067, Orleans Cedex 2, France.
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Rouleau FD, Dubé AK, Gagnon-Arsenault I, Dibyachintan S, Pageau A, Després PC, Lagüe P, Landry CR. Deep mutational scanning of Pneumocystis jirovecii dihydrofolate reductase reveals allosteric mechanism of resistance to an antifolate. PLoS Genet 2024; 20:e1011252. [PMID: 38683847 PMCID: PMC11125491 DOI: 10.1371/journal.pgen.1011252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 05/24/2024] [Accepted: 04/08/2024] [Indexed: 05/02/2024] Open
Abstract
Pneumocystis jirovecii is a fungal pathogen that causes pneumocystis pneumonia, a disease that mainly affects immunocompromised individuals. This fungus has historically been hard to study because of our inability to grow it in vitro. One of the main drug targets in P. jirovecii is its dihydrofolate reductase (PjDHFR). Here, by using functional complementation of the baker's yeast ortholog, we show that PjDHFR can be inhibited by the antifolate methotrexate in a dose-dependent manner. Using deep mutational scanning of PjDHFR, we identify mutations conferring resistance to methotrexate. Thirty-one sites spanning the protein have at least one mutation that leads to resistance, for a total of 355 high-confidence resistance mutations. Most resistance-inducing mutations are found inside the active site, and many are structurally equivalent to mutations known to lead to resistance to different antifolates in other organisms. Some sites show specific resistance mutations, where only a single substitution confers resistance, whereas others are more permissive, as several substitutions at these sites confer resistance. Surprisingly, one of the permissive sites (F199) is without direct contact to either ligand or cofactor, suggesting that it acts through an allosteric mechanism. Modeling changes in binding energy between F199 mutants and drug shows that most mutations destabilize interactions between the protein and the drug. This evidence points towards a more important role of this position in resistance than previously estimated and highlights potential unknown allosteric mechanisms of resistance to antifolate in DHFRs. Our results offer unprecedented resources for the interpretation of mutation effects in the main drug target of an uncultivable fungal pathogen.
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Affiliation(s)
- Francois D. Rouleau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Centre de recherche en données massives de l’Université Laval (CRDM_UL), Québec, Québec, Canada
| | - Alexandre K. Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
| | - Isabelle Gagnon-Arsenault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
| | - Soham Dibyachintan
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Centre de recherche en données massives de l’Université Laval (CRDM_UL), Québec, Québec, Canada
| | - Alicia Pageau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Centre de recherche en données massives de l’Université Laval (CRDM_UL), Québec, Québec, Canada
| | - Philippe C. Després
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Centre de recherche en données massives de l’Université Laval (CRDM_UL), Québec, Québec, Canada
| | - Patrick Lagüe
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Centre de recherche en données massives de l’Université Laval (CRDM_UL), Québec, Québec, Canada
| | - Christian R. Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, Québec, Canada
- Centre de recherche en données massives de l’Université Laval (CRDM_UL), Québec, Québec, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Québec, Canada
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Sayson SG, Ashbaugh A, Cushion MT. Extracellular vesicles from Pneumocystis carinii-infected rats impair fungal viability but are dispensable for macrophage functions. Microbiol Spectr 2024; 12:e0365323. [PMID: 38236033 PMCID: PMC10845964 DOI: 10.1128/spectrum.03653-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 11/28/2023] [Indexed: 01/19/2024] Open
Abstract
Pneumocystis spp. are host obligate fungal pathogens that can cause severe pneumonia in mammals and rely heavily on their host for essential nutrients. The lack of a sustainable in vitro culture system poses challenges in understanding their metabolism, and the acquisition of essential nutrients from host lungs remains unexplored. Transmission electron micrographs show that extracellular vesicles (EVs) are found near Pneumocystis spp. within the lung. We hypothesized that EVs transport essential nutrients to the fungi during infection. To investigate this, EVs from P. carinii- and P. murina-infected rodents were biochemically and functionally characterized. These EVs contained host proteins involved in cellular, metabolic, and immune processes as well as proteins with homologs found in other fungal EV proteomes, indicating that Pneumocystis may release EVs. Notably, EV uptake by P. carinii indicated their potential involvement in nutrient acquisition and a possibility for using engineered EVs for efficient therapeutic delivery. However, EVs added to P. carinii in vitro did not show increased growth or viability, implying that additional nutrients or factors are necessary to support their metabolic requirements. Exposure of macrophages to EVs increased proinflammatory cytokine levels but did not affect macrophages' ability to kill or phagocytose P. carinii. These findings provide vital insights into P. carinii and host EV interactions, yet the mechanisms underlying P. carinii's survival in the lung remain uncertain. These studies are the first to isolate, characterize, and functionally assess EVs from Pneumocystis-infected rodents, promising to enhance our understanding of host-pathogen dynamics and therapeutic potential.IMPORTANCEPneumocystis spp. are fungal pathogens that can cause severe pneumonia in mammals, relying heavily on the host for essential nutrients. The absence of an in vitro culture system poses challenges in understanding their metabolism, and the acquisition of vital nutrients from host lungs remains unexplored. Extracellular vesicles (EVs) are found near Pneumocystis spp., and it is hypothesized that these vesicles transport nutrients to the pathogenic fungi. Pneumocystis proteins within the EVs showed homology to other fungal EV proteomes, suggesting that Pneumocystis spp. release EVs. While EVs did not significantly enhance P. carinii growth in vitro, P. carinii displayed active uptake of these vesicles. Moreover, EVs induced proinflammatory cytokine production in macrophages without compromising their ability to combat P. carinii. These findings provide valuable insights into EV dynamics during host-pathogen interactions in Pneumocystis pneumonia. However, the precise underlying mechanisms remain uncertain. This research also raises the potential for engineered EVs in therapeutic applications.
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Affiliation(s)
- Steven G. Sayson
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- The Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Alan Ashbaugh
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- The Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Melanie T. Cushion
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- The Veterans Affairs Medical Center, Cincinnati, Ohio, USA
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Watson AL, Woodford J, Britton S, Gupta R, Whiley D, McCarthy K. Determining Pneumocystis jirovecii Colonisation from Infection Using PCR-Based Diagnostics in HIV-Negative Individuals. Diagnostics (Basel) 2024; 14:114. [PMID: 38201422 PMCID: PMC10802892 DOI: 10.3390/diagnostics14010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Pneumocystis jirovecii pneumonia is increasingly diagnosed with highly sensitive PCR diagnostics in immunocompromised, HIV-negative individuals. We assessed the performance of our in-house quantitative PCR with the aim to optimise interpretation. METHODS Retrospective audit of all positive P. jirovecii qPCRs on induced sputum or BAL fluid at a single centre from 2012 to 2023. Medical and laboratory records were analysed and people with HIV were excluded. Cases were categorised as colonisation, high-probability PCP or uncertain PCP infection against a clinical gold standard incorporating clinico-radiological data. Quantitative PCR assay targeting the 5s gene was utilised throughout the time period. RESULTS Of the 82 positive qPCRs, 28 were categorised as high-probability PCP infection, 30 as uncertain PCP and 24 as colonisation. There was a significant difference in qPCR values stratified by clinical category but not respiratory sample type. Current assay performance with a cutoff of 2.5 × 105 copies/mL had a sensitivity of 50% (95% CI, 30.65-69.35%) and specificity of 83.33% (95% CI, 62.62-95.26%). Youden Index calculated at 6.5 × 104 copies/mL had a sensitivity of 75% (56.64-87.32%, 95% CI) and specificity of 66.67% (46.71-82.03%, 95% CI). High and low cutoffs were explored. Significant variables associated with infection were age > 70 years old, the presence of fever, hypoxia or ground glass changes. CONCLUSIONS A single qPCR cutoff cannot reliably determine P. jirovecii infection from colonisation. Low and high cutoffs are useful, however, a large "possible infection" cohort will remain where interpretation of clinic-radiological factors remains essential. Standardisation of assays with prospective validation in specific immunocompromised groups will allow greater generalisability and allow large-scale prospective assay validation to be performed.
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Affiliation(s)
- Anna Louise Watson
- Infectious Diseases, Royal Brisbane & Women’s Hospital, Metro North Health, Herston, QLD 4006, Australia
- Herston Infectious Diseases Institute, Herston, QLD 4006, Australia
| | - John Woodford
- Infectious Diseases, Ipswich Hospital, Ipswich, QLD 4305, Australia
| | - Sumudu Britton
- Infectious Diseases, Royal Brisbane & Women’s Hospital, Metro North Health, Herston, QLD 4006, Australia
| | - Rita Gupta
- Pathology Queensland, Herston, QLD 4006, Australia
| | - David Whiley
- Pathology Queensland, Herston, QLD 4006, Australia
- The University of Queensland, Herston, QLD 4006, Australia
| | - Kate McCarthy
- Infectious Diseases, Royal Brisbane & Women’s Hospital, Metro North Health, Herston, QLD 4006, Australia
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Navale AM. Glucose Transporter and Sensor Mechanisms in Fungal Pathogens as Potential Drug Targets. Curr Rev Clin Exp Pharmacol 2024; 19:250-258. [PMID: 37861001 DOI: 10.2174/0127724328263050230923154326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/02/2023] [Accepted: 08/25/2023] [Indexed: 10/21/2023]
Abstract
Fungal infections are emerging as major health challenges in recent years. The development of resistance against existing antifungal agents needs urgent attention and action. The limited classes of antifungal drugs available, their tendency to cause adverse effects, lack of effectiveness, etc., are the major limitations of current therapy. Thus, there is a pressing demand for new antifungal drug classes to cope with the present circumstances. Glucose is the key source of energy for all organisms, including fungi. Glucose plays a crucial role as a source of carbon and energy for processes like virulence, growth, invasion, biofilm formation, and resistance development. The glucose transport and sensing mechanisms are well developed in these organisms as an important strategy to sustain survival. Modulating these transport or sensor mechanisms may serve as an important strategy to inhibit fungal growth. Moreover, the structural difference between human and fungal glucose transporters makes them more appealing as drug targets. Limited literature is available for fungal glucose entry mechanisms. This review provides a comprehensive account of sugar transport mechanisms in common fungal pathogens.
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Affiliation(s)
- Archana Mohit Navale
- Department of Pharmacology, Parul Institute of Pharmacy, Parul University, Limda, India
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Tsvetkova N, Harizanov R, Rainova I, Ivanova A, Yancheva-Petrova N. Molecular Analysis of Dihydropteroate Synthase Gene Mutations in Pneumocystis jirovecii Isolates among Bulgarian Patients with Pneumocystis Pneumonia. Int J Mol Sci 2023; 24:16927. [PMID: 38069248 PMCID: PMC10707730 DOI: 10.3390/ijms242316927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Pneumocystis jirovecii pneumonia (PCP) is a significant cause of morbidity and mortality in immunocompromised people. The widespread use of trimethoprim-sulfamethoxazole (TMP-SMZ) for the treatment and prophylaxis of opportunistic infections (including PCP) has led to an increased selection of TMP-SMZ-resistant microorganisms. Sulfa/sulfone resistance has been demonstrated to result from specific point mutations in the DHPS gene. This study aims to investigate the presence of DHPS gene mutations among P. jirovecii isolates from Bulgarian patients with PCP. A total of 326 patients were examined via real-time PCR targeting the P. jirovecii mitochondrial large subunit rRNA gene and further at the DHPS locus. P. jirovecii DNA was detected in 50 (15.34%) specimens. A 370 bp DHPS locus fragment was successfully amplified in 21 samples from 19 PCP-positive patients, which was then purified, sequenced, and used for phylogenetic analysis. Based on the sequencing analysis, all (n = 21) P. jirovecii isolates showed DHPS genotype 1 (the wild type, with the nucleotide sequence ACA CGG CCT at codons 55, 56, and 57, respectively). In conclusion, infections caused by P. jirovecii mutants potentially resistant to sulfonamides are still rare events in Bulgaria. DHPS genotype 1 at codons 55 and 57 is the predominant P. jirovecii strain in the country.
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Affiliation(s)
- Nina Tsvetkova
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Rumen Harizanov
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Iskra Rainova
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Aleksandra Ivanova
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Nina Yancheva-Petrova
- Department for AIDS, Specialized Hospital for Active Treatment of Infectious and Parasitic Diseases, Ivan Geshev Blvd. 17, 1431 Sofia, Bulgaria
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Park JW, Curtis JR, Choi SR, Kim MJ, Ha YJ, Kang EH, Lee YJ, Lee EB. Risk-Benefit Analysis of Primary Prophylaxis Against Pneumocystis Jirovecii Pneumonia in Patients With Rheumatic Diseases Receiving Rituximab. Arthritis Rheumatol 2023; 75:2036-2044. [PMID: 37096489 DOI: 10.1002/art.42541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/31/2023] [Accepted: 04/20/2023] [Indexed: 04/26/2023]
Abstract
OBJECTIVE To identify a specific population of patients with rheumatic diseases receiving rituximab treatment for whom the benefit from primary prophylaxis against Pneumocystis jirovecii pneumonia (PJP) outweighs the risk of adverse events (AEs). METHODS This study included 818 patients treated with rituximab for rheumatic diseases, among whom 419 received prophylactic trimethoprim/sulfamethoxazole (TMP/SMX) with rituximab, while the remainder did not. Differences in 1-year PJP incidence between the groups were estimated using Cox proportional hazards regression. Risk-benefit assessment was performed in subgroups stratified according to risk factors based on the number needed to treat (NNT) to prevent 1 case of PJP and the number needed to harm (NNH) due to severe AEs. Inverse probability of treatment weighting was applied to minimize the confounding by indication. RESULTS During the 663.1 person-years, there were 11 PJP cases, with a mortality rate of 63.6%. Concomitant use of high-dose glucocorticoids (≥30 mg/day of prednisone or equivalent during 4 weeks after rituximab administration) was the most important risk factor. The PJP incidence (per 100 person-years) was 7.93 (95% confidence interval [95% CI] 2.91-17.25) in the subgroup receiving high-dose glucocorticoids compared with 0.40 (95% CI 0.01-2.25) in the subgroup without high-dose glucocorticoid use. Although prophylactic TMP/SMX significantly reduced the overall PJP incidence (HR 0.11 [95% CI 0.03-0.43]), the NNT to prevent 1 case of PJP (146) was higher than the NNH (86). In contrast, the NNT fell to 20 (95% CI 10.7-65.7) in patients receiving concomitant high-dose glucocorticoids. CONCLUSION The benefit associated with primary PJP prophylaxis outweighs the risk of severe AEs in patients with rheumatic diseases receiving rituximab and concomitant high-dose glucocorticoid treatment.
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Affiliation(s)
- Jun Won Park
- Division of Rheumatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jeffrey R Curtis
- Division of Clinical Immunology & Rheumatology, University of Alabama at Birmingham
| | - Se Rim Choi
- Division of Rheumatology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Min Jung Kim
- Division of Rheumatology, Department of Internal Medicine, Seoul Metropolitan Government-Seoul National University, Boramae Medical Center, Seoul, Republic of Korea
| | - You-Jung Ha
- Division of Rheumatology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Eun Ha Kang
- Division of Rheumatology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Yun Jong Lee
- Division of Rheumatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, and Division of Rheumatology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Eun Bong Lee
- Division of Rheumatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, and Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
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Alselami A, Drummond RA. How metals fuel fungal virulence, yet promote anti-fungal immunity. Dis Model Mech 2023; 16:dmm050393. [PMID: 37905492 PMCID: PMC10629672 DOI: 10.1242/dmm.050393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023] Open
Abstract
Invasive fungal infections represent a significant global health problem, and present several clinical challenges, including limited treatment options, increasing rates of antifungal drug resistance and compounding comorbidities in affected patients. Metals, such as copper, iron and zinc, are critical for various biological and cellular processes across phyla. In mammals, these metals are important determinants of immune responses, but pathogenic microbes, including fungi, also require access to these metals to fuel their own growth and drive expression of major virulence traits. Therefore, host immune cells have developed strategies to either restrict access to metals to induce starvation of invading pathogens or deploy toxic concentrations within phagosomes to cause metal poisoning. In this Review, we describe the mechanisms regulating fungal scavenging and detoxification of copper, iron and zinc and the importance of these mechanisms for virulence and infection. We also outline how these metals are involved in host immune responses and the consequences of metal deficiencies or overloads on how the host controls invasive fungal infections.
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Affiliation(s)
- Alanoud Alselami
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rebecca A. Drummond
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
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Grønseth S, Rogne T, Heggelund L, Åsvold BO, Afset JE, Damås JK. Role of fungal burden in risk stratification of HIV-negative patients with Pneumocystis pneumonia: A 12-year, retrospective, observational, multicenter cohort. Int J Infect Dis 2023; 134:177-186. [PMID: 37339716 DOI: 10.1016/j.ijid.2023.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/22/2023] Open
Abstract
OBJECTIVES This study aimed to explore the role of fungal burden in risk stratification of patients without HIV-negative patients with Pneumocystis pneumonia (PCP). METHODS This was a retrospective analysis of the characteristics associated with 30-day mortality in patients who were positive for P. jirovecii using polymerase chain reaction in bronchoalveolar lavage fluid between 2006 and 2017 in a multicenter cohort from Central Norway. The fungal burden was indicated by the cycle threshold (CT) values from semiquantitative real-time polymerase chain reaction targeting the β-tubulin gene. RESULTS We included 170 patients with proven or probable PCP. The all-cause 30-day mortality was 18.2%. After adjusting for host characteristics and premorbid corticosteroid use, a higher fungal burden was associated with a higher risk of dying: adjusted odds ratio 1.42 (95% confidence interval 0.48-4.25) for a CT value 31-36, increasing to odds ratio 5.43 (95% confidence interval 1.48-19.9) for a CT value ≤30 compared with patients with a CT value ≥37. The Charlson comorbidity index (CCI) improved the risk stratification: patients with a CT value ≥37 and CCI ≤2 had a 9% mortality risk compared with 70% among those with a CT value ≤30 and CCI ≥6. Comorbid cardiovascular disease, solid tumors, immunological disorders, premorbid corticosteroids, hypoxemia, abnormal leukocyte counts, low serum albumin, and C-reactive protein ≥100 were also independently associated with 30-day mortality. The sensitivity analyses did not suggest selection bias. CONCLUSION Fungal burden may improve the risk stratification of patients without HIV-negative patients with PCP.
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Affiliation(s)
- Stine Grønseth
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
| | - Tormod Rogne
- Department of Circulation and Medical Imaging, NTNU, Trondheim, Norway; Department of Chronic Disease Epidemiology and Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, USA
| | - Lars Heggelund
- Department of Internal Medicine, Vestre Viken Hospital Trust, Drammen, Norway; Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Bjørn Olav Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Trondheim, Norway; HUNT Research Center, Department of Public Health and Nursing, The Trøndelag Health Study, NTNU, Levanger, Norway; Department of Endocrinology, St. Olavs hospital, Clinic of Medicine, Trondheim University Hospital, Trondheim, Norway
| | - Jan Egil Afset
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Department of Medical Microbiology, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jan Kristian Damås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Department of Infectious Diseases, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway; Centre of Molecular Inflammation Research, NTNU, Trondheim, Norway
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Abstract
The burden of fungal infections has been on the rise globally and remains a significant public health concern in Kenya. We estimated the incidence and prevalence of fungal infections using all mycology publications in Kenya up to January 2023, and from neighbouring countries where data lacked. We used deterministic modelling using populations at risk to calculate the disease burden. The total burden of serious fungal infections is estimated to affect 6,328,294 persons which translates to 11.57% of the Kenyan population. Those suffering from chronic infections such as chronic pulmonary aspergillosis are estimated to be 100,570 people (0.2% of the population) and probably nearly 200,000 with fungal asthma, all treatable with oral antifungal therapy. Serious acute fungal infections secondary to HIV (cryptococcal meningitis, disseminated histoplasmosis, pneumocystis pneumonia, and mucosal candidiasis) affect 196,543 adults and children (0.4% of the total population), while cancer-related invasive fungal infection cases probably exceed 2,299 and those in intensive care about 1,230 incident cases, including Candida auris bloodstream infection. The burden of fungal infections in Kenya is high; however, limited diagnostic test availability, low clinician awareness and inadequate laboratory capacity constrain the country's health system in responding to the syndemic of fungal disease in Kenya.
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Affiliation(s)
- Stanley N. Ratemo
- Research Department, Kisii Teaching and Referral Hospital, Kisii, Kenya
- CONTACT Stanley N. Ratemo
| | - David W Denning
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Global Action for Fungal Infections (GAFFI), Geneva, Switzerland
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Bereznicka A, Mikolajczyk K, Czerwinski M, Kaczmarek R. Microbial lectome versus host glycolipidome: How pathogens exploit glycosphingolipids to invade, dupe or kill. Front Microbiol 2022; 13:958653. [PMID: 36060781 PMCID: PMC9437549 DOI: 10.3389/fmicb.2022.958653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Glycosphingolipids (GSLs) are ubiquitous components of the cell membranes, found across several kingdoms of life, from bacteria to mammals, including humans. GSLs are a subclass of major glycolipids occurring in animal lipid membranes in clusters named “lipid rafts.” The most crucial functions of GSLs include signal transduction and regulation as well as participation in cell proliferation. Despite the mainstream view that pathogens rely on protein–protein interactions to survive and thrive in their hosts, many also target the host lipids. In particular, multiple pathogens produce adhesion molecules or toxins that bind GSLs. Attachment of pathogens to cell surface receptors is the initial step in infections. Many mammalian pathogens have evolved to recognize GSL-derived receptors. Animal glycosphingolipidomes consist of multiple types of GSLs differing in terminal glycan and ceramide structures in a cell or tissue-specific manner. Interspecies differences in GSLs dictate host specificity as well as cell and tissue tropisms. Evolutionary pressure exerted by pathogens on their hosts drives changes in cell surface glycoconjugates, including GSLs, and has produced a vast number of molecules and interaction mechanisms. Despite that abundance, the role of GSLs as pathogen receptors has been largely overlooked or only cursorily discussed. In this review, we take a closer look at GSLs and their role in the recognition, cellular entry, and toxicity of multiple bacterial, viral and fungal pathogens.
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Nasr M, Mohammad A, Hor M, Baradeiya AM, Qasim H. Exploring the Differences in Pneumocystis Pneumonia Infection Between HIV and Non-HIV Patients. Cureus 2022; 14:e27727. [PMID: 36106266 PMCID: PMC9441775 DOI: 10.7759/cureus.27727] [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] [Accepted: 08/05/2022] [Indexed: 11/06/2022] Open
Abstract
Pneumocystis pneumonia (PCP) is one of the most common opportunistic infections worldwide that affects the lung. Pneumocystis leads to pneumonia, caused by Pneumocystis jirovecii, formerly known as Pneumocystis carinii. In recent decades, PCP has been a major health problem for human immunodeficiency virus (HIV) patients and is responsible for most of mortality and morbidity. However, the increasing number of immunosuppressive-related diseases has led to outbreaks in other patient populations, raising the concern for PCP as it becomes a major concern among those patients. These changes led to marked changes in the prevalence and mortality rates of PCP. Huge variations in those parameters among HIV and non-HIV patients have been seen also. Historically, the diagnosis was made by staining and direct visualization of the organism within the bronchoalveolar lavage (BAL) fluid. The diagnosis is now made by microscopic examination and a real-time polymerase chain reaction (PCR) of BAL. Serum (1,3)-β-D-glucan, which is a component of the Pneumocystis jirovecii cell wall that distinguishes it from other fungi, has become an important diagnostic tool. Early diagnosis and treatment play a vital role in the patient’s survival and in the infection outcome; hence, empirical PCP therapy should be started immediately when the infection is suspected without waiting for the results of the diagnostic test. Steroids play an important role in the treatment of HIV patients, especially patients who present with hypoxia and respiratory failure. Prophylaxis is very effective and should be given to all patients at high risk of PCP. Antiretroviral therapy (ART) should be started as soon as possible in newly diagnosed HIV-infected patients with PCP, and the immune status of immunocompromised patients with PCP should be improved by temporarily withholding immunosuppressive drugs or reducing their doses.
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