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Chew R, Woods ML, Paterson DL. Development and validation of supervised machine learning multivariable prediction models for the diagnosis of Pneumocystis jirovecii pneumonia using nasopharyngeal swab PCR in adults in a low-HIV prevalence setting. Int Health 2024:ihae052. [PMID: 39206512 DOI: 10.1093/inthealth/ihae052] [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: 03/05/2024] [Revised: 05/08/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND The global burden of the opportunistic fungal disease Pneumocystis jirovecii pneumonia (PJP) remains substantial. Polymerase chain reaction (PCR) on nasopharyngeal swabs (NPS) has high specificity and may be a viable alternative to the gold standard diagnostic of PCR on invasively collected lower respiratory tract specimens, but has low sensitivity. Sensitivity may be improved by incorporating NPS PCR results into machine learning models. METHODS Three supervised multivariable diagnostic models (random forest, logistic regression and extreme gradient boosting) were constructed and validated using a 111-person Australian dataset. The predictors were age, gender, immunosuppression type and NPS PCR result. Model performance metrics such as accuracy, sensitivity, specificity and predictive values were compared to select the best-performing model. RESULTS The logistic regression model performed best, with 80% accuracy, improving sensitivity to 86% and maintaining acceptable specificity of 70%. Using this model, positive and negative NPS PCR results indicated post-test probabilities of 84% (likely PJP) and 26% (unlikely PJP), respectively. CONCLUSIONS The logistic regression model should be externally validated in a wider range of settings. As the predictors are simple, routinely collected patient variables, this model may represent a diagnostic advance suitable for settings where collection of lower respiratory tract specimens is difficult but PCR is available.
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Affiliation(s)
- Rusheng Chew
- Mathematical and Economic Modelling Department, Mahidol Oxford Tropical Medicine Research Unit, c/o Faculty of Tropical Medicine, Mahidol University, 3rd floor, 60th Anniversary Chalermprakiat Building, 420/6 Ratchawithi Road, Ratchathewi, Bangkok 10400, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX3 7LG, UK
- Faculty of Medicine, University of Queensland, Herston 4006, Queensland, Australia
| | - Marion L Woods
- Faculty of Medicine, University of Queensland, Herston 4006, Queensland, Australia
- Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Herston 4029, Queensland, Australia
| | - David L Paterson
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549
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Garnacho-Montero J, Barrero-García I, León-Moya C. Fungal infections in immunocompromised critically ill patients. JOURNAL OF INTENSIVE MEDICINE 2024; 4:299-306. [PMID: 39035612 PMCID: PMC11258510 DOI: 10.1016/j.jointm.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/01/2024] [Accepted: 01/02/2024] [Indexed: 07/23/2024]
Abstract
Diverse pathogenic fungi can produce severe infections in immunocompromised patients, thereby justifying intensive care unit (ICU) admissions. In some cases, the infections can develop in immunocompromised patients who were previously admitted to the ICU. Aspergillus spp., Pneumocystis jirovecii, Candida spp., and Mucorales are the fungi that are most frequently involved in these infections. Diagnosis continues to be challenging because symptoms and signs are unspecific. Herein, we provide an in-depth review about the diagnosis, with emphasis on recent advances, and treatment of these invasive fungal infections in the ICU setting.
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Affiliation(s)
- José Garnacho-Montero
- Unidad Clínica de Cuidados Intensivos, Hospital Universitario Virgen Macarena, Sevilla, Spain
| | - Irene Barrero-García
- Unidad Clínica de Cuidados Intensivos, Hospital Universitario Virgen Macarena, Sevilla, Spain
| | - Cristina León-Moya
- Unidad Clínica de Cuidados Intensivos, Hospital Universitario Virgen Macarena, Sevilla, Spain
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Liu L, Ji T, Chen R, Fan L, Dai J, Qiu Y. High prevalence of pneumocystis pneumonia in interstitial lung disease: a retrospective study. Infection 2024; 52:985-993. [PMID: 38147199 DOI: 10.1007/s15010-023-02148-y] [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: 07/09/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Interstitial lung disease (ILD) is a new risk category for pneumocystis pneumonia (PCP) with a high mortality rate. The definite diagnostic criteria of PCP in ILD patients have not been established until now. The aims of this study were to identify potential risk factors of PCP in patients with ILD, and to evaluate the performance of metagenomic next-generation sequencing (mNGS), CD4 + T cell count, (1-3)-β-D-Glucan (BG) and lactate dehydrogenase (LDH) in the diagnosis of PCP in ILD patients. METHODS This is a retrospective, single-center, case-control study. ILD patients who underwent mNGS from December 2018 to December 2022 were included in the study. Based on the diagnosis criteria of PCP, these patients were divided into PCP-ILD and non-PCP-ILD groups. The potential risk factors for PCP occurrence in ILD patients were analysed via logistic regression. The diagnostic efficacy of mNGS was compared with serological biomarkers. RESULTS 92 patients with ILD were enrolled, 31 of which had a definite PCP and were assigned to the PCP-ILD group while 61 were to the non-PCP-ILD group. The infection rate of PJ in ILD patients was 33.7% (31/92). The history of glucocorticoid therapy, CD4 + T cell count, BG level and traction bronchiectasis on HRCT were associated with PCP occurrence in ILD patients. LDH level did not reach statistical significance in the logistic regression analysis. mNGS was confirmed as the most accurate test for PCP diagnosis in ILD patients. CONCLUSION ILD is a new risk group of PCP with high PCP prevalence. Clinicians should pay close attention to the occurrence of PCP in ILD patients who possess the risk factors of previous glucocorticoid therapy, decreased CD4 + T cell count, increased BG level and absence of traction bronchiectasis on HRCT. mNGS showed the most excellent performance for PCP diagnosis in ILD patients. Peripheral blood CD4 + T cell count and BG level are alternative diagnostic methods for PCP in ILD patients. However, the diagnostic value of serum LDH level was limited in ILD patients.
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Affiliation(s)
- Ling Liu
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210008, China
| | - Tong Ji
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210008, China
| | - Ranxun Chen
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210008, China
| | - Li Fan
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210008, China
| | - Jinghong Dai
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210008, China.
| | - Yuying Qiu
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210008, China.
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Rhoads S, Maloney J, Mantha A, Van Hook R, Henao-Martínez AF. Pneumocystis jirovecii Pneumonia in HIV-Negative, Non-transplant Patients: Epidemiology, Clinical Manifestations, Diagnosis, Treatment, and Prevention. CURRENT FUNGAL INFECTION REPORTS 2024; 18:125-135. [PMID: 38948111 PMCID: PMC11213562 DOI: 10.1007/s12281-024-00482-8] [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] [Accepted: 01/03/2024] [Indexed: 07/02/2024]
Abstract
Purpose of Review Pneumocystis jirovecii pneumonia (PJP) is an opportunistic fungal infection that is increasingly seen in HIV-negative patients with immune compromise due to other etiologies. We lack comprehensive clinical recommendations for this population. Recent Findings In non-HIV cases, PJP has a mortality rate of up to 50%, which is unacceptable despite the presence of safe and effective prophylaxis and therapy. Steroid use is one of the most common risk factors for disease development. New data suggests that lower doses of the preferred treatment regimen, TMP-SMX, may be equally effective for treatment while limiting side effects. While commonly used, the benefit of corticosteroids for the treatment of PJP has recently been called into question, with a recent multicenter cohort demonstrating no benefit among solid organ transplant recipients. Summary A high suspicion of PJP in individuals with pneumonia during immunosuppressant use is crucial. Therapeutic options are evolving to decrease potential side effects while maintaining efficacy in this highly morbid disease.
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Affiliation(s)
- Sarah Rhoads
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, USA
| | - James Maloney
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Aditya Mantha
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Reed Van Hook
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Andrés F. Henao-Martínez
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, 12700 E. 19Th Avenue, Mail Stop B168, Aurora, CO 80045, USA
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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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Gulhati V, Desy J, Thornton CS. A case of hypercalcemia from Pneumocystis jirovecii in an immunosuppressed non-HIV patient. BMC Pulm Med 2024; 24:204. [PMID: 38658913 PMCID: PMC11044281 DOI: 10.1186/s12890-024-03007-8] [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: 12/27/2023] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND The prevalence of non-HIV related Pneumocystis jirovecii pneumonia (PJP) is increasing with use of immunosuppressive therapies. There are case reports of solid organ transplant recipients on immunosuppressive therapy presenting with mild hypercalcemia, leading to a diagnosis of PJP. Recent studies have shown efficacy of PJP prophylaxis for patients treated with rituximab with a favourable adverse effect profile. CASE PRESENTATION A 78-year-old male with a history of PR3-ANCA vasculitis, chronic kidney disease and heart failure with reduced ejection fraction presented to our tertiary care hospital with a two-week history of confusion and non-productive cough. Background immunosuppression with rituximab was completed every six months. The patient was found to have hypercalcemia and new infiltrates and ground glass opacities on cross-sectional imaging. Bronchoscopy was performed that was positive for Pneumocystis jirovecii. He was treated with 21 days of trimethoprim-sulfamethoxazole and prednisone with resolution of symptoms and hypercalcemia. CONCLUSIONS Herein, we present a novel case of PJP in a non-transplant recipient preceded by hypercalcemia. Our case demonstrates the importance for a high suspicion for PJP in chronically immunosuppressed patients on rituximab presenting with PTH-independent hypercalcemia.
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Affiliation(s)
- Vishrut Gulhati
- Division of Respiratory Medicine, Department of Medicine, University of Calgary, T2N 4N1, Calgary, AB, Canada
| | - Janeve Desy
- Division of Respiratory Medicine, Department of Medicine, University of Calgary, T2N 4N1, Calgary, AB, Canada
| | - Christina S Thornton
- Division of Respiratory Medicine, Department of Medicine, University of Calgary, T2N 4N1, Calgary, AB, Canada.
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary Cumming School of Medicine, Calgary, AB, Canada.
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Chew R, Tozer S, Ulett K, Paterson DL, Whiley D, Sloots T, Fielding D, Zappala C, Bashirzadeh F, Hundloe J, Bletchley C, Woods ML. Comparing Polymerase Chain Reaction Testing of Nasopharyngeal Swab and Lower Respiratory Tract Specimens for the Diagnosis of Pneumocystis jirovecii Pneumonia. Open Forum Infect Dis 2024; 11:ofae071. [PMID: 38444816 PMCID: PMC10913836 DOI: 10.1093/ofid/ofae071] [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: 11/21/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
Using nasopharyngeal (NP) swab samples instead of lower respiratory tract specimens for polymerase chain reaction (PCR) to diagnose Pneumocystis jirovecii pneumonia (PJP) may be better tolerated and improve diagnostic accessibility. In this 2-year Australian retrospective cohort study of patients with clinically suspected PJP, P jirovecii PCR on NP swab samples had perfect specificity but low sensitivity (0.66).
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Affiliation(s)
- Rusheng Chew
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Mathematical and Economic Modelling Department, Mahidol Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Sarah Tozer
- Central Laboratory, Pathology Queensland, Central Laboratory, Brisbane, Australia
| | - Kimberly Ulett
- Department of Medicine, Gold Coast Hospital and Health Service, Gold Coast, Australia
| | - David L Paterson
- Central Laboratory, Pathology Queensland, Central Laboratory, Brisbane, Australia
- UQ Centre for Clinical Research, University of Queensland, Brisbane, Australia
- Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - David Whiley
- UQ Centre for Clinical Research, University of Queensland, Brisbane, Australia
| | - Theo Sloots
- Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - David Fielding
- Faculty of Medicine, University of Queensland, Brisbane, Australia
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Christopher Zappala
- Faculty of Medicine, University of Queensland, Brisbane, Australia
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Farzad Bashirzadeh
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Justin Hundloe
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Cheryl Bletchley
- Central Laboratory, Pathology Queensland, Central Laboratory, Brisbane, Australia
| | - Marion L Woods
- Faculty of Medicine, University of Queensland, Brisbane, Australia
- Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Brisbane, Australia
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Wang C, Yin X, Ma W, Zhao L, Wu X, Ma N, Cao Y, Zhang Q, Ma S, Xu L, Wang X. Clinical application of bronchoalveolar lavage fluid metagenomics next-generation sequencing in cancer patients with severe pneumonia. Respir Res 2024; 25:68. [PMID: 38317206 PMCID: PMC10840150 DOI: 10.1186/s12931-023-02654-5] [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: 10/13/2023] [Accepted: 12/25/2023] [Indexed: 02/07/2024] Open
Abstract
OBJECTIVE Metagenomic next-generation sequencing (mNGS), as an emerging technique for pathogen detection, has been widely used in clinic. However, reports on the application of mNGS in cancer patients with severe pneumonia remain limited. This study aims to evaluate the diagnostic performance of bronchoalveolar lavage fluid (BALF) mNGS in cancer patients complicated with severe pneumonia. METHODS A total of 62 cancer patients with severe pneumonia simultaneously received culture and mNGS of BALF were enrolled in this study. We systematically analyzed the diagnostic significance of BALF mNGS. Subsequently, optimization of anti-infective therapy based on the distribution of pathogens obtained from BALF mNGS was also assessed. RESULTS For bacteria and fungi, the positive detection rate of mNGS was significantly higher than culture method (91.94% versus 51.61%, P < 0.001), especially for poly-microbial infections (70.97% versus 12.90%, P < 0.001). Compared with the culture method, mNGS exhibited a diagnostic sensitivity of 100% and a specificity of 16.67%, with the positive predictive value (PPV) and negative predictive value (NPV) being 56.14% and 100%, respectively. The agreement rate between these two methods was 59.68%, whereas kappa consensus analysis indicated a poor concordance (kappa = 0.171). After receipt of BALF mNGS results, anti-infective treatment strategies in 39 out of 62 cases (62.90%) were optimized. Moreover, anti-tumor therapy was a high-risk factor for mixed infections (87.18% versus 65.22%, P = 0.04). CONCLUSIONS The present study showed that cancer patients with severe pneumonia, especially those received anti-tumor therapy, were more likely to have poly-microbial infections. BALF mNGS can provide a rapid and comprehensive pathogen distribution of pulmonary infection, making it a promising technique in clinical practice, especially for optimizing therapeutic strategies for cancer patients.
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Affiliation(s)
- Chao Wang
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China
| | - Xiaojuan Yin
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China
| | - Wenqing Ma
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China
| | - Li Zhao
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China
| | - Xuhong Wu
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
| | - Nan Ma
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
| | - Yuepeng Cao
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
| | - Quanli Zhang
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, Jiangsu, 210009, China
| | - Shuliang Ma
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
| | - Lin Xu
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China.
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, Jiangsu, 210009, China.
| | - Xuerong Wang
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China.
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Sagas D, Adler A, Kasher C, Khamaysi K, Strauss M, Chazan B. The effect of the transition to molecular diagnosis on the epidemiology and the clinical characteristics of bacterial gastroenteritis in Northern Israel. Infect Dis (Lond) 2024; 56:157-163. [PMID: 37975631 DOI: 10.1080/23744235.2023.2282713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The transition to PCR-based diagnosis of bacterial gastroenteritis (BGE) can increase the sensitivity but might reduce the clinical specificity. The aims of this study were (1) to compare the effect of the change from culture to PCR-based diagnostics on the reported incidence and positivity rates of BGE due to Salmonella, Shigella and Campylobacter species and (2) to compare the demographics, medical background, clinical characteristics and pre-analytic variables between cases with PCR-positive, culture-negative samples to cases with PCR-positive, culture-positive samples. METHODS The study was performed at the Emek Medical Centre that serves a population of 0.5 million people in Northern Israel. The study included two parts: (1) a retrospective cohort study, comparing the incidence and positivity rates of laboratory-diagnosed BGE from January 2016 until December 22nd, 2019 when culture was the sole method to January 2020 until April 2023 when PCR was used; (2) a prospective cohort study, conducted between November 2020 until April 2023 that compared the demographics and clinical characteristics of BGE cases that were diagnosed by PCR alone versus cases that were diagnosed by both PCR and culture. RESULTS The incidence rate between-periods comparability ratio was only 113% since the incidence rate did not increase during 2020, the first year of the COVID-19 pandemic. The sample positivity rate increased since 2020, with between-periods comparability ratio of 159%. In the second period, the sample positivity rates of culture vs. PCR alone differed between the pathogens and were 90.2%, 63.8% and 54.2% for Salmonella, Campylobacter and Shigella species, respectively (p < 0.001). The following variables were identified as independent predictors of culture positivity: (1) Salmonella infection (O.R. = 10.6, 95% C.I. 3.6-31.1, p < 0.001); (2) Shigella infection (O.R. = 0.46, 95% C.I.0.23-0.93, p = 0.032); (3) time from sample submission to culture (O.R.=0.73, 95% C.I. 0.58-0.92, p = 0.008); (4) the presence of abdominal pain (O.R. = 1.98, 95% C.I. 1.04-3.79, p = 0.038) and the PCR mean Ct value (O.R. = 0.89, 95% C.I.0.85-0.94, p < 0.001). CONCLUSIONS The use of PCR had led to improved sensitivity, without noticeable decrease in the clinical specificity. This was especially important in the case of the more fastidious organisms.
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Affiliation(s)
- Dana Sagas
- Clinical Microbiology, Emek Medical Center, Clalit Health Services, Afula, Israel
- Department of Epidemiology and Preventative Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amos Adler
- Department of Epidemiology and Preventative Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Clinical Microbiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Carmel Kasher
- Infectious Diseases Unit, Emek Medical Center, Clalit Health Services, Afula, Israel
| | | | - Merav Strauss
- Clinical Microbiology, Emek Medical Center, Clalit Health Services, Afula, Israel
| | - Bibiana Chazan
- Infectious Diseases Unit, Emek Medical Center, Clalit Health Services, Afula, Israel
- Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
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10
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Li X, Xiong X, Liang Z, Tang Y. A machine learning diagnostic model for Pneumocystis jirovecii pneumonia in patients with severe pneumonia. Intern Emerg Med 2023; 18:1741-1749. [PMID: 37530943 DOI: 10.1007/s11739-023-03353-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/17/2023] [Indexed: 08/03/2023]
Abstract
BACKGROUND The diagnosis of Pneumocystis jirovecii pneumonia (PCP) in patients presenting with severe pneumonia is challenging and delays in treatment were associated with worse prognosis. This study aimed to develop a rapid, easily available, noninvasive machine learning diagnostic model for PCP among patients with severe pneumonia. METHODS A retrospective study was performed in West China Hospital among consecutive patients with severe pneumonia who had undergone bronchoalveolar lavage for etiological evaluation between October 2010 and April 2021. Factors associated with PCP were identified and four diagnostic models were established using machine learning algorithms including Logistic Regression, eXtreme Gradient Boosting, Random Forest (RF) and LightGBM. The performance of these models were evaluated by the area under the receiver operating characteristic curve (AUC). RESULTS Ultimately, 704 patients were enrolled and randomly divided into a training set (n = 564) and a testing set (n = 140). Four factors were ultimately selected to establish the model including neutrophil, globulin, β-D-glucan and ground glass opacity. The RF model exhibited the greatest diagnostic performance with an AUC of 0.907. The calibration curve and decision curve analysis also demonstrated its accuracy and applicability. CONCLUSIONS We constructed a PCP diagnostic model in patients with severe pneumonia using four easily available and noninvasive clinical indicators. With satisfying diagnostic performance and good clinical practicability, this model may help clinicians to make early diagnosis of PCP, reduce the delays of treatment and improve the prognosis among these patients.
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Affiliation(s)
- Xiaoqian Li
- Department of Critical Care Medicine, West China Hospital of Sichuan University, No. 37 Guoxue Alley, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xingyu Xiong
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, No. 37 Guoxue Alley, Chengdu, 610041, Sichuan, People's Republic of China
| | - Zongan Liang
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, No. 37 Guoxue Alley, Chengdu, 610041, Sichuan, People's Republic of China
| | - Yongjiang Tang
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, No. 37 Guoxue Alley, Chengdu, 610041, Sichuan, People's Republic of China.
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Grønseth S, Rogne T, Heggelund L, Åsvold BO, Afset JE, Damås JK. Role of fungal burden in risk stratification of HIV-negative patients with Pneumocystis pneumonia: A 12-year, retrospective, observational, multicenter cohort. Int J Infect Dis 2023; 134:177-186. [PMID: 37339716 DOI: 10.1016/j.ijid.2023.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/22/2023] Open
Abstract
OBJECTIVES This study aimed to explore the role of fungal burden in risk stratification of patients without HIV-negative patients with Pneumocystis pneumonia (PCP). METHODS This was a retrospective analysis of the characteristics associated with 30-day mortality in patients who were positive for P. jirovecii using polymerase chain reaction in bronchoalveolar lavage fluid between 2006 and 2017 in a multicenter cohort from Central Norway. The fungal burden was indicated by the cycle threshold (CT) values from semiquantitative real-time polymerase chain reaction targeting the β-tubulin gene. RESULTS We included 170 patients with proven or probable PCP. The all-cause 30-day mortality was 18.2%. After adjusting for host characteristics and premorbid corticosteroid use, a higher fungal burden was associated with a higher risk of dying: adjusted odds ratio 1.42 (95% confidence interval 0.48-4.25) for a CT value 31-36, increasing to odds ratio 5.43 (95% confidence interval 1.48-19.9) for a CT value ≤30 compared with patients with a CT value ≥37. The Charlson comorbidity index (CCI) improved the risk stratification: patients with a CT value ≥37 and CCI ≤2 had a 9% mortality risk compared with 70% among those with a CT value ≤30 and CCI ≥6. Comorbid cardiovascular disease, solid tumors, immunological disorders, premorbid corticosteroids, hypoxemia, abnormal leukocyte counts, low serum albumin, and C-reactive protein ≥100 were also independently associated with 30-day mortality. The sensitivity analyses did not suggest selection bias. CONCLUSION Fungal burden may improve the risk stratification of patients without HIV-negative patients with PCP.
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Affiliation(s)
- Stine Grønseth
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
| | - Tormod Rogne
- Department of Circulation and Medical Imaging, NTNU, Trondheim, Norway; Department of Chronic Disease Epidemiology and Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, USA
| | - Lars Heggelund
- Department of Internal Medicine, Vestre Viken Hospital Trust, Drammen, Norway; Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Bjørn Olav Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Trondheim, Norway; HUNT Research Center, Department of Public Health and Nursing, The Trøndelag Health Study, NTNU, Levanger, Norway; Department of Endocrinology, St. Olavs hospital, Clinic of Medicine, Trondheim University Hospital, Trondheim, Norway
| | - Jan Egil Afset
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Department of Medical Microbiology, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jan Kristian Damås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Department of Infectious Diseases, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway; Centre of Molecular Inflammation Research, NTNU, Trondheim, Norway
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12
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Belanger CR, Locher K, Velapatino B, Dufresne PJ, Eckbo E, Charles M. Quick versus Quantitative: Evaluation of Two Commercial Real-Time PCR Assays for the Detection of Pneumocystis jirovecii from Bronchoalveolar Lavage Fluids. Microbiol Spectr 2023; 11:e0102123. [PMID: 37260378 PMCID: PMC10434167 DOI: 10.1128/spectrum.01021-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023] Open
Abstract
Two commercial real-time PCR assays for the detection of Pneumocystis jirovecii were compared, the quantitative RealStar P. jirovecii assay and the qualitative DiaSorin P. jirovecii assay, the latter of which can be used without nucleic acid extraction. Archived bronchoalveolar lavage (BAL) specimens (n = 66), previously tested by molecular methods, were tested by both assays, and the results were compared to the respective original result. The RealStar P. jirovecii assay demonstrated good positive percent agreement (PPA) (90% [95% confidence interval (CI), 72 to 97%]; 27/30) and negative percent agreement (NPA) (100% [95% CI, 88 to 100%]; 36/36) with the reference method. The DiaSorin P. jirovecii assay concordantly detected P. jirovecii in 19 of 24 positive BAL samples (PPA = 73% [95% CI, 52 to 88%]). All negative BAL samples gave concordant results (NPA = 100% [95% CI, 87 to 100%]; 34/34). Discordant results occurred mostly in samples with low fungal loads. In conclusion, the RealStar assay demonstrated good concordance with reference results, and the DiaSorin P. jirovecii assay performed well for negative BAL and positive BAL samples with P. jirovecii concentrations of greater than 260 copies/mL. IMPORTANCE Pneumonia, caused by the opportunistic fungus Pneumocystis jirovecii, poses a significant risk for immunocompromised individuals. Laboratory testing for P. jirovecii is progressively shifting toward the use of molecular tests such as real-time PCR; however, this is often performed at reference laboratories. Many frontline laboratories are looking into improving their service and reducing turnaround times for obtaining P. jirovecii results by bringing molecular P. jirovecii testing in-house. We evaluated and compared two commercial real-time PCR assays with different workflows for the detection of P. jirovecii from bronchoalveolar lavage specimens. The RealStar P. jirovecii assay requires nucleic acid extraction and provides a quantification of fungal load for positive samples. The DiaSorin P. jirovecii assay offers a simple workflow without nucleic extraction from patient samples and qualitative results. Results from this study provide valuable information on performance and workflow considerations for laboratories that wish to implement P. jirovecii molecular testing.
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Affiliation(s)
- Corrie R. Belanger
- Division of Medical Microbiology, Vancouver Coastal Health, Vancouver, British Columbia, Canada
| | - Kerstin Locher
- Division of Medical Microbiology, Vancouver Coastal Health, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Billie Velapatino
- Division of Medical Microbiology, Vancouver Coastal Health, Vancouver, British Columbia, Canada
| | - Philippe J. Dufresne
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Eric Eckbo
- Division of Medical Microbiology, Vancouver Coastal Health, Vancouver, British Columbia, Canada
| | - Marthe Charles
- Division of Medical Microbiology, Vancouver Coastal Health, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Harizanov R, Tsvetkova N, Ivanova A, Enikova R, Videnova M, Rainova I, Kaneva E, Kaftandjiev I, Strashimirov D, Yancheva-Petrova N, Simeonovski I, Levterova V, Yanev N. Study on the Prevalence of Pneumocystis jirovecii as a Causative Agent of Lung Pathology in People with Different Immune Status. Biomedicines 2023; 11:1851. [PMID: 37509491 PMCID: PMC10376562 DOI: 10.3390/biomedicines11071851] [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: 06/02/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Pneumocystis pneumonia (PCP) commonly affects immunocompromised individuals, whereas in immunocompetent persons, it occurs relatively rarely, and in most cases, the Pneumocystis infection is detected as an asymptomatic colonization. The present study aimed to establish the prevalence of Pneumocystis jirovecii infection in human hosts with different immune status (immunocompromised and immunocompetent), using molecular diagnostic methods, and to compare their diagnostic value with that of classical staining methods. METHODS We used the collected-to-this-moment data from a prospective study on the prevalence of pneumocystosis among the Bulgarian population. Clinical specimens (including throat secretions, induced sputum, tracheal aspirates, and bronchoalveolar lavage) collected from 220 patients suspected of PCP (153 immunocompetent and 67 immunocompromised patients) were examined with microscopic staining methods and real-time PCR for detection of P. jirovecii. Results: DNA of the pathogen was detected in 38 (17%) specimens (32 immunocompromised patients and 6 immunocompetent subjects). From all 220 clinical samples examined by staining methods, only five (2%) P. jirovecii cysts were detected by the Gomori stain. All patients with PCP were treated with trimethoprim-sulfamethoxazole, but in ten of them (HIV-positive patients), the disease had a fatal outcome. CONCLUSIONS This study is the first in Bulgaria including the main available laboratory methods for diagnosis of human pneumocystosis. Regarding the etiological diagnosis of PCP, in our study the sensitivity of real-time PCR was higher compared to the staining methods. The choice of a method for sample collection and examination has an important role in the efficiency of the laboratory diagnostics.
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Affiliation(s)
- Rumen Harizanov
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Nina Tsvetkova
- 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
| | - Raina Enikova
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Mihaela Videnova
- 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
| | - Eleonora Kaneva
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Iskren Kaftandjiev
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Dimitar Strashimirov
- Department for AIDS, Specialized Hospital for Active Treatment of Infectious and Parasitic Diseases, Ivan Geshev Blvd. 17, 1431 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
| | - Ivan Simeonovski
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Viktoria Levterova
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Nikolay Yanev
- Department of Bronchology, University Multi-Profile Hospital (UMBAL) for Active Treatment of Lung Diseases "Sveti Ivan Rilski" EAD, Ivan Geshev Blvd. 19, 1431 Sofia, Bulgaria
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Huang JJ, Zhang SS, Liu ML, Yang EY, Pan Y, Wu J. Next-generation sequencing technology for the diagnosis of Pneumocystis pneumonia in an immunocompetent female: A case report. World J Clin Cases 2023; 11:4425-4432. [PMID: 37449225 PMCID: PMC10337001 DOI: 10.12998/wjcc.v11.i18.4425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND Pneumocystis pneumonia (PCP) is a serious fungal infection usually seen in patients with human immunodeficiency virus, and it is more frequently found and has a high fatality rate in immunocompromised people. Surprisingly, it rarely occurs in immunocompetent patients. However, the clinical diagnosis of this pathogen is made more difficult by the difficulty of obtaining accurate microbiological evidence with routine tests. This case reports a PCP patient with normal immune function who was diagnosed through next-generation sequencing (NGS).
CASE SUMMARY A 23-year-old female who had no special disease in the past was admitted to the hospital with a persistent fever and cough. Based on the initial examination results, the patient was diagnosed with bipulmonary pneumonia, and empirical broad-spectrum antibiotic therapy was administered. However, due to the undetermined etiology, the patient's condition continued to worsen. She was transferred to the intensive care unit because of acute respiratory failure. After the diagnosis of Pneumocystis jirovecii infection through NGS in bronchoalveolar lavage fluid and treatment with trimethoprim/sulfamethoxazole and caspofungin, the patient gradually recovered and had a good prognosis.
CONCLUSION This case emphasizes that, for patients with normal immune function the possibility of PCP infection, although rare, cannot be ignored. NGS plays an important role in the diagnosis of refractory interstitial pneumonia and acute respiratory failure.
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Affiliation(s)
- Jing-Ji Huang
- The Second Clinical Medical College, Guizhou University of Traditional Chinese Medicine, Guiyang 550000, Guizhou Province, China
| | - Song-Song Zhang
- Intensive Care Unit, Guizhou Provincial People's Hospital, Guiyang 550000, Guizhou Province, China
| | - Man-Li Liu
- Intensive Care Unit, Guizhou Provincial People's Hospital, Guiyang 550000, Guizhou Province, China
| | - En-Yu Yang
- Intensive Care Unit, Guizhou Provincial People's Hospital, Guiyang 550000, Guizhou Province, China
| | - Yu Pan
- Intensive Care Unit, Guizhou Provincial People's Hospital, Guiyang 550000, Guizhou Province, China
| | - Jing Wu
- Intensive Care Unit, Guizhou Provincial People's Hospital, Guiyang 550000, Guizhou Province, China
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15
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Fang W, Wu J, Cheng M, Zhu X, Du M, Chen C, Liao W, Zhi K, Pan W. Diagnosis of invasive fungal infections: challenges and recent developments. J Biomed Sci 2023; 30:42. [PMID: 37337179 DOI: 10.1186/s12929-023-00926-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/13/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND The global burden of invasive fungal infections (IFIs) has shown an upsurge in recent years due to the higher load of immunocompromised patients suffering from various diseases. The role of early and accurate diagnosis in the aggressive containment of the fungal infection at the initial stages becomes crucial thus, preventing the development of a life-threatening situation. With the changing demands of clinical mycology, the field of fungal diagnostics has evolved and come a long way from traditional methods of microscopy and culturing to more advanced non-culture-based tools. With the advent of more powerful approaches such as novel PCR assays, T2 Candida, microfluidic chip technology, next generation sequencing, new generation biosensors, nanotechnology-based tools, artificial intelligence-based models, the face of fungal diagnostics is constantly changing for the better. All these advances have been reviewed here giving the latest update to our readers in the most orderly flow. MAIN TEXT A detailed literature survey was conducted by the team followed by data collection, pertinent data extraction, in-depth analysis, and composing the various sub-sections and the final review. The review is unique in its kind as it discusses the advances in molecular methods; advances in serology-based methods; advances in biosensor technology; and advances in machine learning-based models, all under one roof. To the best of our knowledge, there has been no review covering all of these fields (especially biosensor technology and machine learning using artificial intelligence) with relevance to invasive fungal infections. CONCLUSION The review will undoubtedly assist in updating the scientific community's understanding of the most recent advancements that are on the horizon and that may be implemented as adjuncts to the traditional diagnostic algorithms.
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Affiliation(s)
- Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Junqi Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Mingrong Cheng
- Department of Anorectal Surgery, The Third Affiliated Hospital of Guizhou Medical University, Guizhou, 558000, China
| | - Xinlin Zhu
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Mingwei Du
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Wanqing Liao
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Kangkang Zhi
- Department of Vascular and Endovascular Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
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Lugat A, Lasolle H, François M, Benhenda N, Bricaire L, Cornu E, Cristante J, Gitton A, Hadoux J, Kerlan V, Le Bras M, Mezzaroba V, Puerto M, Storey C, Ouzounian S, Donadille B, Raverot G, Drui D, Haissaguerre M. Pneumocystis pneumonia in patients with Cushing's syndrome: A French multicenter retrospective study. ANNALES D'ENDOCRINOLOGIE 2023; 84:37-44. [PMID: 36183804 DOI: 10.1016/j.ando.2022.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022]
Abstract
OBJECTIVE Pneumocystis pneumonia (PcP) is an opportunistic infection occurring in immunocompromised patients. Cushing's syndrome (CS) impairs the immune system, and several authors have reported PcP in patients with CS. The present study aimed to characterize PcP occurring in a CS context and its management in French tertiary centers, in order to highlight the similarities in clinical presentation and treatment according to whether prophylaxis is implemented or not. METHODS This was a multicenter retrospective study conducted in several French University Hospitals and Cancer Centers. Patients with PcP and confirmed CS regardless of etiology were included. We excluded patients with other known causes of acquired immunodeficiency with increased risk of PcP. RESULTS Twenty-five patients were included. CS etiology was neoplastic in 84.0% of cases. CS clinical presentation associated predominant catabolic signs (76.0%), hypokalemia (91.7%) and lymphopenia (89.5%). CS was intense in most patients, with mean plasma cortisol levels at diagnosis of 2.424±1.102nmol/L and urinary free cortisol>10× the upper limit of normal in 85.0%. In all patients, PcP onset followed introduction of cortisol blockers, at a median 5.5 days. Patients were treated with 1 to 3 cortisol blockers, mainly metyrapone (88%), which significatively lowered plasma cortisol levels to 667±541nmol/L at the onset of PcP (P<0.001). PcP occurred in 7 patients despite prophylaxis. Finally, 60.0% patients were admitted to intensive care, and 20.0% died of PcP. CONCLUSION High mortality in patients with PcP implies that clinicians should be better informed about this rare infectious complication. Prophylaxis remains controversial, requiring comparative studies.
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Affiliation(s)
- Alexandre Lugat
- Medical Oncology Department, CHU de Nantes, 44000 Nantes, France; Nantes Université, Inserm 1307, CNRS 6075, Université d'Angers, CRCI2NA, Nantes, France
| | - Hélène Lasolle
- Endocrinology Department, Reference Centre for Rare Pituitary Diseases HYPO, "Groupement Hospitalier Est", Hospices Civils de Lyon, Bron, France; Lyon 1 University, Villeurbanne, France; INSERM U1052, CNRC UMR5286, Cancer Research Centre of Lyon (CRLC), Lyon, France
| | - Maud François
- Endocrinology, Diabetology and Nutrition, Centre Hospitalier Universitaire de Reims, Reims, France
| | | | - Léopoldine Bricaire
- Department of Endocrinology and National Reference Center for Rare Adrenal Disorders, Hôpital Cochin, Assistance publique-Hôpitaux de Paris, 75014 Paris, France
| | - Erika Cornu
- Hypertension Unit, Hôpital Européen George-Pompidou, Paris, France
| | | | - Anne Gitton
- Endocrinology, Diabetology and Nutrition, Centre Hospitalier Universitaire de Reims, Reims, France
| | - Julien Hadoux
- Department of Endocrine Oncology and Nuclear Medicine, Gustave-Roussy and University Paris-Saclay, Villejuif, France
| | - Véronique Kerlan
- Department of Endocrinology, Diabetes and Metabolic Diseases, Hôpital de la Cavale-Blanche, Brest, France
| | - Maëlle Le Bras
- Department of Endocrinology, Diabetology and Nutrition, l'institut du thorax, CHU Nantes, Nantes, France
| | - Vincent Mezzaroba
- Endocrinology Department, Reference Centre for Rare Pituitary Diseases HYPO, "Groupement Hospitalier Est", Hospices Civils de Lyon, Bron, France; Lyon 1 University, Villeurbanne, France; INSERM U1052, CNRC UMR5286, Cancer Research Centre of Lyon (CRLC), Lyon, France
| | - Marie Puerto
- Department of Endocrinology, Haut Levêque University Hospital, Bordeaux, France
| | - Caroline Storey
- Department of Paediatric Endocrinology and Diabetology, Robert-Debré Teaching Hospital, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Sophie Ouzounian
- Endocrinology Department, Saint-Antoine Hospital, Sorbonne Université, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Bruno Donadille
- Endocrinology Department, Saint-Antoine Hospital, Sorbonne Université, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Gérald Raverot
- Endocrinology Department, Reference Centre for Rare Pituitary Diseases HYPO, "Groupement Hospitalier Est", Hospices Civils de Lyon, Bron, France; Lyon 1 University, Villeurbanne, France; INSERM U1052, CNRC UMR5286, Cancer Research Centre of Lyon (CRLC), Lyon, France
| | - Delphine Drui
- Department of Endocrinology, Diabetology and Nutrition, l'institut du thorax, CHU Nantes, Nantes, France
| | - Magalie Haissaguerre
- Department of Endocrinology, Haut Levêque University Hospital, Bordeaux, France.
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Amstutz P, Bahr NC, Snyder K, Shoemaker DM. Pneumocystis jirovecii Infections Among COVID-19 Patients: A Case Series and Literature Review. Open Forum Infect Dis 2023; 10:ofad043. [PMID: 36817747 PMCID: PMC9933943 DOI: 10.1093/ofid/ofad043] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/24/2023] [Indexed: 01/30/2023] Open
Abstract
Background Pneumocystis jirovecii pneumonia (PCP) is a serious, emerging complication of coronavirus disease 2019 (COVID-19). Methods We performed a systematic review of published cases. We describe 6 new cases of PCP/COVID-19 coinfection. Among our cases (n = 6) and those in the literature (n = 69) with available data, the median age (interquartile range [IQR]) was 59 (44-77) years (n = 38), 72% (47/65) were male, and the mortality rate was 30.9% (21/68). Results Long-term corticosteroid use was noted in 45.1% (23/51), advanced HIV infection (defined as a CD4 count <200 cells/μL) in 17.6% (9/51), and antineoplastic chemotherapy in 13.7% (7/51), consistent with known PCP risk factors. Notably, 56.7% (38/47) had verifiable risk factors for PCP (high-dose corticosteroids, immunosuppressive therapy, and HIV infection) before COVID-19 infection. A median absolute lymphocyte count (IQR) of 0.61 (0.28-0.92) ×103 cells/mm3 (n = 23) and CD4 count (IQR) of 66 (33-291.5) cells/mm3 (n = 20) were also discovered among the study population. Conclusions These findings suggest a need for greater attention to PCP risk factors among COVID-19 patients and consideration of PCP prophylaxis in these high-risk populations.
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Affiliation(s)
- Paul Amstutz
- School of Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Nathan C Bahr
- Division of Infectious Diseases, Department of Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Karen Snyder
- Division of Infectious Diseases, Department of Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - D Matthew Shoemaker
- Correspondence: D. Matthew Shoemaker, DO, 3901 Rainbow Boulevard, Kansas City, KS 66103 ()
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18
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Li X, Liang S, Zhang D, He M, Zhang H. The clinical application of metagenomic next-generation sequencing in sepsis of immunocompromised patients. Front Cell Infect Microbiol 2023; 13:1170687. [PMID: 37168393 PMCID: PMC10164957 DOI: 10.3389/fcimb.2023.1170687] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/27/2023] [Indexed: 05/13/2023] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) was commonly applied given its ability to identify and type all infections without depending upon culture and to retrieve all DNA with unbiasedness. In this study, we strive to compare outcomes of mNGS with conventional culture methods in adults with sepsis, investigate the differences between the immunocompromised and control group, and assess the clinical effects of mNGS. Methods In our study, 308 adult sepsis patients were included. We used both mNGS and conventional culture methods to analyze diagnostic results, pathogens, and sample types. The correlation between some laboratory tests and the frequency of pathogens by groups was also analyzed. Furthermore, the clinical impacts of mNGS were estimated. Results 308 samples were assigned to an immunocompromised group (92/308,29.9%) and a control group (216/308,70.1%). There was the sensitivity of mNGS considered greater than that of the culture method in all samples (88.0% vs 26.3%; P < 0.001), in the immunocompromised group (91.3% vs 26.1%; P < 0.001), and the control group (86.6% vs 26.4%; P < 0.001), particularly in all sample types of blood (P < 0.001), BALF (P < 0.001), CSF (P < 0.001), sputum (P < 0.001) and ascitic fluid (P = 0.008). When examining the mNGS results between groups, Pneumocystis jirovecii (P < 0.001), Mucoraceae (P = 0.014), and Klebsiella (P = 0.045) all showed significant differences. On the whole, mNGS detected more pathogens than culture methods (111 vs 25), found 89 organisms that were continuously overlooked in entire samples by culture methods, and showed a favorable positive clinical effect in 76.3% (235 of 308) of patients. In 185 (60.1%) patients, mNGS prompted a modification in the course of management, which included antibiotic de-escalation in 61(19.8%) patients. Conclusions The research discovered that mNGS was more sensitive than the culture method, particularly in samples of blood, BALF, CSF, sputum, and ascitic fluid. When examining the mNGS results, Pneumocystis jirovecii and Mucoraceae were the pathogens seen more commonly in immunocompromised patients with sepsis, which required more attention from clinicians. There was a substantial benefit of mNGS in enhancing the diagnosis of sepsis and advancing patient treatment.
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Kim HS, Nam HW, Ahn HJ, Lee SH, Kim YH. Spatiotemporal Clusters and Trends of Pneumocystis Pneumonia in Korea. THE KOREAN JOURNAL OF PARASITOLOGY 2022; 60:327-338. [DOI: 10.3347/kjp.2022.60.5.327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/04/2022] [Indexed: 11/06/2022]
Abstract
This study determined the recent status and trend of <i>Pneumocystis jirovecii</i> pneumonia (PcP) in the non-human immunodeficiency virus (HIV) (non-HIV-PcP) and HIV (HIV-PcP) infected populations using data from the Health Insurance Review & Assessment Service (HIRA) and the Korea Disease Control and Prevention Agency (KDCA). SaTScan and Joinpoint were used for statistical analyses. Non-HIV-PcP cases showed an upward trend during the study period from 2010 to 2021, with the largest number in 2021 (551 cases). The upward trend was similar until 2020 after adjusting for the population. Seoul had the highest number of cases (1,597) in the non-HIV-PcP group, which was the same after adjusting for the population (162 cases/1,000,000). It was followed by Jeju-do (89 cases/1,000,000). The most likely cluster (MLC) for the non-HIV-PCP group was Seoul (Relative Risk (RR)=4.59, Log Likelihood Ratio (LLR)=825.531), followed by Jeju-do (RR=1.59, LLR=5.431). An upward trend was observed among the non-HIV-PcP group in the Jeju-do/Jeollanam-do/Jeollabuk-do/Gyeongsangnam-do/Busan/Daejeon/Daegu/Ulsan joint cluster (29.02%, LLR=11.638, <i>P</i><0.001) located in the southern part of Korea. Both women and men in the non-HIV groups showed an overall upward trend of PcP during the study period. Men in the 60-69 age group had the highest annual percentage change (APC 41.8) during 2014-2019. In contrast, the HIV groups showed a falling trend of PcP recently. Men in the 60-69 age group had the most decrease (APC -17.6) during 2018-2021. This study provides an analytic basis for health measures and a nationwide epidemiological surveillance system for the management of PcP.
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Liu W, Li M, Xu Y, Wang F, Wang J, Wang H, Xu X, Wang Y, Sun H. Evaluation of the Performance of a Multiplex Real-Time PCR Assay for the Identification of Aspergillus, Cryptococcus neoformans, and Pneumocystis jirovecii Simultaneously from Sputum in Multicenter. Infect Drug Resist 2022; 15:6009-6017. [PMID: 36267265 PMCID: PMC9576602 DOI: 10.2147/idr.s379043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 09/28/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose To evaluate the performance of a multiplex real-time polymerase chain reaction (PCR) assay for the simultaneous identification of Aspergillus, Cryptococcus neoformans, and Pneumocystis jirovecii from sputum. Patients and Methods Sputum samples (n=537) from patients with suspected invasive fungal infection (IFI) were collected from four centers; they were tested by both multiplex real-time PCR assay and DNA sequencing. DNA sequencing was considered as the reference method, and the performance of the multiplex real-time assay was evaluated by determining the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). The interference experiment, repeatability, reproducibility, and stability of the multiplex real-time PCR assay were also evaluated. Results The detection performance of the multiplex real-time assay, compared with that of DNA sequencing, for the three pathogens was as follows: sensitivity, specificity, PPV, and NPV for Aspergillus, Cryptococcus neoformans, and Pneumocystis jirovecii were 99.40%, 98.64%, 97.09%, and 99.73%; 100%, 99.59%, 96.36%, and 100.00%; and 99.28%, 98.50%, 95.80%, and 99.75%, respectively. The consistency of the two methods was almost perfect: the kappa value was between 0.97 and 0.98. The minimum detection limit of the multiplex real-time assay for each of the three pathogens was 1250 copies/mL. Interference experiment showed that blood and normally used antifungal drugs had no effect on the results. No cross-reactivity was detected for any bacteria or fungi. In 40 patients, mixed infections by Aspergillus and/or Cryptococcus neoformans and/or Pneumocystis jirovecii were detected by the multiplex real-time assay. Among these patients, those with acquired immune deficiency syndrome (AIDS) ranked first, with Aspergillus and Pneumocystis mixed infection accounting for 75%. Conclusion The multiplex real-time PCR assay is fast, sensitive, and specific and has good clinical application prospects.
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Affiliation(s)
- Wenjing Liu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, 100730, People’s Republic of China
| | - Min Li
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, People’s Republic of China
| | - Yingchun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, 100730, People’s Republic of China
| | - Fengchao Wang
- The First Affiliated Hospital of Bengbu Medical College, Anhui, 233004, People’s Republic of China
| | - Jing Wang
- Chongqing Public Health Medical Center, Chongqing, 400036, People’s Republic of China
| | - Huizhu Wang
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, People’s Republic of China
| | - Xinmin Xu
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, People’s Republic of China
| | - Yajie Wang
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, People’s Republic of China,Yajie Wang, Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, People’s Republic of China, Tel +86-13611269270, Email
| | - Hongli Sun
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, 100730, People’s Republic of China,Correspondence: Hongli Sun, Peking Union Medical College Hospital (Dongdan Campus), No. 1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, People’s Republic of China, Tel +86-1069159788, Fax +86-1069159766, Email
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21
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Hou JN, Liu HD, Tan QY, Cao FA, Wang SL, Yao MY, Zhao YC. Risk factors of in-hospital mortality in patients with pneumocystis pneumonia diagnosed by metagenomics next-generation sequencing. Front Cell Infect Microbiol 2022; 12:994175. [PMID: 36225233 PMCID: PMC9549864 DOI: 10.3389/fcimb.2022.994175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives The metagenomic next-generation sequencing (mNGS) test is useful for rapid and accurate detection and identification of pathogenic microorganisms. The aim of the present study was to investigate the factors associated with in-hospital mortality in pneumocystis pneumonia (PCP) patients with mNGS-assisted diagnosis. Methods Our study enrolled 154 patients with mNGS-positive PCP from August 2018 to February 2022 at the First Affiliated Hospital of Zhengzhou University respectively. Patients were divided into the survivor group (n=98) and the death group (n=56) according to whether in-hospital death occurred. Baseline characteristics, patients’ pre-hospital symptoms and patients’ CT imaging performance during hospitalization were carefully compared between the two groups. Risk factors for the occurrence of in-hospital death were sought by selecting indicators that were significantly different between the two groups for modelling and performing multiple logistic regression analysis. Results Compared with the in-hospital death patients, the survivors were younger and had higher levels of albumin (ALB) (age: 50.29 ± 14.63 years vs 59.39 ± 12.27 years, p<0.001; ALB: 32.24 ± 5.62 g/L vs 29.34 ± 5.42g/L, p=0.002; respectively), while the levels of lactate dehydrogenase (LDH) and C-reactive protein CRP were lower (LDH: 574.67 ± 421.24 U/L vs 960.80 ± 714.94 U/L, p=0.001; CRP: 54.97 ± 55.92 mg/L vs80.45 ± 73.26 mg/L, p=0.018; respectively). Multiple logistic regression analysis revealed that age, the baseline LDH and CRP levels were all positively associated with high in-hospital mortality [age: OR(95%CI): 1.115 (1.062-1.172), p<0.001; LDH: OR(95%CI): 1.002 (1.001-1.003), p<0.001; CRP: OR(95%CI): 1.008 (1.000-1.017), p=0.045; respectively] while the platelet counts was negatively associated with it [OR(95%CI): 0.986 (0.979-0.992), p<0.001]. Conclusions Old age, high baseline levels of LDH and CRP and low platelet counts were risk factors of the in-hospital mortality in mNGS positive PCP patients.
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Affiliation(s)
- Jun-Na Hou
- Department of Pulmonary, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Heng-Dao Liu
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qiu-Yue Tan
- Department of Pulmonary, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Feng-An Cao
- Department of Pulmonary, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shi-Lei Wang
- Department of Pulmonary, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Meng-Ying Yao
- Department of Pulmonary, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Meng-Ying Yao, ; Yang-Chao Zhao,
| | - Yang-Chao Zhao
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Meng-Ying Yao, ; Yang-Chao Zhao,
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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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Sohani ZN, Butler-Laporte G, Aw A, Belga S, Benedetti A, Carignan A, Cheng MP, Coburn B, Costiniuk CT, Ezer N, Gregson D, Johnson A, Khwaja K, Lawandi A, Leung V, Lother S, MacFadden D, McGuinty M, Parkes L, Qureshi S, Roy V, Rush B, Schwartz I, So M, Somayaji R, Tan D, Trinh E, Lee TC, McDonald EG. Low-dose trimethoprim-sulfamethoxazole for the treatment of Pneumocystis jirovecii pneumonia (LOW-TMP): protocol for a phase III randomised, placebo-controlled, dose-comparison trial. BMJ Open 2022; 12:e053039. [PMID: 35863836 PMCID: PMC9310160 DOI: 10.1136/bmjopen-2021-053039] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Pneumocystis jirovecii pneumonia (PJP) is an opportunistic infection of immunocompromised hosts with significant morbidity and mortality. The current standard of care, trimethoprim-sulfamethoxazole (TMP-SMX) at a dose of 15-20 mg/kg/day, is associated with serious adverse drug events (ADE) in 20%-60% of patients. ADEs include hypersensitivity reactions, drug-induced liver injury, cytopenias and renal failure, all of which can be treatment limiting. In a recent meta-analysis of observational studies, reduced dose TMP-SMX for the treatment of PJP was associated with fewer ADEs, without increased mortality. METHODS AND ANALYSIS A phase III randomised, placebo-controlled, trial to directly compare the efficacy and safety of low-dose TMP-SMX (10 mg/kg/day of TMP) with the standard of care (15 mg/kg/day of TMP) among patients with PJP, for a composite primary outcome of change of treatment, new mechanical ventilation, or death. The trial will be undertaken at 16 Canadian hospitals. Data will be analysed as intention to treat. Primary and secondary outcomes will be compared using logistic regression adjusting for stratification and presented with 95% CI. ETHICS AND DISSEMINATION This study has been conditionally approved by the McGill University Health Centre; Ethics approval will be obtained from all participating centres. Results will be submitted for publication in a peer-reviewed journal. TRIAL REGISTRATION NUMBER NCT04851015.
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Affiliation(s)
- Zahra N Sohani
- Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada
| | - Guillaume Butler-Laporte
- Department of Epidemiology, Occupational Health, and Biostatistics, McGill University, Montreal, Quebec, Canada
- Division of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada
| | - Andrew Aw
- Division of Hematology, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Sara Belga
- Division of Infectious Diseases, Department of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrea Benedetti
- Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada
- Department of Epidemiology, Occupational Health, and Biostatistics, McGill University, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Alex Carignan
- Division of Microbiology and Infectious Diseases, Centre hospitalier universitaire de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Matthew P Cheng
- Division of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Bryan Coburn
- Division of Infectious Diseases, Department of Medicine, University Health Network, Toronto, Ontario, Canada
| | - Cecilia T Costiniuk
- Division of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Chronic Viral Illness Service, McGill University, Montreal, Quebec, Canada
| | - Nicole Ezer
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Division of Respirology, Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada
| | - Dan Gregson
- Departments of Pathology and Laboratory Medicine and Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Andrew Johnson
- Division of Infectious Diseases, Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kosar Khwaja
- Department of Epidemiology, Occupational Health, and Biostatistics, McGill University, Montreal, Quebec, Canada
- Department of Critical Care Medicine, McGill University Health Centre, Montreal, Quebec, Canada
| | - Alexander Lawandi
- Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Victor Leung
- Department of Laboratory Medicine & Pathology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Sylvain Lother
- Department of Critical Care Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Derek MacFadden
- Division of Infectious Diseases, Department of Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - Michaeline McGuinty
- Division of Infectious Diseases, Department of Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - Leighanne Parkes
- Division of Medical Microbiology and Infectious Diseases, Lady Davis Institute for Medical Research, Montreal, Quebec, Canada
| | - Salman Qureshi
- Department of Epidemiology, Occupational Health, and Biostatistics, McGill University, Montreal, Quebec, Canada
- Division of Respirology, Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada
- Department of Critical Care Medicine, McGill University Health Centre, Montreal, Quebec, Canada
| | - Valerie Roy
- Division of Microbiology and Infectious Diseases, Centre Hospitalier Universitaire de Sherbrooke Hôtel-Dieu, Sherbrooke, Quebec, Canada
| | - Barret Rush
- Department of Critical Care Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ilan Schwartz
- Division of Infectious Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Miranda So
- Sinai Health System-University Health Network Antimicrobial Stewardship Program, University Health Network, Toronto, Ontario, Canada
| | - Ranjani Somayaji
- Division of Infectious Diseases, Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Darrell Tan
- Division of Infectious Diseases, St Michael's Hospital, Toronto, Ontario, Canada
| | - Emilie Trinh
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Division of Nephrology, Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Todd C Lee
- Division of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Clinical Practice Assessment Unit, Montreal, Quebec, Canada
| | - Emily G McDonald
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Clinical Practice Assessment Unit, Montreal, Quebec, Canada
- Division of General Internal Medicine, McGill University Health Centre, Montreal, Quebec, Canada
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Tiantian C, Jin Y, Jing Z, Jing F, Xiaoyan J. Pneumocystis jirovecii pneumonia in a patient receiving chemotherapy for advanced prostatic cancer: a case report. J Int Med Res 2022; 50:3000605221105358. [PMID: 35751409 PMCID: PMC9237926 DOI: 10.1177/03000605221105358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Pneumocystis jirovecii pneumonia (PJP) in advanced prostatic cancer patients not receiving high-dose glucocorticoids has been reported rarely. A 73-year-old man underwent chemotherapy with cisplatin and docetaxel for advanced prostatic cancer. After nine cycles of chemotherapy, he developed a high fever, dry cough, shortness of breath, and severe fatigue, with rapid-onset hypoxic respiratory failure. Investigations demonstrated bilateral ground-glass opacities with positive bronchoalveolar lavage fluid (BALF) for Pneumocystis jirovecii by next-generation sequencings (NGS). The patient recovered well with treatment with trimethoprim-sulfamethoxazole, caspofungin, and corticosteroids. This case report describes a case of PJP in a patient with a solid tumor who did not receive high-dose glucocorticoids and emphasizes the importance of early diagnosis and treatment.
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Affiliation(s)
- Chen Tiantian
- Department of Pulmonary Medicine and Critical Medicine, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yan Jin
- Department of Pulmonary Medicine and Critical Medicine, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhang Jing
- Department of Pulmonary Medicine and Critical Medicine, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Feng Jing
- Department of Pulmonary Medicine and Critical Medicine, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jin Xiaoyan
- Department of Pulmonary Medicine and Critical Medicine, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Franconi I, Leonildi A, Erra G, Fais R, Falcone M, Ghelardi E, Lupetti A. Comparison of different microbiological procedures for the diagnosis of Pneumocystis jirovecii pneumonia on bronchoalveolar-lavage fluid. BMC Microbiol 2022; 22:143. [PMID: 35597925 PMCID: PMC9123786 DOI: 10.1186/s12866-022-02559-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The current diagnostic gold standard for Pneumocystis jirovecii is represented by microscopic visualization of the fungus from clinical respiratory samples, as bronchoalveolar-lavage fluid, defining "proven" P. jirovecii pneumonia, whereas qPCR allows defining "probable" diagnosis, as it is unable to discriminate infection from colonization. However, molecular methods, such as end-point PCR and qPCR, are faster, easier to perform and interpret, thus allowing the laboratory to give back the clinician useful microbiological data in a shorter time. The present study aims at comparing microscopy with molecular assays and beta-D-glucan diagnostic performance on bronchoalveolar-lavage fluids from patients with suspected Pneumocystis jirovecii pneumonia. Bronchoalveolar-lavage fluid from eighteen high-risk and four negative control subjects underwent Grocott-Gomori's methenamine silver-staining, end-point PCR, RT-PCR, and beta-D-glucan assay. RESULTS All the microscopically positive bronchoalveolar-lavage samples (50%) also resulted positive by end-point and real time PCR and all, but two, resulted positive also by beta-D-glucan quantification. End-point PCR and RT-PCR detected 10 (55%) and 11 (61%) out of the 18 samples, respectively, thus showing an enhanced sensitivity in comparison to microscopy. All RT-PCR with a Ct < 27 were confirmed microscopically, whereas samples with a Ct ≥ 27 were not. CONCLUSIONS Our work highlights the need of reshaping and redefining the role of molecular diagnostics in a peculiar clinical setting, like P. jirovecii infection, which is a rare but also severe and rapidly progressive clinical condition affecting immunocompromised hosts that would largely benefit from a faster diagnosis. Strictly selected patients, according to the inclusion criteria, resulting negative by molecular methods could be ruled out for P. jirovecii pneumonia.
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Affiliation(s)
- Iacopo Franconi
- Department of Traslational Research and of New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
| | - Alessandro Leonildi
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Gianluca Erra
- Department of Traslational Research and of New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
| | - Roberta Fais
- Department of Traslational Research and of New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
| | - Marco Falcone
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Emilia Ghelardi
- Department of Traslational Research and of New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
| | - Antonella Lupetti
- Department of Traslational Research and of New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy.
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Co-Infection of COVID-19 and Pneumocystosis Following Rituximab Infusion—A Case Report. TRANSPLANTOLOGY 2022. [DOI: 10.3390/transplantology3010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Immunocompromised patients with respiratory viral infections are at increased risk of fungal superinfections, including Pneumocystosis. Within the scope of the COVID-19 pandemic, Pneumocystis jirovecii co-infections are being increasingly reported. Differential diagnosis often creates a dilemma, due to multiple overlapping clinical and radiographic features. Awareness of fungal co-infections in the context of the COVID-19 pandemic is crucial to initiate prophylactic measures, especially in high-risk individuals. We report the second case of Pneumocystis jirovecii pneumonia and COVID-19 co-infection in a renal transplant recipient in Poland.
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Watanabe Y, Hayashi K, Terai S. A Rare Case of Ulcerative Colitis with Severe Pneumocystis jirovecii Pneumonia and Cytomegalovirus Colitis: A Case Report and Literature Review. Intern Med 2022; 61:339-344. [PMID: 34373380 PMCID: PMC8866792 DOI: 10.2169/internalmedicine.7953-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Pneumocystis jirovecii pneumonia (PJP) and cytomegalovirus (CMV) colitis are opportunistic infections that occur during immunosuppressive treatments for ulcerative colitis (UC). The prognosis of PJP and CMV colitis is very poor. We herein report a rare case of a 74-year-old UC patient with PJP and CMV colitis that was successfully treated with intensive therapy. PJP progresses rapidly, so the timing and choice of treatment are critical. Furthermore, a literature review of similar cases suggested that prophylactic therapy for opportunistic infections might be important, especially in the elderly. This case will serve as a reference for successful treatment in future cases.
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Affiliation(s)
- Yusuke Watanabe
- Division of Preemptive Medicine for Digestive Disease and Healthy Active Life, School of Medicine, Niigata University, Japan
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, Japan
| | - Kazunao Hayashi
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, Japan
- Department of Preventive and Minimally Invasive Medicine for Digestive Desease, Niigata University, Japan
| | - Shuji Terai
- Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, Japan
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28
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Fuller K, Bultas MW. Management of Common Opportunistic Infections in People Living With HIV. J Nurse Pract 2022. [DOI: 10.1016/j.nurpra.2021.08.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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Identification of Pneumocystis jirovecii with Fluorescence In-Situ Hybridization (FISH) in Patient Samples-A Proof-of-Principle. J Fungi (Basel) 2021; 8:jof8010013. [PMID: 35049953 PMCID: PMC8778293 DOI: 10.3390/jof8010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022] Open
Abstract
In resource-limited settings, where pneumocystosis in immunocompromised patients is infrequently observed, cost-efficient, reliable, and sensitive approaches for the diagnostic identification of Pneumocystis jirovecii in human tissue samples are desirable. Here, an in-house fluorescence in situ hybridization assay was comparatively evaluated against Grocott’s staining as a reference standard with 30 paraffin-embedded tissue samples as well as against in-house real-time PCR with 30 respiratory secretions from immunocompromised patients with clinical suspicion of pneumocystosis. All pneumocystosis patients included in the study suffered from HIV/AIDS. Compared with Grocott’s staining as the reference standard, sensitivity of the FISH assay was 100% (13/13), specificity was 41% (7/17), and the overall concordance was 66.7% with tissue samples. With respiratory specimens, sensitivity was 83.3% (10/12), specificity was 100% (18/18), and the overall concordance was 93.3% as compared with real-time PCR. It remained unresolved to which proportions sensitivity limitations of Grocott’s staining or autofluorescence phenomena affecting the FISH assay accounted for the recorded reduced specificity with the tissue samples. The assessment confirmed Pneumocystis FISH in lung tissue as a highly sensitive screening approach; however, dissatisfying specificity in paraffin-embedded biopsies calls for confirmatory testing with other techniques in case of positive FISH screening results. In respiratory secretions, acceptable sensitivity and excellent specificity were demonstrated for the diagnostic application of the P. jirovecii-specific FISH assay.
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Yi J, Wang N, Wu J, Tang Y, Zhang J, Zhu L, Rui X, Guo Y, Xu Y. Development of a Droplet Digital Polymerase Chain Reaction for Sensitive Detection of Pneumocystis jirovecii in Respiratory Tract Specimens. Front Med (Lausanne) 2021; 8:761788. [PMID: 35004733 PMCID: PMC8727342 DOI: 10.3389/fmed.2021.761788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/25/2021] [Indexed: 11/24/2022] Open
Abstract
Background:Pneumocystis jirovecii is a human-specific opportunistic fungus that causes Pneumocystis pneumonia (PCP), a life-threatening opportunistic lung infection that affects immunocompromised patients. P. jirovecii colonization may be linked to the transmission of the infection. The detection of P. jirovecii in immunocompromised patients is thus especially important. The low fungal load and the presence of PCR inhibitors limit the usefulness of quantitative PCR (qPCR) for accurate absolute quantification of P. jirovecii in specimens. Droplet digital PCR (ddPCR), however, presents a methodology that allows higher sensitivity and accuracy. Here, we developed a ddPCR method for detecting P. jirovecii DNA in respiratory specimens, and evaluated its sensitivity against qPCR. Materials and Methods: One bronchoalveolar fluid (BALF) sample each was collected from 82 patients with potential PCP to test the presence of P. jirovecii DNA using both ddPCR and qPCR, and samples with inconsistent results between the two methods were further tested by metagenomic next generation sequencing (mNGS). In addition, 37 sputum samples from 16 patients diagnosed with PCP, as well as continuous respiratory tract specimens from nine patients with PCP and treated with sulfonamides, were also collected for P. jirovecii DNA testing using both ddPCR and qPCR. Results: ddPCR and qPCR gave the same results for 95.12% (78/82) of the BALF samples. The remaining four specimens tested positive using ddPCR but negative using qPCR, and they were found to be positive by mNGS. Detection results of 78.37% (29/37) sputum samples were consistent between ddPCR and qPCR, while the other eight samples tested positive using ddPCR but negative using qPCR. The P. jirovecii load of patients with PCP decreased to undetectable levels after treatment according to qPCR, but P. jirovecii was still detectable using ddPCR. Conclusions: ddPCR was more sensitive than qPCR, especially at detecting low-pathogen-load P. jirovecii. Thus, ddPCR represents a useful, viable, and reliable alternative to qPCR in P. jirovecii testing in patients with immunodeficiency.
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Affiliation(s)
- Jie Yi
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Nan Wang
- Human Genetic Resource Center, National Research Institute for Family Planning, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Jie Wu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yueming Tang
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jingjia Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | | | - Xiao Rui
- TargetingOne Corporation, Beijing, China
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
- Yong Guo
| | - Yingchun Xu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Yingchun Xu
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McDonald EG, Butler-Laporte G, Del Corpo O, Hsu JM, Lawandi A, Senecal J, Sohani ZN, Cheng MP, Lee TC. On the Treatment of Pneumocystis jirovecii Pneumonia: Current Practice Based on Outdated Evidence. Open Forum Infect Dis 2021; 8:ofab545. [PMID: 34988242 PMCID: PMC8694206 DOI: 10.1093/ofid/ofab545] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
Pneumocystis jirovecii pneumonia (PCP) is a common opportunistic infection causing more than 400000 cases annually worldwide. Although antiretroviral therapy has reduced the burden of PCP in persons with human immunodeficiency virus (HIV), an increasing proportion of cases occur in other immunocompromised populations. In this review, we synthesize the available randomized controlled trial (RCT) evidence base for PCP treatment. We identified 14 RCTs that were conducted 25-35 years ago, principally in 40-year-old men with HIV. Trimethoprim-sulfamethoxazole, at a dose of 15-20 mg/kg per day, is the treatment of choice based on historical practice rather than on quality comparative, dose-finding studies. Treatment duration is similarly based on historical practice and is not evidence based. Corticosteroids have a demonstrated role in hypoxemic patients with HIV but have yet to be studied in RCTs as an adjunctive therapy in non-HIV populations. The echinocandins are potential synergistic treatments in need of further investigation.
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Affiliation(s)
- Emily G McDonald
- Division of General Internal Medicine, Department of Medicine, McGill University Health Centre, Montréal, Canada
- Clinical Practice Assessment Unit, Department of Medicine, McGill University Health Centre, Montréal, Canada
| | - Guillaume Butler-Laporte
- Department of Epidemiology, Occupational Health, and Biostatistics, McGill University, Montréal, Canada
| | - Olivier Del Corpo
- Faculty of Medicine and Health Sciences, McGill University, Montréal, Canada
| | - Jimmy M Hsu
- Faculty of Medicine and Health Sciences, McGill University, Montréal, Canada
| | - Alexander Lawandi
- Department of Critical Care Medicine, National Institutes of Health, Clinical Center, Bethesda, Maryland, USA
| | - Julien Senecal
- Faculty of Medicine and Health Sciences, McGill University, Montréal, Canada
| | - Zahra N Sohani
- Department of Medicine, McGill University, Montréal, Canada
| | - Matthew P Cheng
- Division of Medical Microbiology, Department of Laboratory Medicine, McGill University Health Centre, Montréal, Canada
- Division of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montréal, Canada
| | - Todd C Lee
- Clinical Practice Assessment Unit, Department of Medicine, McGill University Health Centre, Montréal, Canada
- Department of Epidemiology, Occupational Health, and Biostatistics, McGill University, Montréal, Canada
- Division of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montréal, Canada
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Souza TN, Valdez AF, Rizzo J, Zamith-Miranda D, Guimarães AJ, Nosanchuk JD, Nimrichter L. Host cell membrane microdomains and fungal infection. Cell Microbiol 2021; 23:e13385. [PMID: 34392593 PMCID: PMC8664998 DOI: 10.1111/cmi.13385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/14/2021] [Accepted: 07/24/2021] [Indexed: 01/13/2023]
Abstract
Lipid microdomains or lipid rafts are dynamic and tightly ordered regions of the plasma membrane. In mammalian cells, they are enriched in cholesterol, glycosphingolipids, Glycosylphosphatidylinositol-anchored and signalling-related proteins. Several studies have suggested that mammalian pattern recognition receptors are concentrated or recruited to lipid domains during host-pathogen association to enhance the effectiveness of host effector processes. However, pathogens have also evolved strategies to exploit these domains to invade cells and survive. In fungal organisms, a complex cell wall network usually mediates the first contact with the host cells. This cell wall may contain virulence factors that interfere with the host membrane microdomains dynamics, potentially impacting the infection outcome. Indeed, the microdomain disruption can dampen fungus-host cell adhesion, phagocytosis and cellular immune responses. Here, we provide an overview of regulatory strategies employed by pathogenic fungi to engage with and potentially subvert the lipid microdomains of host cells. TAKE AWAY: Lipid microdomains are ordered regions of the plasma membrane enriched in cholesterol, glycosphingolipids (GSL), GPI-anchored and signalling-related proteins. Pathogen recognition by host immune cells can involve lipid microdomain participation. During this process, these domains can coalesce in larger complexes recruiting receptors and signalling proteins, significantly increasing their signalling abilities. The antifungal innate immune response is mediated by the engagement of pathogen-associated molecular patterns to pattern recognition receptors (PRRs) at the plasma membrane of innate immune cells. Lipid microdomains can concentrate or recruit PRRs during host cell-fungi association through a multi-interactive mechanism. This association can enhance the effectiveness of host effector processes. However, virulence factors at the fungal cell surface and extracellular vesicles can re-assembly these domains, compromising the downstream signalling and favouring the disease development. Lipid microdomains are therefore very attractive targets for novel drugs to combat fungal infections.
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Affiliation(s)
- Taiane N Souza
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alessandro F Valdez
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana Rizzo
- Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Institut Pasteur, Paris, France
| | - Daniel Zamith-Miranda
- Departments of Medicine (Division of Infectious Diseases) and Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Allan Jefferson Guimarães
- Departamento de Microbiologia e Parasitologia-MIP, Instituto Biomédico, Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Joshua D Nosanchuk
- Departments of Medicine (Division of Infectious Diseases) and Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Leonardo Nimrichter
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Wilson D. The role of zinc in the pathogenicity of human fungal pathogens. ADVANCES IN APPLIED MICROBIOLOGY 2021; 117:35-61. [PMID: 34742366 DOI: 10.1016/bs.aambs.2021.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Fungal pathogens now account for an unprecedented burden on human health. Like all microorganisms, these fungi must successfully forage for essential micronutrients such as zinc in order to proliferate. However, pathogenic microbes face an additional hurdle in securing zinc from their environment: the action of host nutritional immunity which strictly manipulates microbial access to this essential, but also potentially toxic trace metal. This review introduces the relevant pathogenic species and goes on to cover the molecular mechanisms of zinc uptake by human fungal pathogens. Fungi scavenge zinc from their environment via two basic mechanisms: via a family of cellular zinc importers-the ZIP transporters; and via a unique secreted zinc binding protein-the zincophore. However the genetic requirement of these systems for fungal virulence is highly species-specific. As well as zinc scarcity, potential intoxification with this heavy metal can occur and, unlike bacteria, fungi deal with environmental insult this via intraorganellar compartmentalization. Zinc availability also modulates the morphogenic behavior of a subset of pathogenic yeast species. This chapter will cover these different aspects of zinc availability on the physiology of human fungal pathogens with emphasis on the major pathogenic species Candida albicans.
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Affiliation(s)
- Duncan Wilson
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom.
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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.
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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
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35
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Liotti FM, Posteraro B, De Angelis G, Torelli R, De Carolis E, Speziale D, Menchinelli G, Spanu T, Sanguinetti M. A New PCR-Based Assay for Testing Bronchoalveolar Lavage Fluid Samples from Patients with Suspected Pneumocystis jirovecii Pneumonia. J Fungi (Basel) 2021; 7:jof7090681. [PMID: 34575719 PMCID: PMC8466016 DOI: 10.3390/jof7090681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 11/23/2022] Open
Abstract
To support the clinical laboratory diagnosis of Pneumocystis jirovecii (PJ) pneumonia (PCP), an invasive fungal infection mainly occurring in HIV-negative patients, in-house or commercial PJ-specific real-time quantitative PCR (qPCR) assays are todays’ reliable options. The performance of these assays depends on the type of PJ gene (multi-copy mitochondrial versus single-copy nuclear) targeted by the assay. We described the development of a PJ-PCR assay targeting the dihydrofolate reductase (DHFR)-encoding gene. After delineating its analytical performance, the PJ-PCR assay was used to test bronchoalveolar lavage (BAL) fluid samples from 200 patients (only seven were HIV positive) with suspected PCP. Of 211 BAL fluid samples, 18 (8.5%) were positive and 193 (91.5%) were negative by PJ-PCR. Of 18 PJ-PCR-positive samples, 11 (61.1%) tested positive and seven (38.9%) tested negative with the immunofluorescence assay (IFA). All (100%) of the 193 PJ-PCR-negative samples were IFA negative. Based on IFA/PCR results, patients were, respectively, classified as having (n = 18) and not having (n = 182) proven (PJ-PCR+/IFA+) or probable (PJ-PCR+/IFA−) PCP. For 182 patients without PCP, alternative infectious or non-infectious etiologies were identified. Our PJ-PCR assay was at least equivalent to IFA, fostering studies aimed at defining a qPCR-based standard for PCP diagnosis in the future.
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Affiliation(s)
- Flora Marzia Liotti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo A. Gemelli 8, 00168 Roma, Italy; (F.M.L.); (B.P.); (G.D.A.); (G.M.); (T.S.)
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy; (R.T.); (E.D.C.); (D.S.)
| | - Brunella Posteraro
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo A. Gemelli 8, 00168 Roma, Italy; (F.M.L.); (B.P.); (G.D.A.); (G.M.); (T.S.)
- Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy
| | - Giulia De Angelis
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo A. Gemelli 8, 00168 Roma, Italy; (F.M.L.); (B.P.); (G.D.A.); (G.M.); (T.S.)
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy; (R.T.); (E.D.C.); (D.S.)
| | - Riccardo Torelli
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy; (R.T.); (E.D.C.); (D.S.)
| | - Elena De Carolis
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy; (R.T.); (E.D.C.); (D.S.)
| | - Domenico Speziale
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy; (R.T.); (E.D.C.); (D.S.)
| | - Giulia Menchinelli
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo A. Gemelli 8, 00168 Roma, Italy; (F.M.L.); (B.P.); (G.D.A.); (G.M.); (T.S.)
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy; (R.T.); (E.D.C.); (D.S.)
| | - Teresa Spanu
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo A. Gemelli 8, 00168 Roma, Italy; (F.M.L.); (B.P.); (G.D.A.); (G.M.); (T.S.)
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy; (R.T.); (E.D.C.); (D.S.)
| | - Maurizio Sanguinetti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo A. Gemelli 8, 00168 Roma, Italy; (F.M.L.); (B.P.); (G.D.A.); (G.M.); (T.S.)
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy; (R.T.); (E.D.C.); (D.S.)
- Correspondence: ; Tel.: +39-06-3054-411; Fax: +39-06-3051-152
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Pulmonary cannonballs in a patient with Acquired Immunodeficiency Syndrome (AIDS). IDCases 2021; 25:e01229. [PMID: 34367917 PMCID: PMC8326746 DOI: 10.1016/j.idcr.2021.e01229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/15/2021] [Accepted: 07/15/2021] [Indexed: 11/20/2022] Open
Abstract
Pneumocystis jirovecii pneumonia (PJP) remains one of the most common and life-threatening complications in patients with AIDS. PJP typically presents subacutely with a dry cough, shortness of breath with exertion, fever, and bilateral ground-glass opacities on imaging. However, atypical imaging findings have been reported including cysts, isolated lymphadenopathy, and small to large nodules. This case highlights the importance of considering unusual presentations of a relatively common entity in order to prevent delays in diagnosis and treatment.
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Grønseth S, Rogne T, Hannula R, Åsvold BO, Afset JE, Damås JK. Epidemiological and clinical characteristics of immunocompromised patients infected with Pneumocystis jirovecii in a twelve-year retrospective study from Norway. BMC Infect Dis 2021; 21:659. [PMID: 34233631 PMCID: PMC8262122 DOI: 10.1186/s12879-021-06144-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/08/2021] [Indexed: 01/10/2023] Open
Abstract
Background Pneumocystis pneumonia (PCP) severely menaces modern chemotherapy and immunosuppression. Detailed description of the epidemiology of Pneumocystis jirovecii today is needed to identify candidates for PCP-prophylaxis. Methods We performed a 12-year retrospective study of patients with P. jirovecii detected by polymerase chain reaction in Central Norway. In total, 297 patients were included. Comprehensive biological, clinical and epidemiological data were abstracted from patients’ medical records. Regional incidence rates and testing trends were also assessed. Results From 2007 to 2017 we found a 3.3-fold increase in testing for P. jirovecii accompanied by a 1.8-fold increase in positive results. Simultaneously, regional incidence rates doubled from 5.0 cases per 100,000 person years to 10.8. A majority of the study population had predisposing conditions other than human immunodeficiency virus (HIV). Hematological (36.0%) and solid cancers (25.3%) dominated. Preceding corticosteroids were a common denominator for 72.1%. Most patients (74.4%) presented with at least two cardinal symptoms; cough, dyspnea or fever. Main clinical findings were hypoxia, cytopenias and radiological features consistent with PCP. A total of 88 (29.6%) patients required intensive care and 121 (40.7%) suffered at least one complication. In-hospital mortality was 21.5%. Three patients (1.0%) had received prophylaxis. Conclusions P. jirovecii is re-emerging; likely due to increasing immunosuppressants use. This opportunistic pathogen threatens the life of heterogenous non-HIV immunosuppressed populations currently at growth. Corticosteroids seem to be a major risk factor. A strategy to increase prophylaxis is called for. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06144-1.
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Affiliation(s)
- Stine Grønseth
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, NO-7491, Trondheim, Norway.
| | - Tormod Rogne
- Department of Circulation and Medical Imaging, NTNU, Trondheim, Norway
| | - Raisa Hannula
- Department of Infectious Diseases, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Bjørn Olav Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Trondheim, Norway.,HUNT Research Center, Department of Public Health and Nursing, NTNU, Levanger, Norway.,Department of Endocrinology, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jan Egil Afset
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, NO-7491, Trondheim, Norway.,Department of Medical Microbiology, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jan Kristian Damås
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, NO-7491, Trondheim, Norway.,Department of Infectious Diseases, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway.,Centre of Molecular Inflammation Research, NTNU, Trondheim, Norway
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38
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Kumar A, Mahajan A, Salazar EA, Pruitt K, Guzman CA, Clauss MA, Almodovar S, Dhillon NK. Impact of human immunodeficiency virus on pulmonary vascular disease. Glob Cardiol Sci Pract 2021; 2021:e202112. [PMID: 34285903 PMCID: PMC8272407 DOI: 10.21542/gcsp.2021.12] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/31/2021] [Indexed: 01/08/2023] Open
Abstract
With the advent of anti-retroviral therapy, non-AIDS-related comorbidities have increased in people living with HIV. Among these comorbidities, pulmonary hypertension (PH) is one of the most common causes of morbidity and mortality. Although chronic HIV-1 infection is independently associated with the development of pulmonary arterial hypertension, PH in people living with HIV may also be the outcome of various co-morbidities commonly observed in these individuals including chronic obstructive pulmonary disease, left heart disease and co-infections. In addition, the association of these co-morbidities and other risk factors, such as illicit drug use, can exacerbate the development of pulmonary vascular disease. This review will focus on these complex interactions contributing to PH development and exacerbation in HIV patients. We also examine the interactions of HIV proteins, including Nef, Tat, and gp120 in the pulmonary vasculature and how these proteins alter the endothelial and smooth muscle function by transforming them into susceptible PH phenotype. The review also discusses the available infectious and non-infectious animal models to study HIV-associated PAH, highlighting the advantages and disadvantages of each model, along with their ability to mimic the clinical manifestations of HIV-PAH.
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Affiliation(s)
- Ashok Kumar
- Pulmonary, Critical Care and Sleep Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Aatish Mahajan
- Pulmonary, Critical Care and Sleep Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Ethan A Salazar
- Department of Immunology & Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Kevin Pruitt
- Department of Immunology & Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Christian Arce Guzman
- Pulmonary, Critical Care, Sleep & Occupational Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Matthias A Clauss
- Pulmonary, Critical Care, Sleep & Occupational Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Sharilyn Almodovar
- Department of Immunology & Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Navneet K Dhillon
- Pulmonary, Critical Care and Sleep Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
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Zhou H, Larkin PMK, Zhao D, Ma Q, Yao Y, Wu X, Wang J, Zhou X, Li Y, Wang G, Feng M, Wu L, Chen J, Zhou C, Hua X, Zhou J, Yang S, Yu Y. Clinical Impact of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage in the Diagnosis and Management of Pneumonia: A Multicenter Prospective Observational Study. J Mol Diagn 2021; 23:1259-1268. [PMID: 34197923 DOI: 10.1016/j.jmoldx.2021.06.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/20/2021] [Accepted: 06/11/2021] [Indexed: 12/18/2022] Open
Abstract
Rapid and accurate pathogen identification is necessary for appropriate treatment of pneumonia. Here, we describe the use of shotgun metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage for pathogen identification in pneumonia in a large-scale multicenter prospective study with 159 patients enrolled. We compared the results of mNGS with standard methods including culture, staining, and targeted PCR, and evaluated the clinical impact of mNGS. A positive impact was defined by a definitive diagnosis made using the mNGS results, or change of management because of the mNGS results, leading to a favorable clinical outcome. Overall, mNGS identified more organisms than standard methods (117 versus 72), detected 17 pathogens that consistently were missed in all cases by standard methods, and had an overall positive clinical impact in 40.3% (64 of 159) of cases. mNGS was especially useful in identification of fastidious and atypical organisms causing pneumonia, contributing to detection of definitive pathogens in 45 (28.3%) cases in which standard results were either negative or insufficient. mNGS also helped reassure antibiotic de-escalation in 19 (11.9%) cases. Overall, mNGS led to a change of treatment in 59 (37.1%) cases, including antibiotic de-escalation in 40 (25.2%) cases. This study showed the significant value of mNGS of bronchoalveolar lavage for improving the diagnosis of pneumonia and contributing to better patient care.
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Affiliation(s)
- Hua Zhou
- Department of Respiratory Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Paige M K Larkin
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, Illinois
| | - Dongdong Zhao
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qiang Ma
- Department of Respiratory Diseases, Yuhang Second People's Hospital, Hangzhou, Zhejiang, China
| | - Yake Yao
- Department of Respiratory Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaohong Wu
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jiaoli Wang
- Department of Respiratory Diseases, Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - XiaoHu Zhou
- Department of Respiratory Diseases, The People's Hospital of Jiangshan, Quzhou, Zhejiang, China
| | - Yaqing Li
- Department of Respiratory Medicine, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, China
| | - Gang Wang
- Department of Respiratory Diseases, Anji People's Hospital, Huzhou, Zhejiang, China
| | - Malong Feng
- Department of Respiratory Diseases, Fenghua People's Hospital of Ningbo, Ningbo, Zhejiang, China
| | - Lei Wu
- Department of Pulmonology and Endoscopy Center, The Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jinyin Chen
- Department of Respiratory Diseases, Zhuji People's Hospital, Shaoxing, Zhejiang, China
| | - Changsheng Zhou
- Department of Respiratory Diseases, People's Hospital of Cangnan, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaoting Hua
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Department of Respiratory Diseases, Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jianying Zhou
- Department of Respiratory Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shangxin Yang
- Zhejiang-California International Nanosystems Institute, Zhejiang University, Hangzhou, Zhejiang, China; Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California.
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Department of Respiratory Diseases, Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China.
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Albulushi K, Jung-Hynes B, Chen D. Detection of Pneumocystis jirovecii from Clinical Specimens Utilizing a TaqMan-Based Real-Time PCR Assay on the Luminex ARIES. Curr Protoc 2021; 1:e95. [PMID: 33818923 DOI: 10.1002/cpz1.95] [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: 11/10/2022]
Abstract
Pneumocystis jirovecii can cause severe pneumonia in immunocompromised patients, which can be life threatening if left untreated. Despite the widespread use of polymerase chain reaction (PCR) within the clinical laboratory setting, FDA-approved PCR assays are not readily available for the detection of Pneumocystis from respiratory samples. Using the Luminex ARIES system-an open-channel, automated, sample-to-answer PCR platform-the cell division cycle 2 (cdc-2) gene can be targeted for the detection of Pneumocystis. This novel TaqMan-based, real-time PCR assay offers improved sensitivity compared to staining or immunofluorescence while reducing turnaround time and eliminating the challenges surrounding microscopic identification. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Primer/probe master mix preparation Basic Protocol 2: Positive control (cdc-2) plasmid preparation Basic Protocol 3: Mucus digestion Basic Protocol 4: Cell lysis Basic Protocol 5: Carrier RNA/proteinase K preparation Basic Protocol 6: Cassette assembly Basic Protocol 7: Running the assay Basic Protocol 8: Interpreting results.
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Affiliation(s)
- Kyle Albulushi
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Brittney Jung-Hynes
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Derrick Chen
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
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Weyant RB, Kabbani D, Doucette K, Lau C, Cervera C. Pneumocystis jirovecii: a review with a focus on prevention and treatment. Expert Opin Pharmacother 2021; 22:1579-1592. [PMID: 33870843 DOI: 10.1080/14656566.2021.1915989] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: Pneumocystis jirovecii (PJ) is an opportunistic fungal pathogen that can cause severe pneumonia in immunocompromised hosts. Risk factors for Pneumocystis jirovecii pneumonia (PJP) include HIV, organ transplant, malignancy, certain inflammatory or rheumatologic conditions, and associated therapies and conditions that result in cell-mediated immune deficiency. Clinical signs of PJP are nonspecific and definitive diagnosis requires direct detection of the organism in lower respiratory secretions or tissue. First-line therapy for prophylaxis and treatment remains trimethoprim-sulfamethoxazole (TMP-SMX), though intolerance or allergy, and rarely treatment failure, may necessitate alternate therapeutics, such as dapsone, pentamidine, atovaquone, clindamycin, primaquine and most recently, echinocandins as adjunctive therapy. In people living with HIV (PLWH), adjunctive corticosteroid use in treatment has shown a mortality benefit.Areas covered: This review article covers the epidemiology, pathophysiology, diagnosis, microbiology, prophylaxis indications, prophylactic therapies, and treatments.Expert opinion: TMP-SMX has been first-line therapy for treating and preventing pneumocystis for decades. However, its adverse effects are not uncommon, particularly during treatment. Second-line therapies may be better tolerated, but often sacrifice efficacy. Echinocandins show some promise for new combination therapies; however, further studies are needed to define optimal antimicrobial therapy for PJP as well as the role of corticosteroids in those without HIV.
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Affiliation(s)
- R Benson Weyant
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Dima Kabbani
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Karen Doucette
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Cecilia Lau
- Department of Pharmacy, Alberta Health Services, Edmonton, Alberta, Canada
| | - Carlos Cervera
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
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Neumonía por Pneumocystis en artritis reumatoide en tratamiento con biológicos: a propósito de un caso. OPEN RESPIRATORY ARCHIVES 2021. [PMID: 37497066 PMCID: PMC10369516 DOI: 10.1016/j.opresp.2021.100093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Gingerich AD, Norris KA, Mousa JJ. Pneumocystis Pneumonia: Immunity, Vaccines, and Treatments. Pathogens 2021; 10:pathogens10020236. [PMID: 33669726 PMCID: PMC7921922 DOI: 10.3390/pathogens10020236] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 12/18/2022] Open
Abstract
For individuals who are immunocompromised, the opportunistic fungal pathogen Pneumocystis jirovecii is capable of causing life-threatening pneumonia as the causative agent of Pneumocystis pneumonia (PCP). PCP remains an acquired immunodeficiency disease (AIDS)-defining illness in the era of antiretroviral therapy. In addition, a rise in non-human immunodeficiency virus (HIV)-associated PCP has been observed due to increased usage of immunosuppressive and immunomodulating therapies. With the persistence of HIV-related PCP cases and associated morbidity and mortality, as well as difficult to diagnose non-HIV-related PCP cases, an improvement over current treatment and prevention standards is warranted. Current therapeutic strategies have primarily focused on the administration of trimethoprim-sulfamethoxazole, which is effective at disease prevention. However, current treatments are inadequate for treatment of PCP and prevention of PCP-related death, as evidenced by consistently high mortality rates for those hospitalized with PCP. There are no vaccines in clinical trials for the prevention of PCP, and significant obstacles exist that have slowed development, including host range specificity, and the inability to culture Pneumocystis spp. in vitro. In this review, we overview the immune response to Pneumocystis spp., and discuss current progress on novel vaccines and therapies currently in the preclinical and clinical pipeline.
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Affiliation(s)
- Aaron D. Gingerich
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (A.D.G.); (K.A.N.)
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Karen A. Norris
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (A.D.G.); (K.A.N.)
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Jarrod J. Mousa
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (A.D.G.); (K.A.N.)
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Correspondence:
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Chotiprasitsakul D, Pewloungsawat P, Setthaudom C, Santanirand P, Pornsuriyasak P. Performance of real-time PCR and immunofluorescence assay for diagnosis of Pneumocystis pneumonia in real-world clinical practice. PLoS One 2020; 15:e0244023. [PMID: 33347478 PMCID: PMC7751978 DOI: 10.1371/journal.pone.0244023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/01/2020] [Indexed: 11/21/2022] Open
Abstract
Background PCR is more sensitive than immunofluorescence assay (IFA) for detection of Pneumocystis jirovecii. However, PCR cannot always distinguish infection from colonization. This study aimed to compare the performance of real-time PCR and IFA for diagnosis of P. jirovecii pneumonia (PJP) in a real-world clinical setting. Methods A retrospective cohort study was conducted at a 1,300-bed hospital between April 2017 and December 2018. Patients whose respiratory sample (bronchoalveolar lavage or sputum) were tested by both Pneumocystis PCR and IFA were included. Diagnosis of PJP was classified based on multicomponent criteria. Sensitivity, specificity, 95% confidence intervals (CI), and Cohen's kappa coefficient were calculated. Results There were 222 eligible patients. The sensitivity and specificity of PCR was 91.9% (95% CI, 84.0%–96.7%) and 89.7% (95% CI, 83.3%–94.3%), respectively. The sensitivity and specificity of IFA was 7.0% (95% CI, 2.6%–14.6%) and 99.2% (95% CI, 95.6%–100.0%), respectively. The percent agreement between PCR and IFA was 56.7% (Cohen's kappa -0.02). Among discordant PCR-positive and IFA-negative samples, 78% were collected after PJP treatment. Clinical management would have changed in 14% of patients using diagnostic information, mainly based on PCR results. Conclusions PCR is highly sensitive compared with IFA for detection of PJP. Combining clinical, and radiological features with PCR is useful for diagnosis of PJP, particularly when respiratory specimens cannot be promptly collected before initiation of PJP treatment.
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Affiliation(s)
- Darunee Chotiprasitsakul
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pataraporn Pewloungsawat
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Chavachol Setthaudom
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pitak Santanirand
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Prapaporn Pornsuriyasak
- Division of Pulmonary and Critical Care, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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Hedvat J, Poladi N, Salerno DM, Dube GK, Lange NW. An evaluation of PJP prophylaxis and anemia among renal transplant recipients. Transpl Infect Dis 2020; 23:e13543. [PMID: 33280205 DOI: 10.1111/tid.13543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/19/2020] [Accepted: 11/29/2020] [Indexed: 12/01/2022]
Abstract
BACKGROUND Dapone and atovaquone are therapeutic options for PJP prophylaxis in renal transplant recipients. The objective of this study was to evaluate the incidence of anemia in renal transplant recipients receiving these agents. METHODS This is an IRB-approved, retrospective analysis of adult renal transplant recipients who received either dapsone or atovaquone. The primary endpoint was the change in hemoglobin within 90 days of drug initiation. Other endpoints of interest included incidence and management of anemia at multiple time points post-transplant. Categorical variables were compared with Pearson's chi-squared or Fischer's exact test and continuous data were compared utilizing Wilcoxon rank-sum test. Statistical analyses were performed using Stata 14.2. RESULTS A total of 478 patients were screened for inclusion; 50 patients were evaluated in both the dapsone and atovaquone groups. In the dapsone and atovaquone groups, the median age was 52 and 50.5 years, 44% and 42% were Caucasian, and median time to treatment initiation was 27 and 39 days post-transplant, respectively. All patients receiving dapsone had normal G6PD function. There was no difference in baseline hemoglobin between groups (9.7 g/dL vs 9.8 g/dL, P = .83). The median nadir hemoglobin values were 8.6 g/dL and 9.6 g/dL in the dapsone and atovaquone groups, respectively (P = .047). The median decrease in hemoglobin from baseline to nadir was 1.3 g/dL in dapsone patients and 0.2 g/dL in atovaquone patients (P = .001). Dapsone was discontinued in 46% of patients, whereas atovaquone was discontinued in 18% (P = .001). CONCLUSION Among renal transplant recipients with normal G6PD activity, dapsone is associated with greater hemoglobin reductions and rates of drug discontinuation as compared to atovaquone.
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Affiliation(s)
- Jessica Hedvat
- Department of Pharmacy, NewYork-Presbyterian Hospital, New York, NY, USA
| | - Neha Poladi
- Department of Pharmacy, Wake Forest Baptist Health Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - David M Salerno
- Department of Pharmacy, NewYork-Presbyterian Hospital, New York, NY, USA
| | - Geoffrey K Dube
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Nicholas W Lange
- Department of Pharmacy, NewYork-Presbyterian Hospital, New York, NY, USA
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Merrill K, Coffey E, Furrow E, Masseau I, Rindt H, Reinero C. X-linked CD40 ligand deficiency in a 1-year-old male Shih Tzu with secondary Pneumocystis pneumonia. J Vet Intern Med 2020; 35:497-503. [PMID: 33274522 PMCID: PMC7848317 DOI: 10.1111/jvim.15988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 12/17/2022] Open
Abstract
An approximately 1‐year‐old male intact Shih Tzu dog was referred to a tertiary facility with a history of progressive tachypnea, increased respiratory effort, and weight loss over a 3‐month period that failed to improve with empirical antimicrobial treatment. Upon completion of a comprehensive respiratory evaluation, the dog was diagnosed with severe Pneumocystis pneumonia and secondary pulmonary hypertension. Clinical signs resolved and disease resolution was confirmed after completion of an 8‐week course of trimethoprim‐sulfonamide, 4‐week tapering dose of prednisone to decrease an inflammatory response secondary to acute die‐off of organisms, a 2‐week course of clopidogrel to prevent clot formation, and a 2‐week course of a phosphodiesterase‐5 inhibitor to treat pulmonary hypertension. Immunodiagnostic testing and genetic sequencing were performed to evaluate for potential immunodeficiency as an underlying cause for the development Pneumocystis pneumonia, and identified an X‐linked CD40 ligand deficiency.
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Affiliation(s)
- Kristen Merrill
- Department of Veterinary Medicine and Surgery, University of Missouri, Ringgold Standard Institution - Small Animal Internal Medicine, Columbia, Missouri, USA
| | - Emily Coffey
- University of Minnesota, Ringgold Standard Institution, Minneapolis, Minnesota, USA
| | - Eva Furrow
- University of Minnesota, Internal Medicine Veterinary Medical Center, St. Paul, Minnesota, USA
| | - Isabelle Masseau
- Department of Sciences Cliniques, Universite de Montreal, St. Hyacinthe, Quebec, Canada
| | - Hansjörg Rindt
- University of Missouri, College of Veterinary Medicine, Veterinary Medicine and Surgery, Columbia, Missouri, USA
| | - Carol Reinero
- University of Missouri, Veterinary Medicine and Surgery, Columbia, Missouri, USA
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Verbeke K, Verbuyst R, Brands C, Slabbynck H. Dyspnea in homosexual male patients: throwback to an occasionally forgotten but severe clinical presentation of HIV/AIDS. Acta Clin Belg 2020; 75:411-415. [PMID: 31130106 DOI: 10.1080/17843286.2019.1622880] [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: 10/26/2022]
Abstract
Pneumocystis jirovecii pneumonia (PJP) can be a severe indicator disease of acquired immunodeficiency syndrome (AIDS). We present two cases of homosexual male patients who came to the emergency unit of a Belgian hospital because of shortness of breath. Both men had been sent back home, initially diagnosed with a benign viral infection. Because of worsening symptoms and gradually evolving hypoxemia, both patients came back and were admitted to the hospital with a diagnosis of (microbiology proven) Pneumocystis jirovecii pneumonia. HIV serology in both men was tested and was clearly positive, indicating a new diagnosis of HIV infection. In this article, we provide an overview of this possibly severe AIDS defining condition. First, we give an introduction of the history of HIV/AIDS and its occurrence in homosexual males in Europe. Secondly, we provide an overview of the diagnosis and treatment of Pneumocystis jirovecii pneumonia. Finally, since the first case reports of Pneumocystis jirovecii pneumonia at the beginning of the AIDS epidemic also included homosexual men, we emphasize the potential importance of a sexual anamnesis in young male patients with an initial complaint of dyspnea.
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Affiliation(s)
- Koen Verbeke
- Department of Pulmonology, ZNA Middelheim, Antwerp, Belgium
| | - Roel Verbuyst
- Department of Pulmonology, ZNA Stuyvenberg, Antwerp, Belgium
| | | | - Hans Slabbynck
- Department of Pulmonology, ZNA Middelheim, Antwerp, Belgium
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King LD, Sia H, Anoopkumar‐Dukie S. Trimethoprim‐sulfamethoxazole as
Pneumocystis jiroveci
pneumonia prevention in patients undergoing methotrexate therapy for hematological malignancies: A review of the literature. Hematol Oncol 2020. [DOI: 10.1002/hon.2823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Liam D. King
- Ramsay Pharmacy John Flynn Private Hospital Tugun Queensland Australia
- School of Pharmacy and Pharmacology Griffith University Southport Queensland Australia
| | - Hanlon Sia
- First in Haematology and Oncology Pindara Private Hospital Benowa Queensland Australia
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Consensus Multilocus Sequence Typing Scheme for Pneumocystis jirovecii. J Fungi (Basel) 2020; 6:jof6040259. [PMID: 33143112 PMCID: PMC7711988 DOI: 10.3390/jof6040259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/10/2020] [Accepted: 10/18/2020] [Indexed: 12/26/2022] Open
Abstract
Pneumocystis jirovecii is an opportunistic human pathogenic fungus causing severe pneumonia mainly in immunocompromised hosts. Multilocus sequence typing (MLST) remains the gold standard for genotyping of this unculturable fungus. However, the lack of a consensus scheme impedes a global comparison, large scale population studies and the development of a global MLST database. To overcome this problem this study compared all genetic regions (19 loci) currently used in 31 different published Pneumocystis MLST schemes. The most diverse/commonly used eight loci, β-TUB, CYB, DHPS, ITS1, ITS1/2, mt26S and SOD, were further assess for their ability to be successfully amplified and sequenced, and for their discriminatory power. The most successful loci were tested to identify genetically related and unrelated cases. A new consensus MLST scheme consisting of four genetically independent loci: β-TUB, CYB, mt26S and SOD, is herein proposed for standardised P. jirovecii typing, successfully amplifying low and high fungal burden specimens, showing adequate discriminatory power, and correctly identifying suspected related and unrelated isolates. The new consensus MLST scheme, if accepted, will for the first time provide a powerful tool to investigate outbreak settings and undertake global epidemiological studies shedding light on the spread of this important human fungal pathogen.
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Mercer DK, O'Neil DA. Innate Inspiration: Antifungal Peptides and Other Immunotherapeutics From the Host Immune Response. Front Immunol 2020; 11:2177. [PMID: 33072081 PMCID: PMC7533533 DOI: 10.3389/fimmu.2020.02177] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 08/10/2020] [Indexed: 12/17/2022] Open
Abstract
The purpose of this review is to describe antifungal therapeutic candidates in preclinical and clinical development derived from, or directly influenced by, the immune system, with a specific focus on antimicrobial peptides (AMP). Although the focus of this review is AMP with direct antimicrobial effects on fungi, we will also discuss compounds with direct antifungal activity, including monoclonal antibodies (mAb), as well as immunomodulatory molecules that can enhance the immune response to fungal infection, including immunomodulatory AMP, vaccines, checkpoint inhibitors, interferon and colony stimulating factors as well as immune cell therapies. The focus of this manuscript will be a non-exhaustive review of antifungal compounds in preclinical and clinical development that are based on the principles of immunology and the authors acknowledge the incredible amount of in vitro and in vivo work that has been conducted to develop such therapeutic candidates.
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