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Rattin J, Marigney K, Miranda C, Arrossi AV, Misra A, Wang H. The Brief Case: False-negative Pneumocystis PCR. J Clin Microbiol 2024; 62:e0009424. [PMID: 39012140 PMCID: PMC11250520 DOI: 10.1128/jcm.00094-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024] Open
Affiliation(s)
- Jacob Rattin
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Pathology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Kelly Marigney
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Cyndee Miranda
- Department of Infectious Disease, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Anisha Misra
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Hannah Wang
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
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Walker AM, Timbrook TT, Hommel B, Prinzi AM. Breaking Boundaries in Pneumonia Diagnostics: Transitioning from Tradition to Molecular Frontiers with Multiplex PCR. Diagnostics (Basel) 2024; 14:752. [PMID: 38611665 PMCID: PMC11012095 DOI: 10.3390/diagnostics14070752] [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: 02/25/2024] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
The advent of rapid molecular microbiology testing has revolutionized infectious disease diagnostics and is now impacting pneumonia diagnosis and management. Molecular platforms offer highly multiplexed assays for diverse viral and bacterial detection, alongside antimicrobial resistance markers, providing the potential to significantly shape patient care. Despite the superiority in sensitivity and speed, debates continue regarding the clinical role of multiplex molecular testing, notably in comparison to standard methods and distinguishing colonization from infection. Recent guidelines endorse molecular pneumonia panels for enhanced sensitivity and rapidity, but implementation requires addressing methodological differences and ensuring clinical relevance. Diagnostic stewardship should be leveraged to optimize pneumonia testing, emphasizing pre- and post-analytical strategies. Collaboration between clinical microbiologists and bedside providers is essential in developing implementation strategies to maximize the clinical utility of multiplex molecular diagnostics in pneumonia. This narrative review explores these multifaceted issues, examining the current evidence on the clinical performance of multiplex molecular assays in pneumonia, and reflects on lessons learned from previous microbiological advances. Additionally, given the complexity of pneumonia and the sensitivity of molecular diagnostics, diagnostic stewardship is discussed within the context of current literature, including implementation strategies that consider pre-analytical and post-analytical modifications to optimize the clinical utility of advanced technologies like multiplex PCR.
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Affiliation(s)
| | - Tristan T. Timbrook
- bioMerieux, 69280 Marcy L’etoile, France (A.M.P.)
- Department of Pharmacotherapy, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
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Gudisa R, Harchand R, Rudramurthy SM. Nucleic-Acid-Based Molecular Fungal Diagnostics: A Way to a Better Future. Diagnostics (Basel) 2024; 14:520. [PMID: 38472992 DOI: 10.3390/diagnostics14050520] [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: 01/03/2024] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
The world has seen a tremendous increase in the number of fungal infections during the past two decades. Recently, the World Health Organisation released the pathogen priority list for fungal infections, signifying the importance of these infections in the fields of research and public health. Microbiology laboratories demand an upgrade in the diagnostic system to keep up with the increased burden of these infections. Diagnosis of fungal infections using conventional techniques has always faced limitations in terms of specificity, sensitivity, and turnaround time. Although these methods are the core pillars of the diagnosis, there is an increased need for molecular approaches. Molecular techniques have revolutionised the field of fungal diagnostics. The diverse array of molecular techniques, including techniques like Polymerase Chain Reaction (PCR), have emerged as a cornerstone in fungal diagnostics. Molecular techniques have transformed fungal diagnostics, providing powerful tools for the rapid and accurate identification of pathogens. As these technologies continue to evolve, their integration into routine clinical practice holds the promise of improving patient outcomes through timely and targeted antifungal interventions. This review will cover the molecular approaches involved in fungal diagnostics, moving from the basic techniques to the advanced-level nucleic-acid-based molecular approaches providing a high throughput and decreased turnaround time for the diagnosis of serious fungal infections.
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Affiliation(s)
- Rajendra Gudisa
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Ritika Harchand
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
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Watson AL, Woodford J, Britton S, Gupta R, Whiley D, McCarthy K. Determining Pneumocystis jirovecii Colonisation from Infection Using PCR-Based Diagnostics in HIV-Negative Individuals. Diagnostics (Basel) 2024; 14:114. [PMID: 38201422 PMCID: PMC10802892 DOI: 10.3390/diagnostics14010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Pneumocystis jirovecii pneumonia is increasingly diagnosed with highly sensitive PCR diagnostics in immunocompromised, HIV-negative individuals. We assessed the performance of our in-house quantitative PCR with the aim to optimise interpretation. METHODS Retrospective audit of all positive P. jirovecii qPCRs on induced sputum or BAL fluid at a single centre from 2012 to 2023. Medical and laboratory records were analysed and people with HIV were excluded. Cases were categorised as colonisation, high-probability PCP or uncertain PCP infection against a clinical gold standard incorporating clinico-radiological data. Quantitative PCR assay targeting the 5s gene was utilised throughout the time period. RESULTS Of the 82 positive qPCRs, 28 were categorised as high-probability PCP infection, 30 as uncertain PCP and 24 as colonisation. There was a significant difference in qPCR values stratified by clinical category but not respiratory sample type. Current assay performance with a cutoff of 2.5 × 105 copies/mL had a sensitivity of 50% (95% CI, 30.65-69.35%) and specificity of 83.33% (95% CI, 62.62-95.26%). Youden Index calculated at 6.5 × 104 copies/mL had a sensitivity of 75% (56.64-87.32%, 95% CI) and specificity of 66.67% (46.71-82.03%, 95% CI). High and low cutoffs were explored. Significant variables associated with infection were age > 70 years old, the presence of fever, hypoxia or ground glass changes. CONCLUSIONS A single qPCR cutoff cannot reliably determine P. jirovecii infection from colonisation. Low and high cutoffs are useful, however, a large "possible infection" cohort will remain where interpretation of clinic-radiological factors remains essential. Standardisation of assays with prospective validation in specific immunocompromised groups will allow greater generalisability and allow large-scale prospective assay validation to be performed.
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Affiliation(s)
- Anna Louise Watson
- Infectious Diseases, Royal Brisbane & Women’s Hospital, Metro North Health, Herston, QLD 4006, Australia
- Herston Infectious Diseases Institute, Herston, QLD 4006, Australia
| | - John Woodford
- Infectious Diseases, Ipswich Hospital, Ipswich, QLD 4305, Australia
| | - Sumudu Britton
- Infectious Diseases, Royal Brisbane & Women’s Hospital, Metro North Health, Herston, QLD 4006, Australia
| | - Rita Gupta
- Pathology Queensland, Herston, QLD 4006, Australia
| | - David Whiley
- Pathology Queensland, Herston, QLD 4006, Australia
- The University of Queensland, Herston, QLD 4006, Australia
| | - Kate McCarthy
- Infectious Diseases, Royal Brisbane & Women’s Hospital, Metro North Health, Herston, QLD 4006, Australia
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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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Veintimilla C, Álvarez-Uría A, Martín-Rabadán P, Valerio M, Machado M, Padilla B, Alonso R, Diez C, Muñoz P, Marín M. Pneumocystis jirovecii Pneumonia Diagnostic Approach: Real-Life Experience in a Tertiary Centre. J Fungi (Basel) 2023; 9:jof9040414. [PMID: 37108869 PMCID: PMC10142180 DOI: 10.3390/jof9040414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/14/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023] Open
Abstract
Pneumocystis jirovecii pneumonia (PJP) in immunocompromised patients entails high mortality and requires adequate laboratory diagnosis. We compared the performance of a real time-PCR assay against the immunofluorescence assay (IFA) in the routine of a large microbiology laboratory. Different respiratory samples from HIV and non-HIV-infected patients were included. The retrospective analysis used data from September 2015 to April 2018, which included all samples for which a P. jirovecii test was requested. A total of 299 respiratory samples were tested (bronchoalveolar lavage fluid (n = 181), tracheal aspirate (n = 53) and sputum (n = 65)). Forty-eight (16.1%) patients fulfilled the criteria for PJP. Five positive samples (10%) had only colonization. The PCR test was found to have a sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of 96%, 98%, 90% and 99%, compared to 27%, 100%, 100% and 87%, for the IFA, respectively. PJ-PCR sensitivity and specificity were >80% and >90% for all tested respiratory samples. Median cycle threshold values in definite PJP cases were 30 versus 37 in colonized cases (p < 0.05). Thus, the PCR assay is a robust and reliable test for the diagnosis PJP in all respiratory sample types. Ct values of ≥36 could help to exclude PJP diagnosis.
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Borojevic B, Johns E, Raju N, Sycamnias LA. Pneumocystis pneumonia with respiratory failure in a HIV-negative patient following short course of low-dose to moderate-dose prednisolone for a dermatological condition. BMJ Case Rep 2022; 15:e249346. [PMID: 35675962 PMCID: PMC9185496 DOI: 10.1136/bcr-2022-249346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2022] [Indexed: 12/15/2022] Open
Abstract
A woman in her 80s was admitted with 5 days of progressive dyspnoea and hypoxic respiratory failure, in the setting of receiving a 3-week course of low-dose to moderate-dose prednisolone for a pruritic skin rash. Her medical history was not significant for major medical comorbidities or any other clear risk factors for secondary immunosuppression apart from advanced age. CT revealed widespread small-airway and parenchymal disease with ground-glass opacities consistent with atypical respiratory infection. Sputum PCR confirmed Pneumocystis jirovecii She was diagnosed with Pneumocystis jirovecii pneumonia (PJP) in the context of her clinical presentation, radiological features and PCR result. Her HIV status was negative. The patient was treated with 4 weeks of trimethoprim-sulfamethoxazole and 3 weeks of adjunctive prednisolone. She initially required high-dependency unit support with non-invasive ventilation. In this case report, we review the literature regarding PJP in the dermatology setting.
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Affiliation(s)
- Branko Borojevic
- General Medicine, Austin Health, Heidelberg, Victoria, Australia
| | - Esther Johns
- General Medicine, Austin Health, Heidelberg, Victoria, Australia
| | - Nihal Raju
- General Medicine, Austin Health, Heidelberg, Victoria, Australia
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White PL, Alanio A, Brown L, Cruciani M, Hagen F, Gorton R, Lackner M, Millon L, Morton CO, Rautemaa-Richardson R, Barnes RA, Donnelly JP, Loffler J. An overview of using fungal DNA for the diagnosis of invasive mycoses. Expert Rev Mol Diagn 2022; 22:169-184. [PMID: 35130460 DOI: 10.1080/14737159.2022.2037423] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Fungal PCR has undergone considerable standardization and together with the availability of commercial assays, external quality assessment schemes and extensive performance validation data, is ready for widespread use for the screening and diagnosis of invasive fungal disease (IFD). AREAS COVERED Drawing on the experience and knowledge of the leads of the various working parties of the Fungal PCR initiative, this review will address general considerations concerning the use of molecular tests for the diagnosis of IFD, before focussing specifically on the technical and clinical aspects of molecular testing for the main causes of IFD and recent technological developments. EXPERT OPINION For infections caused by Aspergillus, Candida and Pneumocystis jirovecii, PCR testing is recommended, combination with serological testing will likely enhance the diagnosis of these diseases. For other IFD (e.g. Mucormycosis) molecular diagnostics, represent the only non-classical mycological approach towards diagnoses and continued performance validation and standardization has improved confidence in such testing. The emergence of antifungal resistance can be diagnosed, in part, through molecular testing. Next-generation sequencing has the potential to significantly improve our understanding of fungal phylogeny, epidemiology, pathogenesis, mycobiome/microbiome and interactions with the host, while identifying novel and existing mechanisms of antifungal resistance and novel diagnostic/therapeutic targets.
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Affiliation(s)
- P Lewis White
- Public Health Wales Microbiology Cardiff, UHW, Cardiff, UK CF14 4XW
| | - Alexandre Alanio
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Université de Paris, Paris, France.,Institut Pasteur, CNRS UMR2000, Unité de Mycologie Moléculaire, Centre National de Reference Mycoses invasives et Antifongiques, Paris, France
| | - Lottie Brown
- NHS Mycology Reference Centre Manchester, ECMM Centre of Excellence, Manchester University NHS Foundation Trust, Wythenshawe Hospital; and Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | | | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands & Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rebecca Gorton
- Dept. of Infection Sciences, Health Services Laboratories (HSL) LLP, London, UK
| | - Michaela Lackner
- Institute of Hygiene and Medical Microbiology, Department of Hygiene, Medical Microbiology and Publics Health, Medical University Innsbruck, Innsbruck, Austria
| | - Laurence Millon
- Parasitology-Mycology Department, University Hospital of Besançon, 25000 Besançon, France.,UMR 6249 CNRS Chrono-Environnement, University of Bourgogne Franche-Comté, 25000 Besançon, France
| | - C Oliver Morton
- Western Sydney University, School of Science, Campbelltown, NSW 2560, Australia
| | - Riina Rautemaa-Richardson
- NHS Mycology Reference Centre Manchester, ECMM Centre of Excellence, Manchester University NHS Foundation Trust, Wythenshawe Hospital; and Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | | | | | - Juergen Loffler
- Department of Internal Medicine II, WÜ4i, University Hospital Wuerzburg, Wuerzburg, Germany
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Lim W, Suhail M, Diaz K. Diagnostic Challenges of Pneumocystis Pneumonia during the COVID-19 Pandemic: A Case of a Young Patient with Ground Glass Opacities and Pulmonary Embolism on Chest CT. Case Rep Infect Dis 2021; 2021:5669543. [PMID: 34373796 PMCID: PMC8349278 DOI: 10.1155/2021/5669543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/01/2021] [Accepted: 07/23/2021] [Indexed: 12/15/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is wreaking havoc across the globe. This pandemic has given rise to a mindset where physicians tend to neglect other causes of pneumonia, especially if the patient presents with signs and symptoms commonly associated with COVID-19. Herein, we report a case of a young man presenting to the emergency department with common clinical, radiological, and laboratory features of COVID-19 pneumonia such as shortness of breath, hypoxia, pulmonary embolism, elevated D-dimer, and bilateral ground glass opacities on computed tomography of the chest but was later diagnosed with Pneumocystis pneumonia that was treated with appropriate antibiotics and corticosteroids. This case highlights the importance of performing a thorough clinical history and differentiating the clinical and radiological features of COVID-19 pneumonia from pneumonia of other etiologies.
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Affiliation(s)
- William Lim
- Department of Internal Medicine, Richmond University Medical Center, Staten Island, New York, NY, USA
| | - Maham Suhail
- Department of Internal Medicine, Richmond University Medical Center, Staten Island, New York, NY, USA
| | - Keith Diaz
- Department of Internal Medicine, Richmond University Medical Center, Staten Island, New York, NY, USA
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Banerjee S, Denning DW, Chakrabarti A. One Health aspects & priority roadmap for fungal diseases : A mini-review. Indian J Med Res 2021; 153:311-319. [PMID: 33906993 PMCID: PMC8204821 DOI: 10.4103/ijmr.ijmr_768_21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Indexed: 11/29/2022] Open
Abstract
Fungal diseases have not been taken seriously in public health agendas as well as research priorities, despite of globally causing an estimated two million deaths every year, and the emergence of many troublesome fungal pathogens like Candida auris, azole resistant Aspergillus fumigatus, terbinafine and azole resistant dermatophytes, and zoonotic sporotrichosis in humans. Fungi are also responsible for huge losses of agricultural products and stored crops as well as recent massive and unexpected mortality in animals caused by white-nose syndrome in the bats and Chytridiomycosis in amphibians. This review aims to underscore the need for collaborative, multisectoral, and trans-disciplinary approach to include the One Health approach as an essential component of surveillance, prevention, and control of globally emerging fungal diseases. Rigorous evidence based surveillance of the environment as well as strengthening rapid and quality diagnosis of fungal diseases can save millions of lives and reduce significant morbidity.
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Affiliation(s)
- Sayantan Banerjee
- Department of Infectious Diseases, Beleghata Infectious Diseases & BG Hospitals, Beleghata, Kolkata, West Bengal, India
| | - David W. Denning
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- Global Action Fund for Fungal Infections, Geneva, Switzerland
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
- Center of Advanced Research in Medical Mycology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
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Giacobbe DR, Cortegiani A, Karaiskos I, Mercier T, Tejada S, Peghin M, Grecchi C, Rebuffi C, Asperges E, Zuccaro V, Scudeller L, Bassetti M. Performance of Existing Definitions and Tests for the Diagnosis of Invasive Fungal Diseases other than Invasive Candidiasis and Invasive Aspergillosis in Critically Ill, Adult Patients: A Systematic Review with Qualitative Evidence Synthesis. J Fungi (Basel) 2021; 7:jof7030176. [PMID: 33670864 PMCID: PMC7997529 DOI: 10.3390/jof7030176] [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: 01/18/2021] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 12/19/2022] Open
Abstract
The Fungal Infections Definitions in Intensive Care Unit (ICU) patients (FUNDICU) project aims to provide standard sets of definitions for invasive fungal diseases (IFDs) in critically ill, adult patients, including invasive aspergillosis (IA), invasive candidiasis (IC), Pneumocystis jirovecii pneumonia (PJP), and other non-IA, non-IC IFDs. The first step of the project was the conduction of separated systematic reviews of the characteristics and applicability to critically ill, adult patients outside classical populations at risk (hematology patients, solid organ transplant recipients) of available definitions and diagnostic tests for IFDs. We report here the results of two systematic reviews exploring the performance of available definitions and tests, for PJP and for other non-IA, non-IC IFDs. Starting from 2585 and 4584 records for PJP and other IFDs, respectively, 89 and 61 studies were deemed as eligible for full-text evaluation. However, only two studies for PJP and no studies for other IFDs met the FUNDICU protocol criteria for inclusion in qualitative synthesis. Currently, there is no sufficient solid data for directly evaluating the performance of existing definitions and laboratory tests for the diagnosis of PJP and other non-IA, non-IC IFDs in critically ill adult patients outside classical populations at risk.
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Affiliation(s)
- Daniele R. Giacobbe
- Department of Health Sciences, University of Genoa, 16132 Genoa, Italy;
- Clinica Malattie Infettive, Ospedale Policlinico San Martino–IRCCS, 16132 Genoa, Italy
- Correspondence: ; Tel.: +39-01-0555-4652
| | - Andrea Cortegiani
- Department of Surgical, Oncological and Oral Science (Di.Chir.On.S.), University of Palermo, 90127 Palermo, Italy;
- Department of Anaesthesia Intensive Care and Emergency, Policlinico Paolo Giaccone, 90127 Palermo, Italy
| | | | - Toine Mercier
- Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium;
- Department of Hematology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Sofia Tejada
- Clinical Research/Epidemiology in Pneumonia & Sepsis (CRIPS), Vall d’Hebron Institute of Research (VHIR), 08035 Barcelona, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - Maddalena Peghin
- Infectious Diseases Division, Department of Medicine, University of Udine and Azienda Sanitaria Universitaria Integrata di Udine, 33100 Udine, Italy;
| | - Cecilia Grecchi
- Infectious Diseases Unit, IRCCS San Matteo, 27100 Pavia, Italy; (C.G.); (E.A.); (V.Z.)
- Department of Internal Medicine and Therapeutics, University of Pavia, 27100 Pavia, Italy
| | - Chiara Rebuffi
- Scientific Direction, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
| | - Erika Asperges
- Infectious Diseases Unit, IRCCS San Matteo, 27100 Pavia, Italy; (C.G.); (E.A.); (V.Z.)
| | - Valentina Zuccaro
- Infectious Diseases Unit, IRCCS San Matteo, 27100 Pavia, Italy; (C.G.); (E.A.); (V.Z.)
| | - Luigia Scudeller
- Scientific Direction, Clinical Epidemiology and Biostatistics IRCCS, Ca’ Granda Ospedale Maggiore Policlinico di Milano Foundation, 20122 Milan, Italy;
| | - Matteo Bassetti
- Department of Health Sciences, University of Genoa, 16132 Genoa, Italy;
- Clinica Malattie Infettive, Ospedale Policlinico San Martino–IRCCS, 16132 Genoa, Italy
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Alshahrani MY, Alfaifi M, Al Shahrani M, Alshahrani AS, Alkhathami AG, Dera AA, Ahmad I, Wahab S, Beg MMA, Hakamy A, Hamid ME. Increased mRNA expression of key cytokines among suspected cases of Pneumocystis jirovecii infection. BMC Infect Dis 2021; 21:28. [PMID: 33413198 PMCID: PMC7792013 DOI: 10.1186/s12879-020-05729-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/21/2020] [Indexed: 12/16/2022] Open
Abstract
Background Pneumocystis pneumonia (PCP) is a fatal infectious disease caused by Pneumocystis jirovecii (PJP). The major factor relevant to morbidity and mortality seems to be the host inflammatory reaction. The objective of this study was to evaluate the role of IL-2, IL-4, IL-10, and IL-13 cytokine mRNA expression among suspected P. jirovecii infection. Methods This was a cross-sectional analytical study undertaken in Aseer region, Saudi Arabia. One hundred suspected PCP cases and 100 healthy controls were included in the study. Basic clinical manifestations, radiological findings, microbiological and immunological findings were extracted from the hospital records from January 2019 to August 2019, Pneumocystis detection was done by immune-fluorescent staining (IFAT, Gomorimethanamine silver staining (GMSS), Giemsa staining, Toluidine blue O (TBO), and Pneumocystis RT-PCR. Results Increased more than 5 fold, 3 fold, 4 fold, and 7 fold of IL-2, IL-4, IL-10, and IL-13 mRNA expression were observed in PCP cases compared to controls. Higher expression of IL-2 mRNA was connected with crept, wheezing and chest X-ray findings like central perihilar infiltrate, patchy infiltrate, consolidation, hilar lymphadenopathy, pneumothorax, pleural effusion which showed higher expression compared to counterpart (p< 0.0001). Higher expression of IL-4 mRNA was found to be significantly associated with weight loss (p=0.002), dyspnea (p=0.003), crept (p=0.01), and chest X-ray findings (p< 0.0001). Significantly increased expression of IL-10 mRNA was observed to be associated with weight loss, dyspnea, night sweats, wheezing, and different findings of chest X-ray compared to their counterparts, whereas, IL-13 mRNA was observed in cases with fever. Suspected cases of PCP confirmed positive by IFTA with higher IL-2, IL-4, and IL-10 mRNA expression compared to negative cases. RT-PCR confirmed PCP cases had significantly higher expression of IL-2, IL-4, and IL-10 as well as IL-13 mRNA compared to negative cases. Positive detected cases by GMSS showed higher IL-2, IL-10 mRNA expression, while Giemsa showed only higher IL-4 mRNA expression compared to negative cases. Conclusion Confirmed cases of P. jirovecii showed higher IL-2, IL-4, IL-10, and IL-13 mRNA expression comparatively to negative cases. Increased expression of cytokines may be indicative of infection severity and could help in patients’ management.
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Affiliation(s)
- Mohammad Y Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mohammed Alfaifi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mesfer Al Shahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | | | - Ali G Alkhathami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Ayed A Dera
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Mirza M A Beg
- Department of Biochemistry, Maulana Azad Medical College, New Delhi, India
| | - Ali Hakamy
- Respiratory Therapy Department, Faculty of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Mohamed E Hamid
- Department of Microbiology and Clinical Parasitology, College of Medicine, King Khalid University, Abha, Saudi Arabia.
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Du CJ, Liu JY, Chen H, Yan S, Pu L, Xiong HF, Xiang P, Li CS, Zhang M, Xie RM, Chen BD, Li A. Differences and similarities of high-resolution computed tomography features between pneumocystis pneumonia and cytomegalovirus pneumonia in AIDS patients. Infect Dis Poverty 2020; 9:149. [PMID: 33106188 PMCID: PMC7586649 DOI: 10.1186/s40249-020-00768-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Accurately differentiating pneumocystis from cytomegalovirus pneumonia is crucial for correct therapy selection in AIDS patients. Hence, the goal of this study was to compare the computerized tomography (CT) features of pneumocystis pneumonia and cytomegalovirus pneumonia in AIDS patients and identify clinical hallmarks to accurately distinguish these two pathologies. METHODS A total of 112 AIDS patients (78 with pneumocystis pneumonia and 34 cytomegalovirus pneumonia) at Beijing Ditan Hospital from January 2017 to May 2019 were included in this study. Two experienced chest radiologists retrospectively reviewed CT images for 17 features including ground-glass opacity, consolidation, nodules, and halo sign. Binary logistic regression analyses were conducted to identify the significant parameters that distinguished pneumocystis pneumonia from cytomegalovirus pneumonia. Correlations were analyzed by Pearson or Spearman correlation analyses. Result were considered significant if P < 0.05. RESULTS The presence of consolidation, halo signs, and nodules (all P < 0.05) were significantly more frequent in patients with cytomegalovirus pneumonia than in those with pneumocystis pneumonia. Small nodules (32.5% in cytomegalovirus pneumonia, 6.41% in pneumocystis pneumonia, P < 0.001) without perilymphatic distribution were particularly common in patients with cytomegalovirus pneumonia. Large nodules were not found in any of patients with cytomegalovirus pneumonia. The presence of ground-glass opacity, reticulation, and bronchial wall thickening (all P > 0.05) were common in both groups. CONCLUSIONS Analysis of consolidation, nodules, and halo signs may contribute to the differential diagnosis of pneumocystis pneumonia or cytomegalovirus pneumonia. However, some CT features considered typical in one or other diseases appear with similar frequency in both cohorts of AIDS patients. CT features are potentially useful for the differential diagnosis of pneumocystis pneumonia and cytomegalovirus pneumonia in AIDS patients.
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Affiliation(s)
- Chun-Jing Du
- Department of Critical Care Medicine, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundong Street, Chaoyang District, Beijing, 100015, China
| | - Jing-Yuan Liu
- Department of Critical Care Medicine, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundong Street, Chaoyang District, Beijing, 100015, China
| | - Hui Chen
- Department of Radiology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundong Street, Chaoyang District, Beijing, 100015, China
| | - Shuo Yan
- Department of Radiology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundong Street, Chaoyang District, Beijing, 100015, China
| | - Lin Pu
- Department of Critical Care Medicine, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundong Street, Chaoyang District, Beijing, 100015, China
| | - Hao-Feng Xiong
- Department of Critical Care Medicine, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundong Street, Chaoyang District, Beijing, 100015, China
| | - Pan Xiang
- Department of Critical Care Medicine, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundong Street, Chaoyang District, Beijing, 100015, China
| | - Chuan-Sheng Li
- Department of Critical Care Medicine, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundong Street, Chaoyang District, Beijing, 100015, China
| | - Ming Zhang
- Department of Critical Care Medicine, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundong Street, Chaoyang District, Beijing, 100015, China
| | - Ru-Ming Xie
- Department of Radiology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundong Street, Chaoyang District, Beijing, 100015, China
| | - Bu-Dong Chen
- Department of Radiology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundong Street, Chaoyang District, Beijing, 100015, China.
| | - Ang Li
- Department of Critical Care Medicine, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundong Street, Chaoyang District, Beijing, 100015, China.
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Liu B, Totten M, Nematollahi S, Datta K, Memon W, Marimuthu S, Wolf LA, Carroll KC, Zhang SX. Development and Evaluation of a Fully Automated Molecular Assay Targeting the Mitochondrial Small Subunit rRNA Gene for the Detection of Pneumocystis jirovecii in Bronchoalveolar Lavage Fluid Specimens. J Mol Diagn 2020; 22:1482-1493. [PMID: 33069878 DOI: 10.1016/j.jmoldx.2020.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/10/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022] Open
Abstract
The fungal pathogen Pneumocystis jirovecii causes Pneumocystis pneumonia. Although the mitochondrial large subunit rRNA gene (mtLSU) is commonly used as a PCR target, a mitochondrial small subunit rRNA gene (mtSSU)-targeted MultiCode PCR assay was developed on the fully automated ARIES platform for detection of P. jirovecii in bronchoalveolar lavage fluid specimens in 2.5 hours. The assay showed a limit of detection of 800 copies/mL (approximately equal to 22 organisms/mL), with no cross-reactivity with other respiratory pathogens. Compared with the reference Pneumocystis-specific direct fluorescent antibody assay (DFA) and mtLSU-targeted PCR assay, the new assay demonstrated sensitivity of 96.9% (31/32) and specificity of 94.6% (139/147) in detecting P. jirovecii in 180 clinical bronchoalveolar lavage fluid specimens. This assay was concordant with all DFA-positive samples and all but one mtLSU PCR-positive sample, and detected eight positive samples that were negative by DFA and mtLSU PCR. Receiver operating characteristic curve analysis revealed an area under the curve of 0.98 and a threshold cycle (CT) cutoff of 39.1 with sensitivity of 90.9% and specificity of 99.3%. The detection of 39.1 <CT < 40.0 indicates the presence of a low load of the organism and needs further determination of either colonization or probable/possible Pneumocystis pneumonia. Overall, the new assay demonstrates excellent analytical and clinical performance and may be more sensitive than mtLSU PCR target for the detection of P. jirovecii.
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Affiliation(s)
- Baoming Liu
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marissa Totten
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Saman Nematollahi
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kausik Datta
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Warda Memon
- Microbiology Laboratory, Johns Hopkins Hospital, Baltimore, Maryland
| | - Subathra Marimuthu
- Division of Infectious Diseases, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky
| | - Leslie A Wolf
- Division of Infectious Diseases, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Microbiology Laboratory, Johns Hopkins Hospital, Baltimore, Maryland
| | - Sean X Zhang
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Microbiology Laboratory, Johns Hopkins Hospital, Baltimore, Maryland.
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15
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Missed diagnosis and misdiagnosis of infectious diseases in hematopoietic cell transplant recipients: an autopsy study. Blood Adv 2020; 3:3602-3612. [PMID: 31743391 DOI: 10.1182/bloodadvances.2019000634] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/10/2019] [Indexed: 01/20/2023] Open
Abstract
Hematopoietic cell transplantation (HCT) is potentially curative for patients with hematologic disorders, but carries significant risks of infection-related morbidity and mortality. Infectious diseases are the second most common cause of death in HCT recipients, surpassed only by progression of underlying disease. Many infectious diseases are difficult to diagnose and treat, and may only be first identified by autopsy. However, autopsy rates are decreasing despite their value. The clinical and autopsy records of adult HCT recipients at our center who underwent autopsy between 1 January 2000 and 31 December 2017 were reviewed. Discrepancies between premortem clinical diagnoses and postmortem autopsy diagnoses were evaluated. Of 185 patients who underwent autopsy, 35 patients (18.8%) had a total of 41 missed infections. Five patients (2.7%) had >1 missed infection. Of the 41 missed infections, 18 (43.9%) were viral, 16 (39.0%) were fungal, 5 (12.2%) were bacterial, and 2 (4.9%) were parasitic. According to the Goldman criteria, 31 discrepancies (75.6%) were class I, 5 (12.2%) were class II, 1 (2.4%) was class III, and 4 (9.8%) were class IV. Autopsies of HCT recipients frequently identify clinically significant infectious diseases that were not suspected premortem. Had these infections been suspected, a change in management might have improved patient survival in many of these cases. Autopsy is underutilized and should be performed regularly to help improve infection-related morbidity and mortality. Illustrative cases are presented and the lessons learned from them are also discussed.
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16
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Alshahrani MY, Alfaifi M, Ahmad I, Alkhathami AG, Hakami AR, Ahmad H, Alshehri OM, Dhakad MS. Pneumocystis Jirovecii detection and comparison of multiple diagnostic methods with quantitative real-time PCR in patients with respiratory symptoms. Saudi J Biol Sci 2020; 27:1423-1427. [PMID: 32489277 PMCID: PMC7254037 DOI: 10.1016/j.sjbs.2020.04.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 01/04/2023] Open
Abstract
Pneumocystis jirovecii (PCP) remains a significant cause of mortality and morbidity in patients with respiratory infections. Accurate diagnosis of PCP is still a diagnostic challenge. Hence, the main objectives were to study the incidence of Pneumocystis Jirovecii pneumonia infection among respiratory problems patients and to compare the real-time quantitative PCR technique with various diagnostic methodologies. Patients who have respiratory symptoms of PCP like breathlessness, cough, and fever were enrolled. Bronchoalveolar lavage (BAL) samples were collected and homogenized, and then smears were prepared for examination by Gomorimethanamine silver staining (GMSS), Immunofluorescent staining (IFAT), Toludine blue O (TBO), and Giemsa staining. Further, RT-PCR was also performed for the detection of PCP. The mean patients’ age was 52 (SD ± 16) years. 41% were female, and 59% of the patients were male. Weight loss (80%), fever (92%), cough (100%), and dyspnea (76%) were the most common complaints. Twenty-eight patients have been diagnosed with pulmonary infiltrates using chest X-ray. Out of 100 patients, 35% were positive for PCP. The organism was detected using IFAT in all the 35 specimens, 15 of 35 (42.86%) by GMSS, 8 of 35 (17.6%) by Giemsa stain, and 1 of 35 (2.8%) was detected by TBO stains. RT-PCR showed that 39 patients was found to be positive for PCP. Thirty-five of these 39 patients had a positive IFAT (89.74%); the IFAT was negative or undefined in 4 samples. All 39 patients (100%) had signs and symptoms for PCP. Our results suggest that RT-PCR is still the most highly sensitive method for Pneumocystis Jirovecii detection. In poor resource settings where RT-PCR and IFAT is not available, diagnosis of Pneumocystis jirovecii pneumonia remains a complicated issue. In settings where RT-PCR & IFAT are not available, GMSS staining may be the next best choice to detect PCP.
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Affiliation(s)
- Mohammad Y. Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
- Corresponding author at: Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha 9088, Saudi Arabia.
| | - Mohammed Alfaifi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Ali Gaithan Alkhathami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Abdulrahim Refdan Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Hafiz Ahmad
- Department of Medical Microbiology and Immunology, RAK Medical & Health Sciences University, Ras Al Khaimah, United Arab Emirates
| | - Osama M. Alshehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Megh Singh Dhakad
- Department of Microbiology, Lady Hardinge Medical College, New Delhi, India
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17
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Comparison of Positive Results With End-Point and Real-Time Polymerase Chain Reaction Assays for the Diagnosis of Pneumocystis Pneumonia. INFECTIOUS DISEASES IN CLINICAL PRACTICE 2020. [DOI: 10.1097/ipc.0000000000000817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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18
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Molecular Diagnosis of Pneumocystis jirovecii Pneumonia by Use of Oral Wash Samples in Immunocompromised Patients: Usefulness and Importance of the DNA Target. J Clin Microbiol 2019; 57:JCM.01287-19. [PMID: 31578265 DOI: 10.1128/jcm.01287-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/26/2019] [Indexed: 12/23/2022] Open
Abstract
Pneumocystis jirovecii pneumonia (PJP) is an important cause of pneumonia in the HIV-negative immunocompromised population, for whom the fungal load is low, the differential diagnosis is difficult, and a bronchoalveolar lavage (BAL) sample is often not readily available. Molecular techniques have improved the microbiological diagnosis in this scenario. The usefulness of two real-time PCR techniques targeting nuclear single-copy and mitochondrial multicopy genes, respectively, applied to oral wash specimens (OW) for PJP diagnosis was assessed, and its accuracy was compared to a BAL fluid-based diagnosis. Immunocompromised patients having PJP in the differential diagnosis of an acute respiratory episode, and from whom OW and BAL or lung biopsy specimens were obtained ≤48 h apart, were retrospectively included. PCRs targeting the dihydropteroate synthase gene (DHPS) and the mitochondrial small-subunit (mtSSU) rRNA gene were performed in paired OW-BAL specimens. Thirty-six patients were included (88.6% HIV negative). Fifteen patients (41.7%) were classified as PJP, and a further 8 were considered P. jirovecii colonized. Quantification of DHPS and mtSSU in BAL fluid showed an accuracy of 96.9% and 93.0%, respectively, for PJP diagnosis, whereas a qualitative approach performed better when applied to OW (accuracy, 91.7%) irrespective of the PCR target studied (kappa = 1). Qualitative molecular diagnosis applied to OW showed an excellent performance for PJP diagnosis regardless of the target studied, being easier to interpret than the quantitative approach needed for BAL fluid.
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19
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Abstract
Pneumocystis jirovecii pneumonia (PcP) has for many years been reported mostly in human immunodeficiency virus-infected patients. Increasingly, it also affects other immunocompromised patients, e.g. after organ or allogeneic stem cell/bone marrow transplantation, patients with hematologic malignancies or autoimmune diseases. The diagnosis of PcP relies on a critical evaluation of clinical symptoms, risk factors, radiologic features and microbiological tests. High dose cotrimoxazole is the most effective therapeutic option. Rapid initiation is essential, since mortality is especially high in patients admitted to intensive care with respiratory failure. This article reviews the current epidemiology of PcP and highlights the diagnostic and therapeutic options. Recommendations for primary and secondary prophylaxis are summarized.
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Grigoropoulos I, Thomas K, Christoforou P, Fanidi I, Papavdi M, Kyriakou F, Deutsch M, Pirounaki M, Vassilopoulos D. Pneumocystis Jirovecii Pneumonia after Initiation of Tofacitinib Therapy in Rheumatoid Arthritis: Case-Based Review. Mediterr J Rheumatol 2019; 30:167-170. [PMID: 32185360 PMCID: PMC7045858 DOI: 10.31138/mjr.30.3.167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/30/2022] Open
Abstract
The use of biologic and targeted synthetic disease-modifying anti-rheumatic drugs (tsDMARDs) in rheumatic diseases is constantly increasing during the last decade. Tofacitinib is a new oral Janus Kinase (JAK) inhibitor, approved for rheumatoid arthritis (RA), psoriatic arthritis and ulcerative colitis. Safety data of tofacitinib derived from randomized controlled trials and long-term extension studies has demonstrated a moderate increase in the risk for common serious infections. We describe a case of Pneumocystis jirovecii pneumonia (PJP) in a woman on tofacitinib therapy for RA. Although tofacitinib use has been associated with the development of opportunistic infections, PJP has been rarely reported. PJP should be included in the differential diagnosis of patients with autoimmune disorders under newer oral JAK inhibitors therapy who present with fever, hypoxia and pulmonary infiltrates.
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Affiliation(s)
- Ioannis Grigoropoulos
- 2 Department of Medicine and Laboratory, National and Kapodistrian University of Athens Medical School, Hippokration General Hospital, Athens, Greece
| | - Konstantinos Thomas
- 2 Department of Medicine and Laboratory, National and Kapodistrian University of Athens Medical School, Hippokration General Hospital, Athens, Greece
| | - Panagiotis Christoforou
- 2 Department of Medicine and Laboratory, National and Kapodistrian University of Athens Medical School, Hippokration General Hospital, Athens, Greece
| | - Iliana Fanidi
- 2 Department of Medicine and Laboratory, National and Kapodistrian University of Athens Medical School, Hippokration General Hospital, Athens, Greece
| | - Maria Papavdi
- 2 Department of Medicine and Laboratory, National and Kapodistrian University of Athens Medical School, Hippokration General Hospital, Athens, Greece
| | - Fani Kyriakou
- 2 Department of Medicine and Laboratory, National and Kapodistrian University of Athens Medical School, Hippokration General Hospital, Athens, Greece
| | - Melanie Deutsch
- 2 Department of Medicine and Laboratory, National and Kapodistrian University of Athens Medical School, Hippokration General Hospital, Athens, Greece
| | - Maria Pirounaki
- 2 Department of Medicine and Laboratory, National and Kapodistrian University of Athens Medical School, Hippokration General Hospital, Athens, Greece
| | - Dimitrios Vassilopoulos
- 2 Department of Medicine and Laboratory, National and Kapodistrian University of Athens Medical School, Hippokration General Hospital, Athens, Greece
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Petini M, Furlanello T, Danesi P, Zoia A. Nested-polymerase chain reaction detection of Pneumocystis carinii f. sp. canis in a suspected immunocompromised Cavalier King Charles spaniel with multiple infections. SAGE Open Med Case Rep 2019; 7:2050313X19841169. [PMID: 31065354 PMCID: PMC6487761 DOI: 10.1177/2050313x19841169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/27/2019] [Indexed: 11/16/2022] Open
Abstract
A 7-month-old Cavalier King Charles Spaniel female was referred due to a chronic cough refractory to antibiotic treatments. Laboratory findings showed leukocytosis, increased serum C-reactive protein, hypogammaglobulinemia, and decreased total serum immunoglobulin G concentration. Thoracic radiographs showed a mild bronchial pattern. Cytology of the bronchoalveolar lavage fluid revealed a septic inflammation. Bordetella bronchiseptica, Mycoplasma spp., and Pneumocystis carinii were identified by polymerase chain reaction testing, and Klebsiella pneumonia was cultured from the bronchoalveolar lavage fluid. Moreover, Escherichia coli was also cultured from urine. Pneumocystis spp. identification was done by sequencing of genetic amplicons. The dog died due to cardiopulmonary arrest secondary to a spontaneous pneumothorax on the day following the procedure. This report documents the detection of Pneumocystis carinii f. sp. canis in a suspected immunocompromised Cavalier King Charles Spaniel with concurrent pulmonary and urinary tract infections involving four different pathogens, and highlights the importance of the use of polymerase chain reaction testing to detect canine Pneumocystis spp. in cases with negative bronchoalveolar lavage cytology.
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Affiliation(s)
| | | | - Patrizia Danesi
- Operative Unit of Mycology, Parasitology Lab, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVE), Legnaro, Italy
| | - Andrea Zoia
- San Marco Veterinary Clinic, Veggiano, Italy
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Cereser L, Dallorto A, Candoni A, Volpetti S, Righi E, Zuiani C, Girometti R. Pneumocystis jirovecii pneumonia at chest High-resolution Computed Tomography (HRCT) in non-HIV immunocompromised patients: Spectrum of findings and mimickers. Eur J Radiol 2019; 116:116-127. [PMID: 31153552 DOI: 10.1016/j.ejrad.2019.04.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/21/2019] [Accepted: 04/30/2019] [Indexed: 01/08/2023]
Abstract
Pneumocystis jirovecii pneumonia (PJP) has emerged as a main issue in non Human Immunodeficiency Virus (HIV) immunocompromised hosts, exposing patients to high mortality rates, especially when the diagnosis is delayed. Since microbiological confirmation is often unfeasible or difficult to obtain, High-resolution Computed Tomography (HRCT) represents a main tool for guiding the diagnosis in the appropriate clinical scenario. Nevertheless, radiologists must be aware that PJP at HRCT is a multifaceted process, with a variety of common and less frequent findings, along with a broad spectrum of infectious (e.g., viral and certain fungal and bacterial pneumonias) and non-infectious (e.g., pulmonary oedema, diffuse alveolar haemorrhage, and drug toxicity) differential diagnoses. In this review we resume background clinical information on PJP in non-HIV immunocompromised patients, illustrate both typical and less frequent HRCT findings, and present the spectrum of infectious and non-infectious mimickers at HRCT, highlighting the similarities with PJP and providing clues for the differential diagnosis.
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Affiliation(s)
- Lorenzo Cereser
- Institute of Radiology, Department of Medicine, University of Udine, Azienda Sanitaria Universitaria Integrata di Udine, p.le S. Maria della Misericordia 15, 33100, Udine, Italy.
| | - Anna Dallorto
- Institute of Radiology, Department of Medicine, University of Udine, Azienda Sanitaria Universitaria Integrata di Udine, p.le S. Maria della Misericordia 15, 33100, Udine, Italy.
| | - Anna Candoni
- Division of Haematology and Stem Cell Transplantation, University Hospital of Udine, Azienda Sanitaria Universitaria Integrata di Udine, p.le S. Maria della Misericordia 15, 33100, Udine, Italy.
| | - Stefano Volpetti
- Division of Haematology and Stem Cell Transplantation, University Hospital of Udine, Azienda Sanitaria Universitaria Integrata di Udine, p.le S. Maria della Misericordia 15, 33100, Udine, Italy.
| | - Elda Righi
- Infectious Diseases, Santa Maria della Misericordia University Hospital, Azienda Sanitaria Universitaria Integrata di Udine, p.le S. Maria della Misericordia 15, 33100, Udine, Italy.
| | - Chiara Zuiani
- Institute of Radiology, Department of Medicine, University of Udine, Azienda Sanitaria Universitaria Integrata di Udine, p.le S. Maria della Misericordia 15, 33100, Udine, Italy.
| | - Rossano Girometti
- Institute of Radiology, Department of Medicine, University of Udine, Azienda Sanitaria Universitaria Integrata di Udine, p.le S. Maria della Misericordia 15, 33100, Udine, Italy.
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Stempak LM, Vogel SA, Richter SS, Wyllie R, Procop GW. Routine Broad-Range Fungal Polymerase Chain Reaction With DNA Sequencing in Patients With Suspected Mycoses Does Not Add Value and Is Not Cost-Effective. Arch Pathol Lab Med 2018; 143:634-638. [DOI: 10.5858/arpa.2017-0299-oa] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—
New molecular diagnostic tests regularly become available, and they may be assumed to be superior to traditional diagnostic studies. The added cost of these studies should be considered in conjunction with the value provided for patient care.
Objective.—
To assess the cost and diagnostic value of broad-range polymerase chain reaction (PCR) and DNA sequencing for the diagnosis of fungal infections compared with traditional studies.
Design.—
We reviewed the cost and clinical impact of broad-range fungal PCR/DNA sequencing for 65 specimens for which this test, a direct fungal examination, fungal culture, and a histopathologic assessment were performed.
Results.—
The sensitivity, specificity, and positive and negative predictive values for each of the assays studied were, respectively: histopathology (83.3%, 100%, 100%, and 98.3%); direct examination (66.7%, 100%, 100%, and 96.7%); fungal culture (83.3%, 100%, 100%, and 98.3%); and broad-range fungal PCR/DNA sequencing (83.3%, 95.0%, 62.5%, and 98.3%). The cost for broad-range fungal PCR/DNA sequencing was $32,500, compared with $8,591.70 for all traditional tests combined, for the 65 specimens included in this review.
Conclusions.—
Broad-range fungal PCR/DNA sequencing did not detect any infecting fungal pathogen that was not detected by at least 1 of the traditional methods, but 3 false-positives occurred. Broad-range fungal PCR/DNA sequencing is not a substitute for traditional laboratory studies and should be used judiciously to promote care affordability.
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Affiliation(s)
| | | | | | | | - Gary W. Procop
- From the Department of Pathology, The University of Mississippi Medical Center, Jackson (Dr Stempak); and the Pathology and Laboratory Medicine Institute (Ms Vogel and Drs Richter, Wyllie, and Procop) and Medical Operations (Drs Wyllie and Procop), Cleveland Clinic, Cleveland, Ohio
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24
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Pneumocystis Jirovecii (carinii) pneumonia causing lung cystic lesions and pneumomediastinum in non-HIV infected patient. Respir Med Case Rep 2018; 25:174-176. [PMID: 30186757 PMCID: PMC6122305 DOI: 10.1016/j.rmcr.2018.08.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/25/2018] [Accepted: 08/27/2018] [Indexed: 12/31/2022] Open
Abstract
Pneumomediastinum is a rare, potentially life-threatening complication of PCP that occurs in HIV-positive and HIV-negative patients. We are presenting a rare case pneumomediastinum caused by pneumocystis Jirovecii pneumonia in a HIV-negative patient with history of diffuse B-cell lymphoma on R CHOP chemotherapy. What is unique about our case is that the patient developed pneumomediastinum while in the hospital, on atovaquone that improved when switched to clindamycin and primaquine with improvement in her respiratory status. Another interesting point is that diagnosis was entertained due to the characteristic CT scan finding of ground glass opacities with cystic lung lesions and pneumomediastinum in an immunocompromised patient who was started on empirical treatment for PCP. The diagnosis was eventually confirmed with PCP PCR.
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25
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Antinori S, Corbellino M, Parravicini C. Challenges in the Diagnosis of Invasive Fungal Infections in Immunocompromised Hosts. CURRENT FUNGAL INFECTION REPORTS 2018; 12:12-22. [PMID: 32288934 PMCID: PMC7102396 DOI: 10.1007/s12281-018-0306-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Purpose of review The expanding population of immunocompromised patients coupled with the recognition of a growing number of different species of fungi responsible for diseases in such hosts makes the diagnosis of invasive fungal infection (IFI) a challenging task. The recent advances and challenges in the diagnosis of IFI in the setting of immunocompromised hosts are reviewed. The advantages and limitations of histopathology and the role of culture-independent methods, such as those based on the use of nucleic acids applied to fresh and formalin-fixed, paraffin-embedded sections, besides culture- and non-culture-based diagnostic methods, to obtain a timely and correct diagnosis of IFI are highlighted. Recent findings The therapeutic implications of identifying the genus and species of the fungus present in the specimen with the molecular diagnostics applied to tissue specimens are reviewed. No method alone is efficient in correctly identifying fungi and it is essential to combine the traditional histochemical staining with molecular methods to achieve a rapid and genus-/species-specific diagnosis of IFI. Summary We review the recent findings and challenges in the hystopathologic diagnosis of IFI in the setting of immunocompromised hosts. Non method alone is efficient in correctly identify fungi and pathologists should combine classic staining with molecular methods to achieve a rapid and genus/species fungal diagnosis.
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Affiliation(s)
- Spinello Antinori
- 1Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milano, Via GB Grassi, 74, 20157 Milan, Italy.,2III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milan, Italy
| | - Mario Corbellino
- 2III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milan, Italy
| | - Carlo Parravicini
- 3Pathology Unit, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milan, Italy
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