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Riebold D, Mahnkopf M, Wicht K, Zubiria-Barrera C, Heise J, Frank M, Misch D, Bauer T, Stocker H, Slevogt H. Axenic Long-Term Cultivation of Pneumocystis jirovecii. J Fungi (Basel) 2023; 9:903. [PMID: 37755011 PMCID: PMC10533121 DOI: 10.3390/jof9090903] [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: 07/19/2023] [Revised: 08/18/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023] Open
Abstract
Pneumocystis jirovecii, a fungus causing severe Pneumocystis pneumonia (PCP) in humans, has long been described as non-culturable. Only isolated short-term experiments with P. jirovecii and a small number of experiments involving animal-derived Pneumocystis species have been published to date. However, P. jirovecii culture conditions may differ significantly from those of animal-derived Pneumocystis, as there are major genotypic and phenotypic differences between them. Establishing a well-performing P. jirovecii cultivation is crucial to understanding PCP and its pathophysiological processes. The aim of this study, therefore, was to develop an axenic culture for Pneumocystis jirovecii. To identify promising approaches for cultivation, a literature survey encompassing animal-derived Pneumocystis cultures was carried out. The variables identified, such as incubation time, pH value, vitamins, amino acids, and other components, were trialed and adjusted to find the optimum conditions for P. jirovecii culture. This allowed us to develop a medium that produced a 42.6-fold increase in P. jirovecii qPCR copy numbers after a 48-day culture. Growth was confirmed microscopically by the increasing number and size of actively growing Pneumocystis clusters in the final medium, DMEM-O3. P. jirovecii doubling time was 8.9 days (range 6.9 to 13.6 days). In conclusion, we successfully cultivated P. jirovecii under optimized cell-free conditions in a 70-day long-term culture for the first time. However, further optimization of the culture conditions for this slow grower is indispensable.
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Affiliation(s)
- Diana Riebold
- Research Centre of Medical Technology and Biotechnology (FZMB), 99947 Bad Langensalza, Germany; (M.M.); (J.H.)
| | - Marie Mahnkopf
- Research Centre of Medical Technology and Biotechnology (FZMB), 99947 Bad Langensalza, Germany; (M.M.); (J.H.)
| | - Kristina Wicht
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, B-9000 Gent, Belgium;
| | - Cristina Zubiria-Barrera
- Respiratory Infection Dynamics Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (C.Z.-B.); (H.S.)
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, German Center for Lung Research (DZL), BREATH, 30625 Hannover, Germany
| | - Jan Heise
- Research Centre of Medical Technology and Biotechnology (FZMB), 99947 Bad Langensalza, Germany; (M.M.); (J.H.)
| | - Marcus Frank
- Medical Biology and Electron Microscopy Centre (EMZ), University Medicine Rostock, 18057 Rostock, Germany;
| | - Daniel Misch
- Lungenklinik Heckeshorn, Helios Klinikum Emil-von-Behring, 14165 Berlin, Germany; (D.M.); (T.B.)
| | - Torsten Bauer
- Lungenklinik Heckeshorn, Helios Klinikum Emil-von-Behring, 14165 Berlin, Germany; (D.M.); (T.B.)
| | - Hartmut Stocker
- Clinic for Infectiology, St. Joseph’s Hospital Berlin, 12101 Berlin, Germany;
| | - Hortense Slevogt
- Respiratory Infection Dynamics Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (C.Z.-B.); (H.S.)
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, German Center for Lung Research (DZL), BREATH, 30625 Hannover, Germany
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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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Apostolopoulou A, Fishman JA. The Pathogenesis and Diagnosis of Pneumocystis jiroveci Pneumonia. J Fungi (Basel) 2022; 8:1167. [PMID: 36354934 PMCID: PMC9696632 DOI: 10.3390/jof8111167] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 07/29/2023] Open
Abstract
Pneumocystis jiroveci remains an important fungal pathogen in immunocompromised hosts. The environmental reservoir remains unknown. Pneumonia (PJP) results from airborne transmission, including in nosocomial clusters, or with reactivation after an inadequately treated infection. Pneumocystis pneumonia most often occurs within 6 months of organ transplantation, with intensified or prolonged immunosuppression, notably with corticosteroids and following cytomegalovirus (CMV) infections. Infection may be recognized during recovery from neutropenia and lymphopenia. Invasive procedures may be required for early diagnosis and therapy. Despite being a well-established entity, aspects of the pathogenesis of PJP remain poorly understood. The goal of this review is to summarize the data on the pathogenesis of PJP, review the strengths and weaknesses of the pertinent diagnostic modalities, and discuss areas for future research.
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Affiliation(s)
- Anna Apostolopoulou
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jay A. Fishman
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- MGH Transplant Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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Usefulness of ß-d-Glucan Assay for the First-Line Diagnosis of Pneumocystis Pneumonia and for Discriminating between Pneumocystis Colonization and Pneumocystis Pneumonia. J Fungi (Basel) 2022; 8:jof8070663. [PMID: 35887420 PMCID: PMC9318034 DOI: 10.3390/jof8070663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/16/2022] [Accepted: 06/23/2022] [Indexed: 11/17/2022] Open
Abstract
According to the immunodepression status, the diagnosis of Pneumocystis jirovecii pneumonia (PjP) may be difficult. Molecular methods appear very sensitive, but they lack specificity because Pj DNA can be detected in Pneumocystis-colonized patients. The aim of this study was to evaluate the value of a serum ß-d-Glucan (BDG) assay for the diagnosis of PjP in a large cohort of HIV-negative and HIV-positive patients, either as a first-line diagnostic test for PjP or as a tool to distinguish between colonization and PjP in cases of low fungal load. Data of Pj qPCR performed on bronchopulmonary specimens over a 3-year period were retrieved retrospectively. For each result, we searched for a BDG serum assay performed within ±5 days. Among the 69 episodes that occurred in HIV-positive patients and the 609 episodes that occurred in immunocompromised HIV-negative patients, we find an equivalent sensitivity of BDG assays compared with molecular methods to diagnose probable/proven PjP, in a first-line strategy. Furthermore, BDG assay can be used confidently to distinguish between infected and colonized patients using a 80 pg/mL cut-off. Finally, it is necessary to search for causes of false positivity to increase BDG assay performance. BDG assay represents a valuable adjunctive tool to distinguish between colonization and infection.
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Short Communication: Prevalence of Listeria monocytogenes in Raw Milk of Healthy Sheep and Goats. Vet Med Int 2022; 2022:3206172. [PMID: 35646303 PMCID: PMC9135515 DOI: 10.1155/2022/3206172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 03/30/2022] [Accepted: 04/08/2022] [Indexed: 11/29/2022] Open
Abstract
Listeria monocytogenes, one of the most important bacterial pathogens transmitted through milk, causes listeriosis in humans and animals. This study aimed to investigate the prevalence of L. monocytogenes in raw milk of healthy sheep and goats in the west of Iran (Lorestan Province) by touchdown PCR (TD-PCR). Listeria spp. were found in milk samples taken from 21 sheep (29.16%) and 3 goats (10.71%) whereas L. monocytogenes was isolated from milk samples taken from 4 sheep (5.55%) and 1 goat (3.75%). The results showed that there was a significant difference between sheep and goats in the prevalence of Listeria spp. in their raw milk (p < 0.05), but no significant difference was observed between them in the prevalence of L. monocytogenes. The study findings suggested that the raw milk of healthy sheep and goats was infected with L. monocytogenes and warned of the risk of human infection with listeriosis following consumption of raw and unpasteurized milk.
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Meta-analysis of variable-temperature PCR technique performance for diagnosising Schistosoma japonicum infections in humans in endemic areas. PLoS Negl Trop Dis 2022; 16:e0010136. [PMID: 35030167 PMCID: PMC8794272 DOI: 10.1371/journal.pntd.0010136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 01/27/2022] [Accepted: 01/03/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND As China is moving onto schistosomiasis elimination/eradication, diagnostic methods with both high sensitivity and specificity for Schistosoma japonicum infections in humans are urgently needed. Microscopic identification of eggs in stool is proven to have poor sensitivity in low endemic regions, and antibody tests are unable to distinguish between current and previous infections. Polymerase chain reaction (PCR) technologies for the detection of parasite DNA have been theoretically assumed to show high diagnostic sensitivity and specificity. However, the reported performance of PCR for detecting S. japonicum infection varied greatly among studies. Therefore, we performed a meta-analysis to evaluate the overall diagnostic performance of variable-temperature PCR technologies, based on stool or blood, for detecting S. japonicum infections in humans from endemic areas. METHODS We searched literatures in eight electronic databases, published up to 20 January 2021. The heterogeneity and publication bias of included studies were assessed statistically. The risk of bias and applicability of each eligible study were assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 tool (QUADAS-2). The bivariate mixed-effects model was applied to obtain the summary estimates of diagnostic performance. The hierarchical summary receiver operating characteristic (HSROC) curve was applied to visually display the results. Subgroup analyses and multivariate regression were performed to explore the source of heterogeneity. This research was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines and was registered prospectively in PROSPERO (CRD42021233165). RESULTS A total of 2791 papers were retrieved. After assessing for duplications and eligilibity a total of thirteen publications were retained for inclusion. These included eligible data from 4268 participants across sixteen studies. High heterogeneity existed among studies, but no publication bias was found. The pooled analyses of PCR data from all included studies resulted in a sensitivity of 0.91 (95% CI: 0.83 to 0.96), specificity of 0.85 (95% CI: 0.65 to 0.94), positive likelihood ratio of 5.90 (95% CI: 2.40 to 14.60), negative likelihood ratio of 0.10 (95% CI: 0.05 to 0.20) and a diagnostics odds ratio of 58 (95% CI: 19 to 179). Case-control studies showed significantly better performances for PCR diagnostics than cross-sectional studies. This was further evidenced by multivariate analyses. The four types of PCR approaches identified (conventional PCR, qPCR, Droplet digital PCR and nested PCR) differed significantly, with nested PCRs showing the best performance. CONCLUSIONS Variable-temperature PCR has a satisfactory performance for diagnosing S. japonicum infections in humans in endemic areas. More high quality studies on S. japonicum diagnostic techniques, especially in low endemic areas and for the detection of dual-sex and single-sex infections are required. These will likely need to optimise a nested PCR alongside a highly sensitive gene target. They will contribute to successfully monitoring endemic areas as they move towards the WHO 2030 targets, as well as ultimately helping areas to achieve these goals.
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Damhorst GL, Broder KJ, Overton EC, Rara R, Busch LM, Burd EM, Webster AS, Kraft CS, Babiker A. Clinical Utilization of DiaSorin Molecular Polymerase Chain Reaction in Pneumocystis Pneumonia. Open Forum Infect Dis 2022; 9:ofab634. [PMID: 35036467 PMCID: PMC8754379 DOI: 10.1093/ofid/ofab634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/08/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Pneumocystis jirovecii polymerase chain reaction (PCR) testing is a sensitive diagnostic tool but does not distinguish infection from colonization. Cycle threshold (CT) may correlate with fungal burden and could be considered in clinical decision making. Clinical use of PCR and significance of CT values have not previously been examined with the DiaSorin Molecular platform. METHODS Retrospective review of P jirovecii PCR, CT values and clinical data from 18 months in a multihospital academic health system. The diagnostic performance of PCR with respect to pathology and correlation of CT with severity were examined. RESULTS Ninety-nine of 1006 (9.8%) assays from 786 patients in 919 encounters were positive. Among 91 (9.9%) encounters in which P jirovecii pneumonia (PJP) was treated, 41 (45%) were influenced by positive PCR. Negative PCR influenced discontinuation of therapy in 35 cases. Sensitivity and specificity of PCR were 93% (95% CI, 68%-100%) and 94% (95% CI, 91%-96%) with respect to pathology. CT values from deep respiratory specimens were significantly different among treated patients (P = .04) and those with positive pathology results (P < .0001) compared to patients not treated and those with negative pathology, respectively, and was highly predictive of positive pathology results (area under the curve = 0.92). No significant difference was observed in comparisons based on indicators of disease severity. CONCLUSIONS Pneumocystis jirovecii PCR was a highly impactful tool in the diagnosis and management of PJP, and use of CT values may have value in the treatment decision process in select cases. Further investigation in a prospective manner is needed.
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Affiliation(s)
- Gregory L Damhorst
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kari J Broder
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | | | - Lindsay M Busch
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Eileen M Burd
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Andrew S Webster
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Colleen S Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ahmed Babiker
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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Is It Possible to Differentiate Pneumocystis jirovecii Pneumonia and Colonization in the Immunocompromised Patients with Pneumonia? J Fungi (Basel) 2021; 7:jof7121036. [PMID: 34947017 PMCID: PMC8707387 DOI: 10.3390/jof7121036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 11/18/2022] Open
Abstract
Respiratory sample staining is a standard tool used to diagnose Pneumocystis jirovecii pneumonia (PjP). Although molecular tests are more sensitive, their interpretation can be difficult due to the potential of colonization. We aimed to validate a Pneumocystis jirovecii (Pj) real-time PCR (qPCR) assay in bronchoscopic bronchoalveolar lavage (BAL) and oropharyngeal washes (OW). We included 158 immunosuppressed patients with pneumonia, 35 lung cancer patients who underwent BAL, and 20 healthy individuals. We used a SYBR green qPCR assay to look for a 103 bp fragment of the Pj mtLSU rRNA gene in BAL and OW. We calculated the qPCR cut-off as well as the analytical and diagnostic characteristics. The qPCR was positive in 67.8% of BAL samples from the immunocompromised patients. The established cut-off for discriminating between disease and colonization was Ct 24.53 for BAL samples. In the immunosuppressed group, qPCR detected all 25 microscopy-positive PjP cases, plus three additional cases. Pj colonization in the immunocompromised group was 66.2%, while in the cancer group, colonization rates were 48%. qPCR was ineffective at diagnosing PjP in the OW samples. This new qPCR allowed for reliable diagnosis of PjP, and differentiation between PjP disease and colonization in BAL of immunocompromised patients with pneumonia.
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Jitmuang A, Nititammaluk A, Boonsong T, Sarasombath PT, Sompradeekul S, Chayakulkeeree M. A novel droplet digital polymerase chain reaction for diagnosis of Pneumocystis pneumonia (PCP)-a clinical performance study and survey of sulfamethoxazole-trimethoprim resistant mutations. J Infect 2021; 83:701-708. [PMID: 34562541 DOI: 10.1016/j.jinf.2021.09.014] [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: 03/07/2021] [Revised: 09/14/2021] [Accepted: 09/19/2021] [Indexed: 10/20/2022]
Abstract
Objectives To determine the performance of droplet digital polymerase chain reaction (ddPCR) assays in diagnosing Pneumocystis pneumonia (PCP), and to survey the sulfamethoxazole-trimethoprim (SMX-TMP) resistant mutations in our PCP cohort. Methods A prospective study was conducted from January 2017 to June 2018. Adult immunocompromised subjects with pneumonia were enrolled. Bronchoalveolar lavage fluid samples were obtained for standard microscopic testing and ddPCR to quantify the Pneumocystis MSG gene. DHPS and DHFR gene sequencings were performed to detect SMX-TMP resistance. Results Of 54 subjects, 12 had definite PCP, 7 had probable PCP, and 35 were non-PCP. In the PCP cohort, 10 (53%) had HIV infections. Using a cutoff value of ≥ 1.94 copies/µL, the ddPCR exhibited an overall sensitivity of 91.7% (61.5-99.8%) and specificity of 88.1% (74.4-96%). It showed a better performance when different cutoff values were used in subjects with HIV (≥ 1.80 copies/µL) and non-HIV (≥ 4.5 copies/µL). ROC curves demonstrated an AUC of 0.80 (95% CI, 0.56-1.0) for the HIV group, and 0.99 (95% CI, 0.95-1.0) for the non-HIV group. Of 16 PCP samples tested for DHPS- and DHFR-mutations, only DHPS mutations were detected (2). Most of the subjects, including those with DHPS mutations, demonstrated favorable outcomes. Conclusions The ddPCR exhibited a satisfactory diagnostic performance for PCP. Based on very limited data, the treatment outcomes of PCP did not seem to be affected by the DHPS mutations.
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Affiliation(s)
- Anupop Jitmuang
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, Thailand
| | - Anapat Nititammaluk
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, Thailand
| | - Thitaya Boonsong
- Department of Internal Medicine, Hatyai Hospital, Songkhla, Thailand
| | | | - Suree Sompradeekul
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, Thailand
| | - Methee Chayakulkeeree
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, Thailand.
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Grønseth S, Rogne T, Hannula R, Åsvold BO, Afset JE, Damås JK. Semiquantitative Real-Time PCR to Distinguish Pneumocystis Pneumonia from Colonization in a Heterogeneous Population of HIV-Negative Immunocompromised Patients. Microbiol Spectr 2021; 9:e0002621. [PMID: 34346746 PMCID: PMC8552647 DOI: 10.1128/spectrum.00026-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/14/2021] [Indexed: 11/20/2022] Open
Abstract
Pneumocystis jirovecii is a threat to iatrogenically immunosuppressed individuals, a heterogeneous population at rapid growth. We assessed the ability of an in-house semiquantitative real-time PCR assay to discriminate Pneumocystis pneumonia (PCP) from colonization and identified risk factors for infection in these patients. Retrospectively, 242 PCR-positive patients were compared according to PCP status, including strata by immunosuppressive conditions, human immunodeficiency virus (HIV) infection excluded. Associations between host characteristics and cycle threshold (CT) values, semiquantitative real-time PCR correlates of fungal loads in lower respiratory tract specimens, were investigated. CT values differed significantly according to PCP status. Overall, a CT value of 36 allowed differentiation between PCP and colonization with sensitivity and specificity of 71.3% and 77.1%, respectively. A CT value of less than 31 confirmed PCP, whereas no CT value permitted exclusion. A considerable diversity was uncovered; solid organ transplant (SOT) recipients had significantly higher fungal loads than patients with hematological malignancies. In SOT recipients, a CT cutoff value of 36 resulted in sensitivity and specificity of 95.0% and 83.3%, respectively. In patients with hematological malignancies, a higher CT cutoff value of 37 improved sensitivity to 88.5% but reduced specificity to 66.7%. For other conditions, assay validity appeared inferior. Corticosteroid usage was an independent predictor of PCP in a multivariable analysis and was associated with higher fungal loads at PCP expression. Semiquantitative real-time PCR improves differentiation between PCP and colonization in immunocompromised HIV-negative individuals with acute respiratory syndromes. However, heterogeneity in disease evolution requires separate cutoff values across intrinsic and iatrogenic predisposition for predicting non-HIV PCP. IMPORTANCE Pneumocystis jirovecii is potentially life threatening to an increasing number of individuals with compromised immune systems. This microorganism can cause severe pneumonia in susceptible hosts, including patients with cancer and autoimmune diseases and people undergoing solid organ transplantation. Together, these patients constitute an ever-diverse population. In this paper, we demonstrate that the heterogeneity herein has important implications for how we diagnose and assess the risk of Pneumocystis pneumonia (PCP). Specifically, low loads of microorganisms are sufficient to cause infection in patients with blood cancer compared to those in solid organ recipients. With this new insight into host versus P. jirovecii biology, clinicians can manage patients at risk of PCP more accurately. As a result, we take a significant step toward offering precision medicine to a vulnerable patient population. One the one hand, these patients have propensity for adverse effects from antimicrobial treatment. On the other hand, this population is susceptible to life-threatening infections, including PCP.
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Affiliation(s)
- Stine Grønseth
- Department of Clinical and Molecular Medicine, NTNU, Trondheim, Norway
| | - Tormod Rogne
- Department of Circulation and Medical Imaging, NTNU, Trondheim, Norway
- Department of Chronic Disease Epidemiology, Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
| | - 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, NTNU, Trondheim, Norway
- Department of Medical Microbiology, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jan Kristian Damås
- Department of Clinical and Molecular Medicine, 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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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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Gits-Muselli M, White PL, Mengoli C, Chen S, Crowley B, Dingemans G, Fréalle E, L Gorton R, Guiver M, Hagen F, Halliday C, Johnson G, Lagrou K, Lengerova M, Melchers WJG, Novak-Frazer L, Rautemaa-Richardson R, Scherer E, Steinmann J, Cruciani M, Barnes R, Donnelly JP, Loeffler J, Bretagne S, Alanio A. The Fungal PCR Initiative's evaluation of in-house and commercial Pneumocystis jirovecii qPCR assays: Toward a standard for a diagnostics assay. Med Mycol 2021; 58:779-788. [PMID: 31758173 DOI: 10.1093/mmy/myz115] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 10/22/2019] [Accepted: 10/31/2019] [Indexed: 01/04/2023] Open
Abstract
Quantitative real-time PCR (qPCR) is increasingly used to detect Pneumocystis jirovecii for the diagnosis of Pneumocystis pneumonia (PCP), but there are differences in the nucleic acids targeted, DNA only versus whole nucleic acid (WNA), and also the target genes for amplification. Through the Fungal PCR Initiative, a working group of the International Society for Human and Animal Mycology, a multicenter and monocenter evaluation of PCP qPCR assays was performed. For the multicenter study, 16 reference laboratories from eight different countries, performing 20 assays analyzed a panel consisting of two negative and three PCP positive samples. Aliquots were prepared by pooling residual material from 20 negative or positive- P. jirovecii bronchoalveolar lavage fluids (BALFs). The positive pool was diluted to obtain three concentrations (pure 1:1; 1:100; and 1:1000 to mimic high, medium, and low fungal loads, respectively). The monocenter study compared five in-house and five commercial qPCR assays testing 19 individual BALFs on the same amplification platform. Across both evaluations and for all fungal loads, targeting WNA and the mitochondrial small sub-unit (mtSSU) provided the earliest Cq values, compared to only targeting DNA and the mitochondrial large subunit, the major surface glycoprotein or the beta-tubulin genes. Thus, reverse transcriptase-qPCR targeting the mtSSU gene could serve as a basis for standardizing the P. jirovecii load, which is essential if qPCR is to be incorporated into clinical care pathways as the reference method, accepting that additional parameters such as amplification platforms still need evaluation.
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Affiliation(s)
- Maud Gits-Muselli
- Institut Pasteur, Molecular Mycology Unit, CNRS UMR2000, Paris, France.,Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Université de Paris, Paris, France
| | - P Lewis White
- Public Health Wales, Microbiology Cardiff, UHW, Heath Park, Cardiff, UK
| | | | - Sharon Chen
- Clinical Mycology reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, and the University of Sydney, Australia
| | - Brendan Crowley
- Department of Virology, St James's Hospital, Dublin, Ireland
| | | | - Emilie Fréalle
- CHU Lille, Laboratoire de Parasitologie-Mycologie, F-59000 Lille, France & Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL-Centre for Infection and Immunity of Lille, F-59000 Lille, France
| | - Rebecca L Gorton
- Regional UK Clinical Mycology Network (UK CMN) Laboratory, Dept. Infection Sciences, Health Services Laboratories (HSL) LLP, London, UK
| | - Malcom Guiver
- Public Health Laboratory, National Infection Service Public Health England, Manchester University NHS Foundation Trust, Manchester, UK
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands.,Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
| | - Catriona Halliday
- Clinical Mycology reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, and the University of Sydney, Australia
| | | | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, KU Leuven, and Department of Laboratory Medicine and National Reference Centre for Mycosis, Excellence Centre for Medical Mycology (ECMM), University Hospitals Leuven, Leuven, Belgium
| | - Martina Lengerova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Willem J G Melchers
- Radboud University Medical Centre, Department of Medical Microbiology, Nijmegen, The Netherlands
| | - Lily Novak-Frazer
- Mycology Reference Centre Manchester, Manchester University NHS Foundation Trust; and Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Riina Rautemaa-Richardson
- Department of Infectious Diseases and the Mycology Reference Centre Manchester, Manchester University NHS Foundation Trust; and Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Emeline Scherer
- Department of Parasitology-Mycology, University Hospital of Besançon, Besançon, France
| | - Joerg Steinmann
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Klinikum Nürnberg, Paracelsus Medical University, Nuremberg, Germany.,Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Mario Cruciani
- Infectious Diseases Unit, San Bonifacio Hospital, Verona, Italy
| | | | | | - Juergen Loeffler
- University Hospital Wuerzburg, Medical Hospital II, C11, Wuerzburg, Germany
| | - Stéphane Bretagne
- Institut Pasteur, Molecular Mycology Unit, CNRS UMR2000, Paris, France.,Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Université de Paris, Paris, France
| | - Alexandre Alanio
- Institut Pasteur, Molecular Mycology Unit, CNRS UMR2000, Paris, France.,Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Université de Paris, Paris, France
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13
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Wills NK, Lawrence DS, Botsile E, Tenforde MW, Jarvis JN. The prevalence of laboratory-confirmed Pneumocystis jirovecii in HIV-infected adults in Africa: A systematic review and meta-analysis. Med Mycol 2021; 59:802-812. [PMID: 33578417 DOI: 10.1093/mmy/myab002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 11/30/2020] [Accepted: 01/08/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The epidemiology of Pneumocystis jirovecii, known to colonize the respiratory tract and cause a life-threatening HIV-associated pneumonia (PCP), is poorly described in Africa. We conducted a systematic review to evaluate P. jirovecii prevalence in African HIV-positive adults with or without respiratory symptoms. METHODS We searched Medline, Embase, Cochrane library, Africa-Wide, and Web of Science for studies employing PCR and/or microscopy for P. jirovecii detection in respiratory samples from HIV-positive adults in Africa between 1995 and 2020. Prevalence with respiratory symptoms was pooled using random-effect meta-analysis, and stratified by laboratory method, sample tested, study setting, CD4 count, and trimethoprim/sulfamethoxazole prophylaxis. Colonization prevalence in asymptomatic adults and in adults with non-PCP respiratory disease was described, and quantitative PCR (qPCR) thresholds to distinguish colonization from microscopy-confirmed PCP reviewed. RESULTS Thirty-two studies were included, with 27 studies (87%) at high risk of selection bias. P. jirovecii was detected in 19% [95% confidence interval (CI): 12-27%] of 3583 symptomatic and in 9% [95% CI: 0-45%] of 140 asymptomatic adults. Among symptomatic adults, prevalence was 22% [95% CI: 12-35%] by PCR and 15% [95% CI: 9-23%] by microscopy. Seven percent of 435 symptomatic adults had PCR-detected Pneumocystis colonization without evidence of PCP [95% CI: 5-10%, four studies]. One study established a qPCR cutoff of 78 copies/5μl of DNA in 305 induced sputum samples to distinguish Pneumocystis colonization from microscopy-confirmed PCP. CONCLUSION Despite widened access to HIV services, P. jirovecii remains common in Africa. Prevalence estimates and qPCR-based definitions of colonization are limited, and overall quality of studies is low.
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Affiliation(s)
- Nicola K Wills
- Welcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa.,Department of Clinical Research, Faculty of infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.,Department of Medicine, Groote Schuur Hospital University of Cape Town, Cape Town, 7925, South Africa
| | - David S Lawrence
- Department of Clinical Research, Faculty of infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.,Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Elizabeth Botsile
- Department of Medicine, Princess Marina Hospital, Gaborone, Botswana
| | - Mark W Tenforde
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, 98195, USA.,Department of Epidemiology, University of Washington School of Public Health, Seattle, 98195, WA, USA
| | - Joseph N Jarvis
- Department of Clinical Research, Faculty of infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.,Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
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14
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Irinyi L, Hu Y, Hoang MTV, Pasic L, Halliday C, Jayawardena M, Basu I, McKinney W, Morris AJ, Rathjen J, Stone E, Chen S, Sorrell TC, Schwessinger B, Meyer W. Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens: A paradigm shift in mycological diagnostics. Med Mycol 2021; 58:650-660. [PMID: 31758176 DOI: 10.1093/mmy/myz109] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/26/2019] [Accepted: 11/19/2019] [Indexed: 11/14/2022] Open
Abstract
The advent of next generation sequencing technologies has enabled the characterization of the genetic content of entire communities of organisms, including those in clinical specimens, without prior culturing. The MinION from Oxford Nanopore Technologies offers real-time, direct sequencing of long DNA fragments directly from clinical samples. The aim of this study was to assess the ability of unbiased, genome-wide, long-read, shotgun sequencing using MinION to identify Pneumocystis jirovecii directly from respiratory tract specimens and to characterize the associated mycobiome. Pneumocystis pneumonia (PCP) is a life-threatening fungal disease caused by P. jirovecii. Currently, the diagnosis of PCP relies on direct microscopic or real-time quantitative polymerase chain reaction (PCR) examination of respiratory tract specimens, as P. jirovecii cannot be cultured readily in vitro. P. jirovecii DNA was detected in bronchoalveolar lavage (BAL) and induced sputum (IS) samples from three patients with confirmed PCP. Other fungi present in the associated mycobiome included known human pathogens (Aspergillus, Cryptococcus, Pichia) as well as commensal species (Candida, Malassezia, Bipolaris). We have established optimized sample preparation conditions for the generation of high-quality data, curated databases, and data analysis tools, which are key to the application of long-read MinION sequencing leading to a fundamental new approach in fungal diagnostics.
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Affiliation(s)
- Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia
| | - Yiheng Hu
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Minh Thuy Vi Hoang
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia
| | - Lana Pasic
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia
| | - Catriona Halliday
- Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Menuk Jayawardena
- Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Indira Basu
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Wendy McKinney
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Arthur J Morris
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - John Rathjen
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Eric Stone
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,ANU-CSIRO Centre for Genomics, Metabolomics and Bioinformatics, Canberra, ACT, Australia
| | - Sharon Chen
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Tania C Sorrell
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia.,Westmead Hospital (Research and Education Network), Westmead, NSW, Australia
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15
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Evert K, Dienemann T, Brochhausen C, Lunz D, Lubnow M, Ritzka M, Keil F, Trummer M, Scheiter A, Salzberger B, Reischl U, Boor P, Gessner A, Jantsch J, Calvisi DF, Evert M, Schmidt B, Simon M. Autopsy findings after long-term treatment of COVID-19 patients with microbiological correlation. Virchows Arch 2021; 479:97-108. [PMID: 33471172 PMCID: PMC7816067 DOI: 10.1007/s00428-020-03014-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/22/2020] [Accepted: 12/27/2020] [Indexed: 12/11/2022]
Abstract
Between April and June 2020, i.e., during the first wave of pandemic coronavirus disease 2019 (COVID-19), 55 patients underwent long-term treatment in the intensive care unit at the University Hospital of Regensburg. Most of them were transferred from smaller hospitals, often due to the need for an extracorporeal membrane oxygenation system. Autopsy was performed in 8/17 COVID-19-proven patients after long-term treatment (mean: 33.6 days). Autopsy revealed that the typical pathological changes occurring during the early stages of the disease (e.g., thrombosis, endothelitis, capillaritis) are less prevalent at this stage, while severe diffuse alveolar damage and especially coinfection with different fungal species were the most conspicuous finding. In addition, signs of macrophage activation syndrome was detected in 7 of 8 patients. Thus, fungal infections were a leading cause of death in our cohort of severely ill patients and may alter clinical management of patients, particularly in long-term periods of treatment.
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Affiliation(s)
- Katja Evert
- Institute of Pathology, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany.
| | - Thomas Dienemann
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Christoph Brochhausen
- Institute of Pathology, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Dirk Lunz
- Department of Medicine II, University Medical Centre, Regensburg, Germany
| | - Matthias Lubnow
- Department of Anesthesiology and Intensive Care, University Hospital Regensburg, Regensburg, Germany
| | - Markus Ritzka
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Felix Keil
- Institute of Pathology, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Matthias Trummer
- Institute of Pathology, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Alexander Scheiter
- Institute of Pathology, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Bernd Salzberger
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - Udo Reischl
- Institute of Clinical Microbiology and Hygiene, Regensburg University Hospital, Regensburg, Germany
| | - Peter Boor
- Institute of Pathology, University Hospital Aachen, RWTH Aachen, Aachen, Germany
| | - André Gessner
- Institute of Clinical Microbiology and Hygiene, Regensburg University Hospital, Regensburg, Germany
| | - Jonathan Jantsch
- Institute of Clinical Microbiology and Hygiene, Regensburg University Hospital, Regensburg, Germany
| | - Diego F Calvisi
- Institute of Pathology, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Matthias Evert
- Institute of Pathology, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Barbara Schmidt
- Institute of Clinical Microbiology and Hygiene, Regensburg University Hospital, Regensburg, Germany
| | - Michaela Simon
- Institute of Clinical Microbiology and Hygiene, Regensburg University Hospital, Regensburg, Germany
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16
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Sivaraj V, Cliff P, Douthwaite S, Smith M, Kulasegaram R. Pneumocystis jirovecii pneumonia PCR test on upper respiratory tract swab. HIV Med 2020; 22:321-324. [PMID: 33230932 DOI: 10.1111/hiv.13014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/22/2020] [Accepted: 10/09/2020] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Pneumocystis jirovecii pneumonia (PCP) is an opportunistic fungal infection with high morbidity and mortality among people living with HIV. Upper respiratory tract (URT) swabs are routinely taken for testing viral and bacterial pathogens when patients present with respiratory symptoms in our hospital. We conducted a pilot service improvement project to explore the utility of URT swabs for PCP diagnosis using in-house real-time polymerase chain reaction (PCR). METHODS Ten URT swab samples obtained from HIV-positive patients with PCP and a positive PCP PCR (AusDiagnostics) from lower respiratory tract (LRT) samples were retrospectively identified. Nine HIV-positive patients with a negative PCR for PCP from LRT samples were identified. Stored aliquots of DNA extracted from these samples were retrieved and tested by an in-house real-time PCR for the presence of PCP DNA. Among PCP-positive cases, URT swabs collected after PCP treatment initiation were excluded from the study. RESULTS In all, 10 URT samples from PCP-positive patients and nine URT samples from PCP-negative patients were tested for PCP by real-time PCR. Eighteen out of 19 URT sample had a concordant result with the LRT samples. The sensitivity and specificity for URT sample PCR were 90% [confidence interval (CI): 55.50-99.75%] and 100% (CI: 66.37-100%). The positive predictive value was 100% and the negative predictive value was 90.9% (CI: 60.90-98.47%). CONCLUSIONS Upper respiratory tract swab can reliably detect PCP DNA on real-time PCR among people living with HIV with PCP.
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Affiliation(s)
- V Sivaraj
- Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - P Cliff
- Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - S Douthwaite
- Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - M Smith
- King's College hospital NHS foundation trust, London, UK
| | - R Kulasegaram
- Guy's and St Thomas' NHS Foundation Trust, London, UK
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17
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Evaluation of the Amplex eazyplex Loop-Mediated Isothermal Amplification Assay for Rapid Diagnosis of Pneumocystis jirovecii Pneumonia. J Clin Microbiol 2020; 58:JCM.01739-20. [PMID: 32938732 DOI: 10.1128/jcm.01739-20] [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: 07/12/2020] [Accepted: 09/08/2020] [Indexed: 11/20/2022] Open
Abstract
Quantitative PCR (qPCR) assays are the gold standard for diagnosis of Pneumocystis jirovecii pneumonia (PCP). However, they are laborious and require skilled personnel. Therefore, execution outside regular working hours of the molecular biology laboratory is limited. The eazyplex P. jirovecii assay (PJA) uses loop-mediated isothermal amplification for detection of P. jirovecii It is performed directly with respiratory specimens, without the need for special skills, and delivers a result within 3 to 25 min. The goal of our study was to compare the performance of the eazyplex PJA with that of established P. jirovecii qPCR assays. All archived bronchoalveolar lavage fluid (BALF) samples that had previously tested positive for P. jirovecii by qPCR assay and 50 control samples (retrospective part), as well as all BALF samples received for P. jirovecii analysis over a period of 4 months (prospective part), were tested. Forty-nine patients with proven PCP and 126 patients without PCP were included. The sensitivity and specificity of the eazyplex PJA (95.7% and 96.5%, respectively) were comparable to those for three different P. jirovecii qPCR assays. The detection limit of the eazyplex PJA was analogous to 103 copies of the major surface glycoprotein gene per 25 μl of BALF, corresponding to 10 to 20 P. jirovecii cells. The eazyplex PJA reliably discriminated patients with PCP from patients with P. jirovecii colonization. It delivered a positive result within a mean of 9 min 38 s and required a hands-on time of 2 min 45 s. In summary, the eazyplex PJA showed identical performance for the diagnosis of PCP, compared to qPCR assays. However, in terms of time to result, practicability, and robustness, the eazyplex PJA is clearly superior and allows for around-the-clock molecular testing.
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18
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Scharmann U, Kirchhoff L, Schmidt D, Buer J, Steinmann J, Rath PM. Evaluation of a commercial Loop-mediated Isothermal Amplification (LAMP) assay for rapid detection of Pneumocystis jirovecii. Mycoses 2020; 63:1107-1114. [PMID: 32738076 DOI: 10.1111/myc.13152] [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: 06/05/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND Various tools are obtainable for the detection of Pneumocystis jirovecii, among them qPCR promising highest sensitivity. A novel molecular method is commercially available, the loop-mediated isothermal amplification (LAMP) assay. OBJECTIVES We compared the performance of the LAMP eazyplex® Pneumocystis jirovecii with the RealStar Pneumocystis jirovecii PCR 1.0 qPCR. MATERIAL/METHODS Overall, 162 lower respiratory tract specimens from 146 critically ill patients were investigated. LAMP assay and qPCR were carried out according to the manufacturer's recommendations. Positive results of the LAMP were described as time to positivity (TTP). The limit of detection (LOD) of the LAMP was analysed using 10-fold serial dilutions of a high positive P jirovecii respiratory sample. For each serial dilution, TTP of the LAMP was plotted against cycle threshold (Ct) values of the qPCR. RESULTS The LOD of the LAMP was determined to be approximately 4 × 103 copies/mL. While the LAMP revealed 28 (17%) positive signals from 20 patients, by using qPCR 41 (25%) positive samples from 28 patients were identified. Overall agreement with qPCR was 92%. Five false-negative, one false-positive and nine invalid results were detected by the LAMP. Positive and negative predictive values were 96% each, and sensitivity and specificity were 84% and 99%, respectively. There was a low correlation between the TTP and the fungal load. CONCLUSION The LAMP is a time-saving and easy-to-perform method. It can be used as an alternative diagnostic method. However, for quantification purposes the qPCR is still the gold standard.
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Affiliation(s)
- Ulrike Scharmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lisa Kirchhoff
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Dirk Schmidt
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Joerg Steinmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Klinikum Nürnberg, Paracelsus Medical University, Nuremberg, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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19
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Rahimi H, Tukmechi A, Rashidian E. Use of touch-down polymerase chain reaction to enhance the sensitivity of Brucella melitensis detection in raw milk. Anim Biotechnol 2020; 33:104-109. [PMID: 32522080 DOI: 10.1080/10495398.2020.1777149] [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] [Indexed: 10/24/2022]
Abstract
Brucellosis is a highly contagious bacterial zoonotic infectious disease severely affecting the public health and economic features of endemic and non-endemic countries. The present study assessed the potentials of using the touch-down polymerase chain reaction (TD-PCR) compared to the conventional PCR and culture methods in order to detect Brucella melitensis in raw milk samples of 55 sheep and 45 goats through deriving the primers from the omp31 element of the Brucella genome. In addition, nine isolates of B. melitensis were identified using the culture method. No positive cases were found in sediment samples, while the fatty tap layer test by conventional PCR and TD-PCR revealed 6 and 16 positive samples, respectively. Based on the survey of the limits of detection by TD-PCR and conventional PCR, TD protocol had a detection threshold of three logs higher than the conventional protocol under the experimental condition. The developed protocol of this study was highly sensitive and extremely fast. Therefore, this TD-PCR protocol could detect even a very low number of bacteria in milk samples. To our best knowledge, this is the first report on the use of the TD-PCR method to identify B. melitensis in milk.
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Affiliation(s)
- Heidar Rahimi
- Faculty of Veterinary Medicine, Department of Microbiology, Urmia University, Urmia, Iran
| | - Amir Tukmechi
- Faculty of Veterinary Medicine, Department of Microbiology, Urmia University, Urmia, Iran
| | - Ehsan Rashidian
- Faculty of Veterinary Medicine, Department of Microbiology, Lorestan University, Lorestan, Iran
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20
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Bossart S, Mühlethaler K, Garzoni C, Furrer H. Is real time PCR preferable to the direct immunofluorescence in the diagnosis of Pneumocystis jirovecii pneumonia in HIV-infected patients? BMC Res Notes 2020; 13:235. [PMID: 32357915 PMCID: PMC7195742 DOI: 10.1186/s13104-020-05075-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 04/23/2020] [Indexed: 12/12/2022] Open
Abstract
Objectives In this study, we compared IFA and real-time PCR in bronchoalveolar lavage specimens of HIV infected patients. A total of 66 BALs from 62 HIV patients were included in the study. 30 IFA positive and 36 IFA negative specimens were tested with real-time PCR, targeting the major surface glycoprotein. We performed a retrospective analysis of the patient’s medical records, compared the results of the IFA and PCR tests and analyzed costs, expenditure of time and personal expenses. Results All of the 30 IFA positive samples were PCR positive. 35 of 36 IFA negative probes were also negative in the PCR assay. Considering the PCR results as a binary outcome (positive/negative) sensitivity was 100%, specificity 97.2%. The patient with negative IFA and positive PCR had a clear clinical picture of PCP and responded to PCP treatment. PCR was more than twice as expensive and time-consuming as IFA. Diagnostic accuracy for PCP of PCR and IFA was comparable in HIV-infected patients, but IFA was significantly less expensive and less time-consuming. Therefore, IFA testing can continue to be used as gold standard in the diagnosis of PCP in HIV patients. However, in special cases, IFA may lack sensitivity and PCR should be added to the diagnostic armamentarium.
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Affiliation(s)
- Simon Bossart
- Department of Dermatology, University Hospital Inselspital, 3010, Bern, Switzerland. .,Institute for Infectious Diseases, Clinical Microbiology, University of Bern, Bern, Switzerland.
| | - Konrad Mühlethaler
- Institute for Infectious Diseases, Clinical Microbiology, University of Bern, Bern, Switzerland
| | - Christian Garzoni
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland.,Department of Internal Medicine and Infectious Disease, Clinica Luganese Moncucco, Lugano, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
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21
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Yang Z, Le JT, Hutter D, Bradley KM, Overton BR, McLendon C, Benner SA. Eliminating primer dimers and improving SNP detection using self-avoiding molecular recognition systems. Biol Methods Protoc 2020; 5:bpaa004. [PMID: 32395633 PMCID: PMC7200914 DOI: 10.1093/biomethods/bpaa004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 01/25/2023] Open
Abstract
Despite its widespread value to molecular biology, the polymerase chain reaction (PCR) encounters modes that unproductively consume PCR resources and prevent clean signals, especially when high sensitivity, high SNP discrimination, and high multiplexing are sought. Here, we show how "self-avoiding molecular recognition systems" (SAMRS) manage such difficulties. SAMRS nucleobases pair with complementary nucleotides with strengths comparable to the A:T pair, but do not pair with other SAMRS nucleobases. This should allow primers holding SAMRS components to avoid primer-primer interactions, preventing primer dimers, allowing more sensitive SNP detection, and supporting higher levels of multiplex PCR. The experiments here examine the PCR performances of primers containing different numbers of SAMRS components placed strategically at different positions, and put these performances in the context of estimates of SAMRS:standard pairing strengths. The impact of these variables on primer dimer formation, the overall efficiency and sensitivity of SAMRS-based PCR, and the value of SAMRS primers when detecting single nucleotide polymorphisms (SNPs) are also evaluated. With appropriately chosen polymerases, SNP discrimination can be greater than the conventional allele-specific PCR, with the further benefit of avoiding primer dimer artifacts. General rules guiding the design of SAMRS-modified primers are offered to support medical research and clinical diagnostics products.
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Affiliation(s)
- Zunyi Yang
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Jennifer T Le
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
| | - Daniel Hutter
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Benjamin R Overton
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
| | - Chris McLendon
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
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22
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Comparative Analysis of the Wako β-Glucan Test and the Fungitell Assay for Diagnosis of Candidemia and Pneumocystis jirovecii Pneumonia. J Clin Microbiol 2018; 56:JCM.00464-18. [PMID: 29899003 DOI: 10.1128/jcm.00464-18] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/09/2018] [Indexed: 11/20/2022] Open
Abstract
(1→3)-β-d-Glucan (BDG) is a biomarker for invasive fungal disease. Until now, all BDG data in the Western Hemisphere were obtained using the Fungitell assay (FA). How it compares to the Wako β-glucan test (GT), which was recently launched in Europe, is largely unknown. We conducted a case-control study to compare the two assays in serum samples from 120 candidemia and 63 Pneumocystis jirovecii pneumonia (PCP) patients. Two hundred patients with bacteremia or negative blood cultures served as candidemia control group. In patients with candidemia the median BDG values of the FA and the GT were 351 and 8.4 pg/ml, respectively. With both assays, the BDG levels in candidemia were significantly higher than those measured in the control group (P < 0.001). The sensitivity, specificity, and positive and negative predictive values for the diagnosis of candidemia were 86.7%, 85.0%, 6.0%, and 99.8% for the FA and 42.5%, 98.0%, 19.0%, and 99.4% for the GT, respectively. In PCP patients the median BDG values of the FA and the GT were 963 and 57.7 pg/ml, respectively. The sensitivities for PCP diagnosis were 100% for the FA and 88.9% for the GT. In practical terms, the GT proved to be robust and applicable for testing single samples, whereas for economic reasons the FA required the samples to be tested in batch. The sensitivity of the FA is superior to that of the GT. However, the GT is a valuable alternative to the FA, especially for patients with suspected PCP and in laboratories with low sample throughput.
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23
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Dunaiski CM, Janssen L, Erzinger H, Pieper M, Damaschek S, Schildgen O, Schildgen V. Inter-Specimen Imbalance of Mitochondrial Gene Copy Numbers Predicts Clustering of Pneumocystis jirovecii Isolates in Distinct Subgroups. J Fungi (Basel) 2018; 4:jof4030084. [PMID: 29996561 PMCID: PMC6162491 DOI: 10.3390/jof4030084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/04/2018] [Accepted: 07/09/2018] [Indexed: 12/11/2022] Open
Abstract
The molecular detection of Pneumocystis jirovecii is an important therapy-relevant tool in microbiological diagnostics. However, the quantification of this pathogen in the past has revealed discordant results depending on the target gene. As the clinical variety of P. jirovecii infections ranges between life-threatening infections and symptom-free colonization, the question arises if qPCRs are reliable tools for quantitative diagnostics of P. jirovecii. P. jirovecii positive BALs were quantitatively tested for the copy numbers of one mitochondrial (COX-1) and two nuclear single-copy genes (KEX1 and DHPS) compared to the mitochondrial large subunit (mtLSU) by qPCR. Independent of the overall mtLSU copy number P. jirovecii clustered into distinct groups based on the ratio patterns of the respective qPCRs. This study, which compared different mitochondrial to nuclear gene ratio patterns of independent patients, shows that the mtLSU gene represents a highly sensitive qPCR tool for the detection of P. jirovecii, but does not display a reliable target for absolute quantification.
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Affiliation(s)
- Cara Mia Dunaiski
- Kliniken der Stadt Köln gGmbH, Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke, 51109 Köln, Germany.
| | - Lena Janssen
- Kliniken der Stadt Köln gGmbH, Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke, 51109 Köln, Germany.
| | - Hannah Erzinger
- Kliniken der Stadt Köln gGmbH, Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke, 51109 Köln, Germany.
| | - Monika Pieper
- Kliniken der Stadt Köln gGmbH, Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke, 51109 Köln, Germany.
| | - Sarah Damaschek
- Kliniken der Stadt Köln gGmbH, Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke, 51109 Köln, Germany.
| | - Oliver Schildgen
- Kliniken der Stadt Köln gGmbH, Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke, 51109 Köln, Germany.
| | - Verena Schildgen
- Kliniken der Stadt Köln gGmbH, Institut für Pathologie, Klinikum der Privaten Universität Witten/Herdecke, 51109 Köln, Germany.
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24
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25
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Doyle L, Vogel S, Procop GW. Pneumocystis PCR: It Is Time to Make PCR the Test of Choice. Open Forum Infect Dis 2017; 4:ofx193. [PMID: 29062861 PMCID: PMC5641380 DOI: 10.1093/ofid/ofx193] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/31/2017] [Indexed: 11/16/2022] Open
Abstract
Background The testing strategy for Pneumocystis at the Cleveland Clinic changed from toluidine blue staining to polymerase chain reaction (PCR). We studied the differences in positivity rates for these assays and compared each with the detection of Pneumocystis in companion specimens by cytology and surgical pathology. Methods We reviewed the results of all Pneumocystis test orders 1 year before and 1 year after the implementation of a Pneumocystis-specific PCR. We also reviewed the corresponding cytology and surgical pathology results, if performed. Finally, we reviewed the medical records of patients with rare Pneumocystis detected by PCR in an effort to differentiate colonization vs true disease. Results Toluidine blue staining and surgical pathology had similar sensitivities and negative predictive values, both of which were superior to cytology. There was a >4-fold increase in the annual detection of Pneumocystis by PCR compared with toluidine blue staining (toluidine blue staining: 11/1583 [0.69%] vs PCR: 44/1457 [3.0%]; chi-square P < .001). PCR detected 1 more case than surgical pathology and was far more sensitive than cytology. Chart review demonstrated that the vast majority of patients with rare Pneumocystis detected were immunosuppressed, had radiologic findings supportive of this infection, had no other pathogens detected, and were treated for pneumocystosis by the clinical team. Conclusion PCR was the most sensitive method for the detection of Pneumocystis and should be considered the diagnostic test of choice. Correlation with clinical and radiologic findings affords discrimination of early true disease from the far rarer instances of colonization.
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Affiliation(s)
- Laura Doyle
- Section of Clinical Microbiology, Department of Laboratory Medicine, Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Sherilynn Vogel
- Section of Clinical Microbiology, Department of Laboratory Medicine, Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Gary W Procop
- Section of Clinical Microbiology, Department of Laboratory Medicine, Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
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26
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Comparison of quantitative real-time PCR and direct immunofluorescence for the detection of Pneumocystis jirovecii. PLoS One 2017; 12:e0180589. [PMID: 28683092 PMCID: PMC5500343 DOI: 10.1371/journal.pone.0180589] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 06/16/2017] [Indexed: 11/23/2022] Open
Abstract
Background Pneumocystis pneumonia (PCP) is a serious risk for HIV-positive patients. Asymptomatic infection or colonisation with P. jirovecii has been shown to occur frequently. PCR assays frequently identify such cases, due to their high sensitivity. Quantitative real-time PCR (qPCR) gene copy number cut-off values have been suggested to differentiate colonisation and infection; these need to be standardised for routine use. We compared the results of qPCR with an immunofluorescence assay (IFA) to determine a specific cut-off value. Methods From March 2005 through June 2009, induced sputum specimens were collected from adult patients who were clinically suspected of having PCP, at the Chris Hani Baragwanath Hospital in Gauteng, South Africa. Laboratory diagnosis of PCP was done by a conventional direct IFA and a qPCR assay. A receiver operating characteristic (ROC) analysis was performed to determine a suitable copy number cut-off value. Results P. jirovecii was identified in 51% (156/305) and 67% (204/305) of specimens using IFA and qPCR, respectively. The cut-off value for the qPCR that best predicted the IFA results was 78 copies/5 μl (area under ROC curve 0.92). The sensitivity and specificity of qPCR using this cut-off was 94.6% and 89.1%, respectively, compared with the IFA. Discussion The results of the ROC curve analysis indicate an excellent predictive value of the qPCR using the proposed cut-off. However, the IFA test is an imperfect gold standard and so this cut-off should not be used in isolation; clinical data should also contribute to the interpretation of the qPCR result.
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27
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Homayouni MM, Rostami A, Gholizadeh H, Mehbod ASA, Ebrahimi M, Mehravar S. Comparison of three cost effective staining methods for detection of Pneumocystis jirovecii. J Parasit Dis 2017; 41:298-301. [PMID: 28316430 DOI: 10.1007/s12639-016-0776-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 03/08/2016] [Indexed: 11/26/2022] Open
Abstract
Pneumocystis pneumonia due to Pneumocystis jirovecii infection is an emerging health problem not only for HIV-infected patients but also for other immunocompromised patients in many countries. We compared Gomori methenamine silver (GMS), Toluidine Blue O (TBO) and Giemsa staining methods using standard procedures. The sensitivity and specificity of GMS were 100 %. The sensitivity and specificity of TBO were 96 and 100 %, respectively. The sensitivity and specificity of Giemsa stain were 84 and 90 %, respectively. Only GMS had positive and negative predictive values of 100 % while PPV and NPV for TBO were 100 and 90.9 %, and for Giemsa stain were 95.4 and 69.2 %, respectively. Therefore, our results suggest that if TBO or Geimsa stains are used as the primary staining methods in a clinical laboratory, then confirmation with a GMS staining method should be performed to increase the sensitivity and specificity of the final test result.
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Affiliation(s)
- Mohamad Mohsen Homayouni
- Department of Parasitology and Mycology, School of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Ali Rostami
- Department of Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamed Gholizadeh
- Department of Parasitology and Mycology, School of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Amir Sayed Ali Mehbod
- Department of Parasitology and Mycology, School of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Maryam Ebrahimi
- Department of Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeed Mehravar
- Department of Epidemiology and Statistics, School of Public Health, Tehran University of Medical Science, Tehran, Iran
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28
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Chien JY, Liu CJ, Chuang PC, Lee TF, Huang YT, Liao CH, Hung CC, Sheng WH, Yu CJ, Hsueh PR. Evaluation of the automated Becton Dickinson MAX real-time PCR platform for detection of Pneumocystis jirovecii. Future Microbiol 2016; 12:29-37. [PMID: 27936923 DOI: 10.2217/fmb-2016-0115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
AIM We evaluated the performance of the automated quantitative BD MAX (Becton Dickinson) real-time PCR platform for detecting Pneumocystis jirovecii. MATERIALS & METHODS A total of 34 retrospective and 137 prospective samples were included. RESULTS Retrospectively, all (100%) positive samples were correctly detected by this platform compared with a nested PCR. Among prospective samples, the overall sensitivity, specificity, positive likelihood ratio and negative likelihood ratio were 92.6%, 94.5%, 17.0 and 0.1, respectively. All bronchoalveolar lavage fluid (BALF)/bronchial washing samples were correctly identified by this platform. Samples from patients with colonization had significantly higher median amplification cycle threshold values than patients with P. jirovecii pneumonia. CONCLUSION The quantitative BD MAX real-time PCR is a rapid and highly sensitive modality for detecting P. jirovecii, especially in samples from bronchoalveolar lavage fluid/bronchial washing fluid.
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Affiliation(s)
- Jung-Yien Chien
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chia-Jung Liu
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pei-Chien Chuang
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tai-Fen Lee
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Tsung Huang
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan.,Graduate Institute of Clinical Laboratory Sciences & Medical Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Chun-Hsing Liao
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - Chien-Ching Hung
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wan-Huei Sheng
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Po-Ren Hsueh
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
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29
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Nethathe G, Patel N. Survival after Pneumocystis jirovecii pneumonia requiring ventilation: A case report. South Afr J HIV Med 2016; 17:474. [PMID: 29568616 PMCID: PMC5843145 DOI: 10.4102/sajhivmed.v17i1.474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 09/05/2016] [Indexed: 11/08/2022] Open
Abstract
Pneumocystis pneumonia (PCP) in patients with the human immunodeficiency virus (HIV) is associated with a high mortality rate, which increases substantially with the need for mechanical ventilation. Local experience of patients with PCP admitted to the intensive care unit has revealed mortality rates close to 100%. We present a case of a 39-year-old HIV-infected man diagnosed with PCP who was successfully weaned from mechanical ventilation after presenting with respiratory distress and severe hypoxaemia. A short review of the literature will also be presented.
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Affiliation(s)
- Gladness Nethathe
- Intensive Care Unit, Chris Hani Baragwanath Academic Hospital, South Africa
| | - Nirav Patel
- Department of Pediatric Surgery, University of the Witwatersrand, South Africa
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30
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Le Gal S, Robert-Gangneux F, Pépino Y, Belaz S, Damiani C, Guéguen P, Pitous M, Virmaux M, Lissillour E, Pougnet L, Guillaud-Saumur T, Toubas D, Valot S, Hennequin C, Morio F, Hasseine L, Bouchara JP, Totet A, Nevez G. A misleading false-negative result of Pneumocystis real-time PCR assay due to a rare punctual mutation: A French multicenter study. Med Mycol 2016; 55:180-184. [PMID: 27489302 DOI: 10.1093/mmy/myw051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 02/05/2016] [Accepted: 06/18/2016] [Indexed: 11/13/2022] Open
Abstract
This article describes a previously unreported mutation at position 210 (C210T) of the mitochondrial large subunit ribosomal RNA (mtLSUrRNA) gene of Pneumocystis jirovecii, which led to a false-negative result of a real-time polymerase chain reaction (PCR) assay. Since the aforementioned real-time PCR assay is widely used in France, a French multicenter study was conducted to estimate the mutation frequency and its potential impact on the routine diagnosis of Pneumocystis pneumonia (PCP). Through analysis of data obtained from eight centers, the mutation frequency was estimated at 0.28%. This low frequency should not call into question the routine use of this PCR assay. Nonetheless, the occurrence of the false-negative PCR result provides arguments for maintaining microscopic techniques combined to PCR assays to achieve PCP diagnosis.
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Affiliation(s)
- Solène Le Gal
- University of Brest, GEIHP EA 3142, Brest, France .,Laboratory of Parasitology and Mycology, Brest University Hospital, Brest, France
| | - Florence Robert-Gangneux
- University of Rennes 1, INSERM U1085, Rennes, France.,Laboratory of Parasitology and Mycology, Rennes University Hospital, Rennes, France
| | - Yann Pépino
- University of Brest, GEIHP EA 3142, Brest, France
| | - Sorya Belaz
- University of Rennes 1, INSERM U1085, Rennes, France.,Laboratory of Parasitology and Mycology, Rennes University Hospital, Rennes, France
| | - Céline Damiani
- University of Picardy-Jules Verne, EA 4285 UMR-I 01 INERIS, Amiens, France.,Department of Parasitology and Mycology, Amiens University Hospital, Amiens, France
| | - Paul Guéguen
- Laboratory of Molecular Genetics and Histocompatibility, Brest University Hospital, Brest, France.,University of Brest, INSERM 1078, Molecular Genetics and Epidemiological Genetics, SFR 148, Brest, France
| | | | | | | | | | | | - Dominique Toubas
- Parasitology and Mycology laboratory, Reims University Hospital, Reims, France
| | - Stéphane Valot
- Parasitology and Mycology laboratory, Dijon University Hospital, Dijon, France
| | - Christophe Hennequin
- Parasitology and Mycology laboratory, Saint Antoine Hospital, Assistance Publique-Hôpitaux de Paris, France
| | - Florent Morio
- Parasitology and Mycology laboratory, Nantes University Hospital, Nantes, France
| | - Lilia Hasseine
- Parasitology and Mycology laboratory, Nice University Hospital, Nice, France
| | | | - Anne Totet
- University of Picardy-Jules Verne, EA 4285 UMR-I 01 INERIS, Amiens, France.,Department of Parasitology and Mycology, Amiens University Hospital, Amiens, France
| | - Gilles Nevez
- University of Brest, GEIHP EA 3142, Brest, France .,Laboratory of Parasitology and Mycology, Brest University Hospital, Brest, France
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Wozniak A, Geoffroy E, Miranda C, Castillo C, Sanhueza F, García P. Comparison of manual and automated nucleic acid extraction methods from clinical specimens for microbial diagnosis purposes. Diagn Microbiol Infect Dis 2016; 86:268-269. [PMID: 27543377 DOI: 10.1016/j.diagmicrobio.2016.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/21/2016] [Accepted: 07/08/2016] [Indexed: 10/21/2022]
Abstract
The choice of nucleic acids (NAs) extraction method for molecular diagnosis in microbiology is of major importance because of the low microbial load, different nature of microorganisms, and clinical specimens. The NA yield of different extraction methods has been mostly studied using spiked samples. However, information from real human clinical specimens is scarce. The purpose of this study was to compare the performance of a manual low-cost extraction method (Qiagen kit or salting-out extraction method) with the automated high-cost MagNAPure Compact method. According to cycle threshold values for different pathogens, MagNAPure is as efficient as Qiagen for NA extraction from noncomplex clinical specimens (nasopharyngeal swab, skin swab, plasma, respiratory specimens). In contrast, according to cycle threshold values for RNAseP, MagNAPure method may not be an appropriate method for NA extraction from blood. We believe that MagNAPure versatility reduced risk of cross-contamination and reduced hands-on time compensates its high cost.
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Affiliation(s)
- Aniela Wozniak
- Laboratorio de Microbiología, Departamento de Laboratorios Clínicos, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Enrique Geoffroy
- Laboratorio de Microbiología, Departamento de Laboratorios Clínicos, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carolina Miranda
- Laboratorio de Microbiología, Departamento de Laboratorios Clínicos, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudia Castillo
- Laboratorio de Microbiología, Departamento de Laboratorios Clínicos, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Francia Sanhueza
- Laboratorio de Microbiología, Departamento de Laboratorios Clínicos, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Patricia García
- Laboratorio de Microbiología, Departamento de Laboratorios Clínicos, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
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32
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Prickartz A, Lüsebrink J, Khalfaoui S, Schildgen O, Schildgen V, Windisch W, Brockmann M. Low Titer Pneumocystis jirovecii Infections: More than Just Colonization? J Fungi (Basel) 2016; 2:jof2020016. [PMID: 29376933 PMCID: PMC5753078 DOI: 10.3390/jof2020016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/29/2016] [Accepted: 05/26/2016] [Indexed: 01/01/2023] Open
Abstract
Non-pneumonia Pneumocystis jirovecii colonization is thought to occur frequently in immunocompetent individuals. The aim was to analyze if P. jirovecii low-titer detections have more impact than just colonization. From our total cohort of patients for which P. jirovecii testing by qPCR was requested, we selected exclusively those that were fully immunocompetent. Patients were defined as fully immunocompetent if they did not receive immunosuppressive therapy, displayed regular antibody titers, and did not suffer from acquired, inherited or autoimmune diseases. Only those patients with complete medical records available were included. A retrospective analysis identified patients with P. jirovecii colonization and successful antibiotic therapy in response to laboratory pathogen detection. We identified 30 fully immunocompetent patients with P. jirovecii colonization suspected to suffer from infection with the pathogen, but with milder symptoms than pneumonia. All patients were successfully treated with cotrimoxazole against P. jirovecii and resolved from chronic cough and recurrent pulmonary infections. The fact that all patients displayed recovery from their clinical symptoms gives raise to the hypothesis that P. jirovecii infections may also occur in immunocompetent patients but with milder symptoms.
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Affiliation(s)
- Alexander Prickartz
- Lungenklinik Merheim, Kliniken der Stadt Köln gGmbH, Universität Witten-Herdecke, Alfred-Herrhausen-Straße 50, Witten 58448, Germany.
| | - Jessica Lüsebrink
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Ostmerheimer Str. 200, Köln/Cologne D-51109, Germany.
| | - Soumaya Khalfaoui
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Ostmerheimer Str. 200, Köln/Cologne D-51109, Germany.
| | - Oliver Schildgen
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Ostmerheimer Str. 200, Köln/Cologne D-51109, Germany.
| | - Verena Schildgen
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Ostmerheimer Str. 200, Köln/Cologne D-51109, Germany.
| | - Wolfram Windisch
- Lungenklinik Merheim, Kliniken der Stadt Köln gGmbH, Universität Witten-Herdecke, Alfred-Herrhausen-Straße 50, Witten 58448, Germany.
| | - Michael Brockmann
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Klinikum der Privaten Universität Witten/Herdecke mit Sitz in Köln, Ostmerheimer Str. 200, Köln/Cologne D-51109, Germany.
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33
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Ma L, Chen Z, Huang DW, Kutty G, Ishihara M, Wang H, Abouelleil A, Bishop L, Davey E, Deng R, Deng X, Fan L, Fantoni G, Fitzgerald M, Gogineni E, Goldberg JM, Handley G, Hu X, Huber C, Jiao X, Jones K, Levin JZ, Liu Y, Macdonald P, Melnikov A, Raley C, Sassi M, Sherman BT, Song X, Sykes S, Tran B, Walsh L, Xia Y, Yang J, Young S, Zeng Q, Zheng X, Stephens R, Nusbaum C, Birren BW, Azadi P, Lempicki RA, Cuomo CA, Kovacs JA. Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts. Nat Commun 2016; 7:10740. [PMID: 26899007 PMCID: PMC4764891 DOI: 10.1038/ncomms10740] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/13/2016] [Indexed: 02/07/2023] Open
Abstract
Pneumocystis jirovecii is a major cause of life-threatening pneumonia in immunosuppressed patients including transplant recipients and those with HIV/AIDS, yet surprisingly little is known about the biology of this fungal pathogen. Here we report near complete genome assemblies for three Pneumocystis species that infect humans, rats and mice. Pneumocystis genomes are highly compact relative to other fungi, with substantial reductions of ribosomal RNA genes, transporters, transcription factors and many metabolic pathways, but contain expansions of surface proteins, especially a unique and complex surface glycoprotein superfamily, as well as proteases and RNA processing proteins. Unexpectedly, the key fungal cell wall components chitin and outer chain N-mannans are absent, based on genome content and experimental validation. Our findings suggest that Pneumocystis has developed unique mechanisms of adaptation to life exclusively in mammalian hosts, including dependence on the lungs for gas and nutrients and highly efficient strategies to escape both host innate and acquired immune defenses.
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Affiliation(s)
- Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Zehua Chen
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Da Wei Huang
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Geetha Kutty
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Mayumi Ishihara
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
| | - Honghui Wang
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Amr Abouelleil
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Lisa Bishop
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Emma Davey
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Rebecca Deng
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Xilong Deng
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Lin Fan
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Giovanna Fantoni
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Michael Fitzgerald
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Emile Gogineni
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Jonathan M. Goldberg
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Grace Handley
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Xiaojun Hu
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Charles Huber
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Xiaoli Jiao
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Kristine Jones
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Joshua Z. Levin
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Yueqin Liu
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Pendexter Macdonald
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Alexandre Melnikov
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Castle Raley
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Monica Sassi
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Brad T. Sherman
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Xiaohong Song
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Sean Sykes
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Bao Tran
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Laura Walsh
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Yun Xia
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
| | - Jun Yang
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Sarah Young
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Qiandong Zeng
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Xin Zheng
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Robert Stephens
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Chad Nusbaum
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Bruce W. Birren
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
| | - Richard A. Lempicki
- Leidos BioMedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Christina A. Cuomo
- Genome Sequencing and Analysis Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Joseph A. Kovacs
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Building 10, Room 2C145, 10 Center Drive, Bethesda, Maryland 20892, USA
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Harrison N, Mitterbauer M, Tobudic S, Kalhs P, Rabitsch W, Greinix H, Burgmann H, Willinger B, Presterl E, Forstner C. Incidence and characteristics of invasive fungal diseases in allogeneic hematopoietic stem cell transplant recipients: a retrospective cohort study. BMC Infect Dis 2015; 15:584. [PMID: 26715563 PMCID: PMC4696168 DOI: 10.1186/s12879-015-1329-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/18/2015] [Indexed: 11/10/2022] Open
Abstract
Background Allogeneic hematopoietic stem cell transplant (HSCT) recipients experience an increased risk for invasive fungal diseases (IFDs). Methods This retrospective cohort study at the Medical University of Vienna aspired to assess the incidence, characteristics and the outcome of IFDs as well as the associated risk factors in a setting where only 43 % of patients were given systemic antifungal prophylaxis during aplasia. IFDs were classified as probable or proven according to the EORTC/MSG consensus group. All adult patients (n = 242) receiving an allogeneic HSCT at the University Hospital of Vienna from January 2009 to December 2013 were enrolled. Results The primary outcome of this study was the one-year incidence for IFDs after HSCT, which was 10.3 % (25/242). Overall 28 patients experienced an IFD – 20 probable and 8 proven – with invasive aspergillosis being the predominant IFD (n = 18), followed by invasive candidiasis (n = 7) and pneumocystis pneumonia (n = 3). Patients with an IFD were more likely to be admitted to an intensive care unit (64 % versus 12 %, p < 0.0001) and had a significantly higher mortality in the first year after HSCT (48 % versus 25 %, p = 0.02). Multivariate regression analysis revealed that intensified immunosuppressive therapy (high-dose cortisone and basiliximab or etanercept) because of severe graft-versus-host disease (adjusted odds ratio (AOR) 3.6, p = 0.01) and transplant-associated microangiopathy (AOR 3.7, p = 0.04) were associated with an increased risk for IFD, while antifungal prophylaxis given during aplasia and post-engraftment was associated with a decreased risk (AOR 0.3, p = 0.02). Conclusions We documented a one-year incidence for IFDs of 10.3 % and no selection of rare pathogens at a centre with moderate use of antifungal prophylaxis. Intensified immunosuppressive therapy and transplant-associated microangiopathy were significant risk factors for IFDs.
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Affiliation(s)
- Nicole Harrison
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Margit Mitterbauer
- Department of Medicine I, Bone Marrow Transplantation, Medical University of Vienna, Vienna, Austria
| | - Selma Tobudic
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Peter Kalhs
- Department of Medicine I, Bone Marrow Transplantation, Medical University of Vienna, Vienna, Austria
| | - Werner Rabitsch
- Department of Medicine I, Bone Marrow Transplantation, Medical University of Vienna, Vienna, Austria
| | - Hildegard Greinix
- Department of Medicine I, Bone Marrow Transplantation, Medical University of Vienna, Vienna, Austria.,Division of Hematology, Medical University of Graz, Graz, Austria
| | - Heinz Burgmann
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Birgit Willinger
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - Elisabeth Presterl
- Department of Hospital Hygiene and Infection Control, Medical University of Vienna, Vienna, Austria
| | - Christina Forstner
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria. .,Center of Infectious Diseases, Jena University Hospital, Jena, Germany.
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Goto N, Futamura K, Okada M, Yamamoto T, Tsujita M, Hiramitsu T, Narumi S, Watarai Y. Management of Pneumocystis jirovecii Pneumonia in Kidney Transplantation to Prevent Further Outbreak. CLINICAL MEDICINE INSIGHTS-CIRCULATORY RESPIRATORY AND PULMONARY MEDICINE 2015; 9:81-90. [PMID: 26609250 PMCID: PMC4648609 DOI: 10.4137/ccrpm.s23317] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/11/2015] [Accepted: 08/12/2015] [Indexed: 12/19/2022]
Abstract
The outbreak of Pneumocystis jirovecii pneumonia (PJP) among kidney transplant recipients is emerging worldwide. It is important to control nosocomial PJP infection. A delay in diagnosis and treatment increases the number of reservoir patients and the number of cases of respiratory failure and death. Owing to the large number of kidney transplant recipients compared to other types of organ transplantation, there are greater opportunities for them to share the same time and space. Although the use of trimethoprim-sulfamethoxazole (TMP-SMX) as first choice in PJP prophylaxis is valuable for PJP that develops from infections by trophic forms, it cannot prevent or clear colonization, in which cysts are dominant. Colonization of P. jirovecii is cleared by macrophages. While recent immunosuppressive therapies have decreased the rate of rejection, over-suppressed macrophages caused by the higher levels of immunosuppression may decrease the eradication rate of colonization. Once a PJP cluster enters these populations, which are gathered in one place and uniformly undergoing immunosuppressive therapy for kidney transplantation, an outbreak can occur easily. Quick actions for PJP patients, other recipients, and medical staff of transplant centers are required. In future, lifelong prophylaxis may be required even in kidney transplant recipients.
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Affiliation(s)
- Norihiko Goto
- Department of Transplant Surgery, Nagoya Daini Red Cross Hospital, Nagoya, Japan
| | - Kenta Futamura
- Department of Transplant Surgery, Nagoya Daini Red Cross Hospital, Nagoya, Japan
| | - Manabu Okada
- Department of Transplant Surgery, Nagoya Daini Red Cross Hospital, Nagoya, Japan
| | - Takayuki Yamamoto
- Department of Transplant Surgery, Nagoya Daini Red Cross Hospital, Nagoya, Japan
| | - Makoto Tsujita
- Department of Transplant Surgery, Nagoya Daini Red Cross Hospital, Nagoya, Japan
| | - Takahisa Hiramitsu
- Department of Transplant Surgery, Nagoya Daini Red Cross Hospital, Nagoya, Japan
| | - Shunji Narumi
- Department of Transplant Surgery, Nagoya Daini Red Cross Hospital, Nagoya, Japan
| | - Yoshihiko Watarai
- Department of Transplant Surgery, Nagoya Daini Red Cross Hospital, Nagoya, Japan
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36
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Iriart X, Bouar ML, Kamar N, Berry A. Pneumocystis Pneumonia in Solid-Organ Transplant Recipients. J Fungi (Basel) 2015; 1:293-331. [PMID: 29376913 PMCID: PMC5753127 DOI: 10.3390/jof1030293] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 12/27/2022] Open
Abstract
Pneumocystis pneumonia (PCP) is well known and described in AIDS patients. Due to the increasing use of cytotoxic and immunosuppressive therapies, the incidence of this infection has dramatically increased in the last years in patients with other predisposing immunodeficiencies and remains an important cause of morbidity and mortality in solid-organ transplant (SOT) recipients. PCP in HIV-negative patients, such as SOT patients, harbors some specificity compared to AIDS patients, which could change the medical management of these patients. This article summarizes the current knowledge on the epidemiology, risk factors, clinical manifestations, diagnoses, prevention, and treatment of Pneumocystis pneumonia in solid-organ transplant recipients, with a particular focus on the changes caused by the use of post-transplantation prophylaxis.
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Affiliation(s)
- Xavier Iriart
- Department of Parasitology-Mycology, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, Institut Fédératif de biologie (IFB), 330 avenue de Grande Bretagne, TSA 40031, Toulouse 31059, France.
- INSERM U1043, Toulouse F-31300, France.
- CNRS UMR5282, Toulouse F-31300, France.
- Université de Toulouse, UPS, Centre de Physiopathiologie de Toulouse Purpan (CPTP), Toulouse F-31300, France.
| | - Marine Le Bouar
- Department of Parasitology-Mycology, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, Institut Fédératif de biologie (IFB), 330 avenue de Grande Bretagne, TSA 40031, Toulouse 31059, France.
- INSERM U1043, Toulouse F-31300, France.
- CNRS UMR5282, Toulouse F-31300, France.
- Université de Toulouse, UPS, Centre de Physiopathiologie de Toulouse Purpan (CPTP), Toulouse F-31300, France.
| | - Nassim Kamar
- INSERM U1043, Toulouse F-31300, France.
- Université de Toulouse, UPS, Centre de Physiopathiologie de Toulouse Purpan (CPTP), Toulouse F-31300, France.
- Department of Nephrology and Organ Transplantation, CHU Rangueil, TSA 50032, Toulouse 31059, France.
| | - Antoine Berry
- Department of Parasitology-Mycology, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, Institut Fédératif de biologie (IFB), 330 avenue de Grande Bretagne, TSA 40031, Toulouse 31059, France.
- INSERM U1043, Toulouse F-31300, France.
- CNRS UMR5282, Toulouse F-31300, France.
- Université de Toulouse, UPS, Centre de Physiopathiologie de Toulouse Purpan (CPTP), Toulouse F-31300, France.
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37
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Cooley L, Dendle C, Wolf J, Teh BW, Chen SC, Boutlis C, Thursky KA. Consensus guidelines for diagnosis, prophylaxis and management of Pneumocystis jirovecii pneumonia in patients with haematological and solid malignancies, 2014. Intern Med J 2015; 44:1350-63. [PMID: 25482745 DOI: 10.1111/imj.12599] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Pneumocystis jirovecii infection (PJP) is a common cause of pneumonia in patients with cancer-related immunosuppression. There are well-defined patients who are at risk of PJP due to the status of their underlying malignancy, treatment-related immunosuppression and/or concomitant use of corticosteroids. Prophylaxis is highly effective and should be given to all patients at moderate to high risk of PJP. Trimethoprim-sulfamethoxazole is the drug of choice for prophylaxis and treatment, although several alternative agents are available.
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Affiliation(s)
- L Cooley
- Department of Microbiology and Infectious Diseases, Royal Hobart Hospital, Hobart, Tasmania
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Thompson SM, Johnson CP, Lu AY, Frampton RA, Sullivan KL, Fiers MWEJ, Crowhurst RN, Pitman AR, Scott IAW, Wen A, Gudmestad NC, Smith GR. Genomes of 'Candidatus Liberibacter solanacearum' Haplotype A from New Zealand and the United States Suggest Significant Genome Plasticity in the Species. PHYTOPATHOLOGY 2015; 105:863-871. [PMID: 25822188 DOI: 10.1094/phyto-12-14-0363-fi] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
'Candidatus Liberibacter solanacearum' contains two solanaceous crop-infecting haplotypes, A and B. Two haplotype A draft genomes were assembled and compared with ZC1 (haplotype B), revealing inversion and relocation genomic rearrangements, numerous single-nucleotide polymorphisms, and differences in phage-related regions. Differences in prophage location and sequence were seen both within and between haplotype comparisons. OrthoMCL and BLAST analyses identified 46 putative coding sequences present in haplotype A that were not present in haplotype B. Thirty-eight of these loci were not found in sequences from other Liberibacter spp. Quantitative polymerase chain reaction (qPCR) assays designed to amplify sequences from 15 of these loci were screened against a panel of 'Ca. L. solanacearum'-positive samples to investigate genetic diversity. Seven of the assays demonstrated within-haplotype diversity; five failed to amplify loci in at least one haplotype A sample while three assays produced amplicons from some haplotype B samples. Eight of the loci assays showed consistent A-B differentiation. Differences in genome arrangements, prophage, and qPCR results suggesting locus diversity within the haplotypes provide more evidence for genetic complexity in this emerging bacterial species.
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Affiliation(s)
- Sarah M Thompson
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Chris P Johnson
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Ashley Y Lu
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Rebekah A Frampton
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Kerry L Sullivan
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Mark W E J Fiers
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Ross N Crowhurst
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Andrew R Pitman
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Ian A W Scott
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Aimin Wen
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Neil C Gudmestad
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Grant R Smith
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
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Juliano JJ, Barnett E, Parobek CM, Taylor SM, Meshnick SR, Stone S, Chang E, Fong S, Huang L. Use of Oropharyngeal Washes to Diagnose and Genotype Pneumocystis jirovecii. Open Forum Infect Dis 2015; 2:ofv080. [PMID: 26180832 PMCID: PMC4498285 DOI: 10.1093/ofid/ofv080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 06/01/2015] [Indexed: 11/13/2022] Open
Abstract
Pneumocystis jirovecii is a symbiotic respiratory fungus that presents in 2 clinical forms: pneumonia in immunocompromised patients or colonization, defined by the presence of the organism without associated clinical symptoms. Currently, diagnosis requires invasive bronchoscopy, which may not be available in some settings and is inappropriate for detecting colonization in healthy individuals. Noninvasive diagnostic techniques and molecular strain typing tools that can be used on these samples are critical for conducting studies to better understand transmission. We evaluated 2 real-time polymerase chain reaction (PCR) assays targeting dihydropteroate synthase and the major surface glycoprotein for detection in 77 oropharyngeal washes (OPWs) from 43 symptomatic human immunodeficiency virus-infected patients who underwent bronchoscopy. We also evaluated the ability of a new microsatellite (MS) genotyping panel to strain type infections from these samples. Each PCR used individually provided a high sensitivity (>80%) for detection of pneumonia but a modest specificity (<70%). When used in combination, specificity was increased to 100% with a drop in sensitivity (74%). Concentration of organisms by PCR in the OPW tended to be lower in colonized individuals compared with those with pneumonia, but differences in concentration could not clearly define colonization in symptomatic individuals. Oropharyngeal wash samples were genotyped using 6 MSs with ≥4 alleles successfully genotyped in the majority of colonized patients and ≥5 alleles in patients with pneumonia. The MS profile was consistent over time within patients with serial OPWs analyzed. Microsatellite genotyping on noninvasive samples may aid in studying the molecular epidemiology of this pathogen without requiring invasive diagnostic techniques.
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Affiliation(s)
- Jonathan J Juliano
- Division of Infectious Diseases ; Curriculum in Genetics and Molecular Biology , University of North Carolina School of Medicine ; Department of Epidemiology , Gillings School of Global Public Health, University of North Carolina , Chapel Hill
| | | | - Christian M Parobek
- Division of Infectious Diseases ; Curriculum in Genetics and Molecular Biology , University of North Carolina School of Medicine
| | - Steve M Taylor
- Department of Epidemiology , Gillings School of Global Public Health, University of North Carolina , Chapel Hill ; Division of Infectious Diseases and International Health , Duke University Medical Center , Durham
| | - Steven R Meshnick
- Department of Epidemiology , Gillings School of Global Public Health, University of North Carolina , Chapel Hill
| | | | | | | | - Laurence Huang
- HIV/AIDS Division ; Division of Pulmonary and Critical Care Medicine , San Francisco General Hospital, University of California
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Pneumocystis pneumonia in children - the relevance of chemoprophylaxis in different groups of immunocompromised and immunocompetent paediatric patients. Cent Eur J Immunol 2015; 40:91-5. [PMID: 26155189 PMCID: PMC4472545 DOI: 10.5114/ceji.2015.50839] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 02/02/2015] [Indexed: 12/24/2022] Open
Abstract
Introduction Pneumocystis jirovecii is an opportunistic pathogen causing pneumocystis pneumonia (PCP), a life-threatening infection, in immunocompromised patients. In this study, retrospective analysis of the presence of P. jirovecii DNA in different samples collected from children with suspected PCP was carried out. Material and methods Three hundred and six specimens [152 bronchoalveolar lavage (BAL) specimens, 80 blood specimens, 18 bronchial secretions (BS), 34 induced sputum samples, 10 endotracheal aspirates (ETA), and 12 other type samples] obtained from patients with suspected PCP were examined by real-time PCR. Results Forty (13.1%) patients were positive for P. jirovecii: 4 (7.7%) patients with malignancies, 3 (6.8%) transplant recipients, 15 (23.1%) other immunocompromised patients, and 18 (12.4%) immunocompetent patients. Pneumocystis jirovecii DNA was detected in 20.4% of BAL specimens, 11.1% of BS samples, 10% of ETA sample, 8.8% of induced sputum samples, and in 3.7% of blood samples. Comparing the frequency of the presence of P. jirovecii DNA between the group of children treated with PCP chemoprophylaxis (malignancy patients and transplant recipients) and a group of children not receiving this prophylaxis (other immunocompromised and immunocompetent children), we found that the occurrence of PCP was twice as high in the latter group of children (7.3% and 15.7%, respectively). Conclusions Respiratory samples, such as BS, BAL, or ETA specimens, are the material of choice for the diagnosis of PCP. Due to high incidence of PCP in certain groups of immunocompetent and immunocompromised patients, besides cancer patients and transplant recipients, consideration of PCP prophylaxis is required in these groups as well.
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The Clinician and the Microbiology Laboratory. MANDELL, DOUGLAS, AND BENNETT'S PRINCIPLES AND PRACTICE OF INFECTIOUS DISEASES 2015. [PMCID: PMC7151863 DOI: 10.1016/b978-1-4557-4801-3.00016-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Kuik KTH, Trubiano J, Worth LJ, Harun NS, Steinfort D, Johnson D. Pneumocystis jirovecii pneumonia following everolimus treatment of metastatic breast cancer. Med Mycol Case Rep 2014; 6:34-6. [PMID: 25379397 PMCID: PMC4216328 DOI: 10.1016/j.mmcr.2014.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 08/25/2014] [Accepted: 08/29/2014] [Indexed: 01/22/2023] Open
Abstract
Everolimus is an inhibitor of mammalian target of rapamycin with anti-tumour activity. While everolimus is known to cause drug-induced pneumonitis, it is rarely associated with Pneumocystis jirovecii pneumonia (PJP). We report a patient on everolimus therapy for metastatic breast cancer that developed PJP. Diagnosis was based on clinical features and a quantitative polymerase chain reaction for P. jirovecii DNA. Clinicians should consider PJP as a potential cause of pulmonary infiltrates in patients treated with everolimus.
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Affiliation(s)
- Kelvin Teck-Hong Kuik
- Department of General Medicine, Peter MacCallum Cancer Centre, East Melbourne, Australia
| | - Jason Trubiano
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, East Melbourne, Australia
| | - Leon J Worth
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, East Melbourne, Australia ; Department of Medicine, University of Melbourne, Parkville, Australia
| | - Nur-Shirin Harun
- Department of General Medicine, Peter MacCallum Cancer Centre, East Melbourne, Australia
| | - Daniel Steinfort
- Department of General Medicine, Peter MacCallum Cancer Centre, East Melbourne, Australia
| | - Douglas Johnson
- Department of General Medicine, Peter MacCallum Cancer Centre, East Melbourne, Australia
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Diagnosis of Pneumocystis jirovecii Pneumonia: Role of β-D-Glucan Detection and PCR. CURRENT FUNGAL INFECTION REPORTS 2014. [DOI: 10.1007/s12281-014-0198-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Pérez FJ, Ponce CA, Rojas DA, Iturra PA, Bustamante RI, Gallo M, Hananias K, Vargas SL. Fungal colonization with Pneumocystis correlates to increasing chloride channel accessory 1 (hCLCA1) suggesting a pathway for up-regulation of airway mucus responses, in infant lungs. RESULTS IN IMMUNOLOGY 2014; 4:58-61. [PMID: 25379375 PMCID: PMC4213842 DOI: 10.1016/j.rinim.2014.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 01/22/2023]
Abstract
Fungal colonization with Pneumocystis is associated with increased airway mucus in infants during their primary Pneumocystis infection, and to severity of COPD in adults. The pathogenic mechanisms are under investigation. Interestingly, increased levels of hCLCA1 – a member of the calcium-sensitive chloride conductance family of proteins that drives mucus hypersecretion – have been associated with increased mucus production in patients diagnosed with COPD and in immunocompetent rodents with Pneumocystis infection. Pneumocystis is highly prevalent in infants; therefore, the contribution of Pneumocystis to hCLCA1 expression was examined in autopsied infant lungs. Respiratory viruses that may potentially increase mucus, were also examined. hCLCA1 expression was measured using actin-normalized Western-blot, and the burden of Pneumocystis organisms was quantified by qPCR in 55 autopsied lungs from apparently healthy infants who died in the community. Respiratory viruses were diagnosed using RT-PCR for RSV, metapneumovirus, influenza, and parainfluenza viruses; and by PCR for adenovirus. hCLCA1 levels in virus positive samples were comparable to those in virus-negative samples. An association between Pneumocystis and increased hCLCA1 expression was documented (P=0.028). Additionally, increasing Pneumocystis burden correlated with increasing hCLCA1 protein expression levels (P=0.017). Results strengthen the evidence of Pneumocystis-associated up-regulation of mucus-related airway responses in infant lungs. Further characterization of this immunocompetent host-Pneumocystis-interaction, including assessment of potential clinical significance, is warranted.
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Affiliation(s)
- Francisco J Pérez
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina Universidad de Chile, Santiago 8380453, Chile
| | - Carolina A Ponce
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina Universidad de Chile, Santiago 8380453, Chile
| | - Diego A Rojas
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina Universidad de Chile, Santiago 8380453, Chile
| | - Pablo A Iturra
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina Universidad de Chile, Santiago 8380453, Chile
| | - Rebeca I Bustamante
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina Universidad de Chile, Santiago 8380453, Chile
| | | | | | - Sergio L Vargas
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina Universidad de Chile, Santiago 8380453, Chile
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Vanspauwen MJ, Knops VEJ, Bruggeman CA, van Mook WNKA, Linssen CFM. Molecular epidemiology of Pneumocystis jiroveci in human immunodeficiency virus-positive and -negative immunocompromised patients in The Netherlands. J Med Microbiol 2014; 63:1294-1302. [PMID: 25060971 DOI: 10.1099/jmm.0.076257-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pneumocystis jiroveci infections can cause pneumocystis pneumonia (PCP) or lead to colonization without signs of PCP. Over the years, different genotypes of P. jiroveci have been discovered. Genomic typing of P. jiroveci in different subpopulations can contribute to unravelling the pathogenesis, transmission and spread of the different genotypes. In this study, we wanted to determine the distribution of P. jiroveci genotypes in immunocompetent and immunocompromised patients in The Netherlands and determine the clinical relevance of these detected mutations. A real-time PCR targeting the major surface glycoprotein gene (MSG) was used as a screening test for the presence of P. jiroveci DNA. Samples positive for MSG were genotyped based on the internal transcribed spacer (ITS) and dihydropteroate synthase (DHPS) genes. Of the 595 included bronchoalveolar lavage fluid samples, 116 revealed the presence of P. jiroveci DNA. A total of 52 of the 116 samples were ITS genotyped and 58 DHPS genotyped. The ITS genotyping revealed 17 ITS types, including two types that have not been described previously. There was no correlation between ITS genotype and underlying disease. All ITS- and DHPS-genotyped samples were found in immunocompromised patients. Of the 58 DHPS-genotyped samples, 50 were found to be WT. The other eight samples revealed a mixed genotype consisting of WT and type 1. The majority of the latter recovered on trimethoprim-sulfamethoxazole suggesting no clinical relevance for this mutation.
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Affiliation(s)
- Marijke J Vanspauwen
- Department of Medical Microbiology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Vera E J Knops
- Department of Medical Microbiology, Atrium Medical Centre, Heerlen, The Netherlands.,Department of Medical Microbiology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Cathrien A Bruggeman
- Department of Medical Microbiology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Walther N K A van Mook
- Department of Internal Medicine, Maastricht University Medical Centre, Maastricht, The Netherlands.,Department of Intensive Care Medicine, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Catharina F M Linssen
- Department of Medical Microbiology, Atrium Medical Centre, Heerlen, The Netherlands.,Department of Medical Microbiology, Maastricht University Medical Centre, Maastricht, The Netherlands
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Diagnosis of Pneumocystis jirovecii pneumonia in immunocompromised patients by real-time PCR: a 4-year prospective study. J Clin Microbiol 2014; 52:3370-6. [PMID: 25009050 DOI: 10.1128/jcm.01480-14] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pneumocystis jirovecii pneumonia (PCP) is a life-threatening infection in immunocompromised patients. Quantitative real-time PCR (qPCR) is more sensitive than microscopic examination for the detection of P. jirovecii but also detects colonized patients. Hence, its positive predictive value (PPV) needs evaluation. In this 4-year prospective observational study, all immunocompromised patients with acute respiratory symptoms who were investigated for PCP were included, totaling 659 patients (814 bronchoalveolar lavage fluid samples). Patients with negative microscopy but positive qPCR were classified through medical chart review as having retained PCP, possible PCP, or colonization, and their clinical outcomes were compared to those of patients with microscopically proven PCP. Overall, 119 patients were included for analysis, of whom 35, 41, and 43 were classified as having retained PCP, possible PCP, and colonization, respectively. The 35 patients with retained PCP had clinical findings similar to those with microscopically proven PCP but lower fungal loads (P < 0.001) and were mainly non-HIV-infected patients (P < 0.05). Although the mean amplification threshold was higher in colonized patients, it was not possible to determine a discriminant qPCR cutoff. The PPV of qPCR in patients with negative microscopy were 29.4% and 63.8% when considering retained PCP and retained plus possible PCP, respectively. Patients with possible PCP had a higher mortality rate than patients with retained PCP or colonization (63% versus 3% and 16%, respectively); patients who died had not received co-trimoxazole. In conclusion, qPCR is a useful tool to diagnose PCP in non-HIV patients, and treatment might be better targeted through a multicomponent algorithm including both clinical/radiological parameters and qPCR results.
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Lingaratnam SM, Slavin MA, Thursky KA, Teh BW, Haeusler GM, Seymour JF, Rischin D, Worth LJ. Pneumocystis jiroveciipneumonia associated with gemcitabine chemotherapy: experience at an Australian center and recommendations for targeted prophylaxis. Leuk Lymphoma 2014; 56:157-62. [DOI: 10.3109/10428194.2014.911861] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Teh BW, Azzato FA, Lingaratnam SM, Thursky KA, Slavin MA, Worth LJ. Molecular diagnosis of Pneumocystis jirovecii in patients with malignancy: Clinical significance of quantitative polymerase chain reaction. Med Mycol 2014; 52:427-32. [DOI: 10.1093/mmy/myt020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Riedweg-Moreno K, Wallet F, Blazejewski C, Goffard A. Successful management of Panton-Valentine leukocidine-positive necrotising pneumonia and A/H1N12009 influenzavirus coinfection in adult. BMJ Case Rep 2014; 2014:bcr-2013-201120. [PMID: 24436283 DOI: 10.1136/bcr-2013-201120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
This paper presents a case of community-acquired necrotising pneumonia due to Panton-Valentine leukocidine-positive methicillin-susceptible Staphylococcus aureus and A/H1N12009 influenzavirus co-infection in a 26-year-old woman. Despite the presence of pejorative prognostic factors, the clinical course of the patient was favourable.
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Affiliation(s)
- Karena Riedweg-Moreno
- Faculty of Medicine, Department of Microbiology, Lille University Hospital, Lille, France
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