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Apparent Absence of Selective Pressure on Pneumocystis jirovecii Organisms in Patients with Prior Methotrexate Exposure. Antimicrob Agents Chemother 2022; 66:e0099022. [PMID: 36317930 PMCID: PMC9765006 DOI: 10.1128/aac.00990-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Pneumocystis jirovecii infections occur in patients treated with methotrexate (MTX) because of immunosuppressive effects of this highly potent dihydrofolate reductase (DHFR) inhibitor. Conversely, MTX may act as an anti-P. jirovecii drug and consequently may exert a selective pressure on this fungus. In this context, we compared the sequences of the dhfr gene of P. jirovecii isolates obtained from two groups of patients with P. jirovecii infections. The first group, with systemic diseases or malignancies, had prior exposure to MTX (21 patients), whereas the second group (22 patients), the control group, did not. Three single nucleotide polymorphisms (SNPs) were observed at positions 278, 312, and 381. The first one was located in the intronic region and the two others were synonymous. Based on these SNPs, three P. jirovecii dhfr alleles, named A, B, and C, were specified. Allele A was the most frequent, as it was observed in 18 patients (85.7%) and in 16 patients (72.7%) of the first and second groups, respectively. No significant difference in P. jirovecii dhfr gene diversity in the two patient groups was observed. In conclusion, these original results suggest that MTX does not exert an overt selective pressure on P. jirovecii organisms.
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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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Highly conserved gsc1 gene of Pneumocystis jirovecii in patients with or without prior exposure to Echinocandins. Antimicrob Agents Chemother 2021; 66:e0156321. [PMID: 34723629 DOI: 10.1128/aac.01563-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Echinocandins are noncompetitive inhibitors of the GSC1 subunit of the enzymatic complex involved in synthesis of 1,3-beta-D-glucan, a cell wall component of most fungi, including Pneumocystis spp. Echinocandins are widely used for treating systemic candidiasis and rarely used for treating Pneumocystis pneumonia. Consequently, data on P. jirovecii gsc1 gene diversity are still scarce, compared to the homologous fks1 gene of Candida spp. In this study, we analyzed P. jirovecii gsc1 gene diversity and the putative selection pressure of echinocandins on P. jirovecii. Gsc1 gene sequences of P. jirovecii specimens from two patient groups were compared. One group of 27 patients had prior exposure to echinocandins whereas the second group of 24 patients did not, at the time of P. jirovecii infection diagnoses. Two portions of P. jirovecii gsc1 gene, HS1 and HS2, homologous to hot spots described in Candida spp., were sequenced. Three SNPs at positions 2204, 2243, and 2303 close to the HS1 region and another SNP at position 4540 more distant from the HS2 region were identified. These SNPs represent synonymous mutations. Three gsc1 HS1 alleles, A, B, and C, and two gsc1 HS2 alleles, a and b, and four haplotypes, Ca, Cb, Aa, and Ba, were defined, without significant difference in haplotype distribution in both patient groups (p = 0.57). Considering the identical diversity of P. jirovecii gsc1 gene and the detection of synonymous mutations in both patient groups, no selection pressure of echinocandins among P. jirovecii microorganisms can be pointed out so far.
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Damiani C, Demey B, Pauc C, Le Govic Y, Totet A. A Negative (1,3)-β-D-Glucan Result Alone Is Not Sufficient to Rule Out a Diagnosis of Pneumocystis Pneumonia in Patients With Hematological Malignancies. Front Microbiol 2021; 12:713265. [PMID: 34456893 PMCID: PMC8386019 DOI: 10.3389/fmicb.2021.713265] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/21/2021] [Indexed: 12/03/2022] Open
Abstract
Background: Serum (1,3)-β-D-glucan (BG) testing is increasingly being used in the diagnostic armamentarium for invasive fungal diseases. Given its high sensitivity, some studies suggest that a negative BG result contributes to rule out a diagnosis of Pneumocystis pneumonia (PCP). However, recent reports described a suboptimal sensitivity in HIV-negative immunocompromised patients. In this study, we evaluated the performance of BG assay for PCP diagnosis in HIV-negative patients with diverse PCP risk factors. We also assessed the correlation between Pneumocystis jirovecii load in pulmonary samples and serum BG levels. Methods: We retrospectively included HIV-negative patients with microscopically proven PCP and for whom a BG result was available. We also enrolled patients colonized by Pneumocystis as control group. Colonized patients were matched with PCP patients based on their underlying condition that exposed to PCP. Pulmonary fungal loads were determined by an in-house real-time PCR, and BG levels were measured by using the Fungitell® kit (Associates of Cape Cod, Inc.). Results: Thirty-nine patients were included in each of the two groups. Thirty-four of 39 PCP patients and one of 39 colonized patient had a positive BG test, resulting in a sensitivity of 0.87 (95% CI: 0.73–0.94), a specificity of 0.97 (95% CI: 0.87–0.99), a positive predictive value of 0.97 (95% CI: 0.85–0.99), and a negative predictive value of 0.88 (95% CI: 0.75–0.95) for BG assay. Nonetheless, median BG level differed according to the underlying condition. Among the PCP group, the lowest median level of 211 pg/ml was observed in patients with hematological malignancy (HM) and differed significantly from that observed either in solid organ transplants (3,473 pg/ml) or in patients with autoimmune or inflammatory disorder (3,480 pg/ml). Indeed, the sensitivity of BG assay was estimated at 0.64 (95% CI: 0.35–0.85) in HM patients and was lower than the one observed in the whole PCP group. Furthermore, BG level and fungal burden correlated poorly among all PCP patients. Conclusion: BG is not a reliable biomarker for ruling out PCP in HIV-negative patients with HM. Interpretation of a negative BG result should take into account, but not be limited to, the underlying condition predisposing to PCP.
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Affiliation(s)
- Céline Damiani
- Laboratoire de Parasitologie-Mycologie, Centre de Biologie Humaine, CHU Amiens-Picardie, Amiens, France.,Agents Infectieux, Résistance et Chimiothérapie (AGIR), UR 4294, Université de Picardie Jules Verne, Amiens, France
| | - Baptiste Demey
- Laboratoire de Parasitologie-Mycologie, Centre de Biologie Humaine, CHU Amiens-Picardie, Amiens, France.,Agents Infectieux, Résistance et Chimiothérapie (AGIR), UR 4294, Université de Picardie Jules Verne, Amiens, France
| | - Cécile Pauc
- Laboratoire de Parasitologie-Mycologie, Centre de Biologie Humaine, CHU Amiens-Picardie, Amiens, France
| | - Yohann Le Govic
- Laboratoire de Parasitologie-Mycologie, Centre de Biologie Humaine, CHU Amiens-Picardie, Amiens, France.,Agents Infectieux, Résistance et Chimiothérapie (AGIR), UR 4294, Université de Picardie Jules Verne, Amiens, France
| | - Anne Totet
- Laboratoire de Parasitologie-Mycologie, Centre de Biologie Humaine, CHU Amiens-Picardie, Amiens, France.,Agents Infectieux, Résistance et Chimiothérapie (AGIR), UR 4294, Université de Picardie Jules Verne, Amiens, France
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Menu E, Driouich JS, Luciani L, Morand A, Ranque S, L’Ollivier C. Detection of Pneumocystis jirovecii in Hospitalized Children Less Than 3 Years of Age. J Fungi (Basel) 2021; 7:jof7070546. [PMID: 34356925 PMCID: PMC8306698 DOI: 10.3390/jof7070546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/25/2021] [Accepted: 07/07/2021] [Indexed: 11/16/2022] Open
Abstract
Few data are available in the literature regarding Pneumocystis jirovecii infection in children under 3 years old. This retrospective cohort study aimed to describe medically relevant information among them. All children under 3 years old treated in the same medical units from April 2014 to August 2020 and in whom a P. jirovecii evaluation was undertaken were enrolled in the study. A positive case was defined as a child presenting at least one positive PCR for P. jirovecii in a respiratory sample. Medically relevant information such as demographical characteristics, clinical presentation, microbiological co-infections, and treatments were collected. The objectives were to describe the characteristics of these children with P. jirovecii colonization/infection to determine the key underlying diseases and risk factors, and to identify viral respiratory pathogens associated. The PCR was positive for P. jirovecii in 32 children. Cardiopulmonary pathologies (21.9%) were the most common underlying disease in them, followed by severe combined immunodeficiency (SCID) (18.8%), hyaline membrane disease (15.6%), asthma (9.4%) and acute leukaemia (6.3%). All SCID children were diagnosed with pneumocystis pneumonia. Co-infection with Pj/Rhinovirus (34.4%) was not significant. Overall mortality was 18.8%. Paediatric pneumocystis is not restricted to patients with HIV or SCID and should be considered in pneumonia in children under 3 years old.
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Affiliation(s)
- Estelle Menu
- Laboratoire de Parasitologie-Mycologie, IHU Méditerranée Infection, 13385 Marseille, France; (J.-S.D.); (S.R.); (C.L.)
- Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs-Infections Tropicales et Méditerranéennes, 13385 Marseille, France
- Correspondence:
| | - Jean-Sélim Driouich
- Laboratoire de Parasitologie-Mycologie, IHU Méditerranée Infection, 13385 Marseille, France; (J.-S.D.); (S.R.); (C.L.)
- Unité des Virus Emergents (UVE), Aix Marseille Université, IRD 190, INSERM 1207, IHU-Méditerranée Infection, 13385 Marseille, France;
| | - Léa Luciani
- Unité des Virus Emergents (UVE), Aix Marseille Université, IRD 190, INSERM 1207, IHU-Méditerranée Infection, 13385 Marseille, France;
| | - Aurélie Morand
- Institut de Recherche pour le Développement IRD, Aix-Marseille Université, Assistance Publique-Hôpitaux de Marseille, AP-HM, MEPHI: Microbes, Evolution, Phylogénie et Infection, IHU-Méditerranée-Infection, 13385 Marseille, France;
| | - Stéphane Ranque
- Laboratoire de Parasitologie-Mycologie, IHU Méditerranée Infection, 13385 Marseille, France; (J.-S.D.); (S.R.); (C.L.)
- Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs-Infections Tropicales et Méditerranéennes, 13385 Marseille, France
| | - Coralie L’Ollivier
- Laboratoire de Parasitologie-Mycologie, IHU Méditerranée Infection, 13385 Marseille, France; (J.-S.D.); (S.R.); (C.L.)
- Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs-Infections Tropicales et Méditerranéennes, 13385 Marseille, France
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Diagnostic accuracy of (1→3)-β-D-glucan to predict Pneumocystis jirovecii pneumonia in non-HIV-infected patients. Radiol Oncol 2020; 54:221-226. [PMID: 32463392 PMCID: PMC7276650 DOI: 10.2478/raon-2020-0028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/14/2020] [Indexed: 12/19/2022] Open
Abstract
Background Pneumocystis jirovecii pneumonia (PCP) is a common and potentially fatal opportunistic infection in immunocompromised non-HIV individuals. There are problems with clinical and diagnostic protocols for PCP that lack sensitivity and specificity. We designed a retrospective study to compared several methods that were used in diagnostics of PCP. Patients and methods One hundred and eight immunocompromised individuals with typical clinical picture for PCP and suspicious radiological findings were included in the study. Serum samples were taken to measure the values of (1→3)-β-D-glucan (Fungitell, Associates of Cape Cod, USA). Lower respiratory tract samples were obtained to perform direct immunofluorescence (DIF, MERIFLUOR® Pneumocystis, Meridian, USA) stain and real-time PCR (qPCR). Results Fifty-four (50%) of the 108 patients in our study had (1→3)-β-D-glucan > 500 pg/ml. Patients that had (1→3)-β-D-glucan concentrations < 400 pg/ml in serum, had mean threshold cycles (Ct) 35.43 ± 3.32 versus those that had (1→3)-β-D-glucan concentrations >400 pg/mL and mean Ct of 28.97 ± 5.27 (P < 0.001). If we detected P. jirovecii with DIF and qPCR than PCP was proven. If the concentration of (1→3)-β-D-glucan was higher than 400 pg/ml and Ct of qPCR was below 28.97 ± 5.27 than we have been able be certain that P. jirovecii caused pneumonia (odds ratio [OR] 2.31, 95% confidence interval [CI] 1.62–3.27, P < 0.001). Conclusions Measurement of (1→3)-β-D-glucan or qPCR alone could not be used to diagnose PCP. Diagnostic cut-off value for (1→3)-β-D-glucan > 400pg/ml and qPCR below 30 Ct, allow us to conclude that patient has PCP. If the values of (1→3)-β-D-glucan are < 400 pg/ml and qPCR is above 35 Ct than colonization with P. jirovecii is more possible than PCP.
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Cordonnier C, Alanio A, Cesaro S, Maschmeyer G, Einsele H, Donnelly JP, Hauser PM, Lagrou K, Melchers WJG, Helweg-Larsen J, Matos O, Bretagne S, Maertens J. Pneumocystis jirovecii pneumonia: still a concern in patients with haematological malignancies and stem cell transplant recipients-authors' response. J Antimicrob Chemother 2018; 72:1266-1268. [PMID: 28122911 DOI: 10.1093/jac/dkw580] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Catherine Cordonnier
- Department of Haematology, Henri Mondor Teaching Hospital, Assistance Publique-hôpitaux de Paris, and Université Paris-Est-Créteil, Créteil, France
| | - Alexandre Alanio
- Parasitology-Mycology Laboratory, Groupe Hospitalier Lariboisière Saint-Louis Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Diderot, Sorbonne Paris Cité, and Institut Pasteur, Unité de Mycologie Moléculaire, CNRS URA3012, Centre National de Référence Mycoses Invasives et Antifongiques, Paris, France
| | - Simone Cesaro
- Department of Haematology, Oncoematologia Pediatrica, Policlinico G. B. Rossi, Verona, Italy
| | - Georg Maschmeyer
- Department of Haematology, Oncology and Palliative Care, Ernst-von-Bergmann Klinikum, Potsdam, Germany
| | - Hermann Einsele
- Department of Internal Medicine II, Julius Maximilians University, Würzburg, Germany
| | - J Peter Donnelly
- Department of Haematology Radboud University Medical Center, Nijmegen, The Netherlands
| | - Philippe M Hauser
- Institute of Microbiology, Lausanne University Hospital and University, Lausanne, Switzerland
| | - Katrien Lagrou
- Department of Microbiology and Immunology, KU Leuven?-?University of Leuven, Leuven, Belgium and National Reference Center for Mycosis, Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jannik Helweg-Larsen
- Department of Infectious Diseases, Rigshospitalet-Copenhagen University Hospital, Copenhagen, Denmark
| | - Olga Matos
- Medical Parasitology Unit, Group of Opportunistic Protozoa/HIV and Other Protozoa, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Stéphane Bretagne
- Parasitology-Mycology Laboratory, Groupe Hospitalier Lariboisière Saint-Louis Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Diderot, Sorbonne Paris Cité, and Institut Pasteur, Unité de Mycologie Moléculaire, CNRS URA3012, Centre National de Référence Mycoses Invasives et Antifongiques, Paris, France
| | - Johan Maertens
- Department of Haematology, Acute Leukaemia and Stem Cell Transplantation Unit, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium
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Nevez G, Le Gal S, Noel N, Wynckel A, Huguenin A, Le Govic Y, Pougnet L, Virmaux M, Toubas D, Bajolet O. Investigation of nosocomial pneumocystis infections: usefulness of longitudinal screening of epidemic and post-epidemic pneumocystis genotypes. J Hosp Infect 2017; 99:332-345. [PMID: 28943270 DOI: 10.1016/j.jhin.2017.09.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 09/18/2017] [Indexed: 10/18/2022]
Abstract
BACKGROUND Twenty-five patients, of whom 22 were renal transplant recipients, developed Pneumocystis jirovecii infections at the nephrology department of Reims University Hospital (France) from September 2008 to October 2009, whereas only four sporadic cases had been diagnosed in this department over the 14 previous years. AIM This outbreak was investigated by analysing patient encounters and P. jirovecii types. METHODS A transmission map was drawn up. P. jirovecii typing at DHPS, ITS and mtLSU rRNA sequences was performed in the patients of the cluster (18 patients with Pneumocystis pneumonia (PCP) and seven colonized patients), 10 unlinked control patients (six PCP patients and four colonized patients), as well as 23 other patients diagnosed with P. jirovecii (nine PCP patients and 14 colonized patients) in the same department over a three-year post-epidemic period. FINDINGS Eleven encounters between patients harbouring the same types were observed. Three PCP patients and one colonized patient were considered as possible index cases. The most frequent types in the cluster group and the control group were identical. However, their frequency was significantly higher in the first than in the second group (P < 0.01). Identical types were also identified in the post-epidemic group, suggesting a second outbreak due to the same strain, contemporary to a disruption in prevention measures. CONCLUSIONS These results provide additional data on the role of both PCP and colonized patients as infectious sources. Longitudinal screening of P. jirovecii types in infected patients, including colonized patients, is required in the investigation of the fungus's circulation within hospitals.
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Affiliation(s)
- G Nevez
- Université de Bretagne Loire, GEIHP EA 3142, Brest, France; Laboratory of Parasitology and Mycology, Brest University Hospital, Brest, France.
| | - S Le Gal
- Université de Bretagne Loire, GEIHP EA 3142, Brest, France; Laboratory of Parasitology and Mycology, Brest University Hospital, Brest, France
| | - N Noel
- Department of Nephrology, Reims University Hospital, Reims, France
| | - A Wynckel
- Department of Nephrology, Reims University Hospital, Reims, France
| | - A Huguenin
- Laboratory of Parasitology and Mycology, Reims University Hospital, Reims, France
| | - Y Le Govic
- Université de Bretagne Loire, GEIHP EA 3142, Angers, France
| | - L Pougnet
- Université de Bretagne Loire, GEIHP EA 3142, Brest, France
| | - M Virmaux
- Université de Bretagne Loire, GEIHP EA 3142, Brest, France
| | - D Toubas
- Laboratory of Parasitology and Mycology, Reims University Hospital, Reims, France; Université de Reims Champagne-Ardenne, Equipe MéDIAN, Biophotonique et Technologies pour la Santé, Reims, France
| | - O Bajolet
- Université de Reims Champagne-Ardenne, EA 7887, Reims, France; Equipe Opérationnelle d'Hygiène, Reims University Hospital, Reims, France
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Hoarau G, Le Gal S, Zunic P, Poubeau P, Antok E, Jaubert J, Nevez G, Picot S. Evaluation of quantitative FTD-Pneumocystis jirovecii kit for Pneumocystis infection diagnosis. Diagn Microbiol Infect Dis 2017; 89:212-217. [PMID: 28851493 DOI: 10.1016/j.diagmicrobio.2017.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 08/02/2017] [Accepted: 08/04/2017] [Indexed: 11/28/2022]
Abstract
We evaluated the Fast track Diagnostics (FTD) Pneumocystis PCR kit, targeting the mitochondrial large subunit ribosomal RNA gene (mtLSU rRNA) of Pneumocystis jirovecii (P. jirovecii). A hundred and thirty-three patients were prospectively enrolled. Respiratory specimens were examined using both microscopy and the PCR assay. Twenty-six patients led to P. jirovecii detection. Fourteen patients presented with Pneumocystis pneumonia (PCP) whereas 12 patients were considered to be colonized. The median copy numbers in bronchoalveolar lavage fluid were significantly different in the PCP and colonization groups (1.35×108/ml vs. 1.45×105/ml, P < 0.0001). Lower and upper cut-off values of 3.9×105 copies/ml and 3.2×106 copies/ml allowed differentiating PCP and colonization. The FTD P. jirovecii assay was secondarily compared to an in-house reference PCR assay targeting the mtLSUrRNA gene. A concordance rate of 97.5% was observed (Cohen's kappa coefficient κ=0.935). The FTD Pneumocystis PCR kit showed good performance and represents an alternative method to diagnose P. jirovecii infections.
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Affiliation(s)
- Gautier Hoarau
- Department of Microbiology, CHU La Reunion, St Pierre, France; UMR PIMIT « processus infectieux en milieu insulaire tropical », Inserm 1187, CNRS 9192, IRD 249, université de La Réunion, CYROI, 97490 Sainte-Clotilde, Reunion.
| | | | - Patricia Zunic
- Department of Hematology and Medical Oncology, CHU La Reunion, St Pierre, France
| | - Patrice Poubeau
- Department of Infectious Diseases, CHU La Reunion, St Pierre, France
| | | | - Julien Jaubert
- Department of Microbiology, CHU La Reunion, St Pierre, France
| | - Gilles Nevez
- University of Brest, GEIHP EA, 3142, Brest, France
| | - Sandrine Picot
- Department of Microbiology, CHU La Reunion, St Pierre, France
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Alanio A, Gits-Muselli M, Guigue N, Desnos-Ollivier M, Calderon EJ, Di Cave D, Dupont D, Hamprecht A, Hauser PM, Helweg-Larsen J, Kicia M, Lagrou K, Lengerova M, Matos O, Melchers WJG, Morio F, Nevez G, Totet A, White LP, Bretagne S. Diversity of Pneumocystis jirovecii Across Europe: A Multicentre Observational Study. EBioMedicine 2017; 22:155-163. [PMID: 28705464 PMCID: PMC5552205 DOI: 10.1016/j.ebiom.2017.06.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/13/2017] [Accepted: 06/28/2017] [Indexed: 12/30/2022] Open
Abstract
Pneumocystis jirovecii is an airborne human-specific ascomycetous fungus responsible for Pneumocystis pneumonia (PCP) in immunocompromised patients, affecting >500,000 patients per year (www.gaffi.org). The understanding of its epidemiology is limited by the lack of standardised culture. Recent genotyping data suggests a limited genetic diversity of P. jirovecii. The objective of the study was to assess the diversity of P. jirovecii across European hospitals and analyse P. jirovecii diversity in respect to clinical data obtained from the patients. Genotyping was performed using six already validated short tandem repeat (STR) markers on 249 samples (median: 17 per centre interquartile range [11-20]) from PCP patients of 16 European centres. Mixtures of STR markers (i.e., ≥2 alleles for ≥1 locus) were detected in 67.6% (interquartile range [61.4; 76.5]) of the samples. Mixture was significantly associated with the underlying disease of the patient, with an increased proportion in HIV patients (78.3%) and a decreased proportion in renal transplant recipients (33.3%) (p<0.001). The distribution of the alleles was significantly different (p<0.001) according to the centres in three out of six markers. In analysable samples, 201 combinations were observed corresponding to 137 genotypes: 116 genotypes were country-specific; 12 in two; six in three; and two in four and one in five countries. Nine genotypes were recorded more than once in a given country. Genotype 123 (Gt123) was significantly associated with France (14/15, p<0.001) and Gt16 with Belgium (5/5, p<0.001). More specifically, Gt123 was observed mainly in France (14/15/16 patients) and in renal transplant patient (13/15). Our study showed the wide population diversity across Europe, with evidence of local clusters of patients harbouring a given genotype. These data suggest a specific association between genotype and underlying disease, with evidence of a different natural history of PCP in HIV patients and renal transplant recipients.
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Affiliation(s)
- Alexandre Alanio
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Institut Pasteur, CNRS, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, URA3012, Paris, France.
| | - Maud Gits-Muselli
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Nicolas Guigue
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France
| | - Marie Desnos-Ollivier
- Institut Pasteur, CNRS, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, URA3012, Paris, France
| | - Enrique J Calderon
- CIBER de Epidemiología y Salud Pública, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío, CSIC, Universidad de Sevilla, Spain
| | - David Di Cave
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Italy
| | - Damien Dupont
- Hospices Civils de Lyon, Institut des Agents Infectieux, Parasitologie Mycologie, Hôpital de la Croix-Rousse, Integrative Physiology of the Brain Arousal Systems, Centre de Recherche en Neurosciences de Lyon, INSERM U1028-CNRS UMR 5292, Faculté de Médecine, Université Claude Bernard Lyon 1, Lyon F-69000, France
| | - Axel Hamprecht
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Germany
| | - Philippe M Hauser
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Jannik Helweg-Larsen
- Department of Infectious Diseases, Rigshospitalet-Copenhagen University Hospital, Copenhagen, Denmark
| | - Marta Kicia
- Department of Biology & Medical Parasitology, Wroclaw Medical University, Wroclaw, Poland
| | - Katrien Lagrou
- Department of Microbiology and Immunology, Catholic University Leuven, Leuven, Belgium and National Reference Centre for Mycosis, Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Martina Lengerova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Olga Matos
- TB, HIV and Opportunistic Diseases and Pathogens, Global Health and Tropical Medicine, Lisboa, Portugal; Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Willem J G Melchers
- Department of medical microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Florent Morio
- Parasitology and Mycology laboratory, Nantes University Hospital, Nantes, France
| | - Gilles Nevez
- University of Brest, GEIHP EA 3142, Laboratory of Parasitology and Mycology, Brest University Hospital, Brest, France
| | - Anne Totet
- University of Picardy-Jules Verne, EA 4285 UMR-I 01 INERIS, Department of Parasitology and Mycology, Amiens University Hospital, Amiens, France
| | - Lewis P White
- Public Health Wales, Microbiology Cardiff, UHW, Heath Park, Cardiff, UK
| | - Stéphane Bretagne
- Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Institut Pasteur, CNRS, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, URA3012, Paris, France
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11
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Comparison of a commercial real-time PCR assay, RealCycler® PJIR kit, progenie molecular, to an in-house real-time PCR assay for the diagnosis of Pneumocystis jirovecii infections. Diagn Microbiol Infect Dis 2017; 87:335-337. [DOI: 10.1016/j.diagmicrobio.2017.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 11/19/2022]
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12
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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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13
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Guillaud-Saumur T, Le Gal S, Nevez G. Comparison of a new commercial real-time PCR assay (RealCycler PJIR kit, Progenie Molecular) to an in-house real-time PCR assay for the diagnosis of Pneumocystis jirovecii infections. J Mycol Med 2016. [DOI: 10.1016/j.mycmed.2016.04.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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14
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15
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Damiani C, Le Gal S, Goin N, Di Pizio P, Da Costa C, Virmaux M, Bach V, Stéphan-Blanchard E, Nevez G, Totet A. Usefulness of (1,3) ß- d -glucan detection in bronchoalveolar lavage samples in Pneumocystis pneumonia and Pneumocystis pulmonary colonization. J Mycol Med 2015; 25:36-43. [DOI: 10.1016/j.mycmed.2014.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 10/24/2022]
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16
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Le Gal S, Pougnet L, Damiani C, Fréalle E, Guéguen P, Virmaux M, Ansart S, Jaffuel S, Couturaud F, Delluc A, Tonnelier JM, Castellant P, Le Meur Y, Le Floch G, Totet A, Menotti J, Nevez G. Pneumocystis jirovecii in the air surrounding patients with Pneumocystis pulmonary colonization. Diagn Microbiol Infect Dis 2015; 82:137-42. [PMID: 25801779 DOI: 10.1016/j.diagmicrobio.2015.01.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/09/2015] [Accepted: 01/11/2015] [Indexed: 12/23/2022]
Abstract
In this study, Pneumocystis jirovecii was detected and characterized in the air surrounding patients with Pneumocystis pulmonary colonization. Air samples were collected in the rooms of 10 colonized patients using Coriolis® μ air sampler at 1m and 5m from the patient's head. P. jirovecii DNA was amplified and genotyped in pulmonary and air samples at the mitochondrial large subunit ribosomal RNA gene. P. jirovecii DNA was detected in 5 of the 10 air samples collected at 1m and in 5 of the 10 other air samples collected at 5m. P. jirovecii genotyping was successful in 4 pairs or triplets of air and pulmonary samples. Full genotype matches were observed in 3 of the 4 pairs or triplets of air and pulmonary samples. These results provide original data supporting P. jirovecii exhalation from colonized patients and emphasize the risk of P. jirovecii nosocomial transmission from this patient population.
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Affiliation(s)
- Solène Le Gal
- University of Brest, LUBEM EA 3882, SFR 148, Brest, France; Laboratory of Parasitology and Mycology, Brest University Hospital, Brest, France.
| | - Laurence Pougnet
- Laboratory, Military Teaching Hospital Clermont Tonnerre, Brest, France
| | - Céline Damiani
- University of Picardy-Jules Verne, UMR-I 01, SFR Cap Santé, Amiens, France; Laboratory of Parasitology and Mycology, Amiens University Hospital, Amiens, France
| | - Emilie Fréalle
- Laboratory of Parasitology and Mycology, Lille University Hospital, Lille, France
| | - Paul Guéguen
- Laboratory of Molecular Genetics and Histocompatibility, Brest University Hospital, Brest, France; University of Brest, INSERM U1078, Molecular Genetics and Epidemiological Genetics, SFR 148, Brest, France
| | | | - Séverine Ansart
- Department of Infectious Diseases, Brest University Hospital, Brest, France; University of Brest, INSERM UMR 1101, Laboratory of Medical Information Processing, SFR 148, Brest, France
| | - Sylvain Jaffuel
- Department of Infectious Diseases, Brest University Hospital, Brest, France
| | - Francis Couturaud
- Department of Internal Medicine and Pneumology, Brest University Hospital, Brest, France; University of Brest, EA3878 (GETBO), CIC INSERM 0502, SFR 148, Brest, France
| | - Aurélien Delluc
- Department of Internal Medicine and Pneumology, Brest University Hospital, Brest, France; University of Brest, EA3878 (GETBO), CIC INSERM 0502, SFR 148, Brest, France
| | | | | | - Yann Le Meur
- Department of Nephrology and Renal Transplantation Unit, Brest University Hospital, Brest, France; University of Brest, EA 2216, SFR 148, Brest, France
| | | | - Anne Totet
- University of Picardy-Jules Verne, UMR-I 01, SFR Cap Santé, Amiens, France; Laboratory of Parasitology and Mycology, Amiens University Hospital, Amiens, France
| | - Jean Menotti
- Laboratory of Parasitology and Mycology, Saint Louis Hospital APHP, Paris, France; Paris-Diderot University, Paris, France
| | - Gilles Nevez
- University of Brest, LUBEM EA 3882, SFR 148, Brest, France; Laboratory of Parasitology and Mycology, Brest University Hospital, Brest, France.
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17
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Guigue N, Alanio A, Menotti J, Castro ND, Hamane S, Peyrony O, LeGoff J, Bretagne S. Utility of adding Pneumocystis jirovecii DNA detection in nasopharyngeal aspirates in immunocompromised adult patients with febrile pneumonia. Med Mycol 2014; 53:241-7. [PMID: 25550391 PMCID: PMC7107570 DOI: 10.1093/mmy/myu087] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Detection of viral and bacterial DNA in nasopharyngeal aspirates (NPAs) is now a routine practice in emergency cases of febrile pneumonia. We investigated whether
Pneumocystis jirovecii
DNA could also be detected in these cases by conducting retrospective screening of 324 consecutive NPAs from 324 adult patients (198 or 61% were immunocompromised) admitted with
suspected pulmonary infections during the 2012 influenza epidemic season, using a real-time quantitative polymerase chain reaction (PCR) assay (PjqPCR), which targets the
P. jirovecii
mitochondrial large subunit ribosomal RNA gene. These NPAs had already been tested for 22 respiratory pathogens (18 viruses and 4 bacteria), but we found that 16 NPAs (4.9%) were PjqPCR-positive, making
P. jirovecii
the fourth most prevalent of the 23 microorganisms in the screen. Eleven of the 16 PjqPCR-positive patients were immunocompromised, and five had underlying pulmonary conditions. Nine NPAs were also positive for another respiratory pathogen. Six had PjqPCR-positive induced sputa less than 3 days after the NPA procedure, and five were diagnosed with pneumocystis pneumonia (four with chronic lymphoproliferative disorders and one AIDS patient). In all six available pairs quantification of
P. jirovecii
DNA showed fewer copies in NPA than in induced sputum and three PjqPCR-negative NPAs corresponded to PjqPCR-positive bronchoalveolar lavage fluids, underscoring the fact that a negative PjqPCR screen does not exclude a diagnosis of pneumocystosis. Including
P. jirovecii
DNA detection to the panel of microorganisms included in screening tests used for febrile pneumonia may encourage additional investigations or support use of anti-pneumocystis pneumonia prophylaxis in immunocompromised patients.
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Affiliation(s)
- Nicolas Guigue
- Laboratoire de Parasitologie et de Mycologie, APHP, Hôpital Saint Louis Université Paris Diderot, Sorbonne Paris Cité
| | - Alexandre Alanio
- Laboratoire de Parasitologie et de Mycologie, APHP, Hôpital Saint Louis Université Paris Diderot, Sorbonne Paris Cité CNRS URA3012 Institut Pasteur, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, Paris, France
| | - Jean Menotti
- Laboratoire de Parasitologie et de Mycologie, APHP, Hôpital Saint Louis Université Paris Diderot, Sorbonne Paris Cité CNRS URA3012
| | - Nathalie De Castro
- Université Paris Diderot, Sorbonne Paris Cité Service de maladies infectieuses, APHP, Hôpital Saint Louis
| | - Samia Hamane
- Laboratoire de Parasitologie et de Mycologie, APHP, Hôpital Saint Louis
| | | | - Jérôme LeGoff
- Université Paris Diderot, Sorbonne Paris Cité Laboratoire de Microbiologie, APHP, Hôpital Saint Louis
| | - Stéphane Bretagne
- Laboratoire de Parasitologie et de Mycologie, APHP, Hôpital Saint Louis Université Paris Diderot, Sorbonne Paris Cité CNRS URA3012 Institut Pasteur, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses Invasives et Antifongiques, Paris, France
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18
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Multilocus microsatellite genotyping array for investigation of genetic epidemiology of Pneumocystis jirovecii. J Clin Microbiol 2014; 52:1391-9. [PMID: 24523468 DOI: 10.1128/jcm.02531-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pneumocystis jirovecii is a symbiotic respiratory fungus that causes pneumonia (PcP) in immunosuppressed patients. Because P. jirovecii cannot be reliably cultured in vitro, it has proven difficult to study and gaps in our understanding of the organism persist. The release of a draft genome for the organism opens the door for the development of new genotyping approaches for studying its molecular epidemiology and global population structure. We identified and validated 8 putatively neutral microsatellite markers and 1 microsatellite marker linked to the dihydropteroate synthase gene (dhps), the enzymatic target of sulfa drugs used for PcP prevention and treatment. Using these tools, we analyzed P. jirovecii isolates from HIV-infected patients from three geographically distant populations: Uganda, the United States, and Spain. Among the 8 neutral markers, we observed high levels of allelic heterozygosity (average He, 0.586 to 0.842). Consistent with past reports, we observed limited global population structuring, with only the Ugandan isolates showing minor differentiation from the other two populations. In Ugandan isolates that harbored mutations in dhps, the microsatellite locus linked to dhps demonstrated a depressed He, consistent with positive directional selection for sulfa resistance mutations. Using a subset of these microsatellites, analyses of individual and paired samples from infections in San Francisco, CA, showed reliable typeability within a single infection and high discriminatory power between infections. These features suggest that this novel microsatellite typing approach will be an effective tool for molecular-epidemiological investigations into P. jirovecii population structure, transmission, and drug resistance.
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19
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Le Gal S, Rouille A, Gueguen P, Virmaux M, Berthou C, Guillerm G, Couturaud F, Le Meur Y, Damiani C, Totet A, Nevez G. Pneumocystis jirovecii haplotypes at the internal transcribed spacers of the rRNA operon in French HIV-negative patients with diverse clinical presentations of Pneumocystis infections. Med Mycol 2013; 51:851-62. [PMID: 23964829 DOI: 10.3109/13693786.2013.824123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pneumocystis jirovecii, a transmissible fungus, is the causative agent of pulmonary infections. Its genomic diversity has appeared in reports from around the world but data on P. jirovecii genotypes in France are still limited. This study describes the typing of P. jirovecii isolates from 81 HIV-negative patients monitored at Brest University Hospital, Brittany, France, 40 of whom developed Pneumocystis pneumonia (PcP), and remaining 41 patients were colonized by the fungus. The isolates were assayed at the internal transcribed spacer (ITS)1 and ITS2 under improved amplification conditions to avoid in vitro ITS recombination. P. jirovecii ITS haplotypes were identified in 56/81 patients (31 PcP patients and 25 patients who were colonized) which revealed a high diversity in that 27 different haplotypes were identified. Eg was the most frequent haplotype (31/56, 55.3%), followed by Ec and Ai (5/56, 8.9% each). In contrast, Ne, usually the second most frequent haplotype in Europe and the USA, was observed in only 2/56 patients (3.6%). Mixed infections were detected in 18/56 patients (32.1%; 12 PcP patients and six who were colonized). No significant differences were observed in haplotype diversity, frequency of peculiar haplotypes, and mixed infection occurrence, between the two patient populations. The study, conducted with the largest HIV-negative patient population investigated so far, shows that ITS typing remains an efficient method for characterizing P. jirovecii among human populations, whatever their clinical presentation of Pneumocystis infections.
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20
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Combined quantification of pulmonary Pneumocystis jirovecii DNA and serum (1->3)-β-D-glucan for differential diagnosis of pneumocystis pneumonia and Pneumocystis colonization. J Clin Microbiol 2013; 51:3380-8. [PMID: 23903553 DOI: 10.1128/jcm.01554-13] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study assessed a quantitative PCR (qPCR) assay for Pneumocystis jirovecii quantification in bronchoalveolar lavage (BAL) fluid samples combined with serum (1→3)-β-d-glucan (BG) level detection to distinguish Pneumocystis pneumonia (PCP) from pulmonary colonization with P. jirovecii. Forty-six patients for whom P. jirovecii was initially detected in BAL fluid samples were retrospectively enrolled. Based on clinical data and results of P. jirovecii detection, 17 and 29 patients were diagnosed with PCP and colonization, respectively. BAL fluid samples were reassayed using a qPCR assay targeting the mitochondrial large subunit rRNA gene. qPCR results and serum BG levels (from a Fungitell kit) were analyzed conjointly. P. jirovecii DNA copy numbers were significantly higher in the PCP group than in the colonization group (1.3 × 10(7) versus 3.4 × 10(3) copies/μl, P < 0.05). A lower cutoff value (1.6 × 10(3) copies/μl) achieving 100% sensitivity for PCP diagnosis and an upper cutoff value (2 × 10(4) copies/μl) achieving 100% specificity were determined. Applying these two values, 13/17 PCP patients and 19/29 colonized patients were correctly assigned to their patient groups. For the remaining 14 patients with P. jirovecii DNA copy numbers between the cutoff values, PCP and colonization could not be distinguished on the basis of qPCR results. Four of these patients who were initially assigned to the PCP group presented BG levels of ≥100 pg/ml. The other 10 patients, who were initially assigned to the colonization group, presented BG levels of <100 pg/ml. These results suggest that the combination of the qPCR assay, applying cutoff values of 1.6 × 10(3) and 2 × 10(4) copies/μl, and serum BG detection, applying a 100 pg/ml threshold, can differentiate PCP and colonization diagnoses.
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21
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Le Gal S, Robert-Gangneux F, Perrot M, Rouillé A, Virmaux M, Damiani C, Totet A, Gangneux JP, Nevez G. Absence of Pneumocystis dihydropteroate synthase mutants in Brittany, France. Diagn Microbiol Infect Dis 2013; 76:113-5. [PMID: 23433532 DOI: 10.1016/j.diagmicrobio.2013.01.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/16/2013] [Accepted: 01/16/2013] [Indexed: 11/15/2022]
Abstract
Archival Pneumocystis jirovecii specimens from 84 patients monitored at Rennes University Hospital (Rennes, France) were assayed at the dihydropteroate synthase (DHPS) locus. No patient was infected with mutants. The results provide additional data showing that P. jirovecii infections involving DHPS mutants do not represent a public health issue in Brittany, western France.
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Affiliation(s)
- Solène Le Gal
- University of Brest, LUBEM EA 3882, SFR 148, Brest, France; Laboratory of Parasitology and Mycology, Brest University Hospital, Brest, France.
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22
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Abstract
Although the incidence of Pneumocystis pneumonia (PCP) has decreased since the introduction of combination antiretroviral therapy, it remains an important cause of disease in both HIV-infected and non-HIV-infected immunosuppressed populations. The epidemiology of PCP has shifted over the course of the HIV epidemic both from changes in HIV and PCP treatment and prevention and from changes in critical care medicine. Although less common in non-HIV-infected immunosuppressed patients, PCP is now more frequently seen due to the increasing numbers of organ transplants and development of novel immunotherapies. New diagnostic and treatment modalities are under investigation. The immune response is critical in preventing this disease but also results in lung damage, and future work may offer potential areas for vaccine development or immunomodulatory therapy. Colonization with Pneumocystis is an area of increasing clinical and research interest and may be important in development of lung diseases such as chronic obstructive pulmonary disease. In this review, we discuss current clinical and research topics in the study of Pneumocystis and highlight areas for future research.
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23
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Circulation of Pneumocystis dihydropteroate synthase mutants in France. Diagn Microbiol Infect Dis 2012; 74:119-24. [PMID: 22795965 DOI: 10.1016/j.diagmicrobio.2012.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 06/01/2012] [Accepted: 06/04/2012] [Indexed: 11/21/2022]
Abstract
Data on the prevalence of Pneumocystis jirovecii (P. jirovecii) dihydropteroate synthase (DHPS) mutants in France are still limited. In this study, mutant prevalence in the Brest region (western France) was determined. Archival pulmonary specimens from 85 patients infected with P. jirovecii and admitted to our institution (University Hospital, Brest) from October 2007 to February 2010 were retrospectively typed at the DHPS locus using a polymerase chain reaction-restriction fragment length polymorphism assay. Type identification was successful in 66 of 85 patients. Sixty-four patients were infected with a wild type, whereas mutants were found in 2 patients (2/66, 3%). Medical chart analysis revealed that these 2 patients usually lived in Paris. Another patient usually lived on the French Riviera, whereas 63 patients were from the city of Brest. Thus, the corrected prevalence of mutants in patients who effectively lived in our geographic area was 0% (0/63). Taking into account that i) Paris is characterized by a high prevalence of mutants from 18.5% to 40%, ii) infection diagnoses were performed in the 2 Parisians during their vacation <30 days, iii) infection incubation is assumed to last about 2 months, the results provide evidence of mutant circulation from Paris to Brest through infected vacationers. The study shows that the usual city of patient residence, rather than the city of infection diagnosis, is a predictor of mutants and that P. jirovecii infections involving mutants do not represent a public health issue in western France.
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24
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Saltzman RW, Albin S, Russo P, Sullivan KE. Clinical conditions associated with PCP in children. Pediatr Pulmonol 2012; 47:510-6. [PMID: 22009851 DOI: 10.1002/ppul.21577] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 08/16/2011] [Indexed: 01/15/2023]
Abstract
Pneumocystis jirovecii is a leading cause of opportunistic infections among the immune compromised. During the 1980s, attention focused on patients with HIV, however, with the advent of anti-retroviral therapy, we wished to revisit the question of underlying diseases associated with Pneumocystis pneumonia in children. We identified 80 cases from 1986 to 2006 and performed a retrospective chart review to identify clinical characteristics for each of the cases. HIV was the single most common associated underlying condition seen in this cohort, accounting for 39% of the cases overall, however, it was seen in just 15% of the cases since 1998. Transplant recipients and oncology patients together comprised another 39% of the cases, with 9% of cases attributed to primary immune deficiency and another 9% of cases associated with less well-recognized causes of susceptibility. This study documents the ongoing need for vigilance to diagnose Pneumocystis pneumonia in less well-recognized clinical scenarios.
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Affiliation(s)
- Rushani W Saltzman
- Division of Allergy Immunology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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25
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Le Gal S, Damiani C, Rouille A, Grall A, Treguer L, Virmaux M, Moalic E, Quinio D, Moal MC, Berthou C, Saliou P, Le Meur Y, Totet A, Nevez G. A Cluster of Pneumocystis Infections Among Renal Transplant Recipients: Molecular Evidence of Colonized Patients as Potential Infectious Sources of Pneumocystis jirovecii. Clin Infect Dis 2012; 54:e62-71. [DOI: 10.1093/cid/cir996] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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Serum (1->3)-beta-D-glucan levels in primary infection and pulmonary colonization with Pneumocystis jirovecii. J Clin Microbiol 2011; 49:2000-2. [PMID: 21430107 DOI: 10.1128/jcm.00249-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This article describes positive (1 → 3)-β-D-glucan levels in serum from infants with primary Pneumocystis infection and from immunosuppressed patients with Pneumocystis pneumonia (PCP) and negative levels in serum from patients colonized by Pneumocystis jirovecii. Glucan detection is a complementary tool for the diagnosis of the diverse clinical presentations of P. jirovecii infection.
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Catherinot E, Lanternier F, Bougnoux ME, Lecuit M, Couderc LJ, Lortholary O. Pneumocystis jirovecii Pneumonia. Infect Dis Clin North Am 2010; 24:107-38. [PMID: 20171548 DOI: 10.1016/j.idc.2009.10.010] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Pneumocystis jirovecii has gained attention during the last decade in the context of the AIDS epidemic and the increasing use of cytotoxic and immunosuppressive therapies. This article summarizes current knowledge on biology, pathophysiology, epidemiology, diagnosis, prevention, and treatment of pulmonary P jirovecii infection, with a particular focus on the evolving pathophysiology and epidemiology. Pneumocystis pneumonia still remains a severe opportunistic infection, associated with a high mortality rate.
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Affiliation(s)
- Emilie Catherinot
- Université Paris Descartes, Service de Maladies Infectieuses et Tropicales, 149 Rue de Sèvres, Centre d'Infectiologie Necker-Pasteur, Hôpital Necker-Enfants Malades, Paris 75015, France
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Spencer L, Ukwu M, Alexander T, Valadez K, Liu L, Frederick T, Kovacs A, Morris A. Epidemiology of Pneumocystis colonization in families. Clin Infect Dis 2008; 46:1237-40. [PMID: 18444861 PMCID: PMC2613645 DOI: 10.1086/533449] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Whether Pneumocystis colonization is transmitted in families with human immunodeficiency virus (HIV)-infected members is unknown. Using nested polymerase chain reaction of oropharyngeal or nasopharyngeal samples, we detected colonization in 11.4% of HIV-infected adults and in 3.3% of their children, but there was no evidence of clustering.
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Affiliation(s)
- LaShonda Spencer
- Maternal Child and Adolescent Center for Infectious Diseases and Virology, University of Southern California, Los Angeles, CA, United States
| | - Michelle Ukwu
- Department of Medicine, Division of Pulmonary and Critical Care Medicine and the Will Rogers Institute Pulmonary Research Center, University of Southern California, Los Angeles, CA, United States
| | - Travis Alexander
- Department of Medicine, Division of Pulmonary and Critical Care Medicine and the Will Rogers Institute Pulmonary Research Center, University of Southern California, Los Angeles, CA, United States
| | - Karri Valadez
- Department of Medicine, Division of Pulmonary and Critical Care Medicine and the Will Rogers Institute Pulmonary Research Center, University of Southern California, Los Angeles, CA, United States
| | - Lora Liu
- Maternal Child and Adolescent Center for Infectious Diseases and Virology, University of Southern California, Los Angeles, CA, United States
| | - Toni Frederick
- Maternal Child and Adolescent Center for Infectious Diseases and Virology, University of Southern California, Los Angeles, CA, United States
| | - Andrea Kovacs
- Maternal Child and Adolescent Center for Infectious Diseases and Virology, University of Southern California, Los Angeles, CA, United States
| | - Alison Morris
- Department of Medicine, Division of Pulmonary and Critical Care Medicine and the Will Rogers Institute Pulmonary Research Center, University of Southern California, Los Angeles, CA, United States
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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Arcenas RC, Uhl JR, Buckwalter SP, Limper AH, Crino D, Roberts GD, Wengenack NL. A real-time polymerase chain reaction assay for detection of Pneumocystis from bronchoalveolar lavage fluid. Diagn Microbiol Infect Dis 2006; 54:169-75. [PMID: 16423488 DOI: 10.1016/j.diagmicrobio.2005.08.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2005] [Accepted: 08/08/2005] [Indexed: 11/19/2022]
Abstract
Pneumocystis jiroveci is an important cause of pneumonia in immunocompromised individuals. This organism cannot be cultured, and therefore, diagnosis relies on microscopic identification of the organism using stains or antibodies. Although simple, these tests are insensitive and require expertise for accurate interpretation. We developed a real-time polymerase chain reaction (PCR) assay that provides sensitive and objective detection of Pneumocystis from bronchoalveolar lavage fluid. Primers and fluorescence resonance energy transfer probes were developed that target the cdc2 gene of P. jiroveci. Assay sensitivity is 6 copies of target per microliter of sample. No cross-reactivity occurs with other pathogens, and the PCR assay has a 21% increase in clinical sensitivity as compared with Calcofluor white staining. The real-time PCR assay provides a sensitive, rapid, and objective method for the detection of Pneumocystis from bronchoalveolar lavage fluid.
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Affiliation(s)
- Rodney C Arcenas
- Division of Clinical Microbiology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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Espy MJ, Uhl JR, Sloan LM, Buckwalter SP, Jones MF, Vetter EA, Yao JDC, Wengenack NL, Rosenblatt JE, Cockerill FR, Smith TF. Real-time PCR in clinical microbiology: applications for routine laboratory testing. Clin Microbiol Rev 2006; 19:165-256. [PMID: 16418529 PMCID: PMC1360278 DOI: 10.1128/cmr.19.1.165-256.2006] [Citation(s) in RCA: 800] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Real-time PCR has revolutionized the way clinical microbiology laboratories diagnose many human microbial infections. This testing method combines PCR chemistry with fluorescent probe detection of amplified product in the same reaction vessel. In general, both PCR and amplified product detection are completed in an hour or less, which is considerably faster than conventional PCR detection methods. Real-time PCR assays provide sensitivity and specificity equivalent to that of conventional PCR combined with Southern blot analysis, and since amplification and detection steps are performed in the same closed vessel, the risk of releasing amplified nucleic acids into the environment is negligible. The combination of excellent sensitivity and specificity, low contamination risk, and speed has made real-time PCR technology an appealing alternative to culture- or immunoassay-based testing methods for diagnosing many infectious diseases. This review focuses on the application of real-time PCR in the clinical microbiology laboratory.
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Affiliation(s)
- M J Espy
- Mayo Clinic, 200 First St. SW, Hilton 470, Rochester, MN 55905, USA.
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