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de la Horra C, Friaza V, Morilla R, Delgado J, Medrano FJ, Miller RF, de Armas Y, Calderón EJ. Update on Dihydropteroate Synthase (DHPS) Mutations in Pneumocystis jirovecii. J Fungi (Basel) 2021; 7:jof7100856. [PMID: 34682277 PMCID: PMC8540849 DOI: 10.3390/jof7100856] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/28/2021] [Accepted: 10/10/2021] [Indexed: 12/21/2022] Open
Abstract
A Pneumocystis jirovecii is one of the most important microorganisms that cause pneumonia in immunosupressed individuals. The guideline for treatment and prophylaxis of Pneumocystis pneumonia (PcP) is the use of a combination of sulfa drug-containing trimethroprim and sulfamethoxazole. In the absence of a reliable method to culture Pneumocystis, molecular techniques have been developed to detect mutations in the dihydropteroate synthase gene, the target of sulfa drugs, where mutations are related to sulfa resistance in other microorganisms. The presence of dihydropteroate synthase (DHPS) mutations has been described at codon 55 and 57 and found almost around the world. In the current work, we analyzed the most common methods to identify these mutations, their geographical distribution around the world, and their clinical implications. In addition, we describe new emerging DHPS mutations. Other aspects, such as the possibility of transmitting Pneumocystis mutated organisms between susceptible patients is also described, as well as a brief summary of approaches to study these mutations in a heterologous expression system.
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Affiliation(s)
- Carmen de la Horra
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (C.d.l.H.); (R.M.); (J.D.); (F.J.M.)
| | - Vicente Friaza
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (C.d.l.H.); (R.M.); (J.D.); (F.J.M.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
- Correspondence: (V.F.); (E.J.C.); Tel.: +34-955923096 (E.J.C.)
| | - Rubén Morilla
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (C.d.l.H.); (R.M.); (J.D.); (F.J.M.)
- Departamento de Enfermería, Universidad de Sevilla, 41009 Seville, Spain
| | - Juan Delgado
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (C.d.l.H.); (R.M.); (J.D.); (F.J.M.)
| | - Francisco J. Medrano
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (C.d.l.H.); (R.M.); (J.D.); (F.J.M.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
- Departamento de Medicina, Universidad de Sevilla, 41009 Seville, Spain
| | - Robert F. Miller
- Institute for Global Health, University College London, London WC1E 6JB, UK;
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Yaxsier de Armas
- Department of Clinical Microbiology Diagnostic, Hospital Center of Institute of Tropical Medicine “Pedro Kourí”, Havana 11400, Cuba;
- Pathology Department, Hospital Center of Institute of Tropical Medicine “Pedro Kourí,” Havana 11400, Cuba
| | - Enrique J. Calderón
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (C.d.l.H.); (R.M.); (J.D.); (F.J.M.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
- Departamento de Medicina, Universidad de Sevilla, 41009 Seville, Spain
- Correspondence: (V.F.); (E.J.C.); Tel.: +34-955923096 (E.J.C.)
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Szydłowicz M, Jakuszko K, Szymczak A, Piesiak P, Kowal A, Kopacz Ż, Wesołowska M, Lobo ML, Matos O, Hendrich AB, Kicia M. Prevalence and genotyping of Pneumocystis jirovecii in renal transplant recipients-preliminary report. Parasitol Res 2018; 118:181-189. [PMID: 30392033 PMCID: PMC6329730 DOI: 10.1007/s00436-018-6131-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/23/2018] [Indexed: 12/24/2022]
Abstract
Pneumocystis jirovecii is an opportunistic fungus occurring in human lungs. The group at highest risk consists of HIV-infected and non-HIV-infected immunosuppressed individuals. In these patients, P. jirovecii infection may lead to Pneumocystis pneumonia; it may, however, persist also in an asymptomatic form. This study aimed to determine the prevalence of P. jirovecii and potential risk factors for infection in a group of renal transplant recipients and to characterize the genetic diversity of this fungus in the studied population. Sputum specimens from 72 patients were tested for presence of P. jirovecii using immunofluorescence microscopy, as well as nested PCR targeting the mtLSU rRNA gene. Genotyping involving analysis of four loci—mtLSU rRNA, CYB, DHPS, and SOD—was used to characterize the diversity of the detected organisms. Pneumocystis DNA was detected in eight (11.11%) patients. It has been shown that low eosinophil count and dual immunosuppressive treatment combining prednisone and calcineurin inhibitors are potential risk factors for colonization. Analysis of genotype distribution showed an association of the wild-type genotype of mtLSU rRNA with lower average age of patients and shorter time after kidney transplantation. Furthermore, CYB 2 genotype was detected only in patients with the ongoing prophylaxis regimen. In conclusion, renal transplant recipients are at risk of Pneumocystis colonization even a long time after transplantation. The present preliminary study identifies specific polymorphisms that appear to be correlated with certain patient characteristics and highlights the need for deeper investigation of these associations in renal transplant recipients.
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Affiliation(s)
- Magdalena Szydłowicz
- Department of Biology and Medical Parasitology, Wroclaw Medical University, ul. J. Mikulicza-Radeckiego 9, 50-345, Wroclaw, Poland.
| | - Katarzyna Jakuszko
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Anna Szymczak
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Paweł Piesiak
- Department of Pulmonology and Lung Cancer, Wroclaw Medical University, Wroclaw, Poland
| | - Aneta Kowal
- Department of Pulmonology and Lung Cancer, Wroclaw Medical University, Wroclaw, Poland
| | - Żaneta Kopacz
- Department of Biology and Medical Parasitology, Wroclaw Medical University, ul. J. Mikulicza-Radeckiego 9, 50-345, Wroclaw, Poland
| | - Maria Wesołowska
- Department of Biology and Medical Parasitology, Wroclaw Medical University, ul. J. Mikulicza-Radeckiego 9, 50-345, Wroclaw, Poland
| | - Maria Luísa Lobo
- Global Health and Tropical Medicine, Unit of Medical Parasitology, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Olga Matos
- Global Health and Tropical Medicine, Unit of Medical Parasitology, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Andrzej B Hendrich
- Department of Biology and Medical Parasitology, Wroclaw Medical University, ul. J. Mikulicza-Radeckiego 9, 50-345, Wroclaw, Poland
| | - Marta Kicia
- Department of Biology and Medical Parasitology, Wroclaw Medical University, ul. J. Mikulicza-Radeckiego 9, 50-345, Wroclaw, Poland
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Abstract
Pneumocystis pneumonia (PCP) is an opportunistic infection that occurs in humans and other mammals with debilitated immune systems. These infections are caused by fungi in the genus Pneumocystis, which are not susceptible to standard antifungal agents. Despite decades of research and drug development, the primary treatment and prophylaxis for PCP remains a combination of trimethoprim (TMP) and sulfamethoxazole (SMX) that targets two enzymes in folic acid biosynthesis, dihydrofolate reductase (DHFR) and dihydropteroate synthase (DHPS), respectively. There is growing evidence of emerging resistance by Pneumocystis jirovecii (the species that infects humans) to TMP-SMX associated with mutations in the targeted enzymes. In the present study, we report the development of an accurate quantitative model to predict changes in the binding affinity of inhibitors (Ki, IC50) to the mutated proteins. The model is based on evolutionary information and amino acid covariance analysis. Predicted changes in binding affinity upon mutations highly correlate with the experimentally measured data. While trained on Pneumocystis jirovecii DHFR/TMP data, the model shows similar or better performance when evaluated on the resistance data for a different inhibitor of PjDFHR, another drug/target pair (PjDHPS/SMX) and another organism (Staphylococcus aureus DHFR/TMP). Therefore, we anticipate that the developed prediction model will be useful in the evaluation of possible resistance of the newly sequenced variants of the pathogen and can be extended to other drug targets and organisms.
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Esteves F, de Sousa B, Calderón E, Huang L, Badura R, Maltez F, Bassat Q, de Armas Y, Antunes F, Matos O. Multicentre study highlighting clinical relevance of new high-throughput methodologies in molecular epidemiology of Pneumocystis jirovecii pneumonia. Clin Microbiol Infect 2016; 22:566.e9-566.e19. [DOI: 10.1016/j.cmi.2016.03.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 02/19/2016] [Accepted: 03/13/2016] [Indexed: 11/17/2022]
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Alanio A, Hauser PM, Lagrou K, Melchers WJG, Helweg-Larsen J, Matos O, Cesaro S, Maschmeyer G, Einsele H, Donnelly JP, Cordonnier C, Maertens J, Bretagne S. ECIL guidelines for the diagnosis of Pneumocystis jirovecii pneumonia in patients with haematological malignancies and stem cell transplant recipients. J Antimicrob Chemother 2016; 71:2386-96. [PMID: 27550991 DOI: 10.1093/jac/dkw156] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The Fifth European Conference on Infections in Leukaemia (ECIL-5) convened a meeting to establish evidence-based recommendations for using tests to diagnose Pneumocystis jirovecii pneumonia (PCP) in adult patients with haematological malignancies. Immunofluorescence assays are recommended as the most sensitive microscopic method (recommendation A-II: ). Real-time PCR is recommended for the routine diagnosis of PCP ( A-II: ). Bronchoalveolar lavage (BAL) fluid is recommended as the best specimen as it yields good negative predictive value ( A-II: ). Non-invasive specimens can be suitable alternatives ( B-II: ), acknowledging that PCP cannot be ruled out in case of a negative PCR result ( A-II: ). Detecting β-d-glucan in serum can contribute to the diagnosis but not the follow-up of PCP ( A-II: ). A negative serum β-d-glucan result can exclude PCP in a patient at risk ( A-II: ), whereas a positive test result may indicate other fungal infections. Genotyping using multilocus sequence markers can be used to investigate suspected outbreaks ( A-II: ). The routine detection of dihydropteroate synthase mutations in cases of treatment failure is not recommended ( B-II: ) since these mutations do not affect response to high-dose co-trimoxazole. The clinical utility of these diagnostic tests for the early management of PCP should be further assessed in prospective, randomized interventional studies.
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Affiliation(s)
- 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
| | - Philippe M Hauser
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Katrien Lagrou
- Department of Microbiology and Immunology, Catholic University 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, Portugal Universidade Nova de Lisboa, Lisboa, Portugal
| | - Simone Cesaro
- Hematology Department, Oncoematologia Pediatrica, Policlinico G. B. Rossi, Verona, Italy
| | - Georg Maschmeyer
- Department of Hematology, Oncology and Palliative Care, Ernst-von-Bergmann Klinikum, Potsdam, Germany
| | - Hermann Einsele
- Medizinische Klinik und Poliklinik II, Julius Maximilians Universitaet, Würzburg, Germany
| | - J Peter Donnelly
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Catherine Cordonnier
- Hematology Department, Henri Mondor Hospital, APHP and Université Paris-Est-Créteil, Créteil, France
| | - Johan Maertens
- Hematology Department, University Hospital Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - 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
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Friaza V, Morilla R, Respaldiza N, de la Horra C, Calderón EJ. Pneumocystis jiroveciDihydropteroate Synthase Gene Mutations among Colonized Individuals andPneumocystisPneumonia Patients from Spain. Postgrad Med 2015; 122:24-8. [DOI: 10.3810/pgm.2010.11.2219] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Yoon C, Subramanian A, Chi A, Crothers K, Meshnick SR, Taylor SM, Beard CB, Jarlsberg LG, Lawrence GG, Avery M, Swartzman A, Fong S, Roth B, Huang L. Dihydropteroate synthase mutations in Pneumocystis pneumonia: impact of applying different definitions of prophylaxis, mortality endpoints and mutant in a single cohort. Med Mycol 2013; 51:568-75. [PMID: 23470037 DOI: 10.3109/13693786.2013.770604] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pneumocystis jirovecii dihydropteroate synthase (DHPS) gene mutations are well-reported. Although sulfa prophylaxis generally is associated with DHPS mutant infection, whether mutant infection is associated with poorer clinical outcomes is less clear. The differing definitions of sulfa prophylaxis and the different mortality endpoints used in these studies may be one explanation for the conflicting study results. Applying different definitions of prophylaxis, mortality endpoints and DHPS mutant to 301 HIV-infected patients with Pneumocystis pneumonia, we demonstrate that prophylaxis, irrespective of definition, increased the risk of infection with pure mutant (any prophylaxis: AOR 4.00, 95% CI: 1.83-8.76, P < 0.001) but not mixed genotypes (any prophylaxis: AOR 0.78, 95% CI: 0.26-2.36, P = 0.65). However, infection with mutant DHPS, irrespective of definition, was not associated with increased mortality (all-cause or PCP death) at the three time-intervals examined (all P > 0.05). Future studies should standardize key variables associated with DHPS mutant infection as well as examine DHPS mutant subtypes (pure mutant vs. mixed infections) - perhaps even individual DHPS mutant genotypes - so that data can be pooled to better address this issue.
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Affiliation(s)
- Christina Yoon
- San Francisco General Hospital, Division of Pulmonary & Critical Care Medicine, University of California, San Francisco, California 94110, USA.
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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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Beser J, Dini L, Botero-Kleiven S, Krabbe M, Lindh J, Hagblom P. Absence of dihydropteroate synthase gene mutations inPneumocystis jiroveciiisolated from Swedish patients. Med Mycol 2012; 50:320-3. [DOI: 10.3109/13693786.2011.593051] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Matos O, Esteves F. Pneumocystis jirovecii multilocus gene sequencing: findings and implications. Future Microbiol 2010; 5:1257-67. [DOI: 10.2217/fmb.10.75] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Pneumocystis jirovecii pneumonia (PcP) remains a major cause of respiratory illness among immunocompromised patients, especially patients infected with HIV, but it has also been isolated from immunocompetent persons. This article discusses the application of multilocus genotyping analysis to the study of the genetic diversity of P. jirovecii and its epidemiological and clinical parameters, and the important concepts achieved to date with these approaches. The multilocus typing studies performed until now have shown that there is an important genetic diversity of stable and ubiquitous P. jirovecii genotypes; infection with P. jirovecii is not necessarily clonal, recombination between some P. jirovecii multilocus genotypes has been suggested. P. jirovecii-specific multilocus genotypes can be associated with severity of PcP. Patients infected with P. jirovecii, regardless of the form of infection they present with, are part of a common human reservoir for future infections. The CYB, DHFR, DHPS, mtLSU rRNA, SOD and the ITS loci are suitable genetic targets to be used in further epidemiological studies focused on the identification and characterization of P. jirovecii haplotypes correlated with drug resistance and PcP outcome.
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Affiliation(s)
| | - Francisco Esteves
- Unidade de Protozoários Oportunistas/VIH e Outras Protozooses, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
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Costa MC, Gaspar J, Mansinho K, Esteves F, Antunes F, Matos O. Detection of Pneumocystis jirovecii dihydropteroate synthase polymorphisms in patients with Pneumocystis pneumonia. ACTA ACUST UNITED AC 2009; 37:766-71. [PMID: 16191898 DOI: 10.1080/00365540510038505] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In the present study, in order to improve the detection of Pneumocystis jirovecii dihydropteroate synthase (DHPS) mutations in pulmonary specimens of HIV-infected patients with P. jirovecii pneumonia, we evaluated a microfiltration procedure for the removal of human cell contamination and a nested-PCR method, for amplification in specimens with low parasite load. In the studied population, PCR amplification of the DHPS gene was more successful in unfiltered than in filtered specimens, with both touchdown-PCR and nested-PCR procedures (p<0.05 and p<0.001, respectively), but the amount of host DNA in the samples analysed seems to be inversely related with the successful PCR parasite detection. Amplification of P. jirovecii DHPS gene with nested-PCR was achieved in 77.5% of the specimens studied, demonstrating that this is a useful method for the identification of mutations in pulmonary specimens, including samples with low parasite loads, and will facilitate the evaluation of the relationship between the P. jirovecii DHPS polymorphisms and clinical resistance to sulfa drugs.
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Affiliation(s)
- M C Costa
- Unidade de Protozoários Oportunistas/VIH e outras Protozooses, Unidade de Parasitologia e Microbiologia Médicas (UPMM), Instituto de Higiene e Medicina Tropical, Lisboa, Portugal
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Clinical significance and phylogenetic relationship of novel Australian Pneumocystis jirovecii genotypes. J Clin Microbiol 2009; 47:1818-23. [PMID: 19369437 DOI: 10.1128/jcm.02102-08] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Pneumocystis jirovecii is an important opportunistic pathogen in immunocompromised patients. Molecular typing is employed to study this pathogen, as no culture system exists. No Australian P. jirovecii strains have been previously studied. Direct sequencing, targeting the internal transcribed spacer (ITS) regions of the nuclear rRNA operon, the mitochondrial large-subunit rRNA (mt LSU rRNA), and the dihydropteroate synthase (DHPS) gene, was performed on 68 Australian samples, collected between 2001 and 2007. Seven novel Australian ITS haplotypes (a composite of the ITS1 and ITS2 regions) were identified (SYD1m, SYD1g, Isyd2, Esyd3, Osyd4, Ag, and Hc). A dendrogram of published ITS haplotypes revealed that of the seven novel haplotypes, three (SYD1m, SYD1g, and Osyd4) are closely related to the haplotype Eg. Applying statistical parsimony, an Australian haplotype network was constructed which identified Eg as the ancestral haplotype, with two unresolved loops encountered. This suggests that the ITS lacks the resolution required for evolutionary analysis. Only two mt LSU rRNA genotypes were detected, with genotype 1 predominating. Mutant DHPS genotypes were present in 13% (8/60) of the samples. The novel haplotype Isyd2 was associated with less severe disease than the other Australian haplotypes. In contrast, patients with mutant DHPS genotypes were more likely to have severe disease, require invasive ventilation, and have a poor outcome than patients with wild-type DHPS genotypes. In conclusion, genetic clinical correlates continue to be found for Pneumocystis pneumonia; however, they remain controversial and warrant further study.
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Alvarez-Martínez MJ, Moreno A, Miró JM, Valls ME, Rivas PV, de Lazzari E, Sued O, Benito N, Domingo P, Ribera E, Santín M, Sirera G, Segura F, Vidal F, Rodríguez F, Riera M, Cordero ME, Arribas JR, Jiménez de Anta MT, Gatell JM, Wilson PE, Meshnick SR. Pneumocystis jirovecii pneumonia in Spanish HIV-infected patients in the combined antiretroviral therapy era: prevalence of dihydropteroate synthase mutations and prognostic factors of mortality. Diagn Microbiol Infect Dis 2008; 62:34-43. [PMID: 18554841 DOI: 10.1016/j.diagmicrobio.2008.04.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Revised: 03/14/2008] [Accepted: 04/16/2008] [Indexed: 02/08/2023]
Abstract
The incidence of Pneumocystis jirovecii pneumonia (PCP) in HIV-infected patients has decreased thanks to sulfa prophylaxis and combined antiretroviral therapy. The influence of P. jirovecii dihydropteroate synthase (DHPS) gene mutations on survival is controversial and has not been reported in Spain. This prospective multicenter study enrolled 207 HIV-infected patients with PCP from 2000 to 2004. Molecular genotyping was performed on stored specimens. Risk factors for intensive care unit (ICU) admission and mortality were identified using a logistic regression model. Seven patients (3.7%; 95% confidence interval [CI], 1.5-7.5%) had DHPS mutations. Overall mortality was 15% (95% CI, 10-21%), rising to 80% (95% CI, 61-92%) in patients requiring mechanical ventilation. None of the patients with DHPS mutants died, nor did they need ICU admission or mechanical ventilation. PaO(2) <60 mm Hg at admission was a predictor of ICU admission (P = 0.01), and previous antiretroviral therapy predicted non-ICU admission (P = 0.009). PaO(2) <60 mm Hg at admission and ICU admission during the 1st week were predictors of mortality (P = 0.03 and P < 0.001, respectively). The prevalence of DHPS mutants in Spain is low and is not associated with a worse outcome. Severe respiratory failure at admission is the strongest predictor of PCP outcome.
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Esteves F, Montes-Cano M, Horra CDL, Costa M, Calderón E, Antunes F, Matos O. Pneumocystis jirovecii multilocus genotyping profiles in patients from Portugal and Spain. Clin Microbiol Infect 2008; 14:356-62. [DOI: 10.1111/j.1469-0691.2007.01944.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Costa MC, Esteves F, Antunes F, Matos O. Multilocus genotyping of Pneumocystis jirovecii in immunocompromised patients: preliminary results. J Eukaryot Microbiol 2007; 53 Suppl 1:S104-5. [PMID: 17169017 DOI: 10.1111/j.1550-7408.2006.00190.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Marina C Costa
- Instituto de Higiene e Medicina Tropical, Unidade de Protozoários Oportunistas/VIH e outras Protozooses, Unidade de Parasitologia e Microbiologia Médicas, 1349-008 Lisboa, Portugal
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Huang L, Welsh DA, Miller RF, Beard CB, Lawrence GG, Fox M, Swartzman A, Bensley MR, Carbonnet D, Davis JL, Chi A, Yoo BJ, Jones JL. Pneumocystis jirovecii dihydropteroate synthase gene mutations and human immunodeficiency virus-associated Pneumocystis pneumonia. J Eukaryot Microbiol 2007; 53 Suppl 1:S114-6. [PMID: 17169022 DOI: 10.1111/j.1550-7408.2006.00195.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Laurence Huang
- HIV/AIDS Division, Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California 94110, USA.
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Valerio A, Tronconi E, Mazza F, Fantoni G, Atzori C, Tartarone F, Duca P, Cargnel A. Genotyping of Pneumocystis jiroveci pneumonia in Italian AIDS patients. Clinical outcome is influenced by dihydropteroate synthase and not by internal transcribed spacer genotype. J Acquir Immune Defic Syndr 2007; 45:521-8. [PMID: 17558331 DOI: 10.1097/qai.0b013e3180decbe2] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Two Pneumocystis jiroveci independent genomic regions, internal transcribed spacer (ITS) 1 and ITS2, and dihydropteroate synthase (DHPS) gene have been used for typing a cohort of HIV-infected Italian patients with P jiroveci pneumonia (PcP). METHODS Bronchoalveolar lavage samples isolated from 207 HIV-infected adults were ITS and DHPS genotyped by DNA sequencing and by restriction fragment length polymorphism analysis, respectively. Mutant DHPS samples were cloned and ITS typed. Data on severity, treatment, and outcome of PcP were obtained by chart review. RESULTS High diversity with 46 different ITS genotypes was observed. At the DHPS locus, 9.1% of samples analyzed were found to be mutated. A correlation was observed between DHPS mutants and greater severity of PcP, as defined by higher lactate dehydrogenase (P = 0.015) and need for intubation (P = 0.002), and worse outcomes, as defined by failure of sulfa treatment (P = 0.04), death, and/or relapse of PcP (P = 0.008). There was a significant difference in ITS genotype patterns between DHPS wild-type and mutants (P = 0.028). CONCLUSIONS The present data suggest the absence of a correlation between P jiroveci ITS types and specific clinical characteristics. DHPS mutations correlate with possible failure of anti-P jiroveci sulfa therapy, and a trend of association is shown between DHPS mutations and some clinical PcP features.
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Affiliation(s)
- Antonella Valerio
- II Department of Infectious Diseases, Luigi Sacco Hospital, Milan, Italy
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Huang L, Crothers K, Atzori C, Benfield T, Miller R, Rabodonirina M, Helweg-Larsen J. Dihydropteroate synthase gene mutations in Pneumocystis and sulfa resistance. Emerg Infect Dis 2004; 10:1721-8. [PMID: 15504256 PMCID: PMC3323267 DOI: 10.3201/eid1010.030994] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
We review studies of dihydropteroate synthase gene mutations in Pneumocystis jirovecii and summarize the evidence for resistance to sulfamethoxazole and dapsone. Pneumocystis pneumonia (PCP) remains a major cause of illness and death in HIV-infected persons. Sulfa drugs, trimethoprim-sulfamethoxazole (TMP-SMX) and dapsone are mainstays of PCP treatment and prophylaxis. While prophylaxis has reduced the incidence of PCP, its use has raised concerns about development of resistant organisms. The inability to culture human Pneumocystis, Pneumocystis jirovecii, in a standardized culture system prevents routine susceptibility testing and detection of drug resistance. In other microorganisms, sulfa drug resistance has resulted from specific point mutations in the dihydropteroate synthase (DHPS) gene. Similar mutations have been observed in P. jirovecii. Studies have consistently demonstrated a significant association between the use of sulfa drugs for PCP prophylaxis and DHPS gene mutations. Whether these mutations confer resistance to TMP-SMX or dapsone plus trimethoprim for PCP treatment remains unclear. We review studies of DHPS mutations in P. jirovecii and summarize the evidence for resistance to sulfamethoxazole and dapsone.
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Stein CR, Poole C, Kazanjian P, Meshnick SR. Sulfa use, dihydropteroate synthase mutations, and Pneumocystis jirovecii pneumonia. Emerg Infect Dis 2004; 10:1760-5. [PMID: 15504261 PMCID: PMC3323254 DOI: 10.3201/eid1010.040362] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Meta-analysis shows increased risk for DHPS mutations in patients exposed to sulfa prophylaxis for PCP, but clinical relevance of mutations is not known. A systematic review was conducted to examine the associations in Pneumocystis jirovecii pneumonia (PCP) patients between dihydropteroate synthase (DHPS) mutations and sulfa or sulfone (sulfa) prophylaxis and between DHPS mutations and sulfa treatment outcome. Selection criteria included study populations composed entirely of PCP patients and mutation or treatment outcome results for all patients, regardless of exposure status. Based on 13 studies, the risk of developing DHPS mutations is higher for PCP patients receiving sulfa prophylaxis than for PCP patients not receiving sulfa prophylaxis (p < 0.001). Results are too heterogeneous (p < 0.001) to warrant a single summary effect estimate. Estimated effects are weaker after 1996 and stronger in studies that included multiple isolates per patient. Five studies examined treatment outcome. The effect of DHPS mutations on treatment outcome has not been well studied, and the few studies that have been conducted are inconsistent even as to the presence or absence of an association.
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Affiliation(s)
- Cheryl R Stein
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, North Carolina 27599-7435, USA.
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Matos O, Lee CH, Jin S, Li B, Costa MC, Gonçalves L, Antunes F. Pneumocystis jiroveci in Portuguese immunocompromised patients: association of specific ITS genotypes with treatment failure, bad clinical outcome and childhood. INFECTION GENETICS AND EVOLUTION 2003; 3:281-5. [PMID: 14636689 DOI: 10.1016/s1567-1348(03)00092-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We analyzed the genetic variation among isolates of Pneumocystis jiroveci from Portuguese immunocompromised patients with PCP at the internal transcribed spacer (ITS) regions of the nuclear rRNA operon and at the dihydropteroate synthase (DHPS) gene. Pulmonary secretions from 42 patients with PCP corresponding to 43 episodes were studied. Demographic, immunological, and clinical data were obtained from all patients. By combining the two regions ITS1 and ITS2, we found 17 different ITS types of P. jiroveci, two of them were new types (Pb and Pe). The four most prevalent ITS types were Eg (23.3%), Eb and Ne (11.6% each), and Bi (9.3%). A single type was detected in 95.3% of the samples and 4.7% had mixed infections with three different ITS types. DHPS mutants were present in 17 (46%), and the wildtype was present in 20 (54%) of 37 isolates. No association was found between ITS and DHPS types and between DHPS types and therapy or response to anti-PCP treatment. Type Ne presented an association with negative response to anti-PCP treatment (P<0.001) and with death before 120 days after PCP diagnosis (P=0.025). Type Eb was significantly more common in children than in adults (P=0.001). Our data suggest an association of specific ITS genotypes with treatment failure, bad clinical outcome and childhood.
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Affiliation(s)
- Olga Matos
- Instituto de Higiene e Medicina Tropical, Unidade de Protozoários Oportunistas/VIH e outras Protozooses, Unidade de Parasitologia e Microbiologia Médicas (UPMM), Rua da Junqueira 96, 1349-008, Lisboa, Portugal.
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