<italic toggle="yes">De Novo</italic> Assembly of the <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> Genome from a Single Bronchoalveolar Lavage Fluid Specimen from a Patient

ABSTRACT Pneumocystis jirovecii is a fungus that causes severe pneumonia in immunocompromised patients. However, its study is hindered by the lack of an in vitro culture method. We report here the genome of P. jirovecii that was obtained from a single bronchoalveolar lavage fluid specimen from a pat...

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Autores principales:	Ousmane H. Cissé, Marco Pagni, Philippe M. Hauser
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2013
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/3366b893d53a4bb2b8ef633ad79cc2a9
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spelling	oai:doaj.org-article:3366b893d53a4bb2b8ef633ad79cc2a92021-11-15T15:40:24Z<italic toggle="yes">De Novo</italic> Assembly of the <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> Genome from a Single Bronchoalveolar Lavage Fluid Specimen from a Patient10.1128/mBio.00428-122150-7511https://doaj.org/article/3366b893d53a4bb2b8ef633ad79cc2a92013-03-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00428-12https://doaj.org/toc/2150-7511ABSTRACT Pneumocystis jirovecii is a fungus that causes severe pneumonia in immunocompromised patients. However, its study is hindered by the lack of an in vitro culture method. We report here the genome of P. jirovecii that was obtained from a single bronchoalveolar lavage fluid specimen from a patient. The major challenge was the in silico sorting of the reads from a mixture representing the different organisms of the lung microbiome. This genome lacks virulence factors and most amino acid biosynthesis enzymes and presents reduced GC content and size. Together with epidemiological observations, these features suggest that P. jirovecii is an obligate parasite specialized in the colonization of human lungs, which causes disease only in immune-deficient individuals. This genome sequence will boost research on this deadly pathogen. IMPORTANCE Pneumocystis pneumonia is a major cause of mortality in patients with impaired immune systems. The availability of the P. jirovecii genome sequence allows new analyses to be performed which open avenues to solve critical issues for this deadly human disease. The most important ones are (i) identification of nutritional supplements for development of culture in vitro, which is still lacking 100 years after discovery of the pathogen; (ii) identification of new targets for development of new drugs, given the paucity of present treatments and emerging resistance; and (iii) identification of targets for development of vaccines.Ousmane H. CisséMarco PagniPhilippe M. HauserAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 4, Iss 1 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Ousmane H. Cissé Marco Pagni Philippe M. Hauser <italic toggle="yes">De Novo</italic> Assembly of the <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> Genome from a Single Bronchoalveolar Lavage Fluid Specimen from a Patient
description	ABSTRACT Pneumocystis jirovecii is a fungus that causes severe pneumonia in immunocompromised patients. However, its study is hindered by the lack of an in vitro culture method. We report here the genome of P. jirovecii that was obtained from a single bronchoalveolar lavage fluid specimen from a patient. The major challenge was the in silico sorting of the reads from a mixture representing the different organisms of the lung microbiome. This genome lacks virulence factors and most amino acid biosynthesis enzymes and presents reduced GC content and size. Together with epidemiological observations, these features suggest that P. jirovecii is an obligate parasite specialized in the colonization of human lungs, which causes disease only in immune-deficient individuals. This genome sequence will boost research on this deadly pathogen. IMPORTANCE Pneumocystis pneumonia is a major cause of mortality in patients with impaired immune systems. The availability of the P. jirovecii genome sequence allows new analyses to be performed which open avenues to solve critical issues for this deadly human disease. The most important ones are (i) identification of nutritional supplements for development of culture in vitro, which is still lacking 100 years after discovery of the pathogen; (ii) identification of new targets for development of new drugs, given the paucity of present treatments and emerging resistance; and (iii) identification of targets for development of vaccines.
format	article
author	Ousmane H. Cissé Marco Pagni Philippe M. Hauser
author_facet	Ousmane H. Cissé Marco Pagni Philippe M. Hauser
author_sort	Ousmane H. Cissé
title	<italic toggle="yes">De Novo</italic> Assembly of the <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> Genome from a Single Bronchoalveolar Lavage Fluid Specimen from a Patient
title_short	<italic toggle="yes">De Novo</italic> Assembly of the <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> Genome from a Single Bronchoalveolar Lavage Fluid Specimen from a Patient
title_full	<italic toggle="yes">De Novo</italic> Assembly of the <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> Genome from a Single Bronchoalveolar Lavage Fluid Specimen from a Patient
title_fullStr	<italic toggle="yes">De Novo</italic> Assembly of the <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> Genome from a Single Bronchoalveolar Lavage Fluid Specimen from a Patient
title_full_unstemmed	<italic toggle="yes">De Novo</italic> Assembly of the <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> Genome from a Single Bronchoalveolar Lavage Fluid Specimen from a Patient
title_sort	<italic toggle="yes">de novo</italic> assembly of the <named-content content-type="genus-species">pneumocystis jirovecii</named-content> genome from a single bronchoalveolar lavage fluid specimen from a patient
publisher	American Society for Microbiology
publishDate	2013
url	https://doaj.org/article/3366b893d53a4bb2b8ef633ad79cc2a9
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<italic toggle="yes">De Novo</italic> Assembly of the <named-content content-type="genus-species">Pneumocystis jirovecii</named-content> Genome from a Single Bronchoalveolar Lavage Fluid Specimen from a Patient

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