ABSTRACTPneumocystis jiroveciiis a fungus that causes severe pneumonia in immunocompromised patients. However, its study is hindered by the lack of anin vitroculture method. We report here the genome ofP. jiroveciithat was obtained from a single bronchoalveolar lavage fluid specimen from a patient. The major challenge was thein silicosorting 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 thatP. jiroveciiis 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.IMPORTANCEPneumocystispneumonia is a major cause of mortality in patients with impaired immune systems. The availability of theP. jiroveciigenome 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 culturein 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.
De Novo Assembly of the Pneumocystis jirovecii Genome from a Single Bronchoalveolar Lavage Fluid Specimen from a Patient