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This study is part of the project “Pneumocystis Pathogenomics: Unravelling the Colonization-to-Disease Shift,” a Coordination Action supported by the European Commission (ERANET PathoGenoMics). This study was partially supported by the Spanish Ministry of Health (FIS 03/1743). M.A.M.-C. and C.d.l.H. were supported by the Spanish Ministry of Health (FIS CP-04/217 and FIS CM-04/146).