Genomic Insights into the Fungal Pathogens of the Genus Pneumocystis: Obligate Biotrophs of Humans and Other Mammals

Pneumocystis organisms were first believed to be a single protozoan species able to colonize the lungs of all mammals. Subsequently, genetic analyses revealed their affiliation to the fungal Taphrinomycotina subphylum of the Ascomycota, a clade which encompasses plant pathogens and free-living yeasts. It also appeared that, despite their similar morphological appearance, these fungi constitute a family of relatively divergent species, each with a strict specificity for a unique mammalian species [1]. The species colonizing human lungs, Pneumocystis jirovecii, can turn into an opportunistic pathogen that causes Pneumocystis pneumonia (PCP) in immunocompromised individuals, a disease which may be fatal. Although the incidence of PCP diminished in the 1990s thanks to prophylaxis and antiretroviral therapy, PCP is nowadays the second-most-frequent, life-threatening, invasive fungal infection worldwide, with an estimated number of cases per year above 400,000 [2]. Despite this clinical importance, studies of P. jirovecii progressed slowly, at least in part because of the lack of a continuous culture system. Nevertheless, recent genomic findings provided insights into the lifestyle of these fungi.