Genomic insights into the host specific adaptation of the Pneumocystis genus.

Affiliation

Cissé OH(#)(1), Ma L(#)(2), Dekker JP(3)(4), Khil PP(3)(4), Youn JH(4), Brenchley JM(5), Blair R(6), Pahar B(6), Chabé M(7), Van Rompay KKA(8), Keesler R(8), Sukura A(9), Hirsch V(10), Kutty G(11), Liu Y(11), Peng L(12), Chen J(12), Song J(13), Weissenbacher-Lang C(14), Xu J(13), Upham NS(15), Stajich JE(16), Cuomo CA(17), Cushion MT(18), Kovacs JA(19).
Author information:
(1)Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health
(NIH), Bethesda, MD, USA. [Email]
(2)Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health
(NIH), Bethesda, MD, USA. [Email]
(3)Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy and Infectious Diseases
(NIAID), NIH, Bethesda, MD, USA.
(4)Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA.
(5)Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD, USA.
(6)Tulane National Primate Research Center, Tulane University, New Orleans, LA, USA.
(7)Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France.
(8)California National Primate Research Center, University of California, Davis, CA, USA.
(9)Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
(10)Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD, USA.
(11)Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health
(NIH), Bethesda, MD, USA.
(12)Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
(13)Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, University of Michigan Medical School, Ann Arbor, MI, USA.
(14)Institute of Pathology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria.
(15)Arizona State University, School of Life Sciences, Tempe, ARI, USA.
(16)Department of Microbiology and Plant Pathology and Institute for Integrative Genome Biology, University of California, Riverside, Riverside-California, Riverside, CA, USA.
(17)Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA.
(18)Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH, USA.
(19)Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health
(NIH), Bethesda, MD, USA. [Email]
(#)Contributed equally

Abstract

Pneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely related to macaque Pneumocystis. Little is known about other Pneumocystis species in distantly related mammals, none of which are capable of establishing infection in humans. The molecular basis of host specificity in Pneumocystis remains unknown as experiments are limited due to an inability to culture any species in vitro. To explore Pneumocystis evolutionary adaptations, we have sequenced the genomes of species infecting macaques, rabbits, dogs and rats and compared them to available genomes of species infecting humans, mice and rats. Complete whole genome sequence data enables analysis and robust phylogeny, identification of important genetic features of the host adaptation, and estimation of speciation timing relative to the rise of their mammalian hosts. Our data reveals insights into the evolution of P. jirovecii, the sole member of the genus able to infect humans.