A Molecular Window into the Biology and Epidemiology of Pneumocystis spp

Abstract

, a unique atypical fungus with an elusive lifestyle, has had an important medical history. It came to prominence as an opportunistic pathogen that not only can cause life-threatening pneumonia in patients with HIV infection and other immunodeficiencies but also can colonize the lungs of healthy individuals from a very early age. The genus includes a group of closely related but heterogeneous organisms that have a worldwide distribution, have been detected in multiple mammalian species, are highly host species specific, inhabit the lungs almost exclusively, and have never convincingly been cultured, making a fascinating but difficult-to-study organism. Improved molecular biologic methodologies have opened a new window into the biology and epidemiology of. Advances include an improved taxonomic classification, identification of an extremely reduced genome and concomitant inability to metabolize and grow independent of the host lungs, insights into its transmission mode, recognition of its widespread colonization in both immunocompetent and immunodeficient hosts, and utilization of strain variation to study drug resistance, epidemiology, and outbreaks of infection among transplant patients. This review summarizes these advances and also identifies some major questions and challenges that need to be addressed to better understand biology and its relevance to clinical care.

Genotyping of Pneumocystis jirovecii by Use of a New Simplified Nomenclature System Based on the Internal Transcribed Spacer Regions and 5.8S rRNA Gene of the rRNA Operon

“…The high A ϩ T content is accompanied by the presence of many poly(T) and poly(A) tracts, including at least 19 poly(T) tracts and 14 poly(A) tracts in both the ITS1 and ITS2 regions, when regions containing 3 or more T's or A's are counted. These homopolymeric tracts are often highly variable and difficult to sequence accurately by traditional Sanger sequencing, which presents a disadvantage of the ITS1-and ITS2-based typing systems (7). Circumventing such a disadvantage usually requires subcloning of the PCR products into plasmid vectors before sequencing, as described in this study and numerous previous reports (9,14,17).…”

“…widespread use has brought about a number of issues, including inconsistent genotype nomenclatures, difficult data exchangeability between different laboratories (8-12, 16, 19, 29), and uncertain interpretation of the length variation in multiple homopolymeric tracts (7,17). These issues motivated us to refine and improve these typing systems.…”

“…A clear understanding of the epidemiology of P. jirovecii infection and colonization has been difficult largely due to a lack of a reliable in vitro culture system to isolate and propagate this organism from clinical specimens. To overcome this difficulty, a variety of molecular typing methods have been developed, as recently comprehensively reviewed (7). Among the most widely used typing methods is sequence analysis of the internal transcribed spacer 1 (ITS1) and ITS2 regions of the P. jirovecii nuclear rRNA operon.…”

“…In addition, all current nomenclature systems for ITS1 and ITS2 genotypes are complicated by the variation in the length of multiple homopolymers, including poly(T) and poly(A) tracts. It remains unclear whether this variation represents in vivo variation or artifacts during PCR and sequencing (7,17). All these drawbacks call for a refinement of the ITS1-and ITS2-based typing systems.…”

Molecular detection ofPneumocystisin the lungs of cats

“…The Pneumocystis genomes sequenced to date have all demonstrated a contracted genome compared to those of other closely related fungi, revealing adaptative mechanisms to live exclusively in mammalian hosts, very similar to a parasite/host relationship. 6,7 This group of fungi does, however, have the potential to behave as an opportunistic pathogen in certain settings, such as severe malnutrition (e.g., in child refugees after the Second World War), immunosuppressive drug therapy (e.g., after solid organ transplantation) or inherited or acquired immunodeficiency states (including AIDS due to long-standing human immunodeficiency virus (HIV) infection). 3,8 Generally, Pneumocystis species show great host selectivity, such that every mammalian group studied has only one or two specific Pneumocystis species with which it is strongly associated.…”