Delanoë and Delanoë thought that P. carinii could be a coccidian parasite, a concept surviving for about 80 years. However, there was always a degree of uncertainty, and the similarities to fungi was stressed by several investigators during that time (Vavra and Kucera 1970). The recognition of human pneumocystis as a separate species by Frenkel should be noted. He redescribed P. jiroveci n. spp. from humans, including the trophozoite precyst, cyst, intracystic bodies, and empty cyst and showed the forms from man to be distinct with respect to morphology, biology, and physiology compared with those of P. carinii from rats. He concluded that 'These two forms should be regarded as separate species, and forms from other hosts should tentatively be regarded as distinct.' (Frenkel 1976).
Today it is generally agreed that sufficient data is available to regard P. carinii as a fungus (Cushion et al. 1990; Eriksson 1994; Wakefield and Miller 1996), for example, in contrast to the situation in protozoa, the P. carinii genes for the enzymes thymidylate synthase (TS) and dihydrofolate-reductase (DHFR) encode separate proteins (Edman et al. 1989). On the basis of TS, DHFR, actin, and beta-tubulin gene sequences, P. carinii can be placed taxonomically near the ascomycetes and it has been classified as a member of a new family and order (Pneumocystidaceae, Pneumocystidales) in the class Archiascomycetes. Members of this class of saphrophytic and parasitic plant pathogens, for example, the causative agent of peach leaf curl disease and witch brooms, Taphrina, may represent the earliest diverging group of ascomycetes (Eriksson 1994; Miller and Wakefield 1996; Eriksson and Winka 1997). Recent data indicate that P. carinii represents a diverse group of organisms. Thus a revised trinomial nomenclature for P. carinii has been suggested based on the host of origin: P. carinii f. sp. hominis, f. sp. oryctolagi (rabbit), etc. (Bartlett et al. 1994).
Genetic diversity of especially two loci has been studied. These are the mitochondrial large sub-unit rRNA (mt LSU) and the internal transcribed spacer (ITS) of the ribosomal RNA genes (Lee et al. 1993; Latouche et al. 1994, 1996, 1997b; Lu et al. 1995; Jiang et al. 1996; Keely et al. 1996; Wakefield 1996; Wakefield et al. 1997). Organisms isolated from one mammalian host species do not cause infection in another mammalian host species; i.e. P. carinii in man is not a zoonosis. Host specificity of P. carinii has been suggested by unsuccessful transmission studies using several mammalian-derived isolates of P. carinii, including human P. carinii (Furuta and Katsamoto 1987; Gigliotti et al. 1993; Aliouat et al. 1994; Frenkel et al. 1996). Human-derived P. carinii is genetically distinct from parasites isolated from other species of mammalian hosts. Rats and humans can harbour distinct types of P. carinii that are sufficiently different to suggest that P. carinii from the two hosts could be different species
(Stringer 1993). Antigenic differences have been observed between P. carinii isolates from human isolates obtained from different areas of the world (Smulian et al. 1993), in different hosts from the same region (Bauer et al. 1993), and even between P. carinii organisms obtained from the same host. Genetic diversity between P. carinii isolates from different hosts is seen both at the chromosomal and at sequence levels. Genetic diversity has also been demonstrated in P. carinii isolates from the same host, but the extent of diversity is, as expected, lower than that between isolates from different species. Nucleotide sequence variations of P. carinii can be used for typing and studying the epidemiology of P. carinii infections (Lu et al. 1995; Miller and Wakefield 1996; Hauser et al. 1997). Two types of nucleotide sequences (designated types A and B) have been found in the internal transcribed spacer region 1 (ITS1), and three types of nucleotide sequences (designated types a, b, and c) have been found in the ITS2 region. Of the six possible combination types, four have been detected: types Ac, Bb, Ba, and Bc.
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