Genetic diversity of Pneumocystis carinii derived from infected rats, mice, ferrets, and cell cultures

A Molecular Window into the Biology and Epidemiology of Pneumocystis spp

Pneumocystis, 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 Pneumocystis 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 in vitro, making Pneumocystis a fascinating but difficult-to-study organism. Improved molecular biologic methodologies have opened a new window into the biology and epidemiology of Pneumocystis. 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 Pneumocystis biology and its relevance to clinical care.

Biology and Diseases of Mice

Today’s laboratory mouse, Mus musculus, has its origins as the ‘house mouse’ of North America and Europe. Beginning with mice bred by mouse fanciers, laboratory stocks (outbred) derived from M. musculus musculus from eastern Europe and M. m. domesticus from western Europe were developed into inbred strains. Since the mid-1980s, additional strains have been developed from Asian mice (M. m. castaneus from Thailand and M. m. molossinus from Japan) and from M. spretus which originated from the western Mediterranean region.

[Pneumocystis: epidemiology and molecular approaches]

Pneumocystosis is a common opportunistic infection in immunocompromised patients, especially in AIDS patients. The diagnosis of this pneumonia has presented several difficulties due to the low sensitivity of conventional staining methods and the absence of culture system for Pneumocystis. The molecular biology techniques, especially the PCR, have improved the detection of DNA of this fungus in invasive and noninvasive samples, and in the environment which highlighted human transmission and the existence of environmental source of Pneumocystis. In addition, various molecular biology techniques were used for typing of Pneumocystis strains, especially P. jirovecii, which is characterized by a significant genetic biodiversity. Finally, the widespread use of cotrimoxazole for the treatment and prophylaxis of pneumocystosis has raised questions about possible resistance to sulfa drugs in P. jirovecii.

Phylogenetic identification of Pneumocystis murina sp. nov., a new species in laboratory mice

Pneumocystisis a fungal genus that contains multiple species. One member of the genus that has not been formally analysed for its phylogenetic relationships and possible species status is thePneumocystisfound in laboratory mice,Pneumocystis murinasp. nov. (type strain ATCC PRA-111T=CBS 114898T), formerly known asPneumocystis cariniif. sp.muris. To advance research in this area, approximately 3000 bp of additional DNA sequence were obtained from the locus encoding rRNAs. This sequence and others were used to determine genetic distances betweenP. murinaand other members of the genus. These distances indicated thatP. murinaDNA is most similar to that of the species ofPneumocystisfound in laboratory rats. Nevertheless,P. murinais at least as diverged from these otherPneumocystisspecies as species in other fungal genera are from each other. The 18S rRNA gene sequence divergence exhibited byP. murinacould not be ascribed to accelerated evolution of this gene as similar levels of divergence were observed at seven other loci. When five genes were used to construct phylogenetic trees for fivePneumocystistaxa, includingP. murina, all the trees had the same topology, indicating that genes do not flow among these taxa. The gene trees were all strongly supported by statistical tests. When sequences from the rRNA-encoding locus were used to estimate the time of divergence ofP. murina, the results indicated thatP. murinais as old as the mouse. Taken together, these data support previous recognition of multiple species in the genus and indicate thatP. murinais a phylogenetic species as well.

Fungal diseases of ferrets

Although fungal disease in ferrets is uncommon, a few cases have been documented, demonstrating that it should be on the clinician's rule out list, especially if the patient has a long-term illness that is not responding appropriately to antibiotics, as was the clinical presentation in many of these documented cases.

Heterogeneity of Pneumocystis sterol profiles of samples from different sites in the same pair of lungs suggests coinfection by distinct organism populations

Sterol profiles of samples taken from different sites of a Pneumocystis-infected human lung showed large variations in pneumocysterol similar to those that occur among samples from different patients. Thus, the influence of diet or drugs on pneumocysterol accumulation was ruled out, suggesting distinct phenotypic populations as the basis for the heterogeneity.

Characterization of the gene encoding a histidine and aspartic acid-rich protein from Pneumocystis carinii

A cDNA clone derived from Pneumocystis carinii contained an unusual sequence (GTGATG)2(ATGGTG)4(ATG)4 and many GAT repeats. It was found to encode a histidine and aspartic acid-rich protein (HARP). The complete cDNA contained an 888-bp open reading frame encoding a putative protein of 32.6 kDa. The deduced HARP protein contained 39 aspartic acid and 22 histidine residues. The genomic copy of the HARP gene (1203 bp in length) was found to contain 3 small introns of 46, 44, and 38 bp, respectively. HARP was predicted by computer programs to be a plasma membrane protein with nickel-binding activity.

Genetic heterogeneity of Pneumocystis carinii from rats of several regions and strains

Pneumocystis carinii is a major opportunistic pathogen which has been found in the lungs of a wide variety of mammalian host species, and the fact suggests the possibility of intraspecific variation. Until now, P. carinii from different mammalian species are differentiated as subspecies, and the rats are known to be infected by two subspecies. The present study investigated genetic heterogeneity of P. carinii isolates from two strains of rats in Korea and China by molecular karyotyping, RFLP and sequencing analysis. Karyotypes of P. carinii were grouped into three, two from two strains of rats in Korea and one from rats in China. However RFLP of PCR product of ribosomal and MSG gene of the P. carinii isolates showed same pattern. The sequence homology rates of alpha-tubulin DNA of the P. carinii isolates were 96% in Seoul Wistar rats, 93% in Seoul Sprague-Dawley rats, and 85% in Chinese Sprague-Dawley rats. The present finding confirmed that P. carinii from rats in Korea are grouped into two karyotype strains which are different from that of P. carinii from rats in China. The Chinese isolate shows a little different sequences of alpha-tubulin DNA.

Genetic divergence at the SODA locus of six different formae speciales of Pneumocystis carinii

Genetic divergence at the SODA (manganese-dependent superoxide dismutase, MnSOD) locus were compared in six Pneumocystis carinii formae speciales isolated from mouse, rabbit, human, macaque and pig. A degenerate oligonucleotide primer strategy was designed to amplify 85-90% of the full-length SODA gene from P. carinii genomic DNA isolates. DNA sequence analysis revealed an A/T bias in the nucleotide composition (71-77.2%) and the presence of seven small introns (41-142 bp), interrupting each P. carinii open reading frame (ORF) at the same position. The MnSOD deduced amino acid sequences from all P. carinii isolates shared residues which were conserved within the MnSOD family and which are required for enzymatic activity and binding of the cofactor metal. Phylogenetic analysis including MnSOD sequences from representatives of the fungal phyla Basidiomycota and Ascomycota indicated that the P. carinii formae speciales form a monophyletic group that is related to the budding yeasts (subphylum Saccharomycotina, previously called class Hemiascomycetes) in the Ascomycota. In the whole Pneumocystis group, P. carinii f. sp. hominis, P. carinii f. sp. macacae and P. carinii f. sp. oryctolagi MnSOD sequences clustered together, as did the rat-derived P. carinii and P. carinii f. sp. muris sequences.

Ferret respiratory diseases

Ferret behavior often brings them into close contact with potential respiratory pathogens and traumatic insults. Although respiratory disease accounts for a small percentage of cases, they are usually dramatic. Acute and chronic conditions occur, and many lesions are confined to the upper or lower respiratory tree but may not involve both. Pathogens such as influenza A account for a large percentage of upper respiratory infections and often mirror the "flu" season of humans. Traumatic insults to the head and chest are relatively common and account for many veterinary visits. Numerous diseases affecting the upper and lower respiratory systems are discussed, with suggestions for diagnostics and therapies.

C27 to C32 sterols found in Pneumocystis, an opportunistic pathogen of immunocompromised mammals

Pneumocystis carinii is the paradigm of opportunistic infections in immunocompromised mammals. Prior to the acquired immunodeficiency syndrome (AIDS) pandemic and the use of immunosuppressive therapy in organ transplant and cancer patients, P. carinii was regarded as a curiosity, rarely observed clinically. Interest in this organism exploded when it was identified as the agent of P. carinii pneumonia (PcP), the direct cause of death among many AIDS patients. Aggressive prophylaxis has decreased the number of acute PcP cases, but it remains among the most prevalent opportunistic infections found within this patient population. The taxonomic assignment of P. carinii has long been argued; molecular genetics data now demonstrate that it is a fungus. Several antimycotic drugs are targeted against ergosterol or its biosynthesis, but these are not as effective against PcP as they are against other fungal infections. This can now be explained in part by the identification of the sterols of P. carinii. The organism lacks ergosterol but contains distinct C28 and C29 delta7 24-alkylsterols. Also, 24-methylenelanost-8-en-3beta-ol (C31) and pneumocysterol, (24Z)-ethylidenelanost-8-en-3beta-ol (C32) were recently identified in organisms infecting humans. Together, the delta7 24-alkylsterols and pneumocysterol are regarded as signature lipids of the pathogen that can be useful for the diagnosis of PcP, since no other lung pathogen is known to contain them. Cholesterol (C27), the dominant sterol component in P. carinii, is probably totally scavenged from the host. De novo synthesis of sterols has been demonstrated by the presence of lovastatin-sensitive 3-hydroxy-3-methylglutaryl-CoA reductase activity, the incorporation of radiolabeled mevalonate and squalene into P. carinii sterols, and the reduction in cellular ATP in cells treated with inhibitors of enzymes in sterol biosynthesis.

Molecular characterization of KEX1, a kexin-like protease in mouse Pneumocystis carinii

Expression screening of a Pneumocystis carinii-infected mouse lung cDNA library with specific monoclonal antibodies (mAbs) led to the identification of a P. carinii cDNA with extensive homology to subtilisin-like proteases, particularly fungal kexins and mammalian prohormone convertases. The 3.1 kb cDNA contains a single open reading frame encoding 1011 amino acids. Structural similarities to fungal kexins in the deduced primary amino acid sequence include a putative proenzyme domain delineated by a consensus autocatalytic cleavage site (Arg-Glu-Lys-Arg), conserved Asp, His, Asn and Ser residues in the putative catalytic domain, a hydrophobic transmembrane spanning domain, and a carboxy-terminal cytoplasmic domain with a conserved tyrosine motif thought to be important for localization of the protease in the endoplasmic reticulum and/or Golgi apparatus. Based on these structural similarities and the classification of P. carinii as a fungus, the protease was named KEX1. Southern blotting of mouse P. carinii chromosomes localized kex1 to a single chromosome of approximately 610 kb. Southern blotting of restriction enzyme digests of genomic DNA from P. carinii-infected mouse lung demonstrated that kex1 is a single copy gene. The function of kexins in other fungi suggests that KEX1 may be involved in the post-translational processing and maturation of other P. carinii proteins.

Karyotypes of Pneumocystis carinii derived from several mammals

Pneumocystis carinii is the most important opportunistic pathogen of humans in the world. Pneumocystis carinii is experimentally detected in the lungs of rats, mice, rabbits, and monkeys, however, the organisms from different mammals are identical in microscopic morphology. The present study tried to find out more mammalian hosts of P. carinii and also to differentiate the organisms from different mammals by karyotyping. Rats, mice, hamsters, rabbits, cats, and dogs were successfully infected by P. carinii, but guinea pigs and pigs were not. Karyotype of P. carinii from rabbits showed similar size range of chromosomes with that of the prototype, but in different pattern. The patterns from cats and dogs were also different from that of rats. The present study confirms that cats and dogs are infected by P. carinii and at least total three karyotype strains of P. carinii are proven in Korea.

The genome of Pneumocystis carinii

The best understood special form of P. carinii, P. carinii formae specialis (f.sp.) carinii, appears to be haploid and contains about 8 million base pairs of DNA (8.5 fg) per nucleus. The genome of P. carinii f.sp. carinii is divided into 13-15 linear chromosomes that range from 300 to 700 kb in size. Eight different P. carinii f.sp. carinii karyotypes have been observed. The karyotypes of P. carinii f.sp. carinii differ due to slight variations in the lengths of chromosomes, but the 8 karyotype-forms of P. carinii f.sp. carinii exhibit very little variation in DNA sequence. By contrast, the genome of P. carinii f.sp. carinii differs markedly in sequence from the genomes of P. carinii from other hosts, such as mouse, ferret and human. In addition, chromosomes and DNA sequences from P. carinii from mouse, ferret, and human also differ greatly from each other. The genome of a ferret P. carinii appears to be up to 1.7 times larger than those of P. carinii from other hosts. Nearly two dozen P. carinii genes have been cloned and sequenced. The typical P. carinii gene sequence is 60-65% A+T. P. carinii genes usually contain introns, which are typically less than 50 bp in length, but can be as numerous as 9 per gene. A system for naming P. carinii genes is proposed in which each gene would be designated by an italic three-letter lower case symbol. The first allele (i.e. sequence) that is found would have a superscript 1, such as xyz1(1). Any subsequent alleles would be designated as xyz1(2), etc. A protein would have the same symbol as the gene that produced it, but written in roman print with the first letter an uppercase, such as Msg1. Some of the P. carinii genome is comprised of DNA sequences that are present dozens of times. Three families of such repeated DNA sequences have been described. Two of these families (MSG and PRT) encode proteins. The third family is the telomere repeat, which is found at the ends of each chromosome, and sometimes at internal chromosomal sites, in which case it has been called the alpha repeat. Determination of the complete sequence of the P. carinii genome is both practicable and of primary importance to the understanding of this organism. The small size of the P. carinii genome and its packaging into chromosomes that are resolvable by PFGE will facilitate sequence analysis.

Genetic heterogeneity in Pneumocystis carinii: an introduction

Molecular techniques have played an important role in demonstrating a high level of heterogeneity among the different types of organisms which are collectively known as Pneumocystis carinii. Genetic heterogeneity has been observed in Pneumocystis organisms isolated from different host species, suggesting that Pneumocystis infection is host-species specific. On the basis of this genetic divergence a provisional trinomial nomenclature has been adopted, in which different types of Pneumocystis organisms are designated a 'special form'. Multiple special forms of Pneumocystis have been detected in some host species, for example in infected rat and ferret lungs, but not in human lungs. Lower levels of genetic heterogeneity have been observed within each Pneumocystis special form, and in particular in human-derived Pneumocystis. Analysis of the genetic heterogeneity of populations of Pneumocystis is contributing to the understanding of the epidemiology and pathophysiology of this infection.

Typing methods to approach Pneumocystis carinii genetic heterogeneity

The study of the genetic heterogeneity of P. carinii is complicated by the lack of an in vitro culture system, as well as by the likely occurrence of co-infections with several special forms or types in a single host. Karyotyping and multilocus enzyme electrophoresis are useful for studies at the evolutionary level. However, these methods require a large number of cells, which prevents their use for the special form infecting humans. DNA sequence analysis of genomic regions is useful to study P. carinii diversity, both at the evolutionary and epidemiological levels. To type the special form specific to humans, several methods are currently used to detect polymorphism in PCR products of polymorphic regions of the genome: DNA sequencing, type-specific hybridisations, and single-strand conformation polymorphism. All these methods still need evaluation. The frequency of potential co-infections in humans determined by these various methods is different. The differences could be due to methodological problems or to real variations between patient populations, geographical locations and/or prophylaxis regimens. In the future, elucidating the population structure of P. carinii and the frequency of potential co-infections is going to be crucial for a better understanding of its epidemiology, and thus for a better prevention of P. carinii pneumonia in humans.

Natural pathogens of laboratory mice, rats, and rabbits and their effects on research

Laboratory mice, rats, and rabbits may harbor a variety of viral, bacterial, parasitic, and fungal agents. Frequently, these organisms cause no overt signs of disease. However, many of the natural pathogens of these laboratory animals may alter host physiology, rendering the host unsuitable for many experimental uses. While the number and prevalence of these pathogens have declined considerably, many still turn up in laboratory animals and represent unwanted variables in research. Investigators using mice, rats, and rabbits in biomedical experimentation should be aware of the profound effects that many of these agents can have on research.

Pneumocystis carinii: what is it, exactly?

The identity of Pneumocystis carinii has been uncertain for many years. Until recently, it was widely regarded to be a protozoan because it does not grow in culture and is not susceptible to antifungal drugs. Although these and a number of other phenotypic characteristics of P. carinii differ from those of typical fungi, analysis of DNA sequences has shown that P. carinii is a member of the fungal lineage of eukaryotes. However, a close phylogenetic relative of P. carinii has not yet been found. Analysis of gene sequences has also revealed that P. carinii is not a single entity but that the genus Pneumocystis contains a complex group of organisms. P. carinii organisms from one host species do not grow when introduced into another host species, and P. carinii isolates from different host species are more genetically divergent from one another than might be expected for members of the same species. Genetic variation of a lesser degree also occurs among P. carinii organisms from the same host species, suggesting that it may be possible to identify strains and to conduct transmission and epidemiological studies. Results of early studies exploiting genetic variation among P. carinii isolates from patients have suggested that recurrent P. carinii pneumonia may not always be caused by reactivation of latent organisms, as is commonly believed. However, other features of P. carinii suggest that this microbe has established a long-term relationship with its host. A striking new development in this regard is the discovery of a genetic system that is designed to allow variation in the structure of a major antigen on the surface of P. carinii.

Pneumocystis carinii: an atypical fungal micro-organism

The purpose of this review is to assist mycologists in having a better understanding of Pneumocystis carinii and the disease that it causes. Now considered to be a fungus, P. carinii is unusual in its life cycle and relationship with the host. P. carinii pneumonia (PCP) pathogenesis, immunology and host defence mechanisms are examined, as well as epidemiological and control strategies. Most pneumocystosis pathophysiological changes result from the parasite's attachment and proliferation in the lungs, resulting in a filling of the alveoli with masses of the micro-organism. Pathological changes include an increase in alveolar capillary membrane permeability and injury to the alveolar epithelium, which may be mediated by the release of degradative enzymes from the pathogen. A host response takes place by hypertrophy, and hyperplasia involving type II epithelial alveolar cells. P carinii interacts with pulmonary surfactants by binding to the hydrophilic proteins A and D, and by modifying their phospholipid composition. Alveolar macrophages and CD4+ T cells play a key role in the host's defence against Pneumocystis. The epidemiology of PCP remains poorly understood. Airborne transmission has been established, but the actual infective form and its source remains unknown. Studies concerning P. carinii genetic diversity have shown that the parasite polymorphism is related, at least partially, to the host species. A strong host-species specificity in P. carinii has been found. From an epidemiological perspective, there appears to be no animal reservoir for the agent of human PCP. Thus, this disease should not be considered to be zoonotic. Although a significant decrease in the incidence of pneumocystosis has been obtained when employing chemoprophylaxis, anti-P. carinii drugs are not completely successful, often inducing deleterious side-effects. For these reasons, new prophylactic and therapeutic strategies need to be developed. One approach could be based on the anti-P. carinii effect of yeast killer toxins and antibiotic anti-idiotypic antibodies.

Analysis of genetic diversity at the arom locus in isolates of Pneumocystis carinii

The DNA sequences of a portion of the 5-enolpyruvyl shikimate phosphate synthase domain of the arom gene, encoding the pentafunctional AROM protein, were determined from isolates of Pneumocystis carinii from five mammalian host species (rat, human, ferret, rabbit and mouse). High levels of genetic divergence were found among P. carinii derived from different host species, 7-22% at the DNA sequence level, and 7-26% at the derived amino acid sequence level. Two separate and distinct sequences were isolated from infected ferret lungs. Low levels of divergence were seen in human-derived organisms.

Typing of Pneumocystis carinii strains that infect humans based on nucleotide sequence variations of internal transcribed spacers of rRNA genes

Small portions of the 18S and the 26S rRNA genes, the entire 5.8S rRNA gene, and internal transcribed spacers ITS1 and ITS2 (located between the 18S and 5.8S rRNA genes and between the 5.8S and 26S rRNA genes, respectively) of Pneumocystis carinii that infect humans were cloned and sequenced. The nucleotide sequences of the 18S, 5.8S, and 26S rRNA genes determined in the study were approximately 90% homologous to those of P. carinii that infect rats, while the sequences of ITS1 and ITS2 of P. carinii from the two different hosts were only 60% homologous. The 18S, 5.8S, and 26S rRNA gene sequences of P. carinii from 15 patient specimens were determined and were found to be identical to each other, whereas the ITS sequences were found to be variable. With the observed sequence variation, it was possible to classify the ITS1 sequences into two types and the ITS2 sequences into three types. P. carinii strains that had the same type of ITS1 sequence could have a different type of ITS2 sequence. On the basis of the sequence types of the two ITS regions, P. carinii from the 15 patients were classified into four groups. P. carinii from three patient specimens were found to contain two different ITS sequence patterns. More surprisingly, one additional specimen was found to have one ITS sequence typical of P. carinii isolates that infect humans and another typical of P. carinii isolates that infect rats. The studies indicate that it is possible to type P. carinii strains on the basis from one patient, suggesting that coinfection with more than one strain of P. carinii may occur in the same patient.