Phylogenetic systematics and evolution of primate-derived Pneumocystis based on mitochondrial or nuclear DNA sequence comparison

Previous studies have demonstrated that the agent of Pneumocystis pneumonia (PcP), Pneumocystis carinii, is actually a complex of eukaryotic organisms, and cophylogeny could explain the distribution of the hosts and parasites. In the present work, we tested the hypothesis of cophylogeny between the primate-derived Pneumocystis group and their hosts. Specific strains isolated from 20 primate species, including humans, were used to produce a phylogeny of the parasites. Aligned sequences corresponding to DNA sequences of three genes (DHPS, mtSSU-rRNA, and mtLSU-rRNA) were separately analyzed and then combined in a single data set. The resulting parasite phylogeny was compared with different controversial phylogenies for the hosts. This comparison demonstrated that, depending upon which topology is accepted for the hosts, at least 61% and perhaps 77% of the homologous nodes of the respective cladograms of the hosts and parasites may be interpreted as resulting from codivergence events. This finding and the high specificity of these parasites suggests that cophylogeny may be considered the dominant pattern of evolution for Pneumocystis organisms, representing a new example of parallel evolution between primates and their specific parasites. Because the phylogeny of Pneumocystis followed very closely the differentiation of their hosts at the species level, the study of the parasites could provide valuable information on the phylogeny of their hosts. We used this information to explore controversial hypotheses of the phylogeny of the Platyrrhini by comparison with the phylogeny of their specific Pneumocystis parasites. If these organisms were closely associated as lung parasites with primates through the ages, the hypothesis of the Pneumocystis spp. being new pathogenic agents could be refuted. However, these organisms are opportunistic symbionts, becoming pathogenic whenever the immunological defences of their hosts decline. This study also provides support for the hypothesis that the different Pneumocystis species are genetically independent organisms, helping to clarify their taxonomic status.     

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.     

Parallel Phylogenies of Pneumocystis Species and their Mammalian Hosts

ABSTRACT. The single name Pneumocystis carinii consists of an heterogeneous group of specific fungal organisms that colonize a very wide range of mammalian hosts. In the present study, mitochondrial large subunit (mtLSU) and small subunit (mtSSU) rRNA sequences of P. carinii organisms from 24 different mammalian species were compared. The mammals were included in six major groups: Primates (12 species). Rodents (5 species). Carnivores (3 species). Bats (1 species), Lagomorphs (1 species), Marsupials (1 species) and Ungulates (1 species). Direct sequencing of PCR products demonstrated that specific mtSSU and mtLSU rRNA Pneumocystis sequence could be attributed to each mammalian species. No animal harbored P. carinii f. sp. hominis. Comparison of combined mtLSU and mtSSU aligned sequences confirmed cospeciation of P. carinii and corresponding mammalian hosts. P. carinii organisms isolated from mammals of the same zoological group systematically clustered together. Within each cluster, the genetic divergence between P. carinii organisms varied in terms of the phylogenetic divergence existing among the corresponding host species. However, the relative position of P. carinii groups (rodent, carnivore or primate-derived P. carinii) could not be clearly determined. Further resolution will require the integration of additional sequence data.     

Pneumocystis: from a doubtful unique entity to a group of highly diversified fungal species

At the end of the 20th century the unique taxonomically enigmatic entity called Pneumocystis carinii was identified as a heterogeneous group of microscopic Fungi, constituted of multiple stenoxenic biological entities largely spread across ecosystems, closely adapted to, and coevolving in parallel with, mammal species. The discoveries and reasoning that led to the current conceptions about the taxonomy of Pneumocystis at the species level are examined here. The present review also focuses on the biological, morphological and phylogenetical features of Pneumocystis jirovecii, Pneumocystis oryctolagi, Pneumocystis murina, P. carinii and Pneumocystis wakefieldiae, the five Pneumocystis species described until now, mainly on the basis of the phylogenetic species concept. Interestingly, Pneumocystis organisms exhibit a successful adaptation enabling them to dwell and replicate in the lungs of both immunocompromised and healthy mammals, which can act as infection reservoirs. The role of healthy carriers in aerial disease transmission is nowadays recognized as a major contribution to Pneumocystis circulation, and Pneumocystis infection of nonimmunosuppressed hosts has emerged as a public health issue. More studies need to be undertaken both on the clinical consequences of the presence of Pneumocystis in healthy carriers and on the intricate Pneumocystis life cycle to better define its epidemiology, to adapt existing therapies to each clinical context and to discover new drug targets.     

Transmission of Pneumocystis infection in humans

Is Pneumocystis pneumonia (PcP) a transmissible fungal disease? Does nosocomial PcP occur? Is there Pneumocystis transmission in the community? These questions, which could not be tackled before the 2000s, may at present be approached using either noninvasive detection methods or experimental transmission models. Represented by a unique entity (P.?carinii) for almost one century, the Pneumocystis genus was shown to contain several species, being P.?jirovecii the sole species identified in humans hitherto. Molecular methods combined with cross infection experiments revealed strong host specificity that precludes Pneumocystis inter-species transmission. In contrast, respiratory transmission between mammals of a same species is usually highly active, even between immunocompetent hosts. Other transmission ways could also exist. New data show that human being is the unique P.?jirovecii reservoir; it would constitute the sole infection source in both hospital and community.     

Highlights and summaries of the 11th International Workshops on Opportunistic Protists

The 11th in the series of International Workshops on Opportunistic Protists (IWOP-11) was held in August 2010 on the Big Island of Hawaii. These meetings are devoted to agents of infections that cause serious problems in AIDS patients and other individuals with defective immune systems. International Workshops on Opportunistic Protists serves as a forum for exchange of current research information on Pneumocystis, Cryptosporidium and the Microsporidia, Toxoplasma, free-living amoebae, kinetoplastid flagellates and other pathogens that are particularly pathogenic in immunodeficient hosts. Studies on interactions between host and pathogen, especially host responses, were highlighted in this year's symposium. The lack of in vitro cultivation methods for luxuriant growth of Pneumocystis, Cryptosporidium and the Enterocytozoon bieneusi remains a major hindrance to understanding the basic biology of these organisms and precludes genetic manipulations. However, slow but steady progress is being achieved by hard work including data mining of some completed or partially completed genome sequencing of several IWOP organisms. Of great concern is evidence for dramatic decline in research funding for these pathogens and the lack of appreciation by the larger scientific community concerning the state of art and challenges faced by researchers working on these organisms that can provide critical insight into emerging and reemerging pathogens.     

Pneumocystis carinii,Toxoplasma gondii,Cytomegalovirus and the Compromised Host

Pneumocystis carinii and Toxoplasma gondii are the two major parasitic protozoan pathogens in the immunocompromised host. Both organisms cause latent infection in humans and many animals. Cats are the definitive hosts for toxoplasmosis; the animal vector for pneumocystis (if any) has not been defined. Toxoplasma is an obligate intracellular parasite, whereas the available evidence suggests that Pneumocystis carinii exists primarily extracellularly. In compromised hosts, pneumocystis infection usually involves only lungs, whereas toxoplasma causes a generalized infection with encephalitis being the principal clinical manifestation. Both types of infection are treated with combinations of folate antagonists (trimethoprim or pyrimethamine with sulfonamide). Both parasites are associated with cytomegalovirus infection in immunosuppressed hosts, an association which may be due to symbiosis between parasites, or to an additive immunosuppressive effect of dual infection on the hosts.     

Diversity,extinction, and threat status in Lagomorphs

A quarter of all lagomorphs (pikas, rabbits, hares and jackrabbits) are threatened with extinction, including several genera that contain only one species. The number of species in a genus correlates with extinction risk in lagomorphs, but not in other mammal groups, and this is concerning because the non‐random extinction of small clades disproportionately threatens genetic diversity and phylogenetic history. Here, we use phylogenetic analyses to explore the properties of the lagomorph phylogeny and test if variation in evolution, biogeography and ecology between taxa explains current patterns of diversity and extinction risk. Threat status was not related to body size (and, by inference, its biological correlates), and there was no phylogenetic signal in extinction risk. We show that the lagomorph phylogeny has a similar clade‐size distribution to other mammals, and found that genus size was unrelated to present climate, topography, or geographic range size. Extinction risk was greater in areas of higher human population density and negatively correlated with anthropogenically modified habitat. Consistent with this, habitat generalists were less likely to be threatened. Our models did not predict threat status accurately for taxa that experience region‐specific threats. We suggest that pressure from human populations is so severe and widespread that it overrides ecological, biological, and geographic variation in extant lagomorphs.     

Diseases of humans and their domestic mammals: pathogen characteristics, host range and the risk of emergence

Pathogens that can be transmitted between different host species are of fundamental interest and importance from public health, conservation and economic perspectives, yet systematic quantification of these pathogens is lacking. Here, pathogen characteristics, host range and risk factors determining disease emergence were analysed by constructing a database of disease-causing pathogens of humans and domestic mammals. The database consisted of 1415 pathogens causing disease in humans, 616 in livestock and 374 in domestic carnivores. Multihost pathogens were very prevalent among human pathogens (61.6%) and even more so among domestic mammal pathogens (livestock 77.3%, carnivores 90.0%). Pathogens able to infect human, domestic and wildlife hosts contained a similar proportion of disease-causing pathogens for all three host groups. One hundred and ninety-six pathogens were associated with emerging diseases, 175 in humans, 29 in livestock and 12 in domestic carnivores. Across all these groups, helminths and fungi were relatively unlikely to emerge whereas viruses, particularly RNA viruses, were highly likely to emerge. The ability of a pathogen to infect multiple hosts, particularly hosts in other taxonomic orders or wildlife, were also risk factors for emergence in human and livestock pathogens. There is clearly a need to understand the dynamics of infectious diseases in complex multihost communities in order to mitigate disease threats to public health, livestock economies and wildlife.     

Molecular phylogeny of Pneumocystis based on 5.8S rRNA gene and the internal transcribed spacers of rRNA gene sequences

To clarify the phylogenetic relationships and species status of Pneumocystis, the 5.8S rRNA gene and the internal transcribed spacers (ITS, 1 and 2) of Pneumocystis rRNA derived from rat, gerbil and human were amplified, cloned and sequenced. The genetic distance matrix of six Pneumocystis species compared with other fungi like Taphrina and Saccharomyces indicated that the Pneumocystis genus contained multiple species including Pneumocystis from gerbil. The phylogenetic tree also showed that Pneumocystis from human and monkey formed one group and four rodent Pneumocystis formed another group. Among the four members, Pneumocystis wakefieldiae was most closely related to Pneumocystis murina and Pneumocystis carinii, and was least related to gerbil Pneumocystis.     

Biology and Evolution of Beneficial and Detrimental Viruses of Animals, Plants, and Fungi

Virtually every type of organism may serve as a host for viruses. In some hosts, virus presence may be considered beneficial to humans; in other hosts, viruses are considered detrimental. Examples of viruses that are considered beneficial to humans include those that are used for biological control of organisms that themselves are considered detrimental to humans, such as plant pathogenic fungi. Viruses are extremely variable in terms of morphology, structure, and genome organization. However, viruses that attack hosts from different kingdoms may be related, deriving from the same phylogeny. This paper summarizes some of the properties of three related families of viruses that attack hosts in different kingdoms: the animal-infecting Picornaviridae, the plant-infecting Potyviridae, and the fungus-infecting Hypoviridae. Properties of these viruses that set them apart from each other and factors that may affect their evolution are discussed.     

Ecological associations between bacteria of the genus <Emphasis Type="Italic">Bartonella</Emphasis> and mammals

Bacteria of the genus Bartonella are facultative intracellular parasites associated with erythrocytes and endothelial cells of mammals. It has become increasingly obvious that bartonellae are highly adapted to a wide variety of mammals. The present paper reviews associations between Bartonella species and rodents, insectivores, bats, predators, ungulates, and marine mammals. We now have new insights into the adaptive mechanisms of bartonellae. These bacteria usually persist in the bodies of certain mammalian species serving as their reservoir hosts, without causing a disease. When bartonellae accidentally infect other mammals, including humans, they may be responsible for a spectrum of different diseases. Several mammalian species are reservoir hosts for Bartonella species that have been identified as pathogenic for humans.     

Adaptive radiation within marine anisakid nematodes: a zoogeographical modeling of cosmopolitan, zoonotic parasites

Parasites of the nematode genus Anisakis are associated with aquatic organisms. They can be found in a variety of marine hosts including whales, crustaceans, fish and cephalopods and are known to be the cause of the zoonotic disease anisakiasis, a painful inflammation of the gastro-intestinal tract caused by the accidental consumptions of infectious larvae raw or semi-raw fishery products. Since the demand on fish as dietary protein source and the export rates of seafood products in general is rapidly increasing worldwide, the knowledge about the distribution of potential foodborne human pathogens in seafood is of major significance for human health. Studies have provided evidence that a few Anisakis species can cause clinical symptoms in humans. The aim of our study was to interpolate the species range for every described Anisakis species on the basis of the existing occurrence data. We used sequence data of 373 Anisakis larvae from 30 different hosts worldwide and previously published molecular data (n = 584) from 53 field-specific publications to model the species range of Anisakis spp., using a interpolation method that combines aspects of the alpha hull interpolation algorithm as well as the conditional interpolation approach. The results of our approach strongly indicate the existence of species-specific distribution patterns of Anisakis spp. within different climate zones and oceans that are in principle congruent with those of their respective final hosts. Our results support preceding studies that propose anisakid nematodes as useful biological indicators for their final host distribution and abundance as they closely follow the trophic relationships among their successive hosts. The modeling might although be helpful for predicting the likelihood of infection in order to reduce the risk of anisakiasis cases in a given area.     

Viral adaptation to host: a proteome‐based analysis of codon usage and amino acid preferences

Viruses differ markedly in their specificity toward host organisms. Here, we test the level of general sequence adaptation that viruses display toward their hosts. We compiled a representative data set of viruses that infect hosts ranging from bacteria to humans. We consider their respective amino acid and codon usages and compare them among the viruses and their hosts. We show that bacteria‐infecting viruses are strongly adapted to their specific hosts, but that they differ from other unrelated bacterial hosts. Viruses that infect humans, but not those that infect other mammals or aves, show a strong resemblance to most mammalian and avian hosts, in terms of both amino acid and codon preferences. In groups of viruses that infect humans or other mammals, the highest observed level of adaptation of viral proteins to host codon usages is for those proteins that appear abundantly in the virion. In contrast, proteins that are known to participate in host‐specific recognition do not necessarily adapt to their respective hosts. The implication for the potential of viral infectivity is discussed.     

Leishmania parasites: could we consider them as living organisms per se?

Over the last 10 years - in Microbes and Infection - the publications dealing with protozoan parasites were mainly providing insights on the pathogenic processes leading to the local or systemic damages in the mammals, these parasitic organisms exploit/subvert as hosts. As a result, many investigators introduced the objectives of their analysis by referring to "host-pathogen" interactions. Though we, as investigators, are all determined to decipher the pathogenic processes which can indeed be coupled to the parasite uncontrolled development, I think that the parasites - alike the living organisms they subvert as hosts - need to be considered as living organisms per se, instead of being considered as "pathogens". Such a conceptual frame will promote research on the processes on which relies their perpetuation whatever the level under investigations - individual and/or population level. Only the unicellular protozoan parasites of the genus Leishmania known to be hosted by blood-feeding insects and mammals will be further considered in this brief contribution.     

LysM proteins in mammalian fungal pathogens

The LysM domain is a highly conserved carbohydrate-binding module that recognizes polysaccharides containing N-acetylglucosamine residues. LysM domains are found in a wide variety of extracellular proteins and receptors from viruses, bacteria, fungi, plants and animals. LysM proteins are also present in many species of mammalian fungal pathogens, although a limited number of studies have focused on the expression and determination of their putative roles in the infection process. This review summarizes the current knowledge and recent studies on LysM proteins in the main morphological groups of fungal pathogens that cause infections in humans and other mammals. Recent advances towards understanding the biological functions of LysM proteins in infections of mammalian hosts and their use as potential targets in antifungal strategies are also discussed.     

New species, phylogeny, host-associations and geographic distribution of genus Cryptosporella (Gnomoniaceae, Diaporthales)

The phylogeny of Cryptosporella is revised to include recently discovered species. Eight species new to science are described and two new combinations are proposed, raising the total number of species accepted in Cryptosporella to 19. The species delimitation and phylogeny for Cryptosporella are determined based on analyses of DNA sequences from three genes (β-tubulin, ITS and tef1-α), comparative morphology of sexual structures on their host substrate, and host associations. The inferred phylogeny suggests that Cryptosporella has speciated primarily on Betulaceae with 16 species occurring on hosts in that plant family. The host range of most species seems to be narrow with nine species reported from a single host species or subspecies and seven species occurring on plants within a single host genus. A key to species is provided. The known distribution of Cryptosporella is expanded to mountain cloud forests of the provinces of Chiriquí in Panama and Tucumán in Argentina.