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Ma L, Lin I, Hunter ST, Blasi B, Danesi P, Weissenbacher-Lang C, Cisse OH, Rothenburger JL, Kovacs JA. Development of Highly Efficient Universal Pneumocystis Primers and Their Application in Investigating the Prevalence and Genetic Diversity of Pneumocystis in Wild Hares and Rabbits. J Fungi (Basel) 2024; 10:355. [PMID: 38786710 PMCID: PMC11121927 DOI: 10.3390/jof10050355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Despite its ubiquitous infectivity to mammals with strong host specificity, our current knowledge about Pneumocystis has originated from studies of merely 4% of extant mammalian species. Further studies of Pneumocystis epidemiology across a broader range of animal species require the use of assays with high sensitivity and specificity. To this end, we have developed multiple universal Pneumocystis primers targeting different genetic loci with high amplification efficiency. Application of these primers to PCR investigation of Pneumocystis in free-living hares (Lepus townsendii, n = 130) and rabbits (Oryctolagus cuniculus, n = 8) in Canada revealed a prevalence of 81% (105/130) and 25% (2/8), respectively. Genotyping analysis identified five and two variants of Pneumocystis from hares and rabbits, respectively, with significant sequence divergence between the variants from hares. Based on phylogenetic analysis using nearly full-length sequences of the mitochondrial genome, nuclear rRNA operon and dihydropteroate synthase gene for the two most common variants, Pneumocystis in hares and rabbits are more closely related to each other than either are to Pneumocystis in other mammals. Furthermore, Pneumocystis in both hares and rabbits are more closely related to Pneumocystis in primates and dogs than to Pneumocystis in rodents. The high prevalence of Pneumocystis in hares (P. sp. 'townsendii') suggests its widespread transmissibility in the natural environment, similar to P. oryctolagi in rabbits. The presence of multiple distinct Pneumocystis populations in hares contrasts with the lack of apparent intra-species heterogeneity in P. oryctolagi, implying a unique evolution history of P. sp. 'townsendii' in hares.
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Affiliation(s)
- Liang Ma
- Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA; (I.L.); (O.H.C.); (J.A.K.)
| | - Isabella Lin
- Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA; (I.L.); (O.H.C.); (J.A.K.)
| | - Summer T. Hunter
- Faculty of Veterinary Medicine, University of Calgary, Canadian Wildlife Health Cooperative (Alberta Region), Calgary, AB T2N 1N4, Canada; (S.T.H.); (J.L.R.)
| | - Barbara Blasi
- Department of Biological Sciences and Pathobiology, Institute of Pathology, University of Veterinary Medicine Vienna, 1210 Wien, Austria; (B.B.); (C.W.-L.)
| | - Patrizia Danesi
- Laboratory of Parasitology, Mycology and Medical Enthomology, Istituto Zooprofilattico delle Venezie, 35020 Legnaro, Italy;
| | - Christiane Weissenbacher-Lang
- Department of Biological Sciences and Pathobiology, Institute of Pathology, University of Veterinary Medicine Vienna, 1210 Wien, Austria; (B.B.); (C.W.-L.)
| | - Ousmane H. Cisse
- Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA; (I.L.); (O.H.C.); (J.A.K.)
| | - Jamie L. Rothenburger
- Faculty of Veterinary Medicine, University of Calgary, Canadian Wildlife Health Cooperative (Alberta Region), Calgary, AB T2N 1N4, Canada; (S.T.H.); (J.L.R.)
| | - Joseph A. Kovacs
- Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA; (I.L.); (O.H.C.); (J.A.K.)
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Weissenbacher-Lang C, Grenl A, Blasi B. Meta-Analysis and Systematic Literature Review of the Genus Pneumocystis in Pet, Farm, Zoo, and Wild Mammal Species. J Fungi (Basel) 2023; 9:1081. [PMID: 37998885 PMCID: PMC10672670 DOI: 10.3390/jof9111081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
A systematic literature search on Pneumocystis in 276 pet, farm, zoo, and wild mammal species resulted in 124 publications originating from 38 countries that were analyzed descriptively and statistically, for which inclusion and exclusion criteria were exactly defined. The range of recorded Pneumocystis prevalence was broad, yet in half of the citations a prevalence of ≤25% was documented. Prevalence was significantly dependent on the method used for Pneumocystis detection, with PCR revealing the highest percentages. Pet animals showed the lowest median Pneumocystis prevalence, followed by farm, wild, and zoo animals. In contrast, pet and farm animals showed higher proportions of high-grade infection levels compared to zoo and wild mammals. Only in individual cases, all of them associated with severe Pneumocystis pneumonia, was an underlying immunosuppression confirmed. Acquired immunosuppression caused by other diseases was frequently discussed, but its significance, especially in highly immunosuppressive cases, needs to be clarified. This meta-analysis supported a potential influence of the social and environmental factors of the host on Pneumocystis transmission in wildlife, which must be further elucidated, as well as the genetic diversity of the fungus.
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Affiliation(s)
- Christiane Weissenbacher-Lang
- Department for Pathobiology, Institute of Pathology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (A.G.); (B.B.)
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Detection of Pneumocystis and Morphological Description of Fungal Distribution and Severity of Infection in Thirty-Six Mammal Species. J Fungi (Basel) 2023; 9:jof9020220. [PMID: 36836334 PMCID: PMC9960768 DOI: 10.3390/jof9020220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/22/2022] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Pneumocystis spp. are thought to adapt to the lungs of potentially all mammals. However, the full host range, fungal burden and severity of infection are unknown for many species. In this study, lung tissue samples originating from 845 animals of 31 different families of eight mammal orders were screened by in situ hybridization (ISH) using a universal 18S rRNA probe for Pneumocystis, followed by hematoxylin and eosin (H&E) staining for determining histopathological lesions. A total of 216 (26%) samples were positive for Pneumocystis spp., encompassing 36 of 98 investigated mammal species, with 17 of them being described for the first time for the presence of Pneumocystis spp. The prevalence of Pneumocystis spp. as assessed by ISH varied greatly among different mammal species while the organism load was overall low, suggesting a status of colonization or subclinical infection. Severe Pneumocystis pneumonia seemed to be very rare. For most of the Pneumocystis-positive samples, comparative microscopic examination of H&E- and ISH-stained serial sections revealed an association of the fungus with minor lesions, consistent with an interstitial pneumonia. Colonization or subclinical infection of Pneumocystis in the lung might be important in many mammal species because the animals may serve as a reservoir.
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First Molecular Detection of Pneumocystis spp. in the Golden Jackal (Canis aureus). J Wildl Dis 2022; 58:897-901. [PMID: 36300952 DOI: 10.7589/jwd-d-22-00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/24/2022] [Indexed: 12/02/2022]
Abstract
Forty-six golden jackals (Canis aureus) were collected between November 2020 and February 2021 in five counties of Serbia. Lung samples were screened for the presence of Pneumocystis DNA by pan-Pneumocystis PCR on the mtLSU rRNA gene obtaining PCR products of 370 bp in length. Pneumocystis DNA was detected in the lungs from 6/46 (13.04%) golden jackals. Four were females and two were males; four were classified as adults and two as subadults. Positive samples were confirmed in 4/5 investigated counties. No gross pathologic lung lesions were observed in this study. The sequences of Pneumocystis spp. from golden jackals were identical to one another and showed the highest similarity with Pneumocystis spp. sequences of dogs (98% nucleotide identity). The genetic variation was comparable to Pneumocystis spp. of raccoon dogs (95-97% nucleotide identity), red foxes (91-95% nucleotide identity), ferrets (86% nucleotide identity), and another Pneumocystis type in dogs (P. canis Ck2, 81% nucleotide identity) was higher. Golden jackals may be carriers and may play a nonnegligible role in the spread of Pneumocystis spp. Although this finding cannot be directly related to any clinical manifestation or pathologic lesions, a possible role in the exacerbation of different pulmonary disorders should be considered.
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Babb-Biernacki SJ, Esselstyn JA, Doyle VP. Predicting Species Boundaries and Assessing Undescribed Diversity in Pneumocystis, an Obligate Lung Symbiont. J Fungi (Basel) 2022; 8:jof8080799. [PMID: 36012788 PMCID: PMC9409666 DOI: 10.3390/jof8080799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
Far more biodiversity exists in Fungi than has been described, or could be described in several lifetimes, given current rates of species discovery. Although this problem is widespread taxonomically, our knowledge of animal-associated fungi is especially lacking. Fungi in the genus Pneumocystis are obligate inhabitants of mammal lungs, and they have been detected in a phylogenetically diverse array of species representing many major mammal lineages. The hypothesis that Pneumocystis cospeciate with their mammalian hosts suggests that thousands of Pneumocystis species may exist, potentially equal to the number of mammal species. However, only six species have been described, and the true correspondence of Pneumocystis diversity to host species boundaries is unclear. Here, we use molecular species delimitation to estimate the boundaries of Pneumocystis species sampled from 55 mammal species representing eight orders. Our results suggest that Pneumocystis species often colonize several closely related mammals, especially those in the same genus. Using the newly estimated ratio of fungal to host diversity, we estimate ≈4600 to 6250 Pneumocystis species inhabit the 6495 currently recognized extant mammal species. Additionally, we review the literature and find that only 240 (~3.7%) mammal species have been screened for Pneumocystis, and many detected Pneumocystis lineages are not represented by any genetic data. Although crude, our findings challenge the dominant perspective of strict specificity of Pneumocystis to their mammal hosts and highlight an abundance of undescribed diversity.
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Affiliation(s)
- Spenser J. Babb-Biernacki
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
- Correspondence:
| | - Jacob A. Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Vinson P. Doyle
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA 70809, USA;
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6
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Latinne A, Chen HW, Kuo CC, Lorica R, Singleton G, Stuart A, Malbas FF, Demanche C, Chabé M, Michaux J, Morand S. Revisiting the Pneumocystis host specificity paradigm and transmission ecology in wild Southeast Asian rodents. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 93:104978. [PMID: 34175480 DOI: 10.1016/j.meegid.2021.104978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/04/2021] [Accepted: 06/21/2021] [Indexed: 01/16/2023]
Abstract
Pneumocystis fungi are opportunistic parasites of mammalian lungs whose evolution, ecology and host specificity in natural host populations remain poorly understood and controversial. Using an extensive collection of 731 lung samples from 27 rodent species sampled in five Southeast Asian countries, and nested PCR amplification of mitochondrial and nuclear genes, we investigated the host specificity and genetic structure of Pneumocystis lineages infecting wild rodents. We also identified the rodent species playing a central role in the transmission of these parasites using network analysis and centrality measurement and we characterized the environmental conditions allowing Pneumocystis infection in Southeast Asia using generalized linear mixed models. Building upon an unprecedented Pneumocystis sampling from numerous rodent species belonging to closely related genera, our findings provide compelling evidence that the host specificity of Pneumocystis lineages infecting rodents is not restricted to a single host species or genus as often presented in the literature but it encompasses much higher taxonomic levels and more distantly related rodent host species. The phylogenetic species status at both mitochondrial and nuclear genetic markers of at least three new Pneumocystis lineages, highly divergent from Pneumocystis species currently described, is also suggested by our data. Our models show that the probability of Pneumocystis infection in rodent hosts is positively correlated to environmental variables reflecting habitat fragmentation and landscape patchiness. Synanthropic and habitat-generalist rodents belonging to the Rattus, Sundamys and Bandicota genera played a role of bridge host species for Pneumocystis spreading in these heterogeneous habitats, where they can reach high population densities. These are critical findings improving our understanding of the ecology of these enigmatic parasites and the role played by cospeciation and host switches in their evolution. Our results also confirmed the role of land-use change and habitat fragmentation in parasite amplification and spillover in rodents.
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Affiliation(s)
- Alice Latinne
- Wildlife Conservation Society, Viet Nam Country Program, Ha Noi, Viet Nam; Wildlife Conservation Society, Health Program, Bronx, NY, USA; Université de Liège, Laboratoire de Génétique de la Conservation, GeCoLAB, 4000 Liège, Belgium.
| | - Hsuan-Wien Chen
- Department of Biological Resources, National Chiayi University, Chiayi, Taiwan
| | - Chi-Chien Kuo
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Renee Lorica
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Grant Singleton
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines; Natural Resource Institute, University of Greenwich, Chatham Maritime, Kent, UK
| | - Alex Stuart
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Fedelino F Malbas
- Research Institute for Tropical Medicine, Department of Health, Muntinlupa, Metro Manila, Philippines
| | - Christine Demanche
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Magali Chabé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Johan Michaux
- Université de Liège, Laboratoire de Génétique de la Conservation, GeCoLAB, 4000 Liège, Belgium; Animal Santé Territoire Risque Environnement- Unité Mixe de Recherche 117 (ASTRE) Univ. Montpellier, Centre International de Recherche Agronomique pour le Développement (CIRAD), Institut National de la Recherche Agronomique, 34398 Montpellier, France
| | - Serge Morand
- University of Montpellier, Institut des Sciences de l'Evolution, CNRS-IRD, Montpellier, France; University of Kasetsart, Faculty of Veterinary Technology, ASTRE-CIRAD, Bangkok, Thailand
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Affiliation(s)
- Spenser J Babb-Biernacki
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Jacob A Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Vinson P Doyle
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, Louisiana, United States of America
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Riebold D, Lubig J, Wolf P, Wolf C, Russow K, Loebermann M, Slevogt H, Mohr E, Feldhusen F, Reisinger EC. First molecular detection of Pneumocystis spp. in red foxes (Vulpes vulpeslinnaeus, 1758) and raccoon dogs (Nyctereutes procyonoidesgray, 1834). Comp Immunol Microbiol Infect Dis 2020; 73:101531. [PMID: 32871298 DOI: 10.1016/j.cimid.2020.101531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 11/17/2022]
Abstract
Fungal organisms of the genus Pneumocystis may cause Pneumocystis pneumonia (PCP) in humans, but also domestic and wild mammals. Almost every animal species hosts its own genetically distinct Pneumocystis species, however information is sparse. In this study, 62 red foxes (Vulpes vulpes) and 37 raccoon dogs (Nyctereutes procyonoides) were collected in North-East Germany. The lung tissues of the animals were analysed by a new designed specific pan-Pneumocystis mtLSU rRNA gene PCR and sequencing. With this PCR, detection and discrimination of all known Pneumocystis spp. in a single step should be possible. This first detection of Pneumocystis spp. in 29/62 (46.8%) red foxes and 29/37 (78.4%) raccoon dogs indicated, that they harbour two dissimilar strains, as seen by specific single nucleotide position changes (SNPs). Nevertheless, five samples with contrary SNPs showed a probable inter-species transmission.
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Affiliation(s)
- Diana Riebold
- Host Septomics Group, Centre for Innovation Competence (ZIK) Septomics, University Hospital Jena, Jena, Germany; Division of Tropical Medicine and Infectious Diseases, Department of Medicine, University of Rostock, Germany.
| | - Jacob Lubig
- Division of Tropical Medicine and Infectious Diseases, Department of Medicine, University of Rostock, Germany; Chair for Animal Health and Animal Welfare, Faculty of Agriculture and Environmental Sciences, University of Rostock, Germany
| | - Peter Wolf
- State Office for Agriculture, Food Safety and Fishery Mecklenburg-Western Pomerania (LALLF-MV), Rostock, Germany
| | - Carola Wolf
- State Office for Agriculture, Food Safety and Fishery Mecklenburg-Western Pomerania (LALLF-MV), Rostock, Germany
| | - Kati Russow
- Division of Tropical Medicine and Infectious Diseases, Department of Medicine, University of Rostock, Germany
| | - Micha Loebermann
- Division of Tropical Medicine and Infectious Diseases, Department of Medicine, University of Rostock, Germany
| | - Hortense Slevogt
- Host Septomics Group, Centre for Innovation Competence (ZIK) Septomics, University Hospital Jena, Jena, Germany
| | - Elmar Mohr
- Chair for Animal Health and Animal Welfare, Faculty of Agriculture and Environmental Sciences, University of Rostock, Germany
| | - Frerk Feldhusen
- State Office for Agriculture, Food Safety and Fishery Mecklenburg-Western Pomerania (LALLF-MV), Rostock, Germany
| | - Emil Christian Reisinger
- Division of Tropical Medicine and Infectious Diseases, Department of Medicine, University of Rostock, Germany
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Danesi P, Corrò M, Falcaro C, Carminato A, Furlanello T, Cocchi M, Krockenberger MB, Meyer W, Capelli G, Malik R. Molecular detection of Pneumocystis in the lungs of cats. Med Mycol 2020; 57:813-824. [PMID: 30566653 PMCID: PMC7107658 DOI: 10.1093/mmy/myy139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/09/2018] [Accepted: 11/16/2018] [Indexed: 12/23/2022] Open
Abstract
The genus Pneumocystis comprises potential pathogens that reside normally in the lungs of a wide range of mammals. Although they generally behave as transient or permanent commensals, they can occasionally cause life-threatening pneumonia (Pneumocystis pneumonia; PCP) in immunosuppressed individuals. Several decades ago, the presence of Pneumocystis morphotypes (trophic forms and cysts) was described in the lungs of normal cats and cats with experimentally induced symptomatic PCP (after immunosuppression by corticosteroids); yet to date spontaneous or drug-induced PCP has not been described in the clinical feline literature, despite immunosuppression of cats by long-standing retrovirus infections or after kidney transplantation. In this study, we describe the presence of Pneumocystis DNA in the lungs of normal cats (that died of various unrelated causes; n = 84) using polymerase chain reactions (PCRs) targeting the mitochondrial small and large subunit ribosomal RNA gene (mtSSU rRNA and mtLSU rRNA). The presence of Pneumocystis DNA was confirmed by sequencing in 24/84 (29%) cats, with evidence of two different sequence types (or lineages). Phylogenetically, lineage1 (L1; 19 cats) and lineage 2 (L2; 5 cats) formed separate clades, clustering with Pneumocystis from domestic pigs (L1) and carnivores (L2), respectively. Results of the present study support the notion that cats can be colonized or subclinically infected by Pneumocystis, without histological evidence of damage to the pulmonary parenchyma referable to pneumocystosis. Pneumocystis seems most likely an innocuous pathogen of cats’ lungs, but its possible role in the exacerbation of chronic pulmonary disorders or viral/bacterial coinfections should be considered further in a clinical setting.
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Affiliation(s)
- Patrizia Danesi
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Michela Corrò
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Christian Falcaro
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Antonio Carminato
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | | | - Monia Cocchi
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Mark B Krockenberger
- Veterinary Pathology Diagnostic Services, Sydney School of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Westmead Clinical School, Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity, University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Sydney, Australia
| | - Gioia Capelli
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Richard Malik
- Centre for Veterinary Education, B22, University of Sydney, Sydney, New South Wales, Australia
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Petružela J, Bryja J, Bryjová A, Katakweba A, Sabuni C, Baird SJE, de Bellocq JG. Evolutionary history of Pneumocystis fungi in their African rodent hosts. INFECTION GENETICS AND EVOLUTION 2019; 75:103934. [PMID: 31247340 DOI: 10.1016/j.meegid.2019.103934] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/17/2019] [Accepted: 06/20/2019] [Indexed: 02/08/2023]
Abstract
Pneumocystis is a genus of parasitic fungi infecting lung tissues in a wide range of mammal species, displaying a strong host specificity and patterns of co-speciation with their hosts. However, a recent study on Asiatic murids challenged these patterns reporting several Pneumocystis lineages/species shared by different host species or even genera in the Rattini and Murini tribes. Here we screened lung samples of 27 species of African rodents from five families for the presence of Pneumocystis DNA. Using reconstructed multi-locus phylogenies of both hosts and parasites, we tested the hypothesis of their co-evolution. We found that Pneumocystis is widespread in African rodents, detected in all but seven screened host species, with species-level prevalence ranging from 5.9 to 100%. Several host species carry pairs of highly divergent Pneumocystis lineages/species. The retrieved co-phylogenetic signal was highly significant (p = .0017). We found multiple co-speciations, sorting events and two host-shift events, which occurred between Murinae and Deomyinae hosts. Comparison of genetic distances suggests higher substitution rates for Pneumocystis relative to the rodent hosts on neutral loci and slower rates on selected ones. We discuss life-history traits and population dynamics factors which could explain the observed results.
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Affiliation(s)
- Jan Petružela
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic; Faculty of Science, Department of Botany and Zoology, Masaryk University, Brno, Czech Republic.
| | - Josef Bryja
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic; Faculty of Science, Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Abdul Katakweba
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Christopher Sabuni
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Stuart J E Baird
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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Petini M, Furlanello T, Danesi P, Zoia A. Nested-polymerase chain reaction detection of Pneumocystis carinii f. sp. canis in a suspected immunocompromised Cavalier King Charles spaniel with multiple infections. SAGE Open Med Case Rep 2019; 7:2050313X19841169. [PMID: 31065354 PMCID: PMC6487761 DOI: 10.1177/2050313x19841169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/27/2019] [Indexed: 11/16/2022] Open
Abstract
A 7-month-old Cavalier King Charles Spaniel female was referred due to a chronic cough refractory to antibiotic treatments. Laboratory findings showed leukocytosis, increased serum C-reactive protein, hypogammaglobulinemia, and decreased total serum immunoglobulin G concentration. Thoracic radiographs showed a mild bronchial pattern. Cytology of the bronchoalveolar lavage fluid revealed a septic inflammation. Bordetella bronchiseptica, Mycoplasma spp., and Pneumocystis carinii were identified by polymerase chain reaction testing, and Klebsiella pneumonia was cultured from the bronchoalveolar lavage fluid. Moreover, Escherichia coli was also cultured from urine. Pneumocystis spp. identification was done by sequencing of genetic amplicons. The dog died due to cardiopulmonary arrest secondary to a spontaneous pneumothorax on the day following the procedure. This report documents the detection of Pneumocystis carinii f. sp. canis in a suspected immunocompromised Cavalier King Charles Spaniel with concurrent pulmonary and urinary tract infections involving four different pathogens, and highlights the importance of the use of polymerase chain reaction testing to detect canine Pneumocystis spp. in cases with negative bronchoalveolar lavage cytology.
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Affiliation(s)
| | | | - Patrizia Danesi
- Operative Unit of Mycology, Parasitology Lab, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVE), Legnaro, Italy
| | - Andrea Zoia
- San Marco Veterinary Clinic, Veggiano, Italy
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12
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Advances and challenges in barcoding of microbes, parasites, and their vectors and reservoirs. Parasitology 2019; 145:537-542. [PMID: 29900810 DOI: 10.1017/s0031182018000884] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
DNA barcoding is now a common tool in parasitology and epidemiology, which require good methods for identification not only of parasites and pathogens but vectors and reservoirs. This special issue presents some advances and challenges in barcoding of microbes, parasites, and their vectors and reservoirs. DNA barcoding found new applications in disease ecology, conservation parasitology, environmental parasitology and in paleoparasitology. New technologies such as next-generation sequencing and matrix-assisted laser desorption-ionization time-of-flight have made it now possible to investigate large samples of specimens. By allowing the investigation of parasites at the interface between environment, biodiversity, animal and human health, barcoding and biobanking have important policy outcomes as well as ethics and legal implications. The special issue 'Advances and challenges in the barcoding of parasites, vectors and reservoirs' illustrates some recent advances and proposes new avenues for research in barcoding in parasitology.
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Danesi P, Falcaro C, Ravagnan S, Da Rold G, Porcellato E, Corrò M, Iatta R, Cafarchia C, Frangipane di Regalbono A, Meyer W, Capelli G. Real-time PCR assay for screening Pneumocystis in free-living wild squirrels and river rats in Italy. J Vet Diagn Invest 2018; 30:862-867. [PMID: 30204066 DOI: 10.1177/1040638718797379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We used a real-time PCR (rtPCR) targeting a 150-bp amplicon of the mitochondrial small subunit of ribosomal RNA (mtSSU rRNA) to screen for Pneumocystis DNA in lungs of wild squirrels ( Callosciurus finlaysonii, n = 85) and river rats ( Myocastor coypus, n = 43) in Italy. The rtPCR revealed Pneumocystis DNA in 20 of 85 (24%) squirrels and in 35 of 43 (81%) river rats, and was more sensitive than a nested PCR that targets a portion of the mtSSU rRNA and the mitochondrial large subunit of rRNA (mtLSU rRNA). Phylogenetic analysis based on mtSSU rRNA and mtLSU rRNA sequences showed distinct Pneumocystis sequence types in these rodents. The rtPCR assay should be reliable for screening large populations for this potential pathogen, thereby allowing cost-effective monitoring of the disease in wild animals.
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Affiliation(s)
- Patrizia Danesi
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Christian Falcaro
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Silvia Ravagnan
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Graziana Da Rold
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Elena Porcellato
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Michela Corrò
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Roberta Iatta
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Claudia Cafarchia
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Antonio Frangipane di Regalbono
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Wieland Meyer
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
| | - Gioia Capelli
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy (Danesi, Falcaro, Ravagnan, Da Rold, Porcellato, Corrò, Capelli).,Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Bari, Italy (Iatta, Cafarchia).,Dipartimento di Medicina Animale, Produzioni e Salute, Università degli Studi di Padova, Legnaro, Padova, Italy (Frangipane di Regalbono).,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia (Meyer)
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Danesi P, Ravagnan S, Johnson LR, Furlanello T, Milani A, Martin P, Boyd S, Best M, Galgut B, Irwin P, Canfield PJ, Krockenberger MB, Halliday C, Meyer W, Malik R. Molecular diagnosis of Pneumocystis pneumonia in dogs. Med Mycol 2018; 55:828-842. [PMID: 28339756 DOI: 10.1093/mmy/myx007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 01/20/2017] [Indexed: 11/12/2022] Open
Abstract
Pneumocystis pneumonia (PCP) is a life-threatening fungal disease that can occur in dogs. The aim of this study was to provide a preliminary genetic characterisation of Pneumocystis carinii f.sp.'canis' (P. canis) in dogs and thereby develop a reliable molecular protocol to definitively diagnose canine PCP. We investigated P. canis in a variety of lung specimens from dogs with confirmed or strongly suspected PCP (Group 1, n = 16), dogs with non-PCP lower respiratory tract problems (Group 2, n = 65) and dogs not suspected of having PCP or other lower respiratory diseases (Group 3, n = 11). Presence of Pneumocystis DNA was determined by nested PCR of the large and small mitochondrial subunit rRNA loci and by a real-time quantitative polymerase chain reaction (qPCR) assay developed using a new set of primers. Molecular results were correlated with the presence of Pneumocystis morphotypes detected in cytological/histological preparations. Pneumocystis DNA was amplified from 13/16 PCP-suspected dogs (Group 1) and from 4/76 dogs of control Groups 2 and 3 (combined). The latter four dogs were thought to have been colonized by P. canis. Comparison of CT values in 'infected' versus 'colonized' dogs was consistent with this notion, with a distinct difference in molecular burden between groups (CT ≤ 26 versus CT range (26 <CT < 35), respectively). Phylogenetic analyses showed that P. canis is specifically 'canine' associated, being separated from other mammalian Pneumocystis species, thereby confirming the accuracy of qPCR amplicon for Pneumocystis in dogs. Using qPCR, Pneumocystis DNA can be detected in specimens from the respiratory tract and a CT value can be interpreted to distinguish infection versus colonization.
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Affiliation(s)
- Patrizia Danesi
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Silvia Ravagnan
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Lynelle R Johnson
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | | | - Adelaide Milani
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Patricia Martin
- Veterinary Pathology Diagnostic Services, Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Susan Boyd
- QML Vetnostics, Riverview Place, Metroplex on Gateway, Murrarie, QLD Australia
| | - Matthew Best
- Brisbane Veterinary Specialist Centre, Corner Keong & Old Northern Roads, Albany Creek, QLD Australia
| | - Bradley Galgut
- Australian Specialised Animal Pathology (ASAP) Laboratories, Victoria, Australia
| | - Peter Irwin
- School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
| | - Paul J Canfield
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Mark B Krockenberger
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Catriona Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, Westmead Hospital, Sydney, New South Wales, Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity, University of Sydney, Westmead Institute for Medical Research, Sydney, Australia
| | - Richard Malik
- Centre for Veterinary Education, B22, University of Sydney, Sydney, New South Wales, Australia
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Genetic diversity and evolution of Pneumocystis fungi infecting wild Southeast Asian murid rodents. Parasitology 2017; 145:885-900. [PMID: 29117878 DOI: 10.1017/s0031182017001883] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Pneumocystis organisms are airborne-transmitted fungal parasites that infect the lungs of numerous mammalian species with strong host specificity. In this study, we investigated the genetic diversity and host specificity of Pneumocystis organisms infecting Southeast Asian murid rodents through PCR amplification of two mitochondrial genes and tested the co-phylogeny hypothesis among these fungi and their rodent hosts. Pneumocystis DNA was detected in 215 of 445 wild rodents belonging to 18 Southeast Asian murid species. Three of the Pneumocystis lineages retrieved in our phylogenetic trees correspond to known Pneumocystis species, but some of the remaining lineages may correspond to new undescribed species. Most of these Pneumocystis species infect several rodent species or genera and some sequence types are shared among several host species and genera. These results indicated a weaker host specificity of Pneumocystis species infecting rodents than previously thought. Our co-phylogenetic analyses revealed a complex evolutionary history among Pneumocystis and their rodent hosts. Even if a significant global signal of co-speciation has been detected, co-speciation alone is not sufficient to explain the observed co-phylogenetic pattern and several host switches are inferred. These findings conflict with the traditional view of a prolonged process of co-evolution and co-speciation of Pneumocystis and their hosts.
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Demanche C, Deville M, Michaux J, Barriel V, Pinçon C, Aliouat-Denis CM, Pottier M, Noël C, Viscogliosi E, Aliouat EM, Dei-Cas E, Morand S, Guillot J. Correction: What Do Pneumocystis Organisms Tell Us about the Phylogeography of Their Hosts? The Case of the Woodmouse Apodemus sylvaticus in Continental Europe and Western Mediterranean Islands. PLoS One 2017; 12:e0171282. [PMID: 28182721 PMCID: PMC5300120 DOI: 10.1371/journal.pone.0171282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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