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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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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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7
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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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