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Seidl CM, Ferreira FC, Parise KL, Paxton KL, Paxton EH, Atkinson CT, Fleischer RC, Foster JT, Marm Kilpatrick A. Linking avian malaria parasitemia estimates from quantitative PCR and microscopy reveals new infection patterns in Hawai'i. Int J Parasitol 2024; 54:123-130. [PMID: 37922977 DOI: 10.1016/j.ijpara.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/29/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
Plasmodium parasites infect thousands of species and provide an exceptional system for studying host-pathogen dynamics, especially for multi-host pathogens. However, understanding these interactions requires an accurate assay of infection. Assessing Plasmodium infections using microscopy on blood smears often misses infections with low parasitemias (the fractions of cells infected), and biases in malaria prevalence estimates will differ among hosts that differ in mean parasitemias. We examined Plasmodium relictum infection and parasitemia using both microscopy of blood smears and quantitative polymerase chain reaction (qPCR) on 299 samples from multiple bird species in Hawai'i and fit models to predict parasitemias from qPCR cycle threshold (Ct) values. We used these models to quantify the extent to which microscopy underestimated infection prevalence and to more accurately estimate infection patterns for each species for a large historical study done by microscopy. We found that most qPCR-positive wild-caught birds in Hawaii had low parasitemias (Ct scores ≥35), which were rarely detected by microscopy. The fraction of infections missed by microscopy differed substantially among eight species due to differences in species' parasitemia levels. Infection prevalence was likely 4-5-fold higher than previous microscopy estimates for three introduced species, including Zosterops japonicus, Hawaii's most abundant forest bird, which had low average parasitemias. In contrast, prevalence was likely only 1.5-2.3-fold higher than previous estimates for Himatione sanguinea and Chlorodrepanis virens, two native species with high average parasitemias. Our results indicate that relative patterns of infection among species differ substantially from those observed in previous microscopy studies, and that differences depend on variation in parasitemias among species. Although microscopy of blood smears is useful for estimating the frequency of different Plasmodium stages and host attributes, more sensitive quantitative methods, including qPCR, are needed to accurately estimate and compare infection prevalence among host species.
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Affiliation(s)
- Christa M Seidl
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA; Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA.
| | - Francisco C Ferreira
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA; Center for Vector Biology, Rutgers University, New Brunswick, NJ, USA
| | - Katy L Parise
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Kristina L Paxton
- Hawai'i Volcanoes National Park, Resource Management, Hawai'i National Park, HI, USA
| | - Eben H Paxton
- U.S. Geological Survey, Pacific Island Ecosystems Research Center, Hawai'i National Park, HI. USA
| | - Carter T Atkinson
- U.S. Geological Survey, Pacific Island Ecosystems Research Center, Hawai'i National Park, HI. USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
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2
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Ange-Stark M, Parise KL, Cheng TL, Hoyt JR, Langwig KE, Frick WF, Kilpatrick AM, Gillece J, MacManes MD, Foster JT. White-nose syndrome restructures bat skin microbiomes. Microbiol Spectr 2023; 11:e0271523. [PMID: 37888992 PMCID: PMC10714735 DOI: 10.1128/spectrum.02715-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/13/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Inherent complexities in the composition of microbiomes can often preclude investigations of microbe-associated diseases. Instead of single organisms being associated with disease, community characteristics may be more relevant. Longitudinal microbiome studies of the same individual bats as pathogens arrive and infect a population are the ideal experiment but remain logistically challenging; therefore, investigations like our approach that are able to correlate invasive pathogens to alterations within a microbiome may be the next best alternative. The results of this study potentially suggest that microbiome-host interactions may determine the likelihood of infection. However, the contrasting relationship between Pd and the bacterial microbiomes of Myotis lucifugus and Perimyotis subflavus indicate that we are just beginning to understand how the bat microbiome interacts with a fungal invader such as Pd.
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Affiliation(s)
- Meghan Ange-Stark
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Katy L. Parise
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Tina L. Cheng
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA
- Bat Conservation International, Austin, Texas, USA
| | - Joseph R. Hoyt
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Kate E. Langwig
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Winifred F. Frick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA
- Bat Conservation International, Austin, Texas, USA
| | - A. Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA
| | - John Gillece
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Matthew D. MacManes
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Jeffrey T. Foster
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
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Navine AK, Paxton KL, Paxton EH, Hart PJ, Foster JT, McInerney N, Fleischer RC, Videvall E. Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria-resistant introduced birds. Mol Ecol 2023; 32:6659-6670. [PMID: 36281504 DOI: 10.1111/mec.16743] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/30/2022]
Abstract
Of the estimated 55 Hawaiian honeycreepers (subfamily Carduelinae) only 17 species remain, nine of which the International Union for Conservation of Nature considers endangered. Among the most pressing threats to honeycreeper survival is avian malaria, caused by the introduced blood parasite Plasmodium relictum, which is increasing in distribution in Hawai'i as a result of climate change. Preventing further honeycreeper decline will require innovative conservation strategies that confront malaria from multiple angles. Research on mammals has revealed strong connections between gut microbiome composition and malaria susceptibility, illuminating a potential novel approach to malaria control through the manipulation of gut microbiota. One honeycreeper species, Hawai'i 'amakihi (Chlorodrepanis virens), persists in areas of high malaria prevalence, indicating they have acquired some level of immunity. To investigate if avian host-specific microbes may be associated with malaria survival, we characterized cloacal microbiomes and malaria infection for 174 'amakihi and 172 malaria-resistant warbling white-eyes (Zosterops japonicus) from Hawai'i Island using 16S rRNA gene metabarcoding and quantitative polymerase chain reaction. Neither microbial alpha nor beta diversity covaried with infection, but 149 microbes showed positive associations with malaria survivors. Among these were Escherichia and Lactobacillus spp., which appear to mitigate malaria severity in mammalian hosts, revealing promising candidates for future probiotic research for augmenting malaria immunity in sensitive endangered species.
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Affiliation(s)
- Amanda K Navine
- Biology Department, University of Hawai'i at Hilo, Hilo, Hawaii, USA
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Kristina L Paxton
- Hawai'i Cooperative Studies Unit, University of Hawai'i at Hilo, Hawai'i National Park, Hawaii, USA
| | - Eben H Paxton
- U.S. Geological Survey, Pacific Island Ecosystems Research Center, Hawai'i National Park, Hawaii, USA
| | - Patrick J Hart
- Biology Department, University of Hawai'i at Hilo, Hilo, Hawaii, USA
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Nancy McInerney
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Elin Videvall
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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4
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Laggan NA, Parise KL, White JP, Kaarakka HM, Redell JA, DePue JE, Scullon WH, Kath J, Foster JT, Kilpatrick AM, Langwig KE, Hoyt JR. Host infection and disease-induced mortality modify species contributions to the environmental reservoir. Ecology 2023; 104:e4147. [PMID: 37522873 DOI: 10.1002/ecy.4147] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/03/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023]
Abstract
Environmental pathogen reservoirs exist for many globally important diseases and can fuel epidemics, influence pathogen evolution, and increase the threat of host extinction. Species composition can be an important factor that shapes reservoir dynamics and ultimately determines the outcome of a disease outbreak. However, disease-induced mortality can change species communities, indicating that species responsible for environmental reservoir maintenance may change over time. Here we examine the reservoir dynamics of Pseudogymnoascus destructans, the fungal pathogen that causes white-nose syndrome in bats. We quantified changes in pathogen shedding, infection prevalence and intensity, host abundance, and the subsequent propagule pressure imposed by each species over time. We find that highly shedding species are important during pathogen invasion, but contribute less over time to environmental contamination as they also suffer the greatest declines. Less infected species remain more abundant, resulting in equivalent or higher propagule pressure. More broadly, we demonstrate that high infection intensity and subsequent mortality during disease progression can reduce the contributions of high-shedding species to long-term pathogen maintenance.
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Affiliation(s)
- Nichole A Laggan
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, Virginia, USA
| | - Katy L Parise
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - J Paul White
- Wisconsin Department of Natural Resources, Madison, Wisconsin, USA
| | | | | | - John E DePue
- Michigan Department of Natural Resources, Baraga, Michigan, USA
| | | | - Joseph Kath
- Illinois Department of Natural Resources, Springfield, Illinois, USA
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California, USA
| | - Kate E Langwig
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, Virginia, USA
| | - Joseph R Hoyt
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, Virginia, USA
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5
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Moreno E, Middlebrook EA, Altamirano-Silva P, Al Dahouk S, Araj GF, Arce-Gorvel V, Arenas-Gamboa Á, Ariza J, Barquero-Calvo E, Battelli G, Bertu WJ, Blasco JM, Bosilkovski M, Cadmus S, Caswell CC, Celli J, Chacón-Díaz C, Chaves-Olarte E, Comerci DJ, Conde-Álvarez R, Cook E, Cravero S, Dadar M, De Boelle X, De Massis F, Díaz R, Escobar GI, Fernández-Lago L, Ficht TA, Foster JT, Garin-Bastuji B, Godfroid J, Gorvel JP, Güler L, Erdenliğ-Gürbilek S, Gusi AM, Guzmán-Verri C, Hai J, Hernández-Mora G, Iriarte M, Jacob NR, Keriel A, Khames M, Köhler S, Letesson JJ, Loperena-Barber M, López-Goñi I, McGiven J, Melzer F, Mora-Cartin R, Moran-Gilad J, Muñoz PM, Neubauer H, O'Callaghan D, Ocholi R, Oñate Á, Pandey P, Pappas G, Pembroke JT, Roop M, Ruiz-Villalonos N, Ryan MP, Salcedo SP, Salvador-Bescós M, Sangari FJ, de Lima Santos R, Seimenis A, Splitter G, Suárez-Esquivel M, Tabbaa D, Trangoni MD, Tsolis RM, Vizcaíno N, Wareth G, Welburn SC, Whatmore A, Zúñiga-Ripa A, Moriyón I. If You're Not Confused, You're Not Paying Attention: Ochrobactrum Is Not Brucella. J Clin Microbiol 2023; 61:e0043823. [PMID: 37395662 PMCID: PMC10446859 DOI: 10.1128/jcm.00438-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023] Open
Abstract
Bacteria of the genus Brucella are facultative intracellular parasites that cause brucellosis, a severe animal and human disease. Recently, a group of taxonomists merged the brucellae with the primarily free-living, phylogenetically related Ochrobactrum spp. in the genus Brucella. This change, founded only on global genomic analysis and the fortuitous isolation of some opportunistic Ochrobactrum spp. from medically compromised patients, has been automatically included in culture collections and databases. We argue that clinical and environmental microbiologists should not accept this nomenclature, and we advise against its use because (i) it was presented without in-depth phylogenetic analyses and did not consider alternative taxonomic solutions; (ii) it was launched without the input of experts in brucellosis or Ochrobactrum; (iii) it applies a non-consensus genus concept that disregards taxonomically relevant differences in structure, physiology, population structure, core-pangenome assemblies, genome structure, genomic traits, clinical features, treatment, prevention, diagnosis, genus description rules, and, above all, pathogenicity; and (iv) placing these two bacterial groups in the same genus creates risks for veterinarians, medical doctors, clinical laboratories, health authorities, and legislators who deal with brucellosis, a disease that is particularly relevant in low- and middle-income countries. Based on all this information, we urge microbiologists, bacterial collections, genomic databases, journals, and public health boards to keep the Brucella and Ochrobactrum genera separate to avoid further bewilderment and harm.
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Affiliation(s)
- Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Earl A. Middlebrook
- Genomics and Bioanalytics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Pamela Altamirano-Silva
- Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Sascha Al Dahouk
- Department of Environmental Hygiene, German Environment Agency, Berlin, Germany
| | - George F. Araj
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Vilma Arce-Gorvel
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université, CNRS, INSERM, Marseille, France
| | - Ángela Arenas-Gamboa
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Javier Ariza
- Infectious Disease Department, Hospital Universitario de Bellvitge, Universidad de Barcelona, Barcelona, Spain
| | - Elías Barquero-Calvo
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Giorgio Battelli
- Department of Medical Veterinary Sciences, University of Bologna, Bologna, Italy
| | - Wilson J. Bertu
- Brucellosis Research Laboratory, Bacterial Research Division, National Veterinary Research Institute, Vom, Nigeria
| | - José María Blasco
- Departamento de Ciencia Animal, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Zaragoza, Spain
| | - Mile Bosilkovski
- University Hospital for Infectious Diseases and Febrile Conditions, Medical Faculty, Saints Cyril and Methodius University, Skopje, Republic of North Macedonia
| | - Simeon Cadmus
- Centre for Control and Prevention of Zoonoses, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Clayton C. Caswell
- Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia, USA
| | - Jean Celli
- Larner College of Medicine at the University of Vermont, Department of Microbiology and Molecular Genetics, Burlington, Vermont, USA
| | - Carlos Chacón-Díaz
- Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Esteban Chaves-Olarte
- Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Diego J. Comerci
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Raquel Conde-Álvarez
- Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Elizabeth Cook
- International Livestock Research Institute, Nairobi, Kenya
| | - Silvio Cravero
- Centro de Investigación en Ciencias Veterinarias y Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
| | - Maryam Dadar
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Xavier De Boelle
- Research Unit in Biology of Microorganisms, Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
| | - Fabrizio De Massis
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Ramón Díaz
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Gabriela I. Escobar
- Laboratorio de Brucelosis, Laboratorio Nacional de Referencia, INEI-ANLIS Dr. Carlos G. Malbrán, Buenos Aires, Argentina
| | - Luis Fernández-Lago
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Thomas A. Ficht
- Texas A&M University, Veterinary Pathobiology, College Station, Texas, USA
| | - Jeffrey T. Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Bruno Garin-Bastuji
- French Agency for Food, Environmental, and Occupational Health and Safety, Maisons-Alfort, France
| | - Jacques Godfroid
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries, and Economics, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Jean-Pierre Gorvel
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université, CNRS, INSERM, Marseille, France
| | - Leyla Güler
- MG Veterinary Diagnostic Laboratory, Meram, Konya, Turkey
| | - Sevil Erdenliğ-Gürbilek
- Harran University, Faculty of Veterinary Medicine, Microbiology Department, Şanlıurfa, Şanlıurfa, Turkey
| | - Amayel M. Gusi
- Brucellosis Research Laboratory, Bacterial Research Division, National Veterinary Research Institute, Vom, Nigeria
| | - Caterina Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Jiang Hai
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Beijing, People's Republic of China
| | - Gabriela Hernández-Mora
- Servicio Nacional de Salud Animal, Ministerio de Agricultura y Ganadería, Heredia, Costa Rica
| | - Maite Iriarte
- Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Nestor R. Jacob
- Hospital Argerich, Department of Infectious Diseases, Buenos Aires, Argentina
| | - Anne Keriel
- Centre National de Référence des Brucella, U1047, University of Montpellier/INSERM, CHU de Nîmes, Nimes, France
| | - Maamar Khames
- University of Medea, Faculty of Sciences, Department of Biology, Medea, Algeria
| | - Stephan Köhler
- Institut de Recherche en Infectiologie de Montpellier, CNRS, University of Montpellier, Montpellier, France
| | - Jean-Jacques Letesson
- Research Unit in Biology of Microorganisms, Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
| | - Maite Loperena-Barber
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Ignacio López-Goñi
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - John McGiven
- WOAH Reference Laboratory for Brucellosis, Animal and Plant Health Agency, Weybridge, United Kingdom
- FAO Reference Centre for Brucellosis, Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Falk Melzer
- Friedrich Loeffler Institut, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Ricardo Mora-Cartin
- Section of Rheumatology, Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Jacob Moran-Gilad
- Microbiology, Advanced Genomics, and Infection Control Applications Laboratory, Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Pilar M. Muñoz
- Departamento de Ciencia Animal, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Zaragoza, Spain
| | - Heinrich Neubauer
- Friedrich Loeffler Institut, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - David O'Callaghan
- Centre National de Référence des Brucella, U1047, University of Montpellier/INSERM, CHU de Nîmes, Nimes, France
| | - Reuben Ocholi
- Bacteriology, Parasitology, and Virology Department, National Veterinary Research Institute, Vom, Nigeria
| | - Ángel Oñate
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, Assam, India
| | - Georgios Pappas
- Institute of Continuing Medical Education of Ioannina, Ioannina, Greece
| | - J. Tony Pembroke
- School of Natural Sciences and Bernal Institute, University of Limerick, Limerick, Ireland
| | - Martin Roop
- Department of Microbiology and Immunology, East Carolina University School of Medicine, Greenville, North Carolina, USA
| | - Nazaret Ruiz-Villalonos
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Michael P. Ryan
- Department of Applied Science, Technological University of the Shanno, Limerick, Ireland
| | - Suzana P. Salcedo
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Miriam Salvador-Bescós
- Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Félix J. Sangari
- Instituto de Biomedicina y Biotecnología de Cantabria, Consejo Superior de Investigaciones Científicas, Universidad de Cantabria, Santander, Spain
| | - Renato de Lima Santos
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Aristarchos Seimenis
- Mediterranean Zoonoses Control Centre, World Health Organization, Athens, Greece
| | - Gary Splitter
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Marcela Suárez-Esquivel
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Darem Tabbaa
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Hama University, Hama, Syria
| | - Marcos David Trangoni
- Centro de Investigación en Ciencias Veterinarias y Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
| | - Renee M. Tsolis
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Nieves Vizcaíno
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Gamal Wareth
- Friedrich Loeffler Institut, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Susan C. Welburn
- Division of Infection and Pathway Medicine, Centre for Infectious Diseases, School of Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Adrian Whatmore
- WOAH Reference Laboratory for Brucellosis, Animal and Plant Health Agency, Weybridge, United Kingdom
- FAO Reference Centre for Brucellosis, Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Amaia Zúñiga-Ripa
- Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Ignacio Moriyón
- Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
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6
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Pereira CR, Neia RC, Silva SB, Williamson CHD, Gillece JD, O'Callaghan D, Foster JT, Oliveira IRC, Filho JSSB, Lage AP, Azevedo VAC, Dorneles EMS. Comparison of Brucella abortus population structure based on genotyping methods with different levels of resolution. J Microbiol Methods 2023:106772. [PMID: 37343840 DOI: 10.1016/j.mimet.2023.106772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/18/2023] [Accepted: 06/18/2023] [Indexed: 06/23/2023]
Abstract
Numerous genotyping techniques based on different principles and with different costs and levels of resolution are currently available for understanding the transmission dynamics of brucellosis worldwide. We aimed to compare the population structure of the genomes of 53 Brazilian Brucella abortus isolates using eight different genotyping methods: multiple-locus variable-number tandem-repeat analysis (MLVA8, MLVA11, MLVA16), multilocus sequence typing (MLST9, MLST21), core genome MLST (cgMLST) and two techniques based on single nucleotide polymorphism (SNP) detection (parSNP and NASP) from whole genomes. The strains were isolated from six different Brazilian states between 1977 and 2008 and had previously been analyzed using MLVA8, MLVA11, and MLVA16. Their whole genomes were sequenced, assembled, and subjected to MSLT9 MLST21, cgMLST, and SNP analyses. All the genotypes were compared by hierarchical grouping method based on the average distances between the correlation matrices of each technique. MLST9 and MLST21 had the lowest level of resolution, both revealing only four genotypes. MLVA8, MLVA11, and MLVA16 had progressively increasing levels of resolution as more loci were analyzed, identifying 6, 16, and 44 genotypes, respectively. cgMLST showed the highest level of resolution, identifying 45 genotypes, followed by the SNP-based methods, both of which had 44 genotypes. In the assessed population, MLVA was more discriminatory than MLST and was easier and cheaper to perform. SNP techniques and cgMLST provided the highest levels of resolution and the results from the two methods were in close agreement. In conclusion, the choice of genotyping technique can strongly affect one's ability to make meaningful epidemiological conclusions but is dependent on available resources: while the VNTR based techniques are more indicated to high prevalence scenarios, the WGS methods are the ones with the best discriminative power and therefore recommended for outbreaks investigation.
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Affiliation(s)
- Carine R Pereira
- Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Raquel C Neia
- Faculdade de Ciências Básicas, Universidade Federal Fluminense, Nova Friburgo, Rio de Janeiro, Brazil
| | - Saulo B Silva
- Escola de Ciências da Saúde, Univali, Itajaí, Santa Catarina, Brazil
| | | | - John D Gillece
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - David O'Callaghan
- Bacterial Virulence and Infectious Disease, University of Montpellier, Nimes, France
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Izabela R C Oliveira
- Departamento de Estatística, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Júlio S S B Filho
- Departamento de Estatística, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Andrey P Lage
- Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco A C Azevedo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Elaine M S Dorneles
- Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil.
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7
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Kailing MJ, Hoyt JR, White JP, Kaarakka HM, Redell JA, Leon AE, Rocke TE, DePue JE, Scullon WH, Parise KL, Foster JT, Kilpatrick AM, Langwig KE. Sex-biased infections scale to population impacts for an emerging wildlife disease. Proc Biol Sci 2023; 290:20230040. [PMID: 36946110 PMCID: PMC10031401 DOI: 10.1098/rspb.2023.0040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Demographic factors are fundamental in shaping infectious disease dynamics. Aspects of populations that create structure, like age and sex, can affect patterns of transmission, infection intensity and population outcomes. However, studies rarely link these processes from individual to population-scale effects. Moreover, the mechanisms underlying demographic differences in disease are frequently unclear. Here, we explore sex-biased infections for a multi-host fungal disease of bats, white-nose syndrome, and link disease-associated mortality between sexes, the distortion of sex ratios and the potential mechanisms underlying sex differences in infection. We collected data on host traits, infection intensity and survival of five bat species at 42 sites across seven years. We found females were more infected than males for all five species. Females also had lower apparent survival over winter and accounted for a smaller proportion of populations over time. Notably, female-biased infections were evident by early hibernation and likely driven by sex-based differences in autumn mating behaviour. Male bats were more active during autumn which likely reduced replication of the cool-growing fungus. Higher disease impacts in female bats may have cascading effects on bat populations beyond the hibernation season by limiting recruitment and increasing the risk of Allee effects.
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Affiliation(s)
- Macy J Kailing
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, VA 24061, USA
| | - Joseph R Hoyt
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, VA 24061, USA
| | - J Paul White
- Wisconsin Department of Natural Resources, Madison, WI 53707, USA
| | | | | | - Ariel E Leon
- US Geological Survey, National Wildlife Health Center, Madison, WI 53711, USA
| | - Tonie E Rocke
- US Geological Survey, National Wildlife Health Center, Madison, WI 53711, USA
| | - John E DePue
- Michigan Department of Natural Resources, Baraga, MI 49908, USA
| | | | - Katy L Parise
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA
| | - Kate E Langwig
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, VA 24061, USA
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8
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Szentivanyi T, McKee C, Jones G, Foster JT. Trends in Bacterial Pathogens of Bats: Global Distribution and Knowledge Gaps. Transbound Emerg Dis 2023. [DOI: 10.1155/2023/9285855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Bats have received considerable recent attention for infectious disease research because of their potential to host and transmit viruses, including Ebola, Hendra, Nipah, and multiple coronaviruses. These pathogens are occasionally transmitted from bats to wildlife, livestock, and to humans, directly or through other bridging (intermediate) hosts. Due to their public health relevance, zoonotic viruses are a primary focus of research attention. In contrast, other emerging pathogens of bats, such as bacteria, are vastly understudied despite their ubiquity and diversity. Here, we describe the currently known host ranges and geographic distributional patterns of potentially zoonotic bacterial genera in bats, using published presence-absence data of pathogen occurrence. We identify apparent gaps in our understanding of the distribution of these pathogens on a global scale. The most frequently detected bacterial genera in bats are Bartonella, Leptospira, and Mycoplasma. However, a wide variety of other potentially zoonotic bacterial genera are also occasionally found in bats, such as Anaplasma, Brucella, Borrelia, Coxiella, Ehrlichia, Francisella, Neorickettsia, and Rickettsia. The bat families Phyllostomidae, Vespertilionidae, and Pteropodidae are most frequently reported as hosts of bacterial pathogens; however, the presence of at least one bacterial genus was confirmed in all 15 bat families tested. On a spatial scale, molecular diagnostics of samples from 58 countries and four overseas departments and island states (French Guiana, Mayotte, New Caledonia, and Réunion Island) reported testing for at least one bacterial pathogen in bats. We also identified geographical areas that have been mostly neglected during bacterial pathogen research in bats, such as the Afrotropical region and Southern Asia. Current knowledge on the distribution of potentially zoonotic bacterial genera in bats is strongly biased by research effort towards certain taxonomic groups and geographic regions. Identifying these biases can guide future surveillance efforts, contributing to a better understanding of the ecoepidemiology of zoonotic pathogens in bats.
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9
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Langwig KE, Kilpatrick AM, Kailing MJ, Laggan NA, White JP, Kaarakka HM, Redell JA, DePue JE, Parise KL, Foster JT, Hoyt JR. Shifting effects of host physiological condition following pathogen establishment. Biol Lett 2023; 19:20220574. [PMID: 36855852 PMCID: PMC9975657 DOI: 10.1098/rsbl.2022.0574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
Understanding host persistence with emerging pathogens is essential for conserving populations. Hosts may initially survive pathogen invasions through pre-adaptive mechanisms. However, whether pre-adaptive traits are directionally selected to increase in frequency depends on the heritability and environmental dependence of the trait and the costs of trait maintenance. Body condition is likely an important pre-adaptive mechanism aiding in host survival, although can be seasonally variable in wildlife hosts. We used data collected over 7 years on bat body mass, infection and survival to determine the role of host body condition during the invasion and establishment of the emerging disease, white-nose syndrome. We found that when the pathogen first invaded, bats with higher body mass were more likely to survive, but this effect dissipated following the initial epizootic. We also found that heavier bats lost more weight overwinter, but fat loss depended on infection severity. Lastly, we found mixed support that bat mass increased in the population after pathogen arrival; high annual plasticity in individual bat masses may have reduced the potential for directional selection. Overall, our results suggest that some factors that contribute to host survival during pathogen invasion may diminish over time and are potentially replaced by other host adaptations.
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Affiliation(s)
- Kate E Langwig
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, VA 24061, USA
| | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA
| | - Macy J Kailing
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, VA 24061, USA
| | - Nichole A Laggan
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, VA 24061, USA
| | - J Paul White
- Wisconsin Department of Natural Resources, Madison, WI 53707, USA
| | | | | | - John E DePue
- Michigan Department of Natural Resources, Baraga, MI 49908, USA
| | - Katy L Parise
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Joseph R Hoyt
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, VA 24061, USA
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10
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Hoyt JR, Parise KL, DePue JE, Kaarakka HM, Redell JA, Scullon WH, O’Reskie R, Foster JT, Kilpatrick AM, Langwig KE, White JP. Reducing environmentally mediated transmission to moderate impacts of an emerging wildlife disease. J Appl Ecol 2023. [DOI: 10.1111/1365-2664.14371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Affiliation(s)
- Joseph R. Hoyt
- Department of Biological Sciences, Virginia Tech Blacksburg VA USA
| | - Katy L. Parise
- Pathogen and Microbiome Institute Northern Arizona University Flagstaff AZ USA
| | - John E. DePue
- Michigan Department of Natural Resources, Baraga MI USA
| | - Heather M. Kaarakka
- Wisconsin Department of Natural Resources, Bureau of Natural Heritage Conservation Madison WI USA
| | - Jennifer A. Redell
- Wisconsin Department of Natural Resources, Bureau of Natural Heritage Conservation Madison WI USA
| | | | | | - Jeffrey T. Foster
- Pathogen and Microbiome Institute Northern Arizona University Flagstaff AZ USA
| | - A. Marm Kilpatrick
- Department of Ecology and Evolutionary Biology University of California Santa Cruz CA USA
| | - Kate E. Langwig
- Department of Biological Sciences, Virginia Tech Blacksburg VA USA
| | - J. Paul White
- Pathogen and Microbiome Institute Northern Arizona University Flagstaff AZ USA
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11
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Pereira CR, de Jesus Sousa T, Lima da Silva A, Gonçalves Dos Santos R, Minharro S, Costa Custódio DA, Pickard DJ, O'Callaghan D, Foster JT, de Castro Soares S, Juca Ramos RT, Góes-Neto A, Matiuzzi da Costa M, Lage AP, Azevedo V, Seles Dorneles EM. First report and whole-genome sequencing of Pseudochrobactrum saccharolyticum in Latin America. Microbes Infect 2023; 25:105018. [PMID: 35940401 DOI: 10.1016/j.micinf.2022.105018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/24/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023]
Abstract
The Brucellaceae family comprises microorganisms similar both phenotypically and genotypically, making it difficult to identify the etiological agent of these infections. This study reports the first isolation, identification, and characterization of Pseudochrobactrum saccharolyticum (strain 115) from Latin America. Strain 115 was isolated in 2007 from a bovine in Brazil and was initially classified as Brucella spp. by classical microbiological tests and bcsp31 PCR. The antimicrobial susceptibility of strain 115 was tested against drugs used to treat human brucellosis by minimal inhibitory concentration test. Subsequently, the whole genome of the strain was sequenced, assembled, and characterized. Phylogenetic trees built from 16S rRNA and recA gene sequences enabled the classification of strain 115 as Pseudochrobactrum spp. Phylogenomic analysis using Single Nucleotide Polymorphisms and Average Nucleotide Identity allowed the classification of the strain as P. saccharolyticum. Additionally, a Tetra Correlation Search identified one related genome from the same species, which was compared with strain 115 by analyzing genomic islands. This is the first identification and whole-genome sequence of P. saccharolyticum in Latin America and highlights a challenge in the diagnosis of bovine brucellosis, which could be solved by including the sequencing of 16S rRNA and recA genes in routine diagnostics.
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Affiliation(s)
- Carine Rodrigues Pereira
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Thiago de Jesus Sousa
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Alessandra Lima da Silva
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Roselane Gonçalves Dos Santos
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sílvia Minharro
- Centro de Ciência da Saúde - Medicina - Araguaína, Universidade Federal de Tocantins, Tocantins, Brazil
| | - Dirceia Aparecida Costa Custódio
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Derek J Pickard
- Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, United Kingdom
| | - David O'Callaghan
- IVBIC, INSERM, Universite de Montpellier, Nimes, France; CNR Brucella, Laboratoire de Microbiologie, CHU Nimes, Nimes, France
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Siomar de Castro Soares
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Biológicas e Ciências Naturais, Universidade Federal Do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Rommel Thiago Juca Ramos
- Instituto de Ciências Biológicas, Centro de Genômica e Biologia de Sistemas, Universidade Federal Do Pará, Belém, Pará, Brazil
| | - Aristóteles Góes-Neto
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Mateus Matiuzzi da Costa
- Universidade Federal Do Vale Do São Francisco, Departamento de Zootecnia, Petrolina, Pernambuco, Brazil
| | - Andrey Pereira Lage
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Elaine Maria Seles Dorneles
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil.
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12
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Vizentin-Bugoni J, Sperry JH, Kelley JP, Foster JT, Drake DR, Case SB, Gleditsch JM, Hruska AM, Wilcox RC, Tarwater CE. Mechanisms underlying interaction frequencies and robustness in a novel seed dispersal network: lessons for restoration. Proc Biol Sci 2022; 289:20221490. [PMID: 36100025 PMCID: PMC9470274 DOI: 10.1098/rspb.2022.1490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 08/15/2022] [Indexed: 12/25/2022] Open
Abstract
As human-caused extinctions and invasions accumulate across the planet, understanding the processes governing ecological functions mediated by species interactions, and anticipating the effect of species loss on such functions become increasingly urgent. In seed dispersal networks, the mechanisms that influence interaction frequencies may also influence the capacity of a species to switch to alternative partners (rewiring), influencing network robustness. Studying seed dispersal interactions in novel ecosystems on O'ahu island, Hawai'i, we test whether the same mechanisms defining interaction frequencies can regulate rewiring and increase network robustness to simulated species extinctions. We found that spatial and temporal overlaps were the primary mechanisms underlying interaction frequencies, and the loss of the more connected species affected networks to a greater extent. Further, rewiring increased network robustness, and morphological matching and spatial and temporal overlaps between partners were more influential on network robustness than species abundances. We argue that to achieve self-sustaining ecosystems, restoration initiatives can consider optimal morphological matching and spatial and temporal overlaps between consumers and resources to maximize chances of native plant dispersal. Specifically, restoration initiatives may benefit from replacing invasive species with native species possessing characteristics that promote frequent interactions and increase the probability of rewiring (such as long fruiting periods, small seeds and broad distributions).
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Affiliation(s)
- Jeferson Vizentin-Bugoni
- Departamento de Ecologia, Universidade Federal do Rio Grande do Sul, Avenue Bento Gonçalves 9500, Porto Alegre, Rio Grande do Sul 91501-970, Brazil
- US Army Corps of Engineers, Engineer Research Development Center, 2902 Newmark Dr, Champaign, IL 61826, USA
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, 1102 South Goodwin Avenue, Urbana, IL 61801, USA
- Department of Zoology and Physiology, University of Wyoming, 1000 East University Avenue, Laramie, WY 82071, USA
| | - Jinelle H. Sperry
- US Army Corps of Engineers, Engineer Research Development Center, 2902 Newmark Dr, Champaign, IL 61826, USA
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, 1102 South Goodwin Avenue, Urbana, IL 61801, USA
| | - J. Patrick Kelley
- Department of Zoology and Physiology, University of Wyoming, 1000 East University Avenue, Laramie, WY 82071, USA
| | - Jeffrey T. Foster
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Donald R. Drake
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, HI 96822, USA
| | - Samuel B. Case
- Department of Zoology and Physiology, University of Wyoming, 1000 East University Avenue, Laramie, WY 82071, USA
| | - Jason M. Gleditsch
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, 1102 South Goodwin Avenue, Urbana, IL 61801, USA
- Integrative Ecology Laboratory, Center for Biodiversity, Temple University, Philadelphia, PA 19122, USA
| | - Amy M. Hruska
- Department of Botany, University of Hawai‘i at Mānoa, Honolulu, HI 96822, USA
- Smithsonian Environmental Research Center, Edgewater, MD 21037, USA
| | - Rebecca C. Wilcox
- Department of Zoology and Physiology, University of Wyoming, 1000 East University Avenue, Laramie, WY 82071, USA
| | - Corey E. Tarwater
- Department of Zoology and Physiology, University of Wyoming, 1000 East University Avenue, Laramie, WY 82071, USA
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13
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O'Rourke D, Rouillard NP, Parise KL, Foster JT. Spatial and temporal variation in New Hampshire bat diets. Sci Rep 2022; 12:14334. [PMID: 35995911 PMCID: PMC9395357 DOI: 10.1038/s41598-022-17631-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022] Open
Abstract
Insectivorous bats consume a diverse array of arthropod prey, with diets varying by bat species, sampling location, and season. North American bat diets remain incompletely described, which is concerning at a time when many bat and insect populations appear to be declining. Understanding the variability in foraging is thus an essential component for effective bat conservation. To comprehensively evaluate local foraging, we assessed the spatial and temporal variability in prey consumed by the little brown bat, Myotis lucifugus, in New Hampshire, USA. We collected bat guano samples from 20 sites over 2 years and analyzed sequence data for 899 of these samples using a molecular metabarcoding approach targeting the cytochrome oxidase I subunit (COI) gene. Some prey items were broadly shared across locations and sampling dates, with the most frequently detected arthropod orders broadly similar to previous morphological and molecular analyses; at least one representative sequence variant was assigned to Coleoptera in 92% of samples, with other frequently detected orders including Diptera (73%), Lepidoptera (65%), Trichoptera (38%), and Ephemeroptera (32%). More specifically, two turf and forest pests were routinely detected: white grubs in the genus Phyllophaga (50%), and the Asiatic Garden beetle, Maladera castanea (36%). Despite the prevalence of a few taxa shared among many samples and distinct seasonal peaks in consumption of specific arthropods, diet composition varied both temporally and spatially. However, species richness did not strongly vary indicating consumption of a broad diversity of taxa throughout the summer. These data characterize little brown bats as flexible foragers adept at consuming a broad array of locally available prey resources.
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Affiliation(s)
- Devon O'Rourke
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA. .,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
| | - Nicholas P Rouillard
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Katy L Parise
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jeffrey T Foster
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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14
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Case SB, Postelli K, Drake DR, Vizentin-Bugoni J, Foster JT, Sperry JH, Kelley JP, Tarwater CE. Introduced galliforms as seed predators and dispersers in Hawaiian forests. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02830-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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15
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Yang Y, Foster JT, Yi M, Zhan L, Zhang Y, Zhou B, Jiang J, Mei L. Phenotypic homogeneity of emetic Bacillus cereus isolates in China. Lett Appl Microbiol 2021; 73:646-651. [PMID: 34173253 DOI: 10.1111/lam.13527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 11/26/2022]
Abstract
Emetic Bacillus cereus strains produce a potent cereulide cytotoxin, which can cause acute and fatal cases of food poisoning. We isolated 18 emetic B. cereus strains from a food poisoning event, and from clinical and non-random food surveillance in China and phenotypic characteristics of haemolysis, starch hydrolysis, salicin fermentation, gelatin liquefaction, cytotoxicity, and susceptibility to antibiotics were assessed. All isolates were positive for haemolysis and gelatin liquefaction, and negative for starch hydrolysis and salicin fermentation. Their haemolytic potentials were intermediate to Bacillus anthracis and B. cereus ATCC 14579 (a non-emetic strain). All isolates were cytotoxic to CHO, Hep-2, and Vero cells, and were sensitive to ampicillin. The homogeneous phenotypes of emetic isolates from China are similar to the corresponding traits of European and Japanese isolates that have been characterized, suggesting highly similar phenotypes of emetic B. cereus worldwide.
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Affiliation(s)
- Y Yang
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - J T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - M Yi
- Guangzhou Customs Technology Center, Guangzhou, China
| | - L Zhan
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Y Zhang
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - B Zhou
- Department of Science Technology and Information, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - J Jiang
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - L Mei
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
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16
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Bechtel MJ, Drake KK, Esque TC, Nieto NC, Foster JT, Teglas MB. Borreliosis Transmission from Ticks Associated with Desert Tortoise Burrows: Examples of Tick-Borne Relapsing Fever in the Mojave Desert. Vector Borne Zoonotic Dis 2021; 21:635-637. [PMID: 34143676 DOI: 10.1089/vbz.2021.0005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ticks transmit pathogens and parasitize wildlife in turn causing zoonotic diseases in many ecosystems. Argasid ticks, such as Ornithodoros spp., harbor and transmit Borrelia spp., resulting in tick-borne relapsing fever (TBRF) in people. In the western United States, TBRF is typically associated with the bite of an infected Ornithodoros hermsi tick found in habitats at high elevations (>1500 ft). This report describes the first TBRF cases in people in the Mojave Desert (Clark County, NV). Individuals documented in these case studies were exposed to Ornithodoros ticks during excavation of soil burrows associated with Mojave Desert tortoises (Gopherus agassizii), with bacteria from one of the human case's blood sample genetically matching to Borrelia turicatae as determined by quantitative PCR and sequencing. Our findings should serve as a precaution to individuals working with tortoises or animal burrows, or those in contact with Ornithodoros ticks in this region.
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Affiliation(s)
- Molly J Bechtel
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA.,Pathogen and Microbiome Institute, Flagstaff, Arizona, USA
| | - Karla Kristina Drake
- U.S. Geological Survey, Western Ecological Research Center, Henderson, Nevada, USA
| | - Todd C Esque
- U.S. Geological Survey, Western Ecological Research Center, Henderson, Nevada, USA
| | - Nathan C Nieto
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jeffrey T Foster
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA.,Pathogen and Microbiome Institute, Flagstaff, Arizona, USA
| | - Mike B Teglas
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada-Reno, Reno, Nevada, USA
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17
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Ridenour CL, Cocking J, Poidmore S, Erickson D, Brock B, Valentine M, Roe CC, Young SJ, Henke JA, Hung KY, Wittie J, Stefanakos E, Sumner C, Ruedas M, Raman V, Seaton N, Bendik W, Hornstra O'Neill HM, Sheridan K, Centner H, Lemmer D, Fofanov V, Smith K, Will J, Townsend J, Foster JT, Keim PS, Engelthaler DM, Hepp CM. St. Louis Encephalitis Virus in the Southwestern United States: A Phylogeographic Case for a Multi-Variant Introduction Event. Front Genet 2021; 12:667895. [PMID: 34168675 PMCID: PMC8217752 DOI: 10.3389/fgene.2021.667895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/28/2021] [Indexed: 11/14/2022] Open
Abstract
Since the reemergence of St. Louis Encephalitis (SLE) Virus (SLEV) in the Southwest United States, identified during the 2015 outbreak in Arizona, SLEV has been seasonally detected within Culex spp. populations throughout the Southwest United States. Previous work revealed the 2015 outbreak was caused by an importation of SLEV genotype III, which had only been detected previously in Argentina. However, little is known about when the importation occurred or the transmission and genetic dynamics since its arrival into the Southwest. In this study, we sought to determine whether the annual detection of SLEV in the Southwest is due to enzootic cycling or new importations. To address this question, we analyzed 174 SLEV genomes (142 sequenced as part of this study) using Bayesian phylogenetic analyses to estimate the date of arrival into the American Southwest and characterize the underlying population structure of SLEV. Phylogenetic clustering showed that SLEV variants circulating in Maricopa and Riverside counties form two distinct populations with little evidence of inter-county transmission since the onset of the outbreak. Alternatively, it appears that in 2019, Yuma and Clark counties experienced annual importations of SLEV that originated in Riverside and Maricopa counties. Finally, the earliest representatives of SLEV genotype III in the Southwest form a polytomy that includes both California and Arizona samples. We propose that the initial outbreak most likely resulted from the importation of a population of SLEV genotype III variants, perhaps in multiple birds, possibly multiple species, migrating north in 2013, rather than a single variant introduced by one bird.
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Affiliation(s)
- Chase L Ridenour
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States.,The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Jill Cocking
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States.,The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Samuel Poidmore
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Daryn Erickson
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Breezy Brock
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Michael Valentine
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Chandler C Roe
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States.,The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Steven J Young
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ, United States
| | - Jennifer A Henke
- Coachella Valley Mosquito and Vector Control District, Indio, CA, United States
| | - Kim Y Hung
- Coachella Valley Mosquito and Vector Control District, Indio, CA, United States
| | - Jeremy Wittie
- Coachella Valley Mosquito and Vector Control District, Indio, CA, United States
| | | | - Chris Sumner
- Yuma County Pest Abatement District, Yuma, AZ, United States
| | - Martha Ruedas
- Yuma County Pest Abatement District, Yuma, AZ, United States
| | - Vivek Raman
- Southern Nevada Health District, Las Vegas, NV, United States
| | - Nicole Seaton
- Southern Nevada Health District, Las Vegas, NV, United States
| | - William Bendik
- Southern Nevada Health District, Las Vegas, NV, United States
| | | | - Krystal Sheridan
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States.,Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Heather Centner
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Darrin Lemmer
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Viacheslav Fofanov
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States.,The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Kirk Smith
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ, United States
| | - James Will
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ, United States
| | - John Townsend
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ, United States
| | - Jeffrey T Foster
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Paul S Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States.,Translational Genomics Research Institute, Flagstaff, AZ, United States
| | | | - Crystal M Hepp
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States.,The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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18
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Rouzic N, Desmier L, Cariou ME, Gay E, Foster JT, Williamson CHD, Schmitt F, Le Henaff M, Le Coz A, Lorléac'h A, Lavigne JP, O'Callaghan D, Keriel A. First Case of Brucellosis Caused by an Amphibian-type Brucella. Clin Infect Dis 2021; 72:e404-e407. [PMID: 32719850 DOI: 10.1093/cid/ciaa1082] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/24/2020] [Indexed: 11/12/2022] Open
Abstract
We report the first case of brucellosis caused by an isolate whose genome is identical that of a frog isolate from Texas, demonstrating the zoonotic potential of amphibian-type Brucella. Importantly, with such atypical Brucella, correct diagnosis cannot be performed using routine serological tests or identification methods.
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Affiliation(s)
- Nicolas Rouzic
- Unité de Médecine Interne-Maladies Infectieuses, Groupe Hospitalier Bretagne Sud, Lorient, France
| | - Ludovic Desmier
- Centre National de Référence (CNR) des Brucella, CHU de Nîmes, Nîmes, France.,VBMI, U1047, INSERM, Université de Montpellier, Nîmes, France
| | - Marie-Estelle Cariou
- Laboratoire de biologie médicale, Groupe Hospitalier Bretagne Sud, Lorient, France
| | - Eugénie Gay
- Laboratoire de biologie médicale, Groupe Hospitalier Bretagne Sud, Lorient, France
| | - Jeffrey T Foster
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, USA
| | - Charles H D Williamson
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, USA
| | - François Schmitt
- Laboratoire de biologie médicale, Groupe Hospitalier Bretagne Sud, Lorient, France
| | - Mikael Le Henaff
- Service de Pneumologie, Groupe Hospitalier Bretagne Sud, Lorient, France
| | - Alain Le Coz
- Service de Pneumologie, Groupe Hospitalier Bretagne Sud, Lorient, France
| | - Aurélien Lorléac'h
- Unité de Médecine Interne-Maladies Infectieuses, Groupe Hospitalier Bretagne Sud, Lorient, France
| | - Jean-Philippe Lavigne
- Centre National de Référence (CNR) des Brucella, CHU de Nîmes, Nîmes, France.,VBMI, U1047, INSERM, Université de Montpellier, Nîmes, France
| | - David O'Callaghan
- Centre National de Référence (CNR) des Brucella, CHU de Nîmes, Nîmes, France.,VBMI, U1047, INSERM, Université de Montpellier, Nîmes, France
| | - Anne Keriel
- Centre National de Référence (CNR) des Brucella, CHU de Nîmes, Nîmes, France.,VBMI, U1047, INSERM, Université de Montpellier, Nîmes, France
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19
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Whatmore AM, Foster JT. Emerging diversity and ongoing expansion of the genus Brucella. Infect Genet Evol 2021; 92:104865. [PMID: 33872784 DOI: 10.1016/j.meegid.2021.104865] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022]
Abstract
Remarkable genetic diversity and breadth of host species has been uncovered in the Brucella genus over the past decade, fundamentally changing our concept of what it means to be a Brucella. From ocean fishes and marine mammals, to pond dwelling amphibians, forest foxes, desert rodents, and cave-dwelling bats, Brucella have revealed a variety of previously unknown niches. Classical microbiological techniques have been able to help us classify many of these new strains but at times have limited our ability to see the true relationships among or within species. The closest relatives of Brucella are soil bacteria and the adaptations of Brucella spp. to live intracellularly suggest that the genus has evolved to live in vertebrate hosts. Several recently discovered species appear to have phenotypes that are intermediate between soil bacteria and core Brucella, suggesting that they may represent ancestral traits that were subsequently lost in the traditional species. Remarkably, the broad relationships among Brucella species using a variety of sequence and fragment-based approaches have been upheld when using comparative genomics with whole genomes. Nonetheless, genomes are required for fine-scale resolution of many of the relationships and for understanding the evolutionary history of the genus. We expect that the coming decades will reveal many more hosts and previously unknown diversity in a wide range of environments.
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Affiliation(s)
- Adrian M Whatmore
- OIE and FAO Brucellosis Reference Laboratory, Department of Bacteriology, Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey, United Kingdom.
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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20
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Langwig KE, White JP, Parise KL, Kaarakka HM, Redell JA, DePue JE, Scullon WH, Foster JT, Kilpatrick AM, Hoyt JR. Mobility and infectiousness in the spatial spread of an emerging fungal pathogen. J Anim Ecol 2021; 90:1134-1141. [PMID: 33550607 PMCID: PMC8248334 DOI: 10.1111/1365-2656.13439] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 01/11/2021] [Indexed: 12/26/2022]
Abstract
Emerging infectious diseases can have devastating effects on host communities, causing population collapse and species extinctions. The timing of novel pathogen arrival into naïve species communities can have consequential effects that shape the trajectory of epidemics through populations. Pathogen introductions are often presumed to occur when hosts are highly mobile. However, spread patterns can be influenced by a multitude of other factors including host body condition and infectiousness. White-nose syndrome (WNS) is a seasonal emerging infectious disease of bats, which is caused by the fungal pathogen Pseudogymnoascus destructans. Within-site transmission of P. destructans primarily occurs over winter; however, the influence of bat mobility and infectiousness on the seasonal timing of pathogen spread to new populations is unknown. We combined data on host population dynamics and pathogen transmission from 22 bat communities to investigate the timing of pathogen arrival and the consequences of varying pathogen arrival times on disease impacts. We found that midwinter arrival of the fungus predominated spread patterns, suggesting that bats were most likely to spread P. destructans when they are highly infectious, but have reduced mobility. In communities where P. destructans was detected in early winter, one species suffered higher fungal burdens and experienced more severe declines than at sites where the pathogen was detected later in the winter, suggesting that the timing of pathogen introduction had consequential effects for some bat communities. We also found evidence of source-sink population dynamics over winter, suggesting some movement among sites occurs during hibernation, even though bats at northern latitudes were thought to be fairly immobile during this period. Winter emergence behaviour symptomatic of white-nose syndrome may further exacerbate these winter bat movements to uninfected areas. Our results suggest that low infectiousness during host migration may have reduced the rate of expansion of this deadly pathogen, and that elevated infectiousness during winter plays a key role in seasonal transmission. Furthermore, our results highlight the importance of both accurate estimation of the timing of pathogen spread and the consequences of varying arrival times to prevent and mitigate the effects of infectious diseases.
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Affiliation(s)
- Kate E Langwig
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, VA, USA
| | - J Paul White
- Wisconsin Department of Natural Resources, Madison, WI, USA
| | - Katy L Parise
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | | | - John E DePue
- Michigan Department of Natural Resources, Baraga, MI, USA
| | | | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Joseph R Hoyt
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, VA, USA
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21
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O'Rourke DR, Mangan MT, Mangan KE, Bokulich NA, MacManes MD, Foster JT. Lord of the Diptera (and Moths and a Spider): Molecular Diet Analyses and Foraging Ecology of Indiana Bats in Illinois. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.623655] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Effective management of endangered or threatened wildlife requires an understanding of how foraging habitats are used by those populations. Molecular diet analysis of fecal samples offers a cost-effective and non-invasive method to investigate how diets of wild populations vary with respect to spatial and temporal factors. For the federally endangered Indiana bat (Myotis sodalis), documenting its preferred food sources can provide critical information to promote effective conservation of this federally endangered species. Using cytochrome oxidase I amplicon sequence data from Indiana bat guano samples collected at two roosting areas in Cypress Creek National Wildlife Refuge, we found that dipteran taxa (i.e., flies) associated with riparian habitats were the most frequently detected taxon and represented the majority of the sequence diversity among the arthropods sampled. A select few arthropods from other taxa—especially spiders—are also likely important to Indiana bat diets in this refuge. A supervised learning analysis of diet components suggest only a small fraction of the frequently detected taxa are important contributors to spatial and temporal variation. Overall, these data depict the Indiana bat as a generalist consumer whose diet includes some prey items associated with particular seasonal or spatial components, along with other taxa repeatedly consumed throughout the entire foraging season. These molecular diet analyses suggest that protecting foraging resources specifically associated with the riparian habitat of Cypress Creek National Wildlife Refuge is essential to promote effective Indiana bat conservation.
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22
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van Dijk JGB, Iverson SA, Gilchrist HG, Harms NJ, Hennin HL, Love OP, Buttler EI, Lesceu S, Foster JT, Forbes MR, Soos C. Herd immunity drives the epidemic fadeout of avian cholera in Arctic-nesting seabirds. Sci Rep 2021; 11:1046. [PMID: 33441657 PMCID: PMC7806777 DOI: 10.1038/s41598-020-79888-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 12/14/2020] [Indexed: 11/09/2022] Open
Abstract
Avian cholera, caused by the bacterium Pasteurella multocida, is a common and important infectious disease of wild birds in North America. Between 2005 and 2012, avian cholera caused annual mortality of widely varying magnitudes in Northern common eiders (Somateria mollissima borealis) breeding at the largest colony in the Canadian Arctic, Mitivik Island, Nunavut. Although herd immunity, in which a large proportion of the population acquires immunity to the disease, has been suggested to play a role in epidemic fadeout, immunological studies exploring this hypothesis have been missing. We investigated the role of three potential drivers of fadeout of avian cholera in eiders, including immunity, prevalence of infection, and colony size. Each potential driver was examined in relation to the annual real-time reproductive number (Rt) of P. multocida, previously calculated for eiders at Mitivik Island. Each year, colony size was estimated and eiders were closely monitored, and evaluated for infection and serological status. We demonstrate that acquired immunity approximated using antibody titers to P. multocida in both sexes was likely a key driver for the epidemic fadeout. This study exemplifies the importance of herd immunity in influencing the dynamics and fadeout of epidemics in a wildlife population.
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Affiliation(s)
- Jacintha G B van Dijk
- Department of Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada.,Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, 391 82, Kalmar, Sweden
| | - Samuel A Iverson
- Department of Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada.,Environment and Climate Change Canada, Canadian Wildlife Service, Gatineau, QC, K1A 0H3, Canada
| | - H Grant Gilchrist
- Department of Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada.,Environment and Climate Change Canada, National Wildlife Research Center, Ottawa, ON, K1S 5B6, Canada
| | - N Jane Harms
- Department of Veterinary Pathology, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada.,Environment Yukon, Animal Health Unit, Whitehorse, YT, Y1A 4Y9, Canada
| | - Holly L Hennin
- Environment and Climate Change Canada, National Wildlife Research Center, Ottawa, ON, K1S 5B6, Canada.,Department of Integrative Biology, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Oliver P Love
- Department of Integrative Biology, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - E Isabel Buttler
- Department of Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | | | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Mark R Forbes
- Department of Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Catherine Soos
- Department of Veterinary Pathology, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada. .,Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, Saskatoon, SK, S7N 0X4, Canada.
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23
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Janowicz A, De Massis F, Zilli K, Ancora M, Tittarelli M, Sacchini F, Di Giannatale E, Sahl JW, Foster JT, Garofolo G. Evolutionary history and current distribution of the West Mediterranean lineage of Brucella melitensis in Italy. Microb Genom 2020; 6. [PMID: 33030422 PMCID: PMC7725330 DOI: 10.1099/mgen.0.000446] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ovine and caprine brucellosis, caused by Brucella melitensis, is one of the world’s most widespread zoonoses and is a major cause of economic losses in domestic ruminant production. In Italy, the disease remains endemic in several southern provinces, despite an ongoing brucellosis eradication programme. In this study, we used whole-genome sequencing to detail the genetic diversity of circulating strains, and to examine the origins of the predominant sub-lineages of B. melitensis in Italy. We reconstructed a global phylogeny of B. melitensis, strengthened by 339 new whole-genome sequences, from Italian isolates collected from 2011 to 2018 as part of a national livestock surveillance programme. All Italian strains belonged to the West Mediterranean lineage, which further divided into two major clades that diverged roughly between the 5th and 7th centuries. We observed that Sicily serves as a brucellosis burden hotspot, giving rise to several distinct sub-lineages. More than 20 putative outbreak clusters of ovine and caprine brucellosis were identified, several of which persisted over the 8 year survey period despite an aggressive brucellosis eradication campaign. While the outbreaks in Central and Northern Italy were generally associated with introductions of single clones of B. melitensis and their subsequent dissemination within neighbouring territories, we observed weak geographical segregation of genotypes in the southern regions. Biovar determination, recommended in routine analysis of all Brucella strains by the World Organisation for Animal Health (OIE), could not discriminate among the four main global clades. This demonstrates a need for updating the guidelines used for monitoring B. melitensis transmission and spread, both at the national and international level, and to include whole-genome-based typing as the principal method for identification and tracing of brucellosis outbreaks.
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Affiliation(s)
- Anna Janowicz
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", via Campo Boario, 64100 Teramo, Italy
| | - Fabrizio De Massis
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", via Campo Boario, 64100 Teramo, Italy
| | - Katiuscia Zilli
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", via Campo Boario, 64100 Teramo, Italy
| | - Massimo Ancora
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", via Campo Boario, 64100 Teramo, Italy
| | - Manuela Tittarelli
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", via Campo Boario, 64100 Teramo, Italy
| | - Flavio Sacchini
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", via Campo Boario, 64100 Teramo, Italy
| | - Elisabetta Di Giannatale
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", via Campo Boario, 64100 Teramo, Italy
| | - Jason W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Giuliano Garofolo
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", via Campo Boario, 64100 Teramo, Italy
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24
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O'Rourke DR, Bokulich NA, Jusino MA, MacManes MD, Foster JT. A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses. Ecol Evol 2020; 10:9721-9739. [PMID: 33005342 PMCID: PMC7520210 DOI: 10.1002/ece3.6594] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 01/01/2023] Open
Abstract
Metabarcoding studies provide a powerful approach to estimate the diversity and abundance of organisms in mixed communities in nature. While strategies exist for optimizing sample and sequence library preparation, best practices for bioinformatic processing of amplicon sequence data are lacking in animal diet studies. Here we evaluate how decisions made in core bioinformatic processes, including sequence filtering, database design, and classification, can influence animal metabarcoding results. We show that denoising methods have lower error rates compared to traditional clustering methods, although these differences are largely mitigated by removing low-abundance sequence variants. We also found that available reference datasets from GenBank and BOLD for the animal marker gene cytochrome oxidase I (COI) can be complementary, and we discuss methods to improve existing databases to include versioned releases. Taxonomic classification methods can dramatically affect results. For example, the commonly used Barcode of Life Database (BOLD) Classification API assigned fewer names to samples from order through species levels using both a mock community and bat guano samples compared to all other classifiers (vsearch-SINTAX and q2-feature-classifier's BLAST + LCA, VSEARCH + LCA, and Naive Bayes classifiers). The lack of consensus on bioinformatics best practices limits comparisons among studies and may introduce biases. Our work suggests that biological mock communities offer a useful standard to evaluate the myriad computational decisions impacting animal metabarcoding accuracy. Further, these comparisons highlight the need for continual evaluations as new tools are adopted to ensure that the inferences drawn reflect meaningful biology instead of digital artifacts.
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Affiliation(s)
- Devon R. O'Rourke
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNHUSA
- Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffAZUSA
| | - Nicholas A. Bokulich
- Laboratory of Food Systems BiotechnologyInstitute of Food, Nutrition, and HealthETH ZurichZurichSwitzerland
| | - Michelle A. Jusino
- Biology DepartmentWilliam & MaryWilliamsburgVAUSA
- Center for Forest Mycology ResearchUSDA Forest ServiceNorthern Research StationMadisonUSA
| | - Matthew D. MacManes
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNHUSA
| | - Jeffrey T. Foster
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNHUSA
- Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffAZUSA
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffAZUSA
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25
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Ineson KM, O’Shea TJ, Kilpatrick CW, Parise KL, Foster JT. Ambiguities in using telomere length for age determination in two North American bat species. J Mammal 2020. [DOI: 10.1093/jmammal/gyaa064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AbstractThe age of an animal, determined by time (chronological age) as well as genetic and environmental factors (biological age), influences the likelihood of mortality and reproduction and thus the animal’s contribution to population growth. For many long-lived species, such as bats, a lack of external and morphological indicators has made determining age a challenge, leading researchers to examine genetic markers of age for application to demographic studies. One widely studied biomarker of age is telomere length, which has been related both to chronological and biological age across taxa, but only recently has begun to be studied in bats. We assessed telomere length from the DNA of known-age and minimum known-age individuals of two bat species using a quantitative PCR assay. We determined that telomere length was quadratically related to chronological age in big brown bats (Eptesicus fuscus), although it had little predictive power for accurate age determination of unknown-age individuals. The relationship was different in little brown bats (Myotis lucifugus), where telomere length instead was correlated with biological age, apparently due to infection and wing damage associated with white-nose syndrome. Furthermore, we showed that wing biopsies currently are a better tissue source for studying telomere length in bats than guano and buccal swabs; the results from the latter group were more variable and potentially influenced by storage time. Refinement of collection and assessment methods for different non-lethally collected tissues will be important for longitudinal sampling to better understand telomere dynamics in these long-lived species. Although further work is needed to develop a biomarker capable of determining chronological age in bats, our results suggest that biological age, as reflected in telomere length, may be influenced by extrinsic stressors such as disease.
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Affiliation(s)
- Katherine M Ineson
- Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - Thomas J O’Shea
- United States Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
| | | | - Katy L Parise
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jeffrey T Foster
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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26
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Suárez-Esquivel M, Hernández-Mora G, Ruiz-Villalobos N, Barquero-Calvo E, Chacón-Díaz C, Ladner JT, Oviedo-Sánchez G, Foster JT, Rojas-Campos N, Chaves-Olarte E, Thomson NR, Moreno E, Guzmán-Verri C. Persistence of Brucella abortus lineages revealed by genomic characterization and phylodynamic analysis. PLoS Negl Trop Dis 2020; 14:e0008235. [PMID: 32287327 PMCID: PMC7182279 DOI: 10.1371/journal.pntd.0008235] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 04/24/2020] [Accepted: 03/18/2020] [Indexed: 12/27/2022] Open
Abstract
Brucellosis, caused by Brucella abortus, is a major disease of cattle and humans worldwide distributed. Eradication and control of the disease has been difficult in Central and South America, Central Asia, the Mediterranean and the Middle East. Epidemiological strategies combined with phylogenetic methods provide the high-resolution power needed to study relationships between surveillance data and pathogen population dynamics, using genetic diversity and spatiotemporal distributions. This information is crucial for prevention and control of disease spreading at a local and worldwide level. In Costa Rica (CR), the disease was first reported at the beginning of the 20th century and has not been controlled despite many efforts. We characterized 188 B. abortus isolates from CR recovered from cattle, humans and water buffalo, from 2003 to 2018, and whole genome sequencing (WGS) was performed in 95 of them. They were also assessed based on geographic origin, date of introduction, and phylogenetic associations in a worldwide and national context. Our results show circulation of five B. abortus lineages (I to V) in CR, phylogenetically related to isolates from the United States, United Kingdom, and South America. Lineage I was dominant and probably introduced at the end of the 19th century. Lineage II, represented by a single isolate from a water buffalo, clustered with a Colombian sample, and was likely introduced after 1845. Lineages III and IV were likely introduced during the early 2000s. Fourteen isolates from humans were found within the same lineage (lineage I) regardless of their geographic origin within the country. The main CR lineages, introduced more than 100 years ago, are widely spread throughout the country, in contrast to new introductions that seemed to be more geographically restricted. Following the brucellosis prevalence and the farming practices of several middle- and low-income countries, similar scenarios could be found in other regions worldwide.
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Affiliation(s)
- Marcela Suárez-Esquivel
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Gabriela Hernández-Mora
- Servicio Nacional de Salud Animal, Ministerio de Agricultura y Ganadería, Heredia, Costa Rica
| | - Nazareth Ruiz-Villalobos
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Elías Barquero-Calvo
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Carlos Chacón-Díaz
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Jason T. Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, United States of America
| | - Gerardo Oviedo-Sánchez
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Jeffrey T. Foster
- The Pathogen and Microbiome Institute, Northern Arizona University, United States of America
| | - Norman Rojas-Campos
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Esteban Chaves-Olarte
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Nicholas R. Thomson
- Parasites and Microbes from Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Caterina Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
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Pearson T, Sahl JW, Hepp CM, Handady K, Hornstra H, Vazquez AJ, Settles E, Mayo M, Kaestli M, Williamson CHD, Price EP, Sarovich DS, Cook JM, Wolken SR, Bowen RA, Tuanyok A, Foster JT, Drees KP, Kidd TJ, Bell SC, Currie BJ, Keim P. Pathogen to commensal? Longitudinal within-host population dynamics, evolution, and adaptation during a chronic >16-year Burkholderia pseudomallei infection. PLoS Pathog 2020; 16:e1008298. [PMID: 32134991 PMCID: PMC7077878 DOI: 10.1371/journal.ppat.1008298] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 03/17/2020] [Accepted: 01/02/2020] [Indexed: 12/14/2022] Open
Abstract
Although acute melioidosis is the most common outcome of Burkholderia pseudomallei infection, we have documented a case, P314, where disease severity lessened with time, and the pathogen evolved towards a commensal relationship with the host. In the current study, we used whole-genome sequencing to monitor this long-term symbiotic relationship to better understand B. pseudomallei persistence in P314’s sputum despite intensive initial therapeutic regimens. We collected and sequenced 118 B. pseudomallei isolates from P314’s airways over a >16-year period, and also sampled the patient’s home environment, recovering six closely related B. pseudomallei isolates from the household water system. Using comparative genomics, we identified 126 SNPs in the core genome of the 124 isolates or 162 SNPs/indels when the accessory genome was included. The core SNPs were used to construct a phylogenetic tree, which demonstrated a close relationship between environmental and clinical isolates and detailed within-host evolutionary patterns. The phylogeny had little homoplasy, consistent with a strictly clonal mode of genetic inheritance. Repeated sampling revealed evidence of genetic diversification, but frequent extinctions left only one successful lineage through the first four years and two lineages after that. Overall, the evolution of this population is nonadaptive and best explained by genetic drift. However, some genetic and phenotypic changes are consistent with in situ adaptation. Using a mouse model, P314 isolates caused greatly reduced morbidity and mortality compared to the environmental isolates. Additionally, potentially adaptive phenotypes emerged and included differences in the O-antigen, capsular polysaccharide, motility, and colony morphology. The >13-year co-existence of two long-lived lineages presents interesting hypotheses that can be tested in future studies to provide additional insights into selective pressures, niche differentiation, and microbial adaptation. This unusual melioidosis case presents a rare example of the evolutionary progression towards commensalism by a highly virulent pathogen within a single human host. Pathogens frequently jump between different hosts, and associated adaptation may lead to the emergence of new infectious agents. Such host-jumping evolution is witnessed through endpoint analyses but these cannot capture genetic changes in lineages that have gone extinct. In this study, we have identified and monitored an example of the evolution of a bacterium often deadly to its mammalian host, in an unprecedented case whereby disease lessened through time and the pathogen became a part of the commensal human flora. We used genomic analyses to characterize more than 16 years of this evolutionary process and the stepwise mutations that control pathogen interactions with the patient. Soon after infection, mutational changes occurred that allowed the bacterium to remain in the airways without causing disease. This shift towards avirulence was determined based on clinical data and virulence testing in an animal model. In addition, mutations occurred that contributed to the persistence of the bacteria in the patient's lungs. Finally, we found evidence for the evolutionary emergence and persistence of two distinct lineages of the bacterium over the last 13 years, presenting interesting questions about niche utilization. Bacteria are ubiquitous in the human body and almost all are beneficial or benign. In this study, we document the evolutionary conversion of a normally deadly bacterium towards a commensal.
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Affiliation(s)
- Talima Pearson
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W. Sahl
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Crystal M. Hepp
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Karthik Handady
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Heidie Hornstra
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Adam J. Vazquez
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Erik Settles
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Mirjam Kaestli
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Charles H. D. Williamson
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Erin P. Price
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Derek S. Sarovich
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - James M. Cook
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Spenser R. Wolken
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Richard A. Bowen
- Department of Biomedical Sciences, Colorado State University, Colorado, United States of America
| | - Apichai Tuanyok
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jeffrey T. Foster
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Kevin P. Drees
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Timothy J. Kidd
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Scott C. Bell
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, and QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Infectious Diseases Department and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Paul Keim
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail:
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28
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Allen AR, Milne G, Drees K, Presho E, Graham J, McAdam P, Jones K, Wright L, Skuce R, Whatmore AM, Graham J, Foster JT. Genomic epizootiology of a Brucella abortus outbreak in Northern Ireland (1997-2012). Infect Genet Evol 2020; 81:104235. [PMID: 32035245 DOI: 10.1016/j.meegid.2020.104235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/28/2020] [Accepted: 02/04/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND In the recent past (1997-2012), Northern Ireland in the United Kingdom suffered an outbreak of Brucella abortus, which at its height affected over 200 cattle herds. Initially, isolates were characterized using multi-locus variable number tandem repeats analysis (MLVA). While informative in this setting, hyper-variability in some loci limited the resolution necessary to infer fine-scale disease transmission networks. Consequently, we applied whole-genome sequencing to isolates from this outbreak to evaluate higher resolution markers for disease epizootiology. RESULTS Phylogenetic analysis revealed that the B. abortus outbreak in Northern Ireland was caused by two distinct pathogen lineages. One contained isolates consistent with the 1997-2012 outbreak being linked to a previous endemic infection thought eradicated. The dominant second lineage exhibited little genetic diversity throughout the recrudescent outbreak, with limited population sub-structure evident. This finding was inconsistent with prior MLVA molecular characterizations that suggested the presence of seven clonal complexes. Spatio-temporal modeling revealed a significant association of pairwise SNP differences between isolates and geographic distances. However, effect sizes were very small due to reduced pathogen diversity. CONCLUSIONS Genome sequence data suggested that hyper-variability in some MLVA loci contributed to an overestimate of pathogen diversity in the most recent outbreak. The low diversity observed in our genomic dataset made it inappropriate to apply phylodynamic methods to these data. We conclude that maintaining data repositories of genome sequence data will be invaluable for source attribution/epizootiological inference should recrudescence ever re-occur. However genomic epizootiological methods may have limited utility in some settings, such as when applied to recrudescent/re-emergent infections of slowly-evolving bacterial pathogens.
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Affiliation(s)
- Adrian R Allen
- Agri Food and Biosciences Institute (AFBI), AFBI Stormont, Bacteriology Branch, Stoney Road, Belfast, United Kingdom..
| | - Georgina Milne
- Agri Food and Biosciences Institute (AFBI), AFBI Stormont, Bacteriology Branch, Stoney Road, Belfast, United Kingdom
| | - Kevin Drees
- University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, Rudman Hall, 46 College Road, Durham, NH, USA
| | - Eleanor Presho
- Agri Food and Biosciences Institute (AFBI), AFBI Stormont, Bacteriology Branch, Stoney Road, Belfast, United Kingdom
| | - Jordon Graham
- Agri Food and Biosciences Institute (AFBI), AFBI Stormont, Bacteriology Branch, Stoney Road, Belfast, United Kingdom
| | - Paul McAdam
- Fios Genomics, Nine Edinburgh Bioquarter, 9 Little France Road, Edinburgh, United Kingdom
| | - Kerri Jones
- Agri Food and Biosciences Institute (AFBI), AFBI Stormont, Bacteriology Branch, Stoney Road, Belfast, United Kingdom
| | - Lorraine Wright
- Agri Food and Biosciences Institute (AFBI), AFBI Stormont, Bacteriology Branch, Stoney Road, Belfast, United Kingdom
| | - Robin Skuce
- Agri Food and Biosciences Institute (AFBI), AFBI Stormont, Bacteriology Branch, Stoney Road, Belfast, United Kingdom
| | - Adrian M Whatmore
- Department of Bacteriology, Animal and Plant Health Agency (APHA), New Haw, Addlestone, Surrey, United Kingdom
| | - Judith Graham
- Department of Agriculture, Environment and Rural Affairs, Veterinary Service, Belfast, Northern Ireland, United Kingdom
| | - Jeffrey T Foster
- University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, Rudman Hall, 46 College Road, Durham, NH, USA
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29
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Vizentin-Bugoni J, Tarwater CE, Foster JT, Drake DR, Gleditsch JM, Hruska AM, Kelley JP, Sperry JH. Structure, spatial dynamics, and stability of novel seed dispersal mutualistic networks in Hawaiʻi. Science 2019; 364:78-82. [DOI: 10.1126/science.aau8751] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/29/2018] [Accepted: 03/05/2019] [Indexed: 11/02/2022]
Abstract
Increasing rates of human-caused species invasions and extinctions may reshape communities and modify the structure, dynamics, and stability of species interactions. To investigate how such changes affect communities, we performed multiscale analyses of seed dispersal networks on Oʻahu, Hawaiʻi. Networks consisted exclusively of novel interactions, were largely dominated by introduced species, and exhibited specialized and modular structure at local and regional scales, despite high interaction dissimilarity across communities. Furthermore, the structure and stability of the novel networks were similar to native-dominated communities worldwide. Our findings suggest that shared evolutionary history is not a necessary process for the emergence of complex network structure, and interaction patterns may be highly conserved, regardless of species identity and environment. Introduced species can quickly become well integrated into novel networks, making restoration of native ecosystems more challenging than previously thought.
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30
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Koster KJ, Largen A, Foster JT, Drees KP, Qian L, Desmond E, Wan X, Hou S, Douglas JT. Genomic sequencing is required for identification of tuberculosis transmission in Hawaii. BMC Infect Dis 2018; 18:608. [PMID: 30509214 PMCID: PMC6276198 DOI: 10.1186/s12879-018-3502-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/02/2018] [Indexed: 02/08/2023] Open
Abstract
Background Tuberculosis (TB) caused an estimated 1.4 million deaths and 10.4 million new cases globally in 2015. TB rates in the United States continue to steadily decline, yet rates in the State of Hawaii are perennially among the highest in the nation due to a continuous influx of immigrants from the Western Pacific and Asia. TB in Hawaii is composed of a unique distribution of genetic lineages, with the Beijing and Manila families of Mycobacterium tuberculosis (Mtb) comprising over two-thirds of TB cases. Standard fingerprinting methods (spoligotyping plus 24-loci Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats [MIRU-VNTR] fingerprinting) perform poorly when used to identify actual transmission clusters composed of isolates from these two families. Those typing methods typically group isolates from these families into large clusters of non-linked isolates with identical fingerprints. Next-generation whole-genome sequencing (WGS) provides a new tool for molecular epidemiology that can resolve clusters of isolates with identical spoligotyping and MIRU-VNTR fingerprints. Methods We performed WGS and SNP analysis and evaluated epidemiological data to investigate 19 apparent TB transmission clusters in Hawaii from 2003 to 2017 in order to assess WGS’ ability to resolve putative Mtb clusters from the Beijing and Manila families. This project additionally investigated MIRU-VNTR allele prevalence to determine why standard Mtb fingerprinting fails to usefully distinguish actual transmission clusters from these two Mtb families. Results WGS excluded transmission events in seven of these putative clusters, confirmed transmission in eight, and identified both transmission-linked and non-linked isolates in four. For epidemiologically identified clusters, while the sensitivity of MIRU-VNTR fingerprinting for identifying actual transmission clusters was found to be 100%, its specificity was only 28.6% relative to WGS. We identified that the Beijing and Manila families’ significantly lower Shannon evenness of MIRU-VNTR allele distributions than lineage 4 was the cause of standard fingerprinting’s poor performance when identifying transmission in Beijing and Manila family clusters. Conclusions This study demonstrated that WGS is necessary for epidemiological investigation of TB in Hawaii and the Pacific. Electronic supplementary material The online version of this article (10.1186/s12879-018-3502-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Angela Largen
- Hawaii State Department of Health, Honolulu, HI, USA
| | - Jeffrey T Foster
- University of New Hampshire, Durham, NH, USA.,Present Address: Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Lishi Qian
- University of Hawaii at Manoa, Honolulu, HI, USA
| | - Ed Desmond
- California Department of Public Health, Richmond, CA, USA
| | - Xuehua Wan
- Advanced Studies in Genomics, Proteomics and Bioinformatics, Honolulu, HI, USA
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, Honolulu, HI, USA
| | - James T Douglas
- University of Hawaii at Manoa, Honolulu, HI, USA. .,Present Address: Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
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31
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Hoyt JR, Langwig KE, White JP, Kaarakka HM, Redell JA, Kurta A, DePue JE, Scullon WH, Parise KL, Foster JT, Frick WF, Kilpatrick AM. Cryptic connections illuminate pathogen transmission within community networks. Nature 2018; 563:710-713. [PMID: 30455422 DOI: 10.1038/s41586-018-0720-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 09/24/2018] [Indexed: 01/14/2023]
Abstract
Understanding host interactions that lead to pathogen transmission is fundamental to the prediction and control of epidemics1-5. Although the majority of transmissions often occurs within social groups6-9, the contribution of connections that bridge groups and species to pathogen dynamics is poorly understood10-12. These cryptic connections-which are often indirect or infrequent-provide transmission routes between otherwise disconnected individuals and may have a key role in large-scale outbreaks that span multiple populations or species. Here we quantify the importance of cryptic connections in disease dynamics by simultaneously characterizing social networks and tracing transmission dynamics of surrogate-pathogen epidemics through eight communities of bats. We then compared these data to the invasion of the fungal pathogen that causes white-nose syndrome, a recently emerged disease that is devastating North American bat populations13-15. We found that cryptic connections increased links between individuals and between species by an order of magnitude. Individuals were connected, on average, to less than two per cent of the population through direct contact and to only six per cent through shared groups. However, tracing surrogate-pathogen dynamics showed that each individual was connected to nearly fifteen per cent of the population, and revealed widespread transmission between solitarily roosting individuals as well as extensive contacts among species. Connections estimated from surrogate-pathogen epidemics, which include cryptic connections, explained three times as much variation in the transmission of the fungus that causes white-nose syndrome as did connections based on shared groups. These findings show how cryptic connections facilitate the community-wide spread of pathogens and can lead to explosive epidemics.
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Affiliation(s)
- Joseph R Hoyt
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA. .,Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, VA, USA.
| | - Kate E Langwig
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, VA, USA
| | - J Paul White
- Wisconsin Department of Natural Resources, Bureau of Natural Heritage Conservation, Madison, WI, USA
| | - Heather M Kaarakka
- Wisconsin Department of Natural Resources, Bureau of Natural Heritage Conservation, Madison, WI, USA
| | - Jennifer A Redell
- Wisconsin Department of Natural Resources, Bureau of Natural Heritage Conservation, Madison, WI, USA
| | - Allen Kurta
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, USA
| | - John E DePue
- Michigan Department of Natural Resources, Baraga, MI, USA
| | | | - Katy L Parise
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jeffrey T Foster
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Winifred F Frick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA.,Bat Conservation International, Austin, TX, USA
| | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
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Frick WF, Cheng TL, Langwig KE, Hoyt JR, Janicki AF, Parise KL, Foster JT, Kilpatrick AM. Pathogen dynamics during invasion and establishment of white-nose syndrome explain mechanisms of host persistence. Ecology 2018; 98:624-631. [PMID: 27992970 DOI: 10.1002/ecy.1706] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 11/30/2016] [Accepted: 12/06/2016] [Indexed: 12/24/2022]
Abstract
Disease dynamics during pathogen invasion and establishment determine the impacts of disease on host populations and determine the mechanisms of host persistence. Temporal progression of prevalence and infection intensity illustrate whether tolerance, resistance, reduced transmission, or demographic compensation allow initially declining populations to persist. We measured infection dynamics of the fungal pathogen Pseudogymnoascus destructans that causes white-nose syndrome in bats by estimating pathogen prevalence and load in seven bat species at 167 hibernacula over a decade as the pathogen invaded, became established, and some host populations stabilized. Fungal loads increased rapidly and prevalence rose to nearly 100% at most sites within 2 yr of invasion in six of seven species. Prevalence and loads did not decline over time despite huge reductions in colony sizes, likely due to an extensive environmental reservoir. However, there was substantial variation in fungal load among sites with persisting colonies, suggesting that both tolerance and resistance developed at different sites in the same species. In contrast, one species disappeared from hibernacula within 3 yr of pathogen invasion. Variable host responses to pathogen invasion require different management strategies to prevent disease-induced extinction and to facilitate evolution of tolerance or resistance in persisting populations.
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Affiliation(s)
- Winifred F Frick
- Department of Ecology and Evolutionary Biology, University of California, 1156 High St, Santa Cruz, California, 95064, USA.,Bat Conservation International, PO Box 162603, Austin, Texas, 78716, USA
| | - Tina L Cheng
- Department of Ecology and Evolutionary Biology, University of California, 1156 High St, Santa Cruz, California, 95064, USA
| | - Kate E Langwig
- Department of Ecology and Evolutionary Biology, University of California, 1156 High St, Santa Cruz, California, 95064, USA.,Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, 02115, USA
| | - Joseph R Hoyt
- Department of Ecology and Evolutionary Biology, University of California, 1156 High St, Santa Cruz, California, 95064, USA
| | - Amanda F Janicki
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, Tennessee, 37996, USA
| | - Katy L Parise
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, 86011, USA.,Department of Molecular, Cellular & Biomedical Science, University of New Hampshire, 46 College Road, Durham, New Hampshire, 03824, USA
| | - Jeffrey T Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, 86011, USA.,Department of Molecular, Cellular & Biomedical Science, University of New Hampshire, 46 College Road, Durham, New Hampshire, 03824, USA
| | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, 1156 High St, Santa Cruz, California, 95064, USA
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33
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Koster K, Largen A, Foster JT, Drees KP, Qian L, Desmond EP, Wan X, Hou S, Douglas JT. Whole genome SNP analysis suggests unique virulence factor differences of the Beijing and Manila families of Mycobacterium tuberculosis found in Hawaii. PLoS One 2018; 13:e0201146. [PMID: 30036392 PMCID: PMC6056056 DOI: 10.1371/journal.pone.0201146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/09/2018] [Indexed: 02/05/2023] Open
Abstract
While tuberculosis (TB) remains a global disease, the WHO estimates that 62% of the incident TB cases in 2016 occurred in the WHO South-East Asia and Western Pacific regions. TB in the Pacific is composed predominantly of two genetic families of Mycobacterium tuberculosis (Mtb): Beijing and Manila. The Manila family is historically under-studied relative to the families that comprise the majority of TB in Europe and North America (e.g. lineage 4), and it remains unclear why this lineage has persisted in Filipino populations despite the predominance of more globally successful Mtb lineages in most of the world. The Beijing family is of particular interest as it is increasingly associated with drug resistance throughout the world. Both of these lineages are important to the State of Hawaii, where they comprise over two-thirds of TB cases. Here, we performed whole genome sequencing on 82 Beijing family, Manila family, and outgroup clinical Mtb isolates from Hawaii to identify lineage-specific SNPs (SNPs found in all isolates from their respective families, and exclusively in those families) in established virulence factor genes. Six non-silent lineage-specific virulence factor SNPs were found in the Beijing family, including mutations in alternative sigma factor sigG and polyketide synthases pks5 and pks7. The Manila family displayed more than eleven non-silent lineage-specific and characteristic virulence factor mutations, including in genes coding for MCE-family protein Mce1B, two mutations in fatty-acid-AMP ligase FadD26, and virulence-regulating transcriptional regulator VirS. This study further identified an ancient clade that shared some virulence factor mutations with the Manila family, and investigated the relationship of those and other “Manila-like” spoligotypes to the Manila family with this SNP dataset. This work identified a set of virulence genes that are worth pursuing to determine potential differences in transmission or virulence displayed by these two Mtb families.
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Affiliation(s)
- Kent Koster
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Angela Largen
- Hawaii State Department of Health, Honolulu, Hawaii, United States of America
| | - Jeffrey T. Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Kevin P. Drees
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Lishi Qian
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Edward P. Desmond
- California Department of Public Health, Richmond, California, United States of America
| | - Xuehua Wan
- Advanced Studies in Genomics, Proteomics and Bioinformatics, Honolulu, Hawaii, United States of America
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, Honolulu, Hawaii, United States of America
| | - James T. Douglas
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
- * E-mail:
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Campana MG, Kurata NP, Foster JT, Helgen LE, Reeder DM, Fleischer RC, Helgen KM. White-Nose Syndrome Fungus in a 1918 Bat Specimen from France. Emerg Infect Dis 2018; 23:1611-1612. [PMID: 28820367 PMCID: PMC5572869 DOI: 10.3201/eid2309.170875] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
White-nose syndrome, first diagnosed in North America in 2006, causes mass deaths among bats in North America. We found the causative fungus, Pseudogymnoascusdestructans, in a 1918 sample collected in Europe, where bats have now adapted to the fungus. These results are consistent with a Eurasian origin of the pathogen.
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35
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Foster JT, Walker FM, Rannals BD, Hussain MH, Drees KP, Tiller RV, Hoffmaster AR, Al-Rawahi A, Keim P, Saqib M. African Lineage Brucella melitensis Isolates from Omani Livestock. Front Microbiol 2018; 8:2702. [PMID: 29379492 PMCID: PMC5775276 DOI: 10.3389/fmicb.2017.02702] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/29/2017] [Indexed: 11/13/2022] Open
Abstract
Brucellosis is a common livestock disease in the Middle East and North Africa, but remains poorly described in the region both genetically and epidemiologically. Traditionally found in goats and sheep, Brucella melitensis is increasingly recognized as infecting camels. Most studies of brucellosis in camels to date have focused on serological surveys, providing only limited understanding of the molecular epidemiology of circulating strains. We genotyped B. melitensis isolates from Omani camels using whole genome SNP assays and VNTRs to provide context for regional brucellosis cases. We identified a lineage of B. melitensis circulating in camels as well as in goats, sheep, and cattle in Oman. This lineage is genetically distinct from most genotypes from the Arabian Peninsula and from isolates from much of the rest of the Middle East. We then developed diagnostic assays that rapidly identify strains from this lineage. In analyses of genotypes from throughout the region, Omani isolates were genetically most closely related to strains from brucellosis cases in humans and livestock in North Africa. Our findings suggest an African origin for B. melitensis in Oman that has likely occurred through the trade of infected livestock. Moreover, African lineages of B. melitensis appear to be undersampled and consequently are underrepresented in genetic databases for Brucella. As we begin to more fully understand global genomic diversity of B. melitensis, finding and characterizing these unique but widespread lineages is essential. We predict that increased sampling of humans and livestock in Africa will reveal little known diversity in this important zoonotic pathogen.
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Affiliation(s)
- Jeffrey T Foster
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Faith M Walker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Brandy D Rannals
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - M Hammad Hussain
- Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad, Pakistan.,Animal Health Research Center, Ministry of Agriculture and Fisheries, Muscat, Oman
| | - Kevin P Drees
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Rebekah V Tiller
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control, Atlanta, GA, United States
| | - Alex R Hoffmaster
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control, Atlanta, GA, United States
| | | | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Muhammad Saqib
- Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad, Pakistan
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36
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Palmer JM, Drees KP, Foster JT, Lindner DL. Extreme sensitivity to ultraviolet light in the fungal pathogen causing white-nose syndrome of bats. Nat Commun 2018; 9:35. [PMID: 29295979 PMCID: PMC5750222 DOI: 10.1038/s41467-017-02441-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 11/30/2017] [Indexed: 02/08/2023] Open
Abstract
Bat white-nose syndrome (WNS), caused by the fungal pathogen Pseudogymnoascus destructans, has decimated North American hibernating bats since its emergence in 2006. Here, we utilize comparative genomics to examine the evolutionary history of this pathogen in comparison to six closely related nonpathogenic species. P. destructans displays a large reduction in carbohydrate-utilizing enzymes (CAZymes) and in the predicted secretome (~50%), and an increase in lineage-specific genes. The pathogen has lost a key enzyme, UVE1, in the alternate excision repair (AER) pathway, which is known to contribute to repair of DNA lesions induced by ultraviolet (UV) light. Consistent with a nonfunctional AER pathway, P. destructans is extremely sensitive to UV light, as well as the DNA alkylating agent methyl methanesulfonate (MMS). The differential susceptibility of P. destructans to UV light in comparison to other hibernacula-inhabiting fungi represents a potential “Achilles’ heel” of P. destructans that might be exploited for treatment of bats with WNS. White-nose syndrome, caused by the fungus Pseudogymnoascus destructans, is decimating North American bats. Here, Palmer et al. use comparative genomics to examine the evolutionary history of this pathogen, and show that it has lost a crucial DNA repair enzyme and is extremely sensitive to UV light.
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Affiliation(s)
- Jonathan M Palmer
- Center for Forest Mycology Research, Northern Research Station, US Forest Service, Madison, WI, 53726, USA
| | - Kevin P Drees
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
| | - Jeffrey T Foster
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Daniel L Lindner
- Center for Forest Mycology Research, Northern Research Station, US Forest Service, Madison, WI, 53726, USA.
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37
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Langwig KE, Hoyt JR, Parise KL, Frick WF, Foster JT, Kilpatrick AM. Resistance in persisting bat populations after white-nose syndrome invasion. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0044. [PMID: 27920389 DOI: 10.1098/rstb.2016.0044] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2016] [Indexed: 01/07/2023] Open
Abstract
Increases in anthropogenic movement have led to a rise in pathogen introductions and the emergence of infectious diseases in naive host communities worldwide. We combined empirical data and mathematical models to examine changes in disease dynamics in little brown bat (Myotis lucifugus) populations following the introduction of the emerging fungal pathogen Pseudogymnoascus destructans, which causes the disease white-nose syndrome. We found that infection intensity was much lower in persisting populations than in declining populations where the fungus has recently invaded. Fitted models indicate that this is most consistent with a reduction in the growth rate of the pathogen when fungal loads become high. The data are inconsistent with the evolution of tolerance or an overall reduced pathogen growth rate that might be caused by environmental factors. The existence of resistance in some persisting populations of little brown bats offers a glimmer of hope that a precipitously declining species will persist in the face of this deadly pathogen.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.
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Affiliation(s)
- Kate E Langwig
- Department of Ecology and Evolutionary Biology, University of California, EE Biology/EMS, Santa Cruz, CA 95064, USA
| | - Joseph R Hoyt
- Department of Ecology and Evolutionary Biology, University of California, EE Biology/EMS, Santa Cruz, CA 95064, USA
| | - Katy L Parise
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011, USA.,Department of Molecular, Cellular and Biomedical Science, University of New Hampshire, Durham, NH 03824, USA
| | - Winifred F Frick
- Department of Ecology and Evolutionary Biology, University of California, EE Biology/EMS, Santa Cruz, CA 95064, USA.,Bat Conservation International, Austin, TX 78716, USA
| | - Jeffrey T Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011, USA.,Department of Molecular, Cellular and Biomedical Science, University of New Hampshire, Durham, NH 03824, USA
| | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, EE Biology/EMS, Santa Cruz, CA 95064, USA
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38
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Langwig KE, Frick WF, Hoyt JR, Parise KL, Drees KP, Kunz TH, Foster JT, Kilpatrick AM. Drivers of variation in species impacts for a multi-host fungal disease of bats. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0456. [PMID: 28080982 DOI: 10.1098/rstb.2015.0456] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2016] [Indexed: 12/22/2022] Open
Abstract
Disease can play an important role in structuring species communities because the effects of disease vary among hosts; some species are driven towards extinction, while others suffer relatively little impact. Why disease impacts vary among host species remains poorly understood for most multi-host pathogens, and factors allowing less-susceptible species to persist could be useful in conserving highly affected species. White-nose syndrome (WNS), an emerging fungal disease of bats, has decimated some species while sympatric and closely related species have experienced little effect. We analysed data on infection prevalence, fungal loads and environmental factors to determine how variation in infection among sympatric host species influenced the severity of WNS population impacts. Intense transmission resulted in almost uniformly high prevalence in all species. By contrast, fungal loads varied over 3 orders of magnitude among species, and explained 98% of the variation among species in disease impacts. Fungal loads increased with hibernating roosting temperatures, with bats roosting at warmer temperatures having higher fungal loads and suffering greater WNS impacts. We also found evidence of a threshold fungal load, above which the probability of mortality may increase sharply, and this threshold was similar for multiple species. This study demonstrates how differences in behavioural traits among species-in this case microclimate preferences-that may have been previously adaptive can be deleterious after the introduction of a new pathogen. Management to reduce pathogen loads rather than exposure may be an effective way of reducing disease impact and preventing species extinctions.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.
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Affiliation(s)
- Kate E Langwig
- Department of Ecology and Evolutionary Biology, University of California, EE Biology/EMS, Santa Cruz, CA 95064, USA
| | - Winifred F Frick
- Department of Ecology and Evolutionary Biology, University of California, EE Biology/EMS, Santa Cruz, CA 95064, USA
| | - Joseph R Hoyt
- Department of Ecology and Evolutionary Biology, University of California, EE Biology/EMS, Santa Cruz, CA 95064, USA
| | - Katy L Parise
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.,Department of Molecular, Cellular and Biomedical Science, University of New Hampshire, Durham, NH 03824, USA
| | - Kevin P Drees
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.,Department of Molecular, Cellular and Biomedical Science, University of New Hampshire, Durham, NH 03824, USA
| | - Thomas H Kunz
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Jeffrey T Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.,Department of Molecular, Cellular and Biomedical Science, University of New Hampshire, Durham, NH 03824, USA
| | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, EE Biology/EMS, Santa Cruz, CA 95064, USA
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39
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Bernard RF, Willcox EV, Parise KL, Foster JT, McCracken GF. White-nose syndrome fungus, Pseudogymnoascus destructans, on bats captured emerging from caves during winter in the southeastern United States. BMC ZOOL 2017. [DOI: 10.1186/s40850-017-0021-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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40
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Gleditsch JM, Hruska AM, Foster JT. Connecting Resource Tracking by Frugivores to Temporal Variation in Seed Dispersal Networks. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00098] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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41
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Mahoney SM, Theimer TC, Johnson MJ, Foster JT. Similar dietary but different numerical responses to nonnative tamarisk (Tamarix spp.) by two native warblers. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1408-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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42
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Al Dahouk S, Köhler S, Occhialini A, Jiménez de Bagüés MP, Hammerl JA, Eisenberg T, Vergnaud G, Cloeckaert A, Zygmunt MS, Whatmore AM, Melzer F, Drees KP, Foster JT, Wattam AR, Scholz HC. Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts. Sci Rep 2017; 7:44420. [PMID: 28300153 PMCID: PMC5353553 DOI: 10.1038/srep44420] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 02/07/2017] [Indexed: 12/31/2022] Open
Abstract
Twenty-one small Gram-negative motile coccobacilli were isolated from 15 systemically diseased African bullfrogs (Pyxicephalus edulis), and were initially identified as Ochrobactrum anthropi by standard microbiological identification systems. Phylogenetic reconstructions using combined molecular analyses and comparative whole genome analysis of the most diverse of the bullfrog strains verified affiliation with the genus Brucella and placed the isolates in a cluster containing B. inopinata and the other non-classical Brucella species but also revealed significant genetic differences within the group. Four representative but molecularly and phenotypically diverse strains were used for in vitro and in vivo infection experiments. All readily multiplied in macrophage-like murine J774-cells, and their overall intramacrophagic growth rate was comparable to that of B. inopinata BO1 and slightly higher than that of B. microti CCM 4915. In the BALB/c murine model of infection these strains replicated in both spleen and liver, but were less efficient than B. suis 1330. Some strains survived in the mammalian host for up to 12 weeks. The heterogeneity of these novel strains hampers a single species description but their phenotypic and genetic features suggest that they represent an evolutionary link between a soil-associated ancestor and the mammalian host-adapted pathogenic Brucella species.
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Affiliation(s)
- Sascha Al Dahouk
- German Federal Institute for Risk Assessment (BfR), Department of Biological Safety, Berlin, Germany.,RWTH Aachen University, Department of Internal Medicine III, Aachen, Germany
| | - Stephan Köhler
- Université Montpellier, Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), Montpellier, France.,CNRS, FRE3689, CPBS, Montpellier, France
| | - Alessandra Occhialini
- Université Montpellier, Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), Montpellier, France.,CNRS, FRE3689, CPBS, Montpellier, France
| | - María Pilar Jiménez de Bagüés
- Unidad de Producción y Sanidad Animal, Centro de Investigación y Tecnología Agroalimentaria, Instituto Agroalimentario de Aragón - IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Jens Andre Hammerl
- German Federal Institute for Risk Assessment (BfR), Department of Biological Safety, Berlin, Germany
| | | | - Gilles Vergnaud
- I2BC, CNRS, CEA, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Axel Cloeckaert
- ISP, INRA, Université François Rabelais de Tours, UMR1282, Nouzilly, France
| | - Michel S Zygmunt
- ISP, INRA, Université François Rabelais de Tours, UMR1282, Nouzilly, France
| | | | - Falk Melzer
- Friedrich-Loeffler-Institut, German National Reference Laboratory for Animal Brucellosis, Jena, Germany
| | - Kevin P Drees
- University of New Hampshire, Department of Molecular, Cellular, and Biomedical Sciences, Durham, NH, USA
| | - Jeffrey T Foster
- University of New Hampshire, Department of Molecular, Cellular, and Biomedical Sciences, Durham, NH, USA
| | - Alice R Wattam
- Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA
| | - Holger C Scholz
- Bundeswehr Institute of Microbiology and German Center for Infection Research (DZIF), Munich, Germany
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43
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Hoyt JR, Langwig KE, Sun K, Lu G, Parise KL, Jiang T, Frick WF, Foster JT, Feng J, Kilpatrick AM. Host persistence or extinction from emerging infectious disease: insights from white-nose syndrome in endemic and invading regions. Proc Biol Sci 2016; 283:20152861. [PMID: 26962138 DOI: 10.1098/rspb.2015.2861] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Predicting species' fates following the introduction of a novel pathogen is a significant and growing problem in conservation. Comparing disease dynamics between introduced and endemic regions can offer insight into which naive hosts will persist or go extinct, with disease acting as a filter on host communities. We examined four hypothesized mechanisms for host-pathogen persistence by comparing host infection patterns and environmental reservoirs for Pseudogymnoascus destructans (the causative agent of white-nose syndrome) in Asia, an endemic region, and North America, where the pathogen has recently invaded. Although colony sizes of bats and hibernacula temperatures were very similar, both infection prevalence and fungal loads were much lower on bats and in the environment in Asia than North America. These results indicate that transmission intensity and pathogen growth are lower in Asia, likely due to higher host resistance to pathogen growth in this endemic region, and not due to host tolerance, lower transmission due to smaller populations, or lower environmentally driven pathogen growth rate. Disease filtering also appears to be favouring initially resistant species in North America. More broadly, determining the mechanisms allowing species persistence in endemic regions can help identify species at greater risk of extinction in introduced regions, and determine the consequences for disease dynamics and host-pathogen coevolution.
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Affiliation(s)
- Joseph R Hoyt
- Department of Ecology and Evolutionary Biology, University of California, EE Biology/EMS, Santa Cruz, CA 95064, USA
| | - Kate E Langwig
- Department of Ecology and Evolutionary Biology, University of California, EE Biology/EMS, Santa Cruz, CA 95064, USA
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, People's Republic of China
| | - Guanjun Lu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, People's Republic of China Urban and Environmental Science College, Changchun Normal University, Changchun 130032, People's Republic of China
| | - Katy L Parise
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Tinglei Jiang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, People's Republic of China
| | - Winifred F Frick
- Department of Ecology and Evolutionary Biology, University of California, EE Biology/EMS, Santa Cruz, CA 95064, USA
| | - Jeffrey T Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, People's Republic of China
| | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, EE Biology/EMS, Santa Cruz, CA 95064, USA
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44
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Avena CV, Parfrey LW, Leff JW, Archer HM, Frick WF, Langwig KE, Kilpatrick AM, Powers KE, Foster JT, McKenzie VJ. Deconstructing the Bat Skin Microbiome: Influences of the Host and the Environment. Front Microbiol 2016; 7:1753. [PMID: 27909426 PMCID: PMC5112243 DOI: 10.3389/fmicb.2016.01753] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/19/2016] [Indexed: 02/01/2023] Open
Abstract
Bats are geographically widespread and play an important role in many ecosystems, but relatively little is known about the ecology of their associated microbial communities and the role microbial taxa play in bat health, development, and evolution. Moreover, few vertebrate animal skin microbiomes have been comprehensively assessed, and thus characterizing the bat skin microbiome will yield valuable insight into the variability of vertebrate skin microbiomes as a whole. The recent emergence of the skin fungal disease white-nose syndrome highlights the potentially important role bat skin microbial communities could play in bat health. Understanding the determinant of bat skin microbial communities could provide insight into important factors allowing individuals to persist with disease. We collected skin swabs from a total of 11 bat species from the eastern United States (n = 45) and Colorado (n = 119), as well as environmental samples (n = 38) from a subset of sites, and used 16S rRNA marker gene sequencing to observe bacterial communities. In addition, we conducted a literature survey to compare the skin microbiome across vertebrate groups, including the bats presented in this study. Host species, region, and site were all significant predictors of the variability across bat skin bacterial communities. Many bacterial taxa were found both on bats and in the environment. However, some bacterial taxa had consistently greater relative abundances on bat skin relative to their environments. Bats shared many of their abundant taxa with other vertebrates, but also hosted unique bacterial lineages such as the class Thermoleophilia (Actinobacteria). A strong effect of site on the bat skin microbiome indicates that the environment very strongly influences what bacteria are present on bat skin. Bat skin microbiomes are largely composed of site-specific microbiota, but there do appear to be important host-specific taxa. How this translates to differences in host-microbial interactions and bat health remains an important knowledge gap, but this work suggests that habitat variability is very important. We identify some bacterial groups that are more consistent on bats despite site differences, and these may be important ones to study in terms of their function as potential core microbiome members.
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Affiliation(s)
- Christine V Avena
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder Boulder, CO, USA
| | - Laura Wegener Parfrey
- Departments of Botany and Zoology, University of British Columbia Vancouver, BC, Canada
| | - Jonathan W Leff
- Department of Ecology and Evolutionary Biology, University of Colorado BoulderBoulder, CO, USA; Cooperative Institute for Research in Environmental Sciences, University of Colorado BoulderBoulder, CO, USA
| | - Holly M Archer
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder Boulder, CO, USA
| | - Winifred F Frick
- Department of Ecology and Evolutionary Biology, University of California, Santa CruzSanta Cruz, CA, USA; Bat Conservation InternationalAustin, TX, USA
| | - Kate E Langwig
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz Santa Cruz, CA, USA
| | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz Santa Cruz, CA, USA
| | | | - Jeffrey T Foster
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire Durham, NH, USA
| | - Valerie J McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder Boulder, CO, USA
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45
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Vogler AJ, Nottingham R, Busch JD, Sahl JW, Shuey MM, Foster JT, Schupp JM, Smith SR, Rocke TE, Keim P, Wagner DM. VNTR diversity in Yersinia pestis isolates from an animal challenge study reveals the potential for in vitro mutations during laboratory cultivation. Infect Genet Evol 2016; 45:297-302. [PMID: 27664903 DOI: 10.1016/j.meegid.2016.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/30/2016] [Accepted: 09/20/2016] [Indexed: 10/21/2022]
Abstract
Underlying mutation rates and other evolutionary forces shape the population structure of bacteria in nature. Although easily overlooked, similar forces are at work in the laboratory and may influence observed mutations. Here, we investigated tissue samples and Yersinia pestis isolates from a rodent laboratory challenge with strain CO92 using whole genome sequencing and multi-locus variable-number tandem repeat (VNTR) analysis (MLVA). We identified six VNTR mutations that were found to have occurred in vitro during laboratory cultivation rather than in vivo during the rodent challenge. In contrast, no single nucleotide polymorphism (SNP) mutations were observed, either in vivo or in vitro. These results were consistent with previously published mutation rates and the calculated number of Y. pestis generations that occurred during the in vitro versus the in vivo portions of the experiment. When genotyping disease outbreaks, the potential for in vitro mutations should be considered, particularly when highly variable genetic markers such as VNTRs are used.
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Affiliation(s)
- Amy J Vogler
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States
| | - Roxanne Nottingham
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States
| | - Joseph D Busch
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States
| | - Jason W Sahl
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States
| | - Megan M Shuey
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States; Department of Medicine, Vanderbilt University, School of Medicine, Nashville, TN, United States
| | - Jeffrey T Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States; Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - James M Schupp
- Translational Genomics Research Institute North, Flagstaff, AZ, United States
| | - Susan R Smith
- US Geological Survey, National Wildlife Health Center, Madison, WI, United States
| | - Tonie E Rocke
- US Geological Survey, National Wildlife Health Center, Madison, WI, United States
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States; Translational Genomics Research Institute North, Flagstaff, AZ, United States
| | - David M Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States.
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46
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Hoyt JR, Sun K, Parise KL, Lu G, Langwig KE, Jiang T, Yang S, Frick WF, Kilpatrick AM, Foster JT, Feng J. Widespread Bat White-Nose Syndrome Fungus, Northeastern China. Emerg Infect Dis 2016; 22:140-2. [PMID: 26673906 PMCID: PMC4698868 DOI: 10.3201/eid2201.151314] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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Cheng TL, Mayberry H, McGuire LP, Hoyt JR, Langwig KE, Nguyen H, Parise KL, Foster JT, Willis CKR, Kilpatrick AM, Frick WF. Efficacy of a probiotic bacterium to treat bats affected by the disease white‐nose syndrome. J Appl Ecol 2016. [DOI: 10.1111/1365-2664.12757] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Tina L. Cheng
- Department of Ecology and Evolutionary Biology University of California 1156 High Street Santa Cruz CA 95064 USA
| | - Heather Mayberry
- University of Winnipeg Winnipeg MB R3B 2E9 Canada
- University of Toronto 3359 Mississauga Road Mississauga ON L5L 1C6 Canada
| | - Liam P. McGuire
- University of Winnipeg Winnipeg MB R3B 2E9 Canada
- Texas Tech University Lubbock TX 79409 USA
| | - Joseph R. Hoyt
- Department of Ecology and Evolutionary Biology University of California 1156 High Street Santa Cruz CA 95064 USA
| | - Kate E. Langwig
- Department of Ecology and Evolutionary Biology University of California 1156 High Street Santa Cruz CA 95064 USA
- Harvard T.H. Chan School of Public Health Boston MA 02115 USA
| | - Hung Nguyen
- Department of Ecology and Evolutionary Biology University of California 1156 High Street Santa Cruz CA 95064 USA
| | | | | | | | - Auston Marm Kilpatrick
- Department of Ecology and Evolutionary Biology University of California 1156 High Street Santa Cruz CA 95064 USA
| | - Winifred F. Frick
- Department of Ecology and Evolutionary Biology University of California 1156 High Street Santa Cruz CA 95064 USA
- Bat Conservation International PO Box 162603 Austin TX 78716 USA
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48
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Kamath PL, Foster JT, Drees KP, Luikart G, Quance C, Anderson NJ, Clarke PR, Cole EK, Drew ML, Edwards WH, Rhyan JC, Treanor JJ, Wallen RL, White PJ, Robbe-Austerman S, Cross PC. Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock. Nat Commun 2016; 7:11448. [PMID: 27165544 PMCID: PMC4865865 DOI: 10.1038/ncomms11448] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 03/29/2016] [Indexed: 01/09/2023] Open
Abstract
Whole-genome sequencing has provided fundamental insights into infectious disease epidemiology, but has rarely been used for examining transmission dynamics of a bacterial pathogen in wildlife. In the Greater Yellowstone Ecosystem (GYE), outbreaks of brucellosis have increased in cattle along with rising seroprevalence in elk. Here we use a genomic approach to examine Brucella abortus evolution, cross-species transmission and spatial spread in the GYE. We find that brucellosis was introduced into wildlife in this region at least five times. The diffusion rate varies among Brucella lineages (∼3 to 8 km per year) and over time. We also estimate 12 host transitions from bison to elk, and 5 from elk to bison. Our results support the notion that free-ranging elk are currently a self-sustaining brucellosis reservoir and the source of livestock infections, and that control measures in bison are unlikely to affect the dynamics of unrelated strains circulating in nearby elk populations.
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Affiliation(s)
- Pauline L Kamath
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana 59715, USA
| | - Jeffrey T Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona 86011, USA
| | - Kevin P Drees
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona 86011, USA
| | - Gordon Luikart
- Flathead Lake Biological Station, Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA
| | - Christine Quance
- USDA-APHIS, National Veterinary Services Laboratories, Ames, Iowa 50010, USA
| | - Neil J Anderson
- Montana Fish Wildlife and Parks, Bozeman, Montana 59718, USA
| | - P Ryan Clarke
- USDA-APHIS, Veterinary Services, Fort Collins, Colorado 80526, USA
| | - Eric K Cole
- USFWS, National Elk Refuge, Jackson, Wyoming 83001, USA
| | - Mark L Drew
- Wildlife Health Laboratory, Idaho Department of Fish and Game, Caldwell, Idaho 83607, USA
| | | | - Jack C Rhyan
- USDA-APHIS, Veterinary Services, Fort Collins, Colorado 80526, USA
| | - John J Treanor
- National Park Service, Yellowstone National Park, Mammoth, Wyoming 82190, USA
| | - Rick L Wallen
- National Park Service, Yellowstone National Park, Mammoth, Wyoming 82190, USA
| | - Patrick J White
- National Park Service, Yellowstone National Park, Mammoth, Wyoming 82190, USA
| | | | - Paul C Cross
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana 59715, USA
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49
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Affiliation(s)
- Julie A. Blanchong
- Department of Natural Resource Ecology and Management; Iowa State University; 339 Science II Ames IA 50011 USA
| | | | - Michael D. Samuel
- U.S. Geological Survey, Wisconsin Cooperative Wildlife Research Unit; University of Wisconsin; 204 Russell Labs, 1630 Linden Dr. Madison WI 53706 USA
| | - Jeffrey T. Foster
- Department of Molecular, Cellular and Biomedical Sciences; University of New Hampshire; 291 Rudman Hall Durham NH 03824 USA
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50
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McGuire LP, Turner JM, Warnecke L, McGregor G, Bollinger TK, Misra V, Foster JT, Frick WF, Kilpatrick AM, Willis CKR. White-Nose Syndrome Disease Severity and a Comparison of Diagnostic Methods. Ecohealth 2016; 13:60-71. [PMID: 26957435 DOI: 10.1007/s10393-016-1107-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 02/16/2016] [Accepted: 02/16/2016] [Indexed: 06/05/2023]
Abstract
White-nose syndrome is caused by the fungus Pseudogymnoascus destructans and has killed millions of hibernating bats in North America but the pathophysiology of the disease remains poorly understood. Our objectives were to (1) assess non-destructive diagnostic methods for P. destructans infection compared to histopathology, the current gold-standard, and (2) to evaluate potential metrics of disease severity. We used data from three captive inoculation experiments involving 181 little brown bats (Myotis lucifugus) to compare histopathology, quantitative PCR (qPCR), and ultraviolet fluorescence as diagnostic methods of P. destructans infection. To assess disease severity, we considered two histology metrics (wing area with fungal hyphae, area of dermal necrosis), P. destructans fungal load (qPCR), ultraviolet fluorescence, and blood chemistry (hematocrit, sodium, glucose, pCO2, and bicarbonate). Quantitative PCR was most effective for early detection of P. destructans, while all three methods were comparable in severe infections. Correlations among hyphae and necrosis scores, qPCR, ultraviolet fluorescence, blood chemistry, and hibernation duration indicate a multi-stage pattern of disease. Disruptions of homeostasis occurred rapidly in late hibernation. Our results provide valuable information about the use of non-destructive techniques for monitoring, and provide novel insight into the pathophysiology of white-nose syndrome, with implications for developing and implementing potential mitigation strategies.
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Affiliation(s)
- Liam P McGuire
- Department of Biology, University of Winnipeg, 515 Portage Ave., Winnipeg, MB, R3B 2E9, Canada.
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA.
| | - James M Turner
- Department of Biology, University of Winnipeg, 515 Portage Ave., Winnipeg, MB, R3B 2E9, Canada
- Functional Ecology, Biocentre Grindel, University Hamburg, 20146, Hamburg, Germany
| | - Lisa Warnecke
- Department of Biology, University of Winnipeg, 515 Portage Ave., Winnipeg, MB, R3B 2E9, Canada
- Functional Ecology, Biocentre Grindel, University Hamburg, 20146, Hamburg, Germany
| | - Glenna McGregor
- Canadian Wildlife Health Cooperative, Department of Veterinary Pathology, Saskatoon, SK, S7N 5B4, Canada
| | - Trent K Bollinger
- Canadian Wildlife Health Cooperative, Department of Veterinary Pathology, Saskatoon, SK, S7N 5B4, Canada
| | - Vikram Misra
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - Jeffrey T Foster
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
| | - Winifred F Frick
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Craig K R Willis
- Department of Biology, University of Winnipeg, 515 Portage Ave., Winnipeg, MB, R3B 2E9, Canada
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