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Eger E, Homeier-Bachmann T, Adade E, Dreyer S, Heiden SE, Lübcke P, Tawiah PO, Sylverken AA, Knauf S, Schaufler K. Carbapenem- and cefiderocol-resistant Enterobacterales in surface water in Kumasi, Ashanti Region, Ghana. JAC Antimicrob Resist 2024; 6:dlae021. [PMID: 38449514 PMCID: PMC10915899 DOI: 10.1093/jacamr/dlae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/19/2024] [Indexed: 03/08/2024] Open
Abstract
Background MDR pathogens including ESBL- and/or carbapenemase-producing Enterobacterales (ESBL-PE and CPE) increasingly occur worldwide in the One Health context. Objectives This proof-of-principle study investigated the occurrence of ESBL-PE in surface water in the Ashanti Region in Ghana, sub-Saharan Africa (SSA), and investigated their additional genotypic and phenotypic antimicrobial resistance features as part of the Surveillance Outbreak Response Management and Analysis System (SORMAS). Methods From 75 water samples overall, from nine small to medium-sized river streams and one pond spatially connected to a channelled water stream in the greater area of Kumasi (capital of the Ashanti Region in Ghana) in 2021, we isolated 121 putative ESBL-PE that were subsequently subjected to in-depth genotypic and phenotypic analysis. Results Of all 121 isolates, Escherichia coli (70.25%) and Klebsiella pneumoniae (23.14%) were the most prevalent bacterial species. In addition to ESBL enzyme-production of mostly the CTX-M-15 type, one-fifth of the isolates carried carbapenemase genes including blaNDM-5. More importantly, susceptibility testing not only confirmed phenotypic carbapenem resistance, but also revealed two isolates resistant to the just recently approved last-resort antibiotic cefiderocol. In addition, we detected several genes associated with heavy metal resistance. Conclusions ESBL-PE and CPE occur in surface water sources in and around Kumasi in Ghana. Further surveillance and research are needed to not only improve our understanding of their exact prevalence and the reservoir function of water sources in SSA but should include the investigation of cefiderocol-resistant isolates.
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Affiliation(s)
- Elias Eger
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research HZI, Greifswald, Germany
| | - Timo Homeier-Bachmann
- Institute of Epidemiology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald—Insel Riems, Germany
| | - Eugene Adade
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Sylvia Dreyer
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald—Insel Riems, Germany
| | - Stefan E Heiden
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research HZI, Greifswald, Germany
| | - Phillip Lübcke
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Patrick O Tawiah
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Augustina A Sylverken
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald—Insel Riems, Germany
- Faculty of Veterinary Medicine, Justus-Liebig-University, Giessen, Germany
| | - Katharina Schaufler
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research HZI, Greifswald, Germany
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- University Medicine Greifswald, Greifswald, Germany
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2
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Knauf S, Hisgen L, Ågren EO, Barlow AM, Faehndrich M, Voigt U, Fischer L, Grillová L, Hallmaier-Wacker LK, Kik MJL, Klink JC, Křenová J, Lavazza A, Lüert S, Nováková M, Čejková D, Pacioni C, Trogu T, Šmajs D, Roos C. High prevalence and genetic diversity of Treponema paraluisleporidarum isolates in European lagomorphs. Microbiol Spectr 2024; 12:e0177423. [PMID: 38095473 PMCID: PMC10783078 DOI: 10.1128/spectrum.01774-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/17/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Syphilis is an ancient disease of humans and lagomorphs caused by two distinct but genetically closely related bacteria (>98% sequence identity based on the whole genome) of the genus Treponema. While human syphilis is well studied, little is known about the disease in the lagomorph host. Yet, comparative studies are needed to understand mechanisms in host-pathogen coevolution in treponematoses. Importantly, Treponema paraluisleporidarum-infected hare populations provide ample opportunity to study the syphilis-causing pathogen in a naturally infected model population without antibiotic treatment, data that cannot be obtained from syphilis infection in humans. We provide data on genetic diversity and are able to highlight various types of repetitions in one of the two hypervariable regions at the tp0548 locus that have not been described in the human syphilis-causing sister bacterium Treponema pallidum subsp. pallidum.
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Affiliation(s)
- Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
- Infection Biology Unit, Deutsches Primatenzentrum GmbH, Leibniz Institute for Primate Research, Göttingen, Germany
- Professorship for International Animal Health/One Health, Faculty of Veterinary Medicine, Justus Liebig University, Giessen, Germany
| | - Linda Hisgen
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
- Infection Biology Unit, Deutsches Primatenzentrum GmbH, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Erik O. Ågren
- Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden
| | - Alexander M. Barlow
- Wildlife Network for Disease Surveillance, Bristol Veterinary School, Langford, Somerset, United Kingdom
| | - Marcus Faehndrich
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hanover, Foundation, Hanover, Germany
| | - Ulrich Voigt
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hanover, Foundation, Hanover, Germany
| | - Luisa Fischer
- Wildlife Research Institute, State Agency for Nature, Environment and Consumer Protection North Rhine-Westphalia, Bonn, Germany
| | - Linda Grillová
- Department of Biology, Masaryk University, Brno, Czechia
| | - Luisa K. Hallmaier-Wacker
- Infection Biology Unit, Deutsches Primatenzentrum GmbH, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Marja J. L. Kik
- Pathology Division, Department of Biomedical Health Sciences, Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jana C. Klink
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hanover, Foundation, Hanover, Germany
| | - Jitka Křenová
- Department of Biology, Masaryk University, Brno, Czechia
| | - Antonio Lavazza
- Department of Animal Health and Welfare – Virology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Simone Lüert
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
- Infection Biology Unit, Deutsches Primatenzentrum GmbH, Leibniz Institute for Primate Research, Göttingen, Germany
| | | | - Darina Čejková
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czechia
| | - Carlo Pacioni
- Department of Environment, Land, Water and Planning, Arthur Rylah Institute for Environmental Research, Heidelberg, Victoria, Australia
- Environmental and Conservation Sciences, Murdoch University, Murdoch, Australia
| | - Tiziana Trogu
- Department of Animal Health and Welfare – Virology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - David Šmajs
- Department of Biology, Masaryk University, Brno, Czechia
| | - Christian Roos
- Primate Genetics Laboratory, Deutsches Primatenzentrum GmbH, Leibniz Institute for Primate Research, Göttingen, Germany
- Gene Bank of Primates, Deutsches Primatenzentrum GmbH, Leibniz Institute for Primate Research, Göttingen, Germany
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3
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Kuderna LFK, Ulirsch JC, Rashid S, Ameen M, Sundaram L, Hickey G, Cox AJ, Gao H, Kumar A, Aguet F, Christmas MJ, Clawson H, Haeussler M, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Karakikes I, Wang KC, Umapathy G, Roos C, Boubli JP, Siepel A, Kundaje A, Paten B, Lindblad-Toh K, Rogers J, Marques Bonet T, Farh KKH. Identification of constrained sequence elements across 239 primate genomes. Nature 2024; 625:735-742. [PMID: 38030727 PMCID: PMC10808062 DOI: 10.1038/s41586-023-06798-8] [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: 02/09/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3-9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.
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Affiliation(s)
- Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Jacob C Ulirsch
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Sabrina Rashid
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Mohamed Ameen
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Glenn Hickey
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Anthony J Cox
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Arvind Kumar
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Matthew J Christmas
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Hiram Clawson
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | - Mareike C Janiak
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Martin Kuhlwilm
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Joseph D Orkin
- Département d'Anthropologie, Université de Montréal, Montréal, Quebec, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Tefé, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Lidia Agueda
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Julie Blanc
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Marta Gut
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Ian Goodhead
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - David Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City, UT, USA
| | | | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
| | - João Valsecchi
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Brazil
- Rede de Pesquisa em Diversidade, Conservação e Uso da Fauna da Amazônia - RedeFauna, Manaus, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica-ComFauna, Iquitos, Peru
| | - Malu Messias
- Universidade Federal de Rondônia, Porto Velho, Brazil
| | | | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
- Department of Biology, Trinity University, San Antonio, TX, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | | | - Sree Kanthaswamy
- School of Interdisciplinary Forensics, Arizona State University, Phoenix, AZ, USA
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, Addis Ababa, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Long Zhou
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- Professorship for International Animal Health/One Health, Faculty of Veterinary Medicine, Justus Liebig University, Giessen, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Esther Lizano
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelonaβeta Brain Research Center, Pasqual Maragall Foundation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | | | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
- School of Geosciences, Edinburgh, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, Göttingen, Germany
| | - Ivo Gut
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Robin M D Beck
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Kevin C Wang
- Department of Cancer Biology, Stanford University, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Tomas Marques Bonet
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain.
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA.
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4
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Jensen A, Swift F, de Vries D, Beck RMD, Kuderna LFK, Knauf S, Chuma IS, Keyyu JD, Kitchener AC, Farh K, Rogers J, Marques-Bonet T, Detwiler KM, Roos C, Guschanski K. Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation. Mol Biol Evol 2023; 40:msad247. [PMID: 37987553 PMCID: PMC10691879 DOI: 10.1093/molbev/msad247] [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: 07/05/2023] [Revised: 10/17/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023] Open
Abstract
Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.
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Affiliation(s)
- Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala SE-75236, Sweden
| | - Frances Swift
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald – Insel Riems 17493, Germany
| | | | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Edinburgh EH8 9XP, UK
| | - Kyle Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona 08003, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Barcelona 08010, Spain
| | - Kate M Detwiler
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala SE-75236, Sweden
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
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5
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Ndzomo P, Tchatchouang S, Njih Tabah E, Njamnshi T, Tsanga MVN, Bondi JA, Handley R, González Beiras C, Tchatchueng J, Müller C, Lüert S, Knauf S, Boyomo O, Harding-Esch E, Mitja O, Crucitti T, Marks M, Eyangoh S. Prevalence and risk factors associated with Haemophilus ducreyi cutaneous ulcers in Cameroon. PLoS Negl Trop Dis 2023; 17:e0011553. [PMID: 38150487 PMCID: PMC10791135 DOI: 10.1371/journal.pntd.0011553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/09/2024] [Accepted: 12/15/2023] [Indexed: 12/29/2023] Open
Abstract
Epidemics of yaws-like cutaneous ulcers are regularly documented in children in the tropics. They occur mainly in poor and remote communities without access to health facilities. The integration of molecular tools into yaws control efforts has made it possible to describe Haemophilus ducreyi (HD) as a major cause of cutaneous ulcers. The objective of this study was to determine the prevalence of HD as cause of cutaneous ulcers, investigate its presence in asymptomatic individuals and identify associated risk factors. A cross-sectional study was conducted in yaws endemic districts of Cameroon. Participants included people presenting yaws-like ulcers and asymptomatic individuals. Swab samples were collected from each participant and tested for HD and Treponema pallidum (TP) using an established qPCR method. Additionally, demographic, habitat, proximity, and hygiene characteristics were collected using a structured questionnaire. A total of 443 individuals participated in the study, including 271 ulcer cases and 172 asymptomatic contacts. The prevalence of HD in ulcers was 30.3% (Confidence Interval (CI) 95% [24.8-35.7]) and the prevalence of asymptomatic HD carriage was 8.6% (CI95% [4.5-12.9]). TP was also detected in our sample among ulcer cases but in lower proportion (5.2% CI95% [2.5-7.8]) compared to HD. The adjusted logistic regression model showed that women were as much at risk of having HD cutaneous ulcer as men regardless of age. Physical proximity to a confirmed ulcer case was the major factor identified favouring HD transmission. HD ulcers were more likely to be present on Bantu individuals compared to Baka as well as HD colonization. These findings highlight HD as the most common cause of cutaneous ulcers in yaws-endemic communities in Cameroon. The exact implications of detecting HD on intact skin are not yet clear. Further studies are needed to understand the significance of this carriage in the spread dynamics of the disease.
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Affiliation(s)
- Philippe Ndzomo
- Centre Pasteur du Cameroun, Yaounde, Cameroon
- Department of Microbiology, Faculty of Science, University of Yaounde 1, Yaounde, Cameroon
| | | | - Earnest Njih Tabah
- National Yaws, Leishmaniasis, Leprosy and Buruli ulcer Control Programme, Ministry of Public Health, Yaounde, Cameroon
- Department of Public Health, Faculty of Medicine and Pharmaceutical Sciences, University of Dschang, Dschang, West Cameroon
| | - Theophilus Njamnshi
- National Yaws, Leishmaniasis, Leprosy and Buruli ulcer Control Programme, Ministry of Public Health, Yaounde, Cameroon
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Buea, Buea, Cameroon
| | | | | | - Rebecca Handley
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Camila González Beiras
- Department of Infectious Diseases, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | | | - Claudia Müller
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald—Insel Riems, Germany
| | - Simone Lüert
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald—Insel Riems, Germany
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald—Insel Riems, Germany
| | - Onana Boyomo
- Department of Microbiology, Faculty of Science, University of Yaounde 1, Yaounde, Cameroon
| | - Emma Harding-Esch
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Oriol Mitja
- Department of Infectious Diseases, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Tania Crucitti
- Experimental Bacteriology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Michael Marks
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Hospital for Tropical Diseases, University College London Hospital, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
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6
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Adade E, Tawiah PO, Roos C, Chuma IS, Lubinza CC, Mfinanga SGM, Knauf S, Sylverken AA. Antimicrobial susceptibility profile of oral and rectal microbiota of non-human primate species in Ghana: A threat to human health. Vet Med Sci 2023; 10:e1271. [PMID: 37733757 PMCID: PMC10804077 DOI: 10.1002/vms3.1271] [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: 04/03/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND The potential for the transfer of zoonotic diseases, including bacteria between human and non-human primates (NHPs), is expected to rise. It is posited that NHPs that live in close contact with humans serve as sentinels and reservoirs for antibiotic-resistant bacteria. OBJECTIVES The objective was to characterize the oral and rectal bacteria in Ghanaian NHPs and profile the antimicrobial susceptibility of the isolated bacteria. METHODS Oral and rectal swabs were obtained from 40 immobilized wild and captive NHPs from 7 locations in Ghana. Standard bacteriological procedures were used in the isolation, preliminary identification, automated characterization and antimicrobial susceptibility test (AST) of bacteria using the Vitek 2 Compact system. RESULTS Gram-negative bacteria dominated isolates from the rectal swabs (n = 76, 85.4%), whereas Gram-positive bacteria were more common in the oral swabs (n = 41, 82%). Staphylococcus haemolyticus (n = 7, 14%) was the most occurring bacterial species isolated from the oral swabs, whereas Escherichia coli (n = 32, 36%) dominated bacteria isolates from rectal swabs. Enterobacter spp. had the highest (39%) average phenotypic resistance to antimicrobials that were used for AST, whereas a trend of high resistance was recorded against norfloxacin, Ampicillin and Tetracycline in Gram-negative bacteria. Similarly, among Gram-positive bacteria, Staphylococcus spp. had the highest (25%) average phenotypic resistance to antimicrobials used for AST, and a trend of high resistance was recorded against penicillin G and oxacillin. CONCLUSIONS This study has established that apparently healthy NHPs that live in anthropized environments in Ghana harbour zoonotic and antimicrobial resistant bacteria.
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Affiliation(s)
- Eugene Adade
- Department of Theoretical and Applied BiologyKwame Nkrumah University of Science and TechnologyKumasiGhana
- Kumasi Centre for Collaborative Research in Tropical MedicineKwame Nkrumah University of Science and TechnologyKumasiGhana
| | - Patrick Ofori Tawiah
- Department of Theoretical and Applied BiologyKwame Nkrumah University of Science and TechnologyKumasiGhana
- Kumasi Centre for Collaborative Research in Tropical MedicineKwame Nkrumah University of Science and TechnologyKumasiGhana
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics LaboratoryGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
| | | | - Clara Clavery Lubinza
- National Institute for Medical ResearchMuhimbili Medical Research CentreDar es SalaamTanzania
| | | | - Sascha Knauf
- Institute of International Animal Health/One HealthFriedrich‐Loeffler‐InstitutFederal Institute for Animal HealthGreifswald – Insel RiemsGermany
| | - Augustina Angelina Sylverken
- Department of Theoretical and Applied BiologyKwame Nkrumah University of Science and TechnologyKumasiGhana
- Kumasi Centre for Collaborative Research in Tropical MedicineKwame Nkrumah University of Science and TechnologyKumasiGhana
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7
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Janečková K, Roos C, Fedrová P, Tom N, Čejková D, Lueert S, Keyyu JD, Chuma IS, Knauf S, Šmajs D. The genomes of the yaws bacterium, Treponema pallidum subsp. pertenue, of nonhuman primate and human origin are not genomically distinct. PLoS Negl Trop Dis 2023; 17:e0011602. [PMID: 37703251 PMCID: PMC10499264 DOI: 10.1371/journal.pntd.0011602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 08/17/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Treponema pallidum subsp. pertenue (TPE) is the causative agent of human yaws. Yaws is currently reported in 13 endemic countries in Africa, southern Asia, and the Pacific region. During the mid-20th century, a first yaws eradication effort resulted in a global 95% drop in yaws prevalence. The lack of continued surveillance has led to the resurgence of yaws. The disease was believed to have no animal reservoirs, which supported the development of a currently ongoing second yaws eradication campaign. Concomitantly, genetic evidence started to show that TPE strains naturally infect nonhuman primates (NHPs) in sub-Saharan Africa. In our current study we tested hypothesis that NHP- and human-infecting TPE strains differ in the previously unknown parts of the genomes. METHODOLOGY/PRINCIPAL FINDINGS In this study, we determined complete (finished) genomes of ten TPE isolates that originated from NHPs and compared them to TPE whole-genome sequences from human yaws patients. We performed an in-depth analysis of TPE genomes to determine if any consistent genomic differences are present between TPE genomes of human and NHP origin. We were able to resolve previously undetermined TPE chromosomal regions (sequencing gaps) that prevented us from making a conclusion regarding the sequence identity of TPE genomes from NHPs and humans. The comparison among finished genome sequences revealed no consistent differences between human and NHP TPE genomes. CONCLUSION/SIGNIFICANCE Our data show that NHPs are infected with strains that are not only similar to the strains infecting humans but are genomically indistinguishable from them. Although interspecies transmission in NHPs is a rare event and evidence for current spillover events is missing, the existence of the yaws bacterium in NHPs is demonstrated. While the low risk of spillover supports the current yaws treatment campaign, it is of importance to continue yaws surveillance in areas where NHPs are naturally infected with TPE even if yaws is successfully eliminated in humans.
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Affiliation(s)
- Klára Janečková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Christian Roos
- Deutsches Primatenzentrum GmbH, Leibniz-Institute for Primate Research, Göttingen, Germany
| | - Pavla Fedrová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Nikola Tom
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Darina Čejková
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Simone Lueert
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald—Insel Riems, Germany
| | - Julius D. Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Idrissa S. Chuma
- Department of Veterinary Medicine and Public Health, College of Veterinary and Medical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Sascha Knauf
- Deutsches Primatenzentrum GmbH, Leibniz-Institute for Primate Research, Göttingen, Germany
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald—Insel Riems, Germany
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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8
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Sørensen EF, Harris RA, Zhang L, Raveendran M, Kuderna LFK, Walker JA, Storer JM, Kuhlwilm M, Fontsere C, Seshadri L, Bergey CM, Burrell AS, Bergman J, Phillips-Conroy JE, Shiferaw F, Chiou KL, Chuma IS, Keyyu JD, Fischer J, Gingras MC, Salvi S, Doddapaneni H, Schierup MH, Batzer MA, Jolly CJ, Knauf S, Zinner D, Farh KKH, Marques-Bonet T, Munch K, Roos C, Rogers J. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. Science 2023; 380:eabn8153. [PMID: 37262153 DOI: 10.1126/science.abn8153] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 09/27/2022] [Indexed: 06/03/2023]
Abstract
Baboons (genus Papio) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high-coverage whole-genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and interspecies gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes.
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Affiliation(s)
- Erik F Sørensen
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liye Zhang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Artificial Intelligence Lab, Illumina Inc., San Diego, CA 92122, USA
| | - Jerilyn A Walker
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
| | - Claudia Fontsere
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Lakshmi Seshadri
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Christina M Bergey
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Andrew S Burrell
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Jane E Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | - Kenneth L Chiou
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | | | | | - Julia Fischer
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Marie-Claude Gingras
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sejal Salvi
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harshavardhan Doddapaneni
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Kyle K-H Farh
- Artificial Intelligence Lab, Illumina Inc., San Diego, CA 92122, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluis Companys, 23, 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Baldiri i Reixac 4, 08028 Barcelona, Spain
- Institut Catala de Paleontologia Miquel Crusafont, Universitat Autonoma de Barcelona, Edifici ICTA-ICP, cl Columnes s/n, 08193 Cerdanyola del Valles, Barcelona, Spain
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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9
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Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Rogers J, Farh KKH, Marques Bonet T. A global catalog of whole-genome diversity from 233 primate species. Science 2023; 380:906-913. [PMID: 37262161 DOI: 10.1126/science.abn7829] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/06/2023] [Indexed: 06/03/2023]
Abstract
The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
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Affiliation(s)
- Lukas F K Kuderna
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Austria
| | - Joseph D Orkin
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, CEP 69553-225, Tefé, Amazonas, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | | | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City. UT 84102, USA
| | | | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - João Valsecchi
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, Peru
| | - Malu Messias
- Universidade Federal de Rondônia, Porto Velho, Rondônia, Brazil
| | | | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, MT, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | | | - Sree Kanthaswamy
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ 85004, USA
| | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, Addis Ababa, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Long Zhou
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Esther Lizano
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK, and School of Geosciences, Drummond Street, Edinburgh EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Tomas Marques Bonet
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
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10
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Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich ASD, Fiziev PP, Kuderna LFK, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Bataillon T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O'Donnell-Luria A, Rehm HL, Xu J, Rogers J, Marques-Bonet T, Farh KKH. The landscape of tolerated genetic variation in humans and primates. Science 2023; 380:eabn8153. [PMID: 37262156 DOI: 10.1126/science.abn8197] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/22/2023] [Indexed: 06/03/2023]
Abstract
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.
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Affiliation(s)
- Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Tobias Hamp
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Jeffrey Ede
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Jeremy McRae
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
| | - Yanshen Yang
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | | | - Petko P Fiziev
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Yibing Wu
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Aashish Adhikari
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Yair Field
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Chen Chen
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Serafim Batzoglou
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Rebecca Reimers
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Daniel Balick
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
| | - Joseph D Orkin
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Alejandro Valenzuela
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000 Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, Tefé, Amazonas, CEP 69553-225, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels, Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City, UT 84102, USA
| | - Iracilda Sampaio
- Universidade Federal do Para, Guamá, Belém - PA, 66075-110, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
| | - João Valsecchi do Amaral
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, 69553-225, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, 69080-900, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, 16001, Peru
| | - Mariluce Messias
- Universidade Federal de Rondonia, Porto Velho, Rondônia, 78900-000, Brazil
- PPGREN - Programa de Pós-Graduação "Conservação e Uso dos Recursos Naturais and BIONORTE - Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Rede BIONORTE, Universidade Federal de Rondonia, Porto Velho, Rondônia, 78900-000, Brazil
| | - Maria N F da Silva
- Instituto Nacional de Pesquisas da Amazonia, Petrópolis, Manaus - AM, 69067-375, Brazil
| | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Universidade Federal do Mato Grosso, Boa Esperança, Cuiabá - MT, 78060-900, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | | | | | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eduardo Fernandez-Duque
- Yale University, New Haven, CT 06520, USA
- Universidad Nacional de Formosa, Argentina Fundacion ECO, Formosa, Argentina
| | | | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, PoB 16316, Addis Ababa 1000, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald - Insei Riems, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi 100000, Vietnam
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, 70191 Stuttgart, Germany
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province 430000, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore 729826, Republic of Singapore
| | - Patrick Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 168582, Republic of Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 168582, Republic of Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore 168582, Republic of Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz Science Campus Primate Cognition, 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Pg. Luís Companys 23, 08010 Barcelona, Spain
| | - Amanda Melin
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH8 9XP, UK
| | | | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shamil Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jinbo Xu
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
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11
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Ulrich RG, Drewes S, Haring V, Panajotov J, Pfeffer M, Rubbenstroth D, Dreesman J, Beer M, Dobler G, Knauf S, Johne R, Böhmer MM. [Viral zoonoses in Germany: a One Health perspective]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2023:10.1007/s00103-023-03709-0. [PMID: 37261460 DOI: 10.1007/s00103-023-03709-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/26/2023] [Indexed: 06/02/2023]
Abstract
The COVID-19 pandemic and the increasing occurrence of monkeypox (mpox) diseases outside Africa have illustrated the vulnerability of populations to zoonotic pathogens. In addition, other viral zoonotic pathogens have gained importance in recent years.This review article addresses six notifiable viral zoonotic pathogens as examples to highlight the need for the One Health approach in order to understand the epidemiology of the diseases and to derive recommendations for action by the public health service. The importance of environmental factors, reservoirs, and vectors is emphasized, the diseases in livestock and wildlife are analyzed, and the occurrence and frequency of diseases in the population are described. The pathogens selected here differ in their reservoirs and the role of vectors for transmission, the impact of infections on farm animals, and the disease patterns observed in humans. In addition to zoonotic pathogens that have been known in Germany for a long time or were introduced recently, pathogens whose zoonotic potential has only lately been shown are also considered.For the pathogens discussed here, there are still large knowledge gaps regarding the transmission routes. Future One Health-based studies must contribute to the further elucidation of their transmission routes and the development of prevention measures. The holistic approach does not necessarily include a focus on viral pathogens/diseases, but also includes the question of the interaction of viral, bacterial, and other pathogens, including antibiotic resistance and host microbiomes.
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Affiliation(s)
- Rainer G Ulrich
- Institut für neue und neuartige Tierseuchenerreger, Friedrich-Loeffler-Institut, Bundesforschungsinstitut für Tiergesundheit, Südufer 10, 17493, Greifswald-Insel Riems, Deutschland.
| | - Stephan Drewes
- Institut für neue und neuartige Tierseuchenerreger, Friedrich-Loeffler-Institut, Bundesforschungsinstitut für Tiergesundheit, Südufer 10, 17493, Greifswald-Insel Riems, Deutschland
| | - Viola Haring
- Institut für neue und neuartige Tierseuchenerreger, Friedrich-Loeffler-Institut, Bundesforschungsinstitut für Tiergesundheit, Südufer 10, 17493, Greifswald-Insel Riems, Deutschland
| | - Jessica Panajotov
- Fachgruppe Viren in Lebensmitteln, Bundesinstitut für Risikobewertung, Berlin, Deutschland
| | - Martin Pfeffer
- Institut für Tierhygiene und Öffentliches Veterinärwesen, Universität Leipzig, Leipzig, Deutschland
| | - Dennis Rubbenstroth
- Institut für Virusdiagnostik, Friedrich-Loeffler-Institut, Bundesforschungsinstitut für Tiergesundheit, Greifswald-Insel Riems, Deutschland
| | | | - Martin Beer
- Institut für Virusdiagnostik, Friedrich-Loeffler-Institut, Bundesforschungsinstitut für Tiergesundheit, Greifswald-Insel Riems, Deutschland
| | - Gerhard Dobler
- Abteilung Virologie und Rickettsiologie, Institut für Mikrobiologie der Bundeswehr, München, Deutschland
| | - Sascha Knauf
- Institut für Internationale Tiergesundheit/One Health, Friedrich-Loeffler-Institut, Bundesforschungsinstitut für Tiergesundheit, Greifswald-Insel Riems, Deutschland
| | - Reimar Johne
- Fachgruppe Viren in Lebensmitteln, Bundesinstitut für Risikobewertung, Berlin, Deutschland
| | - Merle M Böhmer
- Landesinstitut Gesundheit II - Task Force Infektiologie, Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), München, Deutschland
- Institut für Sozialmedizin und Gesundheitssystemforschung, Otto-von-Guericke Universität, Magdeburg, Deutschland
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12
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Sørensen EF, Harris RA, Zhang L, Raveendran M, Kuderna LFK, Walker JA, Storer JM, Kuhlwilm M, Fontsere C, Seshadri L, Bergey CM, Burrell AS, Bergmann J, Phillips-Conroy JE, Shiferaw F, Chiou KL, Chuma IS, Keyyu JD, Fischer J, Gingras MC, Salvi S, Doddapaneni H, Schierup MH, Batzer MA, Jolly CJ, Knauf S, Zinner D, Farh KKH, Marques-Bonet T, Munch K, Roos C, Rogers J. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. bioRxiv 2023:2023.05.02.539112. [PMID: 37205419 PMCID: PMC10187195 DOI: 10.1101/2023.05.02.539112] [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] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Baboons (genus Papio ) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high coverage whole genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and inter-species gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal novel patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes. One-Sentence Summary Genomic data for 225 baboons reveal novel sites of inter-species gene flow and local effects due to differences in admixture.
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13
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Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich A, Fiziev P, Kuderna L, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath J, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Batallion T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O’Donnell A, Rehm H, Xu J, Rogers J, Marques-Bonet T, Kai-How Farh K. The landscape of tolerated genetic variation in humans and primates. bioRxiv 2023:2023.05.01.538953. [PMID: 37205491 PMCID: PMC10187174 DOI: 10.1101/2023.05.01.538953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases. One Sentence Summary Deep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.
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Affiliation(s)
- Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Tobias Hamp
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Jeffrey Ede
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Joshua G. Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Jeremy McRae
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
| | - Yanshen Yang
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Anastasia Dietrich
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Petko Fiziev
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Lukas Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Yibing Wu
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Aashish Adhikari
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Yair Field
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Chen Chen
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Serafim Batzoglou
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Rebecca Reimers
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Daniel Balick
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Mareike C. Janiak
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna; Djerassiplatz 1, 1030, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna; 1030, Vienna, Austria
| | - Joseph D. Orkin
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Département d’anthropologie, Université de Montréal; 3150 Jean-Brillant, Montréal, QC, H3T 1N8, Canada
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR); Ghaziabad, 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Alejandro Valenzuela
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University; Aarhus, 8000, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University; Aarhus, 8000, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development; Estrada da Bexiga 2584, Tefé, Amazonas, CEP 69553-225, Brazil
- Faculty of Sciences, Department of Organismal Biology, Unit of Evolutionary Biology and Ecology, Université Libre de Bruxelles (ULB); Avenue Franklin D. Roosevelt 50, 1050, Brussels, Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University; SE-75236, Uppsala, Sweden
| | | | - Julie Horvath
- North Carolina Museum of Natural Sciences; Raleigh, North Carolina, 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University; Durham, North Carolina , 27707, USA
- Department of Biological Sciences, North Carolina State University; Raleigh, North Carolina , 27695, USA
- Department of Evolutionary Anthropology, Duke University; Durham, North Carolina , 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | | | - Fabricio Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah; Salt Lake City, Utah, 84102, USA
| | - Iracilda Sampaio
- Universidade Federal do Para; Guamá, Belém - PA, 66075-110, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
| | - João Valsecchi do Amaral
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development; Tefé, Amazonas, 69553-225, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia – RedeFauna; Manaus, Amazonas, 69080-900, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica – ComFauna; Iquitos, Loreto, 16001, Peru
| | - Mariluce Messias
- Universidade Federal de Rondonia; Porto Velho, Rondônia, 78900-000, Brazil
- PPGREN - Programa de Pós-Graduação “Conservação e Uso dos Recursos Naturais and BIONORTE - Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Rede BIONORTE, Universidade Federal de Rondonia; Porto Velho, Rondônia, 78900-000, Brazil
| | - Maria N. F. da Silva
- Instituto Nacional de Pesquisas da Amazonia; Petrópolis, Manaus - AM, 69067-375, Brazil
| | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Rogerio Rossi
- Universidade Federal do Mato Grosso; Boa Esperança, Cuiabá - MT, 78060-900, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
- Department of Biology, Trinity University; San Antonio, Texas, 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | - Clément J. Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | | | | | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center; Houston, Texas, 77030, USA
| | | | - Joe H. Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center; Houston, Texas, 77030, USA
| | - Eduardo Fernandez-Duque
- Yale University; New Haven, Connecticut, 06520, USA
- Universidad Nacional de Formosa, Argentina Fundacion ECO, Formosa, Argentina
| | | | | | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming, Yunnan, 650223, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming, Yunnan, 650223, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen; Copenhagen, DK-2100, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center; 1369 West Wenyi Road, Hangzhou, 311121, China
- Women’s Hospital, School of Medicine, Zhejiang University; 1 Xueshi Road, Shangcheng District, Hangzhou, 310006, China
| | - Julius D. Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office; P.O.Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health; 17493 Greifswald - Isle of Riems, Germany
| | - Minh D. Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University; Hanoi, 100000, Vietnam
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart; 70191 Stuttgart, Germany
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology; Av. Doctor Aiguader, N88, Barcelona, 08003, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation; C. Wellington 30, Barcelona, 08005, Spain
| | - Thomas Batallion
- Bioinformatics Research Centre, Aarhus University; Aarhus, 8000, Denmark
| | - Tilo Nadler
- Cuc Phuong Commune; Nho Quan District, Ninh Binh Province, 430000, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jessica Lee
- Mandai Nature; 80 Mandai Lake Road, Singapore 729826, Republic of Singapore
| | - Patrick Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM); Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School; Singapore 168582, Republic of Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM); Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School; Singapore 168582, Republic of Singapore
- SingHealth Duke-NUS Genomic Medicine Centre; Singapore 168582, Republic of Singapore
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland; Chambers Street, Edinburgh, EH1 1JF, UK
- School of Geosciences, University of Edinburgh; Drummond Street, Edinburgh, EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research; 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen; 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
- Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
| | - Amanda Melin
- Leibniz Science Campus Primate Cognition; 37077 Göttingen, Germany
- Department of Anthropology & Archaeology and Department of Medical Genetics
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University; SE-75236, Uppsala, Sweden
- Alberta Children’s Hospital Research Institute; University of Calgary; 2500 University Dr NW T2N 1N4, Calgary, Alberta, Canada
| | | | - Robin M. D. Beck
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR); Ghaziabad, 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Christian Roos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh; Edinburgh, EH8 9XP, UK
| | - Jean P. Boubli
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Monkol Lek
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research; Kellnerweg 4, 37077 Göttingen, Germany
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- Department of Genetics, Yale School of Medicine; New Haven, Connecticut, 06520, USA
| | - Anne O’Donnell
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Heidi Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Jinbo Xu
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
- Toyota Technological Institute at Chicago; Chicago, Illinois, 60637, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
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14
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Adade E, Roos C, Chuma IS, Sylverken AA, Knauf S. No evidence for yaws infection in a small-scale cross-sectional serosurvey in Ghanaian monkeys. Vet Med Sci 2022; 9:507-512. [PMID: 36480449 PMCID: PMC9856988 DOI: 10.1002/vms3.1016] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Treponema pallidum (TP) is a spirochaete bacterium with subspecies that in humans cause syphilis (subsp. pallidum), bejel (subsp. endemicum) and yaws (subsp. pertenue; TPE). The latter is target for eradication which requires detailed information on yaws epidemiology. It has been shown that African nonhuman primates (NHPs) are infected with TPE strains that are closely related to the human infecting yaws bacterium. While human yaws infection is known to be endemic in Ghana, there is a paucity of information regarding TPE infection of Ghana's native NHPs. OBJECTIVES The objective was to perform a small-scale cross-sectional serological screening for antibodies against TPE in Ghanaian monkeys. Due to the reports of TPE-infected NHPs from neighbouring Côte d'Ivore, we hypothesised that monkeys in Ghana are infected with TPE and, therefore, are seropositive for antibodies against-Treponema. METHODS We sampled blood from 37 NHPs representing four species: Erythrocebus patas (16/37) 43.2%, Papio anubis (15/37) 40.5%, Chlorocebus sabaeus (3/37) 8.1% and Cercopithecus mona (3/37) 8.1%. Samples were tested using the NHP validated treponemal test ESPLINE TP. RESULTS All 37 animals were seronegative for yaws infection. CONCLUSIONS We cannot exclude yaws infection in NHPs in Ghana at this point. Our study, in combination with the absence of reports of clinically infected NHPs in a yaws endemic country is, however, supportive for the current thinking that interspecies infection with TPE is extremely rare. This is an important finding for the current ongoing yaws eradication campaign.
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Affiliation(s)
- Eugene Adade
- Department of Theoretical and Applied BiologyKwame Nkrumah University of Science and TechnologyKumasiGhana,Kumasi Centre for Collaborative Research in Tropical MedicineKwame Nkrumah University of Science and TechnologyKumasiGhana
| | - Christian Roos
- Deutsches Primatenzentrum GmbHLeibniz Institute for Primate ResearchGöttingenGermany
| | | | - Augustina Angelina Sylverken
- Department of Theoretical and Applied BiologyKwame Nkrumah University of Science and TechnologyKumasiGhana,Kumasi Centre for Collaborative Research in Tropical MedicineKwame Nkrumah University of Science and TechnologyKumasiGhana
| | - Sascha Knauf
- Deutsches Primatenzentrum GmbHLeibniz Institute for Primate ResearchGöttingenGermany,Institute of International Animal Health/One HealthFriedrich‐Loeffler‐InstitutGreifswald ‐ Insel RiemsGermany
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15
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Zinner D, Knauf S, Chuma I, Butynski T, De Jong Y, Keyyu J, Kaitila R, Roos C. Mito-phylogenetic relationship of the new subspecies of gentle monkey <i>Cercopithecus mitis manyaraensis</i>, Butynski & De Jong, 2020. Primate Biol 2022; 9:11-18. [PMID: 35855296 PMCID: PMC9285482 DOI: 10.5194/pb-9-11-2022] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/01/2022] [Indexed: 11/11/2022] Open
Abstract
In 2020, a new subspecies was described in the Cercopithecus mitis complex, the Manyara monkey C. m. manyaraensis, Butynski & De Jong, 2020. The internal taxonomy of this species complex is still debated, and the phylogenetic relationships among the taxa are unclear. Here we provide the first mitochondrial sequence data for C. m. manyaraensis to determine its position within the mitochondrial phylogeny of C. mitis. This subspecies clusters within the youngest (internal divergences between 1.01 and 0.42 Ma) of three main taxonomic clades of C. mitis. Its sister lineages are C. m. boutourlinii (Ethiopia), C. m. albotorquatus (Kenya and Somalia), C. m. albogularis (Kenya and Tanzania), and C. m. monoides (Tanzania and Mozambique). In general, the phylogenetic tree of C. mitis based on mitochondrial sequence data indicates several paraphyletic relationships within the C. mitis complex. As in other African cercopithecines (e.g. Papio and Chlorocebus), these data are suitable for reconstructing historic
biogeographical patterns, but they are only of limited value for
delimitating taxa.
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Affiliation(s)
- Dietmar Zinner
- Cognitive Ethology Laboratory, Deutsches Primatenzentrum, Leibniz
Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-University of
Göttingen, 37077, Göttingen, Germany
- Leibniz Science Campus Primate Cognition, 37077 Göttingen,
Germany
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Infection Biology Unit, Deutsches Primatenzentrum, 37077 Göttingen, Germany
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald, Insel Riems, Germany
| | - Idrissa S. Chuma
- Tanzania National Parks (Serengeti National Park), Arusha, Tanzania
| | - Thomas M. Butynski
- Eastern Africa Primate Diversity and Conservation Program &
Lolldaiga Hills Research Programme, Nanyuki, Kenya
| | - Yvonne A. De Jong
- Eastern Africa Primate Diversity and Conservation Program &
Lolldaiga Hills Research Programme, Nanyuki, Kenya
| | | | - Rehema Kaitila
- Tanzania National Parks (Lake Manyara National Park), Arusha, Tanzania
| | - Christian Roos
- Primate Genetics Laboratory, Deutsches Primatenzentrum, Leibniz
Institute for Primate Research, 37077 Göttingen, Germany
- Gene Bank of Primates, Deutsches Primatenzentrum, Leibniz
Institute for Primate Research, 37077 Göttingen, Germany
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16
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Mason B, Petrzelkova KJ, Kreisinger J, Bohm T, Cervena B, Fairet E, Fuh T, Gomez A, Knauf S, Maloueki U, Modry D, Shirley MH, Tagg N, Wangue N, Pafco B. Gastrointestinal symbiont diversity in wild gorilla: a comparison of bacterial and strongylid communities across multiple localities. Mol Ecol 2022; 31:4127-4145. [PMID: 35661299 DOI: 10.1111/mec.16558] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/17/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022]
Abstract
Western lowland gorillas (Gorilla gorilla gorilla) are Critically Endangered and show continued population decline. Consequently, pressure mounts to better understand their conservation threats and ecology. Gastrointestinal symbionts, such as bacterial and eukaryotic communities, are believed to play vital roles in the physiological landscape of the host. Gorillas host a broad spectrum of eucaryotes, so called parasites, with strongylid nematodes being particularly prevalent. While these communities are partially consistent, they are also shaped by various ecological factors, such as diet or habitat type. To investigate gastrointestinal symbionts of wild western lowland gorillas, we analysed 215 faecal samples from individuals in five distinct localities across the Congo Basin, using high-throughput sequencing techniques. We describe the gut bacterial microbiome and genetic diversity of strongylid communities, including strain-level identification of amplicon sequence variants (ASVs). We identified strongylid ASVs from eight genera and bacterial ASVs from twenty phyla. We compared these communities across localities, with reference to varying environmental factors among populations, finding differences in alpha diversity and community compositions of both gastrointestinal components. Moreover, we also investigated covariation between strongylid nematodes and the bacterial microbiome, finding correlations between strongylid taxa and Prevotellaceae and Rikenellaceae ASVs that were consistent across multiple localities. Our research highlights complexity of the bacterial microbiome and strongylid communities in several gorilla populations and emphasizes potential interactions between these two symbiont communities. This study provides a framework for ongoing research into strongylid nematode diversity, and their interactions with the bacterial microbiome, amongst great apes.
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Affiliation(s)
- Bethan Mason
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences
| | - Klara J Petrzelkova
- Institute of Vertebrate Biology, Czech Academy of Sciences.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences.,Liberec Zoo, Liberec, Czech Republic
| | | | - Torsten Bohm
- African Parks, Odzala-Kokoua National Park, Republic of, Congo
| | | | - Emilie Fairet
- SFM Safari Gabon, Loango National Park, Gabon.,Wildlife Conservation Society, New York, NY, USA
| | | | - Andres Gomez
- Department of Animal Science, University of Minnesota Twin Cities, St. Paul, Minnesota
| | - Sascha Knauf
- Institute of International Animal Health / One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany
| | - Ulrich Maloueki
- African Parks, Odzala-Kokoua National Park, Republic of, Congo
| | - David Modry
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences.,Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources/CINeZ, Czech University of Life Sciences Prague
| | - Matthew H Shirley
- SFM Safari Gabon, Loango National Park, Gabon.,Institute of Environment, Florida International University, North Miami, FL, USA
| | - Nikki Tagg
- Project Grands Singes, , Centre for Research and Conservation, Royal Zoological Society of Antwerp
| | | | - Barbora Pafco
- Institute of Vertebrate Biology, Czech Academy of Sciences
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17
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Handley BL, González-Beiras C, Tchatchouang S, Basing LA, Hugues KA, Bakheit M, Becherer L, Ries C, Njih Tabah E, Crucitti T, Borst N, Lüert S, Frischmann S, Haerpfer T, Landmann E, Amanor I, Sylla A, Kouamé-Sina MS, Ndzomo-Ngono JP, Tano A, Arhinful D, Awondo P, Ngazoa Kakou S, Eyangoh S, Addo KK, Harding-Esch EM, Knauf S, Mitjà O, Marks M. LAMP4yaws: Treponema pallidum, Haemophilus ducreyi loop mediated isothermal amplification - protocol for a cross-sectional, observational, diagnostic accuracy study. BMJ Open 2022; 12:e058605. [PMID: 35351731 PMCID: PMC8966536 DOI: 10.1136/bmjopen-2021-058605] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
INTRODUCTION Yaws, caused by the bacterium Treponema pallidum subsp. pertenue, is a neglected tropical disease targeted for eradication by 2030. Improved diagnostics will be essential to meet this goal. Diagnosis of yaws has relied heavily on clinical and serological tools. However, the presence of coendemic cutaneous skin ulcer diseases, such as lesions caused by Haemophilus ducreyi (HD), means these techniques do not provide a reliable diagnosis. Thus, new diagnostic tools are needed. Molecular tools such as PCR are ideal, but often expensive as they require trained technicians and laboratory facilities, which are often not available to national yaws programmes. METHODS AND ANALYSIS The LAMP4yaws project is a cross-sectional, observational, diagnostic accuracy study of a combined Treponema pallidum (TP) and HD loop mediated isothermal amplification (TPHD-LAMP) test performed under real world conditions in three endemic countries in West Africa. Individuals with serologically confirmed yaws will be recruited in Cameroon, Côte d'Ivoire and Ghana. Each participant will provide paired swabs, one of which will be sent to the respective national reference laboratory for yaws quantitative PCR and the other will be tested for both TP and HD using the TPHD-LAMP test at local district laboratories. Sensitivity and specificity of the TPHD-LAMP test will be calculated against the reference standard qPCR. We will also assess the acceptability, feasibility and cost-effectiveness of the test. We anticipate that results from this study will support the adoption of the TPHD-LAMP test for use in global yaws eradication efforts. ETHICS AND DISSEMINATION We have received ethical approval from all relevant institutional and national ethical committees. All participants, or their parents or guardians, must provide written informed consent prior to study enrolment. Study results will be published in an open access journal and disseminated with partners and the World Health Organization. TRIAL REGISTRATION NUMBER NCT04753788.
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Affiliation(s)
- Becca Louise Handley
- Clinical Research Department, London School of Hygiene and Tropical Medicine Faculty of Infectious and Tropical Diseases, London, UK
| | - Camila González-Beiras
- Department of Infectious Diseases, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | | | - Laud Antony Basing
- University of Ghana Noguchi Memorial Institute for Medical Research, Accra, Greater Accra, Ghana
| | - Kouadio Aboh Hugues
- National Program of African Trypanosomiasis Elimination, Abidjan, Côte d'Ivoire
- Institut Pasteur de Cote d'Ivoire, Abidjan, Lagunes, Côte d'Ivoire
| | | | - Lisa Becherer
- IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg im Breisgau, Germany
| | - Christina Ries
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany
| | - Earnest Njih Tabah
- National Buruli Ulcer, Leprosy, Yaws and Leishmaniasis Control Program, Ministry of Public Health, Yaounde, Centre Region, Cameroon
- Public Health & Epidemiology, University of Dschang, Yaounde, West Region, Cameroon
| | - Tania Crucitti
- Experimental Bacteriology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Nadine Borst
- IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg im Breisgau, Germany
| | - Simone Lüert
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany
| | | | - Tamara Haerpfer
- IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg im Breisgau, Germany
| | | | - Ivy Amanor
- University of Ghana Noguchi Memorial Institute for Medical Research, Accra, Greater Accra, Ghana
| | - Aboubacar Sylla
- Institut Pasteur de Cote d'Ivoire, Abidjan, Lagunes, Côte d'Ivoire
| | | | | | - Adingra Tano
- Institut Pasteur de Cote d'Ivoire, Abidjan, Lagunes, Côte d'Ivoire
| | - Daniel Arhinful
- University of Ghana Noguchi Memorial Institute for Medical Research, Accra, Greater Accra, Ghana
| | | | | | | | - Kennedy Kwasi Addo
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Emma Michele Harding-Esch
- Clinical Research Department, London School of Hygiene and Tropical Medicine Faculty of Infectious and Tropical Diseases, London, UK
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany
| | - Oriol Mitjà
- Department of Infectious Diseases, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Michael Marks
- Clinical Research Department, London School of Hygiene and Tropical Medicine Faculty of Infectious and Tropical Diseases, London, UK
- Hospital for Tropical Diseases, London, UK
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18
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Kiffner C, Paciência FMD, Henrich G, Kaitila R, Chuma IS, Mbaryo P, Knauf S, Kioko J, Zinner D. Road-based line distance surveys overestimate densities of olive baboons. PLoS One 2022; 17:e0263314. [PMID: 35108346 PMCID: PMC8809570 DOI: 10.1371/journal.pone.0263314] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 08/29/2021] [Accepted: 01/14/2022] [Indexed: 11/26/2022] Open
Abstract
Estimating population density and population dynamics is essential for understanding primate ecology and relies on robust methods. While distance sampling theory provides a robust framework for estimating animal abundance, implementing a constrained, non-systematic transect design could bias density estimates. Here, we assessed potential bias associated with line distance sampling surveys along roads based on a case study with olive baboons (Papio anubis) in Lake Manyara National Park (Tanzania). This was achieved by comparing density estimates of olive baboons derived from road transect surveys with density estimates derived from estimating the maximum number of social groups (via sleeping site counts) and multiplying this metric with the estimated average size of social groups. From 2011 to 2019, we counted olive baboons along road transects, estimated survey-specific densities in a distance sampling framework, and assessed temporal population trends. Based on the fitted half-normal detection function, the mean density was 132.5 baboons km-2 (95% CI: 110.4–159.2), however, detection models did not fit well due to heaping of sightings on and near the transects. Density estimates were associated with relatively wide confidence intervals that were mostly caused by encounter rate variance. Based on a generalized additive model, baboon densities were greater during the rainy seasons compared to the dry seasons but did not show marked annual trends. Compared to estimates derived from the alternative method (sleeping site survey), distance sampling along road transects overestimated the abundance of baboons more than threefold. Possibly, this overestimation was caused by the preferred use of roads by baboons. While being a frequently used technique (due to its relative ease of implementation compared to spatially randomized survey techniques), inferring population density of baboons (and possibly other species) based on road transects should be treated with caution. Beyond these methodological concerns and considering only the most conservative estimates, baboon densities in LMNP are among the highest across their geographic distribution range.
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Affiliation(s)
- Christian Kiffner
- The School For Field Studies, Center For Wildlife Management Studies, Karatu, Tanzania
- Department of Human Behavior, Max Planck Institute for Evolutionary Anthropology, Ecology and Culture, Leipzig, Germany
- Junior Research Group Human‐Wildlife Conflict & Coexistence, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Filipa M. D. Paciência
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Grace Henrich
- Vassar College, Poughkeepsie, New York State, United States of America
| | - Rehema Kaitila
- Tanzania National Parks, Conservation Science Unit (Veterinary), Arusha, Tanzania
| | - Idrissa S. Chuma
- Tanzania National Parks, Conservation Science Unit (Veterinary), Arusha, Tanzania
| | - Pay Mbaryo
- Tanzania National Parks, Conservation Science Unit (Veterinary), Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health / One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany
- Infection Biology Unit, Germany Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - John Kioko
- The School For Field Studies, Center For Wildlife Management Studies, Karatu, Tanzania
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Department of Primate Cognition, Georg-August-University of Göttingen, Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, Göttingen, Germany
- * E-mail:
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19
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Paciência FMD, Chuma IS, Lipende IF, Knauf S, Zinner D. Female post-copulatory behavior in a group of olive baboons (Papio anubis) infected by Treponema pallidum. PLoS One 2022; 17:e0261894. [PMID: 35051197 PMCID: PMC8775205 DOI: 10.1371/journal.pone.0261894] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 12/13/2021] [Indexed: 11/25/2022] Open
Abstract
Pathogens exert a profound and pervasive cost on various aspects of primate sociality and reproduction. In olive baboons (Papio anubis) at Lake Manyara National Park, Tanzania, genital skin ulcers, caused by the bacterium Treponema pallidum subsp. pertenue, are associated with increased female mating avoidance and altered male mating patterns at a pre-copulatory and copulatory level. Beyond this, mating is also comprised of post-copulatory interactions among sexual partners (i.e., copulation calls, darting [post-copulatory sprint away from the male], and post-copulatory grooming). In baboons, female post-copulatory behavior is hypothesized to incite male-male competition, promote subsequent copulations, and/or strengthen the bonds between the mating pairs. Due to a higher reproductive burden (i.e. pregnancy, lactation, infant rearing), females should avoid proceptive behavior after mating to decrease further exposure to potential pathogens. To investigate whether the presence of genital skin ulcers has an impact at the post-copulatory level, we analyzed 517 copulation events of 33 cycling females and 29 males with and without genital skin ulcers. The occurrence of female post-copulatory behaviors was not altered by genital skin ulcerations in males. Similar to other baboon populations, females in our study group were more likely to utter copulation calls after an ejaculatory copulation. The likelihood of darting was higher after ejaculatory copulations and with the presence of copulation calls. Post-copulatory grooming (i.e., occurring within 15 seconds after a copulation) was not frequently observed. Our results indicate that despite the presence of conspicuous signs of disease, female post-copulatory behavior was not affected by the genital health status of the males. This indicates that in our study group, infection cues caused by T. pallidum subsp. pertenue play a major role before and during mating, but not after mating. The post-copulatory behavior of females is most likely affected by physiological or evolutionary constraints other than sexually transmitted infections.
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Affiliation(s)
- Filipa M. D. Paciência
- Cognitive Ethology Laboratory, Deutsches Primatenzentrum, Leibniz Institute for Primate Research, Göttingen, Germany
- Work Group Neglected Tropical Diseases, Infection Biology Unit, Deutsches Primatenzentrum, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Idrissa S. Chuma
- Sokoine University of Agriculture, Chuo Kikuu, Morogoro, Tanzania
| | - Iddi F. Lipende
- Sokoine University of Agriculture, Chuo Kikuu, Morogoro, Tanzania
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Infection Biology Unit, Deutsches Primatenzentrum, Leibniz Institute for Primate Research, Göttingen, Germany
- Institute of International Animal Health, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald, Isle of Riems, Germany
- Department for Animal Sciences, Georg-August-University, Göttingen, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Deutsches Primatenzentrum, Leibniz Institute for Primate Research, Göttingen, Germany
- Leibniz Science Campus Primate Cognition, Göttingen, Germany
- Department of Primate Cognition, Georg-August-University, Göttingen, Germany
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20
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Tuppurainen E, Dietze K, Wolff J, Bergmann H, Beltran-Alcrudo D, Fahrion A, Lamien CE, Busch F, Sauter-Louis C, Conraths FJ, De Clercq K, Hoffmann B, Knauf S. Review: Vaccines and Vaccination against Lumpy Skin Disease. Vaccines (Basel) 2021; 9:1136. [PMID: 34696244 PMCID: PMC8539040 DOI: 10.3390/vaccines9101136] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [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: 08/31/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 11/16/2022] Open
Abstract
The geographical distribution of lumpy skin disease (LSD), an economically important cattle disease caused by a capripoxvirus, has reached an unprecedented extent. Vaccination is the only way to prevent the spread of the infection in endemic and newly affected regions. Yet, in the event of an outbreak, selection of the best vaccine is a major challenge for veterinary authorities and farmers. Decision makers need sound scientific information to support their decisions and subsequent actions. The available vaccine products vary in terms of quality, efficacy, safety, side effects, and price. The pros and cons of different types of live attenuated and inactivated vaccines, vaccination strategies, and associated risks are discussed. Seroconversion, which typically follows vaccination, places specific demands on the tools and methods used to evaluate the effectiveness of the LSD vaccination campaigns in the field. We aimed to give a comprehensive update on available vaccines and vaccination against LSD, to better prepare affected and at-risk countries to control LSD and ensure the safe trade of cattle.
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Affiliation(s)
- Eeva Tuppurainen
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany; (K.D.); (A.F.); (F.B.); (S.K.)
| | - Klaas Dietze
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany; (K.D.); (A.F.); (F.B.); (S.K.)
| | - Janika Wolff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany; (J.W.); (B.H.)
| | - Hannes Bergmann
- Institute of Epidemiology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany; (H.B.); (C.S.-L.); (F.J.C.)
| | - Daniel Beltran-Alcrudo
- Regional Office for Europe and Central Asia, Food and Agriculture Organization, 20 Kalman Imre utca, H-1054 Budapest, Hungary;
| | - Anna Fahrion
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany; (K.D.); (A.F.); (F.B.); (S.K.)
| | - Charles Euloge Lamien
- FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency (IAEA), Friedenstrasse 1, A-2444 Seibersdorf, Austria;
| | - Frank Busch
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany; (K.D.); (A.F.); (F.B.); (S.K.)
| | - Carola Sauter-Louis
- Institute of Epidemiology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany; (H.B.); (C.S.-L.); (F.J.C.)
| | - Franz J. Conraths
- Institute of Epidemiology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany; (H.B.); (C.S.-L.); (F.J.C.)
| | - Kris De Clercq
- Unit of Exotic and Particular Diseases, Scientific Directorate Infectious Diseases in Animals, Sciensano, Groeselenberg 99, B-1180 Brussels, Belgium;
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany; (J.W.); (B.H.)
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany; (K.D.); (A.F.); (F.B.); (S.K.)
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21
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Hisgen L, Abel L, Hallmaier-Wacker L, Lüert S, Lavazza A, Trogu T, Velarde R, Nováková M, Gyuranecz M, Ågren E, Barlow A, Šmajs D, Knauf S. The distribution of lagomorph syphilis caused by Treponema paraluisleporidarum in Europe. EUR J WILDLIFE RES 2021. [DOI: 10.1007/s10344-021-01535-w] [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: 11/24/2022]
Abstract
AbstractTreponema paraluisleporidarum infects both rabbits (ecovar Cuniculus) and hares (ecovar Lepus). While the occurrence of the bacterium has previously been reported for European brown hares (Lepus europaeus) and domestic rabbits (Oryctolagus cuniculus f. domestica), there are no data available that report infection in the European context. We tested a total of 1,995 serum samples and 287 genital swabs from opportunistically sampled European brown hares (Lepus europaeus; n = 2135), Mountain hares (Lepus timidus; n = 4), European rabbits (Oryctolagus cuniculus; n = 138), and pet rabbits (O. cuniculus f. domestica; n = 5). The samples originated from eight European countries. In case only serum was available, we tested the samples for the presence of anti-treponemal antibodies. For this, we utilized the Treponema pallidum-particle agglutination test (TP-PA), which is suited for the use in lagomorphs due to the antigenic cross-reactivity of anti-T. pallidum and anti-T. paraluisleporidarum antibodies. In addition, the results of 380 sera were confirmed using the fluorescent-Treponema antibody absorption test (FTA-ABS). In all cases where swab samples were available, DNA was extracted and tested using quantitative PCR to test for the presence of the lagomorph syphilis-bacterium. We were able to detect antibodies in 825 of 1,995 lagomorph sera (41.4%; brown hare: 825/1,868; rabbit: 0/127) and obtained positive qPCR results from 182 of 287 swab samples (63.4%; European brown hare: 167/267; mountain hare: 4/4; rabbit: 11/16). While all rabbit sera (n = 127) tested negative for anti-treponemal antibodies, the presence of the bacterium was confirmed in eight wild (n = 8/11) and three domestic rabbits (n = 3/5) from Germany using qPCR.
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22
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Becherer L, Knauf S, Marks M, Lueert S, Frischmann S, Borst N, von Stetten F, Bieb S, Adu-Sarkodie Y, Asiedu K, Mitjà O, Bakheit M. Multiplex Mediator Displacement Loop-Mediated Isothermal Amplification for Detection of Treponema pallidum and Haemophilus ducreyi. Emerg Infect Dis 2021; 26:282-288. [PMID: 31961303 PMCID: PMC6986840 DOI: 10.3201/eid2602.190505] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Yaws, a neglected tropical disease caused by the bacterium Treponema pallidum subspecies pertenue, manifests as ulcerative skin lesions. Nucleic acid amplification tests, like loop-mediated isothermal amplification (LAMP), are versatile tools to distinguish yaws from infections that cause similar skin lesions, primarily Haemophilus ducreyi. We developed a novel molecular test to simultaneously detect T. pallidum and H. ducreyi based on mediator displacement LAMP. We validated the T. pallidum and H. ducreyi LAMP (TPHD-LAMP) by testing 293 clinical samples from patients with yaws-like lesions. Compared with quantitative PCR, the TPHD-LAMP demonstrated high sensitivity and specificity for T. pallidum (84.7% sensitivity, 95.7% specificity) and H. ducreyi (91.6% sensitivity, 84.8% specificity). This novel assay provided rapid molecular confirmation of T. pallidum and H. ducreyi DNA and might be suitable for use at the point of care. TPHD-LAMP could support yaws eradication by improving access to molecular diagnostic tests at the district hospital level.
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23
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Roos C, Knauf S, Chuma IS, Maille A, Callou C, Sabin R, Portela Miguez R, Zinner D. New mitogenomic lineages in Papio baboons and their phylogeographic implications. Am J Phys Anthropol 2020; 174:407-417. [PMID: 33244782 DOI: 10.1002/ajpa.24186] [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: 06/22/2020] [Revised: 10/01/2020] [Accepted: 11/09/2020] [Indexed: 01/20/2023]
Abstract
OBJECTIVES Incomplete and/or biased sampling either on a taxonomic or geographic level can lead to delusive phylogenetic and phylogeographic inferences. However, a complete taxonomic and geographical sampling is often and for various reasons impossible, particularly for widespread taxa such as baboons (Papio spp.). Previous studies on baboon phylogeography identified several sampling gaps, some of which we fill by investigating additional material including samples from museum specimens. MATERIALS AND METHODS We generated 10 new mitochondrial genomes either via conventional PCR and subsequent Sanger sequencing from two blood samples or via high-throughput shotgun sequencing from degraded DNA extracted from eight museum specimens. Phylogenetic relationships and divergence times among baboon lineages were determined using maximum-likelihood and Bayesian inferences. RESULTS We identified new mitochondrial lineages in baboons from Central Africa (Chad, the Central African Republic), from the Mahale, and the Udzungwa Mountains (Tanzania), with the latter likely representing a case of mitochondrial capture from sympatric kipunjis (Rungwecebus kipunji). We also found that the mitochondrial clades of olive baboons found in Ivory Coast and Tanzania extend into Niger and the Democratic Republic of Congo, respectively. Moreover, an olive baboon from Sierra Leone carries a mitochondrial haplotype usually found in Guinea baboons, suggesting gene flow between these two species. DISCUSSION The extension of the geographic sampling by including samples from areas difficult to visit or from populations that are most likely extirpated has improved the geographic and temporal resolution of the mitochondrial phylogeny of baboons considerably. Our study also shows the great value of museum material for genetic analyses even when DNA is highly degraded.
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Affiliation(s)
- Christian Roos
- Primate Genetics Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, Göttingen, Germany.,Gene Bank of Primates, German Primate Center (DPZ), Leibniz Institute for Primate Research, Göttingen, Germany
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Infection Biology Unit, German Primate Center (DPZ), Leibniz Institute for Primate Research, Göttingen, Germany.,Department for Animal Sciences, Georg-August-University, Göttingen, Germany
| | - Idrissa S Chuma
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Audrey Maille
- Unité Eco-Anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Musée de l'Homme, Université de Paris, Paris, France
| | - Cécile Callou
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | | | | | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, Göttingen, Germany.,Leibniz Science Campus Primate Cognition, Göttingen, Germany.,Department of Primate Cognition, Georg-August-University, Göttingen, Germany
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Trede F, Lemkul A, Atickem A, Beehner JC, Bergman TJ, Burke R, Fashing PJ, Knauf S, Mekonnen A, Moges A, Nguyen N, Roos C, Zinner D. Geographic distribution of microsatellite alleles in geladas (Primates, Cercopithecidae): Evidence for three evolutionary units. ZOOL SCR 2020. [DOI: 10.1111/zsc.12451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Franziska Trede
- Cognitive Ethology Laboratory German Primate Center Leibniz Institute for Primate Research Göttingen Germany
- Primate Genetics Laboratory German Primate Center Leibniz Institute for Primate Research Göttingen Germany
| | - Anna Lemkul
- Cognitive Ethology Laboratory German Primate Center Leibniz Institute for Primate Research Göttingen Germany
| | - Anagaw Atickem
- Cognitive Ethology Laboratory German Primate Center Leibniz Institute for Primate Research Göttingen Germany
- Primate Genetics Laboratory German Primate Center Leibniz Institute for Primate Research Göttingen Germany
- Department of Zoological Sciences Addis Ababa University Addis Ababa Ethiopia
| | - Jacinta C. Beehner
- Department of Anthropology University of Michigan Ann Arbor MI USA
- Department of Psychology University of Michigan Ann Arbor MI USA
| | - Thore J. Bergman
- Department of Psychology University of Michigan Ann Arbor MI USA
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA
| | - Ryan Burke
- Long‐Term Ecology Laboratory Department of Zoology University of Oxford Oxford UK
| | - Peter J. Fashing
- Department of Anthropology & Environmental Studies Program California State University Fullerton Fullerton CA USA
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Infection Biology Unit German Primate Center Leibniz Institute for Primate Research Göttingen Germany
- Department for Animal Sciences Georg‐August‐University Göttingen Germany
| | - Addisu Mekonnen
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
- Department of Biology College of Natural Sciences Bahir Dar University Bahir Dar Ethiopia
| | - Amera Moges
- Department of Biology College of Natural Sciences Bahir Dar University Bahir Dar Ethiopia
| | - Nga Nguyen
- Department of Anthropology & Environmental Studies Program California State University Fullerton Fullerton CA USA
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Christian Roos
- Primate Genetics Laboratory German Primate Center Leibniz Institute for Primate Research Göttingen Germany
- Gene Bank of Primates German Primate Center Leibniz Institute for Primate Research Göttingen Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory German Primate Center Leibniz Institute for Primate Research Göttingen Germany
- Leibniz ScienceCampus Primate Cognition Göttingen Germany
- Department for Primate Cognition Georg‐August‐University Göttingen Germany
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25
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Hisgen L, Abel L, Hallmaier-Wacker LK, Lueert S, Siebert U, Faehndrich M, Strauss E, Voigt U, Nováková M, Šmajs D, Knauf S. High syphilis seropositivity in European brown hares (Lepus europaeus), Lower Saxony, Germany. Transbound Emerg Dis 2020; 67:2240-2244. [PMID: 32196988 DOI: 10.1111/tbed.13551] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/17/2020] [Indexed: 12/01/2022]
Abstract
The lagomorph-infecting Treponema paraluisleporidarum is a close relative of the human syphilis-bacterium Treponema pallidum. There is a paucity of information on the epidemiology of hare syphilis and its relationship to the rabbit- and human-infecting treponemes that cause syphilis. In our study, we tested 734 serum samples from European brown hares (Lepus europaeus) collected between 2007 and 2019 in the federal state of Lower Saxony, Germany, for the presence of antibodies against T. paraluisleporidarum. Since T. paraluisleporidarum cross-reacts with T. pallidum antigen, we used a commercially available T. pallidum-particle agglutination (TP-PA) assay to test for the presence of antibodies. A high seropositivity (n = 405/734) was detected. An additional 233 serum samples were retested using a fluorescent treponemal antibody absorption test to confirm the results of the TP-PA assay. Our results show that infection is widespread in Lower Saxony and suggest a horizontal (sexual) transmission mode since adult hares show significantly higher seropositivity than subadults (odds ratio: 0.03 [95% CI 0.02-0.05], p < .0001). No difference was detected based on gender (odds ratio: 0.79 [95% Cl 0.58-1.07], p = .1283). Further studies are warranted to genetically characterize the T. paraluisleporidarum strains that infect wild hares.
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Affiliation(s)
- Linda Hisgen
- Georg-August-University, Goettingen, Germany
- German Primate Center, Goettingen, Germany
| | - Lena Abel
- German Primate Center, Goettingen, Germany
| | | | | | - Ursula Siebert
- University of Veterinary Medicine Hannover - Foundation, Hannover, Germany
| | - Marcus Faehndrich
- University of Veterinary Medicine Hannover - Foundation, Hannover, Germany
| | - Egbert Strauss
- University of Veterinary Medicine Hannover - Foundation, Hannover, Germany
| | - Ulrich Voigt
- University of Veterinary Medicine Hannover - Foundation, Hannover, Germany
| | | | | | - Sascha Knauf
- Georg-August-University, Goettingen, Germany
- German Primate Center, Goettingen, Germany
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26
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Lubinza CKC, Lueert S, Hallmaier-Wacker LK, Ngadaya E, Chuma IS, Kazwala RR, Mfinanga SGM, Failing K, Roos C, Knauf S. Serosurvey of Treponema pallidum infection among children with skin ulcers in the Tarangire-Manyara ecosystem, northern Tanzania. BMC Infect Dis 2020; 20:392. [PMID: 32493291 PMCID: PMC7268494 DOI: 10.1186/s12879-020-05105-4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 05/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The first yaws eradication campaign reduced the prevalence of yaws by 95%. In recent years, however, yaws has reemerged and is currently subject to a second, ongoing eradication campaign. Yet, the epidemiological status of Tanzania and 75 other countries with a known history of human yaws is currently unknown. Contrary to the situation in humans in Tanzania, recent infection of nonhuman primates (NHPs) with the yaws bacterium Treponema pallidum subsp. pertenue (TPE) have been reported. In this study, we consider a One Health approach to investigate yaws and describe skin ulcers and corresponding T. pallidum serology results among children living in the Tarangire-Manyara ecosystem, an area with increasing wildlife-human interaction in northern Tanzania. METHODS To investigate human yaws in Tanzania, we conducted a cross-sectional study to screen and interview skin-ulcerated children aged 6 to 15 years, who live in close proximity to two national parks with high numbers of naturally TPE-infected monkeys. Serum samples from children with skin ulcers were tested for antibodies against the bacterium using a treponemal (Treponema pallidum Particle Agglutination assay) and a non-treponemal (Rapid Plasma Reagin) test. RESULTS A total of 186 children aged between 6 and 15 years (boys: 10.7 ± 2.1 (mean ± SD), N = 132; girls: 10.9 ± 2.0 (mean ± SD), N = 54) were enrolled. Seven children were sampled at health care facilities and 179 at primary schools. 38 children (20.4%) reported active participation in bushmeat hunting and consumption and 26 (13.9%) reported at least one physical contact with a NHP. None of the lesions seen were pathognomonic for yaws. Two children tested positive for treponemal antibodies (1.2%) in the treponemal test, but remained negative in the non-treponemal test. CONCLUSIONS We found no serological evidence of yaws among children in the Tarangire-Manyara ecosystem. Nevertheless, the close genetic relationship of human and NHPs infecting TPE strains should lead to contact prevention with infected NHPs. Further research investigations are warranted to study the causes and possible prevention measures of spontaneous chronic ulcers among children in rural Tanzania and to certify that the country is free from human yaws.
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Affiliation(s)
- Clara K C Lubinza
- National Institute for Medical Research, Muhimbili Medical Research Centre, P.O. Box 3436, Dar es Salaam, Tanzania.,College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3021, Morogoro, Tanzania
| | - Simone Lueert
- Work Group Neglected Tropical Diseases, Infection Biology Unit, Deutsches Primatezentrum GmbH, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Goettingen, Germany.,Primate Genetics Laboratory, Deutsches Primatenzentrum GmbH, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Goettingen, Germany
| | - Luisa K Hallmaier-Wacker
- Work Group Neglected Tropical Diseases, Infection Biology Unit, Deutsches Primatezentrum GmbH, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Goettingen, Germany.,Primate Genetics Laboratory, Deutsches Primatenzentrum GmbH, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Goettingen, Germany
| | - Esther Ngadaya
- National Institute for Medical Research, Muhimbili Medical Research Centre, P.O. Box 3436, Dar es Salaam, Tanzania
| | - Idrissa S Chuma
- College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3021, Morogoro, Tanzania
| | - Rudovick R Kazwala
- College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3021, Morogoro, Tanzania
| | - Sayoki G M Mfinanga
- National Institute for Medical Research, Muhimbili Medical Research Centre, P.O. Box 3436, Dar es Salaam, Tanzania.,Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania.,School of Life Sciences and Bioengineering, Nelson Mandela African Institute of Science and Technology, Arusha, Tanzania
| | - Klaus Failing
- Unit for Biomathematics and Data Processing, Faculty of Veterinary Medicine, Justus Liebig-University-Giessen, Giessen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, Deutsches Primatenzentrum GmbH, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Goettingen, Germany.,Gene Bank of Primates, Deutsches Primatenzentrum GmbH, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Goettingen, Germany
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Infection Biology Unit, Deutsches Primatezentrum GmbH, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Goettingen, Germany. .,Division Microbiology and Animal Hygiene, Department for Animal Sciences, Georg-August-University, Burkhardtweg 2, 37077, Goettingen, Germany.
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27
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Zimmerman DM, Hardgrove EH, von Fricken ME, Kamau J, Chai D, Mutura S, Kivali V, Hussein F, Ambala P, Surmat A, Maina JG, Knauf S. Endemicity of Yaws and Seroprevalence of Treponema pallidum Antibodies in Nonhuman Primates, Kenya. Emerg Infect Dis 2020; 25:2147-2149. [PMID: 31625860 PMCID: PMC6810213 DOI: 10.3201/eid2511.190716] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 11/25/2022] Open
Abstract
Human yaws has historically been endemic to Kenya, but current epidemiologic data are lacking. We report seroprevalence for Treponema pallidum antibodies in olive baboons (Papio anubis) and vervet monkeys (Chlorocebus pygerythrus) in Laikipia County, Kenya. Our results suggest endemicity of the yaws bacterium in monkeys, posing a possible zoonotic threat to humans.
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28
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Affiliation(s)
- Sascha Knauf
- Neglected Tropical Diseases Work Group, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Lena Abel
- Neglected Tropical Diseases Work Group, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Luisa K Hallmaier-Wacker
- Neglected Tropical Diseases Work Group, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
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29
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Delgado SJ, Dehmel S, Twisterling E, Wichmann J, Jonigk D, Warnecke G, Braubach P, Fieguth HG, Wilkens L, Dahlmann F, Kaup FJ, Eggel A, Knauf S, Sewald K, Braun A. Disruptive anti-IgE inhibitors prevent mast cell-dependent early airway response in viable atopic lung tissue. J Allergy Clin Immunol 2019; 145:719-722.e1. [PMID: 31858993 DOI: 10.1016/j.jaci.2019.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 10/02/2019] [Accepted: 11/05/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Sharon Jiménez Delgado
- Fraunhofer Institute for Toxicology and Experimental Medicine, Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH) research network, Hannover, Germany
| | - Susann Dehmel
- Fraunhofer Institute for Toxicology and Experimental Medicine, Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH) research network, Hannover, Germany
| | - Elaine Twisterling
- Fraunhofer Institute for Toxicology and Experimental Medicine, Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH) research network, Hannover, Germany; German Primate Center GmbH, Leibniz-Institute for Primate Research, Goettingen, Germany
| | - Judy Wichmann
- Fraunhofer Institute for Toxicology and Experimental Medicine, Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH) research network, Hannover, Germany; German Primate Center GmbH, Leibniz-Institute for Primate Research, Goettingen, Germany
| | - Danny Jonigk
- Institute for Pathology, Hannover Medical School, Hannover, Germany, Member of the German Center for Lung Research (DZL), Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Research Network, Hannover, Germany
| | - Gregor Warnecke
- Institute for Pathology, Hannover Medical School, Hannover, Germany, Member of the German Center for Lung Research (DZL), Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Research Network, Hannover, Germany
| | - Peter Braubach
- Institute for Pathology, Hannover Medical School, Hannover, Germany, Member of the German Center for Lung Research (DZL), Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Research Network, Hannover, Germany
| | - Hans-Gerd Fieguth
- Institute of Pathology, Klinikum Region Hannover (KRH), Hannover, Germany
| | - Ludwig Wilkens
- Institute of Pathology, Klinikum Region Hannover (KRH), Hannover, Germany
| | - Franziska Dahlmann
- Fraunhofer Institute for Toxicology and Experimental Medicine, Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH) research network, Hannover, Germany
| | - Franz-Josef Kaup
- German Primate Center GmbH, Leibniz-Institute for Primate Research, Goettingen, Germany
| | - Alexander Eggel
- Department of Rheumatology, Immunology and Allergology, University Hospital Bern, Bern, Switzerland
| | - Sascha Knauf
- German Primate Center GmbH, Leibniz-Institute for Primate Research, Goettingen, Germany
| | - Katherina Sewald
- Fraunhofer Institute for Toxicology and Experimental Medicine, Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH) research network, Hannover, Germany.
| | - Armin Braun
- Fraunhofer Institute for Toxicology and Experimental Medicine, Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH) research network, Hannover, Germany
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30
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Paciência FMD, Rushmore J, Chuma IS, Lipende IF, Caillaud D, Knauf S, Zinner D. Mating avoidance in female olive baboons ( Papio anubis) infected by Treponema pallidum. Sci Adv 2019; 5:eaaw9724. [PMID: 31840059 PMCID: PMC6892622 DOI: 10.1126/sciadv.aaw9724] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
Sexually transmitted infections (STIs) are ubiquitous within wild animal populations, yet it remains largely unknown whether animals evolved behavioral avoidance mechanisms in response to STI acquisition. We investigated the mating behavior of a wild population of olive baboons (Papio anubis) infected by the bacterium Treponema pallidum. This pathogen causes highly conspicuous genital ulcerations in males and females, which signal infectious individuals. We analyzed data on 876 mating attempts and associated acceptance or rejection responses in a group of about 170 baboons. Our findings indicate that females are more likely to avoid copulation if either the mating partner or females themselves have ulcerated genitals. We suggest that this outcome is linked to the overall higher choosiness and infection-risk susceptibility typically exhibited by females. Our results show that selection pressures imposed by pathogens induce individual behavioral modifications, leading to altered mate choice and could reduce promiscuity in a wild nonhuman primate population.
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Affiliation(s)
- F. M. D. Paciência
- Cognitive Ethology Laboratory, Leibniz Institute for Primate Research, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
- Work Group Neglected Tropical Diseases, Infection Biology Unit, Leibniz Institute for Primate Research, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - J. Rushmore
- EpiCenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - I. S. Chuma
- Sokoine University of Agriculture, P.O. Box 3000, Chuo Kikuu, Morogoro, Tanzania
| | - I. F. Lipende
- Sokoine University of Agriculture, P.O. Box 3000, Chuo Kikuu, Morogoro, Tanzania
| | - D. Caillaud
- Department of Anthropology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - S. Knauf
- Work Group Neglected Tropical Diseases, Infection Biology Unit, Leibniz Institute for Primate Research, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
- Division of Microbiology and Animal Hygiene, Georg-August-University, Göttingen, Germany
| | - D. Zinner
- Cognitive Ethology Laboratory, Leibniz Institute for Primate Research, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, Göttingen, Germany
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31
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Hallmaier-Wacker LK, Lüert S, Gronow S, Spröer C, Overmann J, Buller N, Vaughan-Higgins RJ, Knauf S. Corrigendum: A Metataxonomic Tool to Investigate the Diversity of Treponema. Front Microbiol 2019; 10:2581. [PMID: 31762772 PMCID: PMC6856545 DOI: 10.3389/fmicb.2019.02581] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/24/2019] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2019.02094.].
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Affiliation(s)
- Luisa K Hallmaier-Wacker
- Neglected Tropical Diseases Work Group, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Simone Lüert
- Neglected Tropical Diseases Work Group, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Department of Microbiology, Braunschweig University of Technology, Braunschweig, Germany
| | - Nicky Buller
- Animal Pathology - Bacteriology Laboratory, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Rebecca J Vaughan-Higgins
- Department of Conservation Medicine, College of Veterinary Medicine, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Sascha Knauf
- Neglected Tropical Diseases Work Group, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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32
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Fischer J, Higham JP, Alberts SC, Barrett L, Beehner JC, Bergman TJ, Carter AJ, Collins A, Elton S, Fagot J, Ferreira da Silva MJ, Hammerschmidt K, Henzi P, Jolly CJ, Knauf S, Kopp GH, Rogers J, Roos C, Ross C, Seyfarth RM, Silk J, Snyder-Mackler N, Staedele V, Swedell L, Wilson ML, Zinner D. Insights into the evolution of social systems and species from baboon studies. eLife 2019; 8:e50989. [PMID: 31711570 PMCID: PMC6850771 DOI: 10.7554/elife.50989] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/16/2019] [Indexed: 01/03/2023] Open
Abstract
Baboons, members of the genus Papio, comprise six closely related species distributed throughout sub-Saharan Africa and southwest Arabia. The species exhibit more ecological flexibility and a wider range of social systems than many other primates. This article summarizes our current knowledge of the natural history of baboons and highlights directions for future research. We suggest that baboons can serve as a valuable model for complex evolutionary processes, such as speciation and hybridization. The evolution of baboons has been heavily shaped by climatic changes and population expansion and fragmentation in the African savanna environment, similar to the processes that acted during human evolution. With accumulating long-term data, and new data from previously understudied species, baboons are ideally suited for investigating the links between sociality, health, longevity and reproductive success. To achieve these aims, we propose a closer integration of studies at the proximate level, including functional genomics, with behavioral and ecological studies.
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Affiliation(s)
- Julia Fischer
- Cognitive Ethology LaboratoryGerman Primate Center, Leibniz-Institute for Primate ResearchGöttingenGermany
- Department of Primate CognitionGeorg-August-University of GöttingenGöttingenGermany
- Leibniz ScienceCampus for Primate CognitionGöttingenGermany
| | - James P Higham
- Department of AnthropologyNew York UniversityNew YorkUnited States
| | - Susan C Alberts
- Department of BiologyDuke UniversityDurhamUnited States
- Department of Evolutionary AnthropologyDuke UniversityDurhamUnited States
- Institute of Primate ResearchNairobiKenya
| | - Louise Barrett
- Department of PsychologyUniversity of LethbridgeLethbridgeCanada
- Applied Behavioural Ecology and Ecosystems Research UnitUniversity of South AfricaPretoriaSouth Africa
| | - Jacinta C Beehner
- Department of PsychologyUniversity of MichiganAnn ArborUnited States
- Department of AnthropologyUniversity of MichiganAnn ArborUnited States
| | - Thore J Bergman
- Department of PsychologyUniversity of MichiganAnn ArborUnited States
- Department of AnthropologyUniversity of MichiganAnn ArborUnited States
| | - Alecia J Carter
- Institut des Sciences de l’Evolution de MontpellierMontpellierFrance
- Université de Montpellier, CNRS, IRD, EPHEMontpellierFrance
| | - Anthony Collins
- Gombe Stream Research CentreJane Goodall InstituteKigomaUnited Republic of Tanzania
| | - Sarah Elton
- Department of AnthropologyDurham UniversityDurhamUnited Kingdom
| | - Joël Fagot
- Aix Marseille UniversitéMarseilleFrance
- Centre National de la Recherche ScientifiqueMontpellierFrance
| | - Maria Joana Ferreira da Silva
- Organisms and Environment Division, School of BiosciencesCardiff UniversityCardiffUnited Kingdom
- Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoPortoPortugal
- Centro de Administração e Políticas Públicas, School of Social and PoliticalSciencesUniversity of LisbonLisbonPortugal
| | - Kurt Hammerschmidt
- Cognitive Ethology LaboratoryGerman Primate Center, Leibniz-Institute for Primate ResearchGöttingenGermany
| | - Peter Henzi
- Applied Behavioural Ecology and Ecosystems Research UnitUniversity of South AfricaPretoriaSouth Africa
| | - Clifford J Jolly
- Department of AnthropologyNew York UniversityNew YorkUnited States
- New York Consortium in Evolutionary PrimatologyNew YorkUnited States
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Infection Biology UnitGerman Primate Center, Leibniz-Institute for Primate ResearchGöttingenGermany
- Division of Microbiology and Animal HygieneGeorg-August-UniversityGöttingenGermany
| | - Gisela H Kopp
- ZukunftskollegUniversity of KonstanzKonstanzGermany
- Department of BiologyUniversity of KonstanzKonstanzGermany
- Centre for the Advanced Study of Collective BehaviourUniversity of KonstanzKonstanzGermany
- Department of MigrationMax Planck Institute for Animal BehaviourKonstanzGermany
| | - Jeffrey Rogers
- Human Genome Sequencing CenterHoustonUnited States
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - Christian Roos
- Gene Bank of PrimatesGerman Primate Center, Leibniz-Institute for Primate ResearchGöttingenGermany
- Primate Genetics LaboratoryGerman Primate Center, Leibniz-Institute for Primate ResearchGöttingenGermany
| | - Caroline Ross
- Department of Life SciencesRoehampton UniversityLondonUnited Kingdom
| | - Robert M Seyfarth
- Department of PsychologyUniversity of PennsylvaniaPhiladelphiaUnited States
| | - Joan Silk
- School of Human Evolution and Social ChangeArizona State UniversityTempeUnited States
- Institute for Human OriginsArizona State UniversityTempeUnited States
| | - Noah Snyder-Mackler
- Department of PsychologyUniversity of WashingtonSeattleUnited States
- Center for Studies in Demography and EcologyUniversity of WashingtonSeattleUnited States
- National Primate Research CenteUniversity of WashingtonSeattleUnited States
| | - Veronika Staedele
- Department of BiologyDuke UniversityDurhamUnited States
- Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Larissa Swedell
- New York Consortium in Evolutionary PrimatologyNew YorkUnited States
- Department of AnthropologyQueens College, City University of New YorkNew YorkUnited States
- Department of ArchaeologyUniversity of Cape TownCape TownSouth Africa
| | - Michael L Wilson
- Department of AnthropologyUniversity of MinnesotaMinneapolisUnited States
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaMinneapolisUnited States
- Institute on the EnvironmentUniversity of MinnesotaSaint PaulUnited States
| | - Dietmar Zinner
- Cognitive Ethology LaboratoryGerman Primate Center, Leibniz-Institute for Primate ResearchGöttingenGermany
- Leibniz ScienceCampus for Primate CognitionGöttingenGermany
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Gogarten JF, Calvignac-Spencer S, Nunn CL, Ulrich M, Saiepour N, Nielsen HV, Deschner T, Fichtel C, Kappeler PM, Knauf S, Müller-Klein N, Ostner J, Robbins MM, Sangmaneedet S, Schülke O, Surbeck M, Wittig RM, Sliwa A, Strube C, Leendertz FH, Roos C, Noll A. Metabarcoding of eukaryotic parasite communities describes diverse parasite assemblages spanning the primate phylogeny. Mol Ecol Resour 2019; 20:204-215. [PMID: 31600853 DOI: 10.1111/1755-0998.13101] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 07/11/2019] [Revised: 10/02/2019] [Accepted: 10/07/2019] [Indexed: 11/28/2022]
Abstract
Despite their ubiquity, in most cases little is known about the impact of eukaryotic parasites on their mammalian hosts. Comparative approaches provide a powerful method to investigate the impact of parasites on host ecology and evolution, though two issues are critical for such efforts: controlling for variation in methods of identifying parasites and incorporating heterogeneity in sampling effort across host species. To address these issues, there is a need for standardized methods to catalogue eukaryotic parasite diversity across broad phylogenetic host ranges. We demonstrate the feasibility of a metabarcoding approach for describing parasite communities by analysing faecal samples from 11 nonhuman primate species representing divergent lineages of the primate phylogeny and the full range of sampling effort (i.e. from no parasites reported in the literature to the best-studied primates). We detected a number of parasite families and regardless of prior sampling effort, metabarcoding of only ten faecal samples identified parasite families previously undescribed in each host (x̅ = 8.5 new families per species). We found more overlap between parasite families detected with metabarcoding and published literature when more research effort-measured as the number of publications-had been conducted on the host species' parasites. More closely related primates and those from the same continent had more similar parasite communities, highlighting the biological relevance of sampling even a small number of hosts. Collectively, results demonstrate that metabarcoding methods are sensitive and powerful enough to standardize studies of eukaryotic parasite communities across host species, providing essential new tools for macroecological studies of parasitism.
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Affiliation(s)
- Jan F Gogarten
- Project Group 3: Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute Berlin, Berlin, Germany.,Viral Evolution, Robert Koch-Institute Berlin, Berlin, Germany
| | - Sébastien Calvignac-Spencer
- Project Group 3: Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute Berlin, Berlin, Germany.,Viral Evolution, Robert Koch-Institute Berlin, Berlin, Germany
| | - Charles L Nunn
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Markus Ulrich
- Project Group 3: Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute Berlin, Berlin, Germany
| | - Nasrin Saiepour
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Henrik Vedel Nielsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Tobias Deschner
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Claudia Fichtel
- Behavioral Ecology & Sociobiology Unit, German Primate Center, Goettingen, Germany.,Leibniz Science Campus Primate Cognition, Goettingen, Germany
| | - Peter M Kappeler
- Behavioral Ecology & Sociobiology Unit, German Primate Center, Goettingen, Germany.,Leibniz Science Campus Primate Cognition, Goettingen, Germany.,Department of Sociobiology/Anthropology, Johann-Friedrich-Blumenbach Institute for Zoology, Georg-August University, Goettingen, Germany
| | - Sascha Knauf
- Neglected Tropical Diseases Work Group, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Nadine Müller-Klein
- Department of Behavioral Ecology, University of Goettingen, Goettingen, Germany
| | - Julia Ostner
- Leibniz Science Campus Primate Cognition, Goettingen, Germany.,Department of Behavioral Ecology, University of Goettingen, Goettingen, Germany.,Research Group Primate Social Evolution, German Primate Center - Leibniz Institute for Primate Research, Goettingen, Germany
| | - Martha M Robbins
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Somboon Sangmaneedet
- Department of Pathobiology, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Oliver Schülke
- Leibniz Science Campus Primate Cognition, Goettingen, Germany.,Department of Behavioral Ecology, University of Goettingen, Goettingen, Germany.,Research Group Primate Social Evolution, German Primate Center - Leibniz Institute for Primate Research, Goettingen, Germany
| | - Martin Surbeck
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Roman M Wittig
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Ivory Coast
| | | | - Christina Strube
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Fabian H Leendertz
- Project Group 3: Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute Berlin, Berlin, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany.,Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Angela Noll
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
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Nováková M, Najt D, Mikalová L, Kostková M, Vrbová E, Strouhal M, Posautz A, Knauf S, Šmajs D. First report of hare treponematosis seroprevalence of European brown hares (Lepus europaeus) in the Czech Republic: seroprevalence negatively correlates with altitude of sampling areas. BMC Vet Res 2019; 15:350. [PMID: 31627750 PMCID: PMC6798448 DOI: 10.1186/s12917-019-2086-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 02/21/2019] [Accepted: 09/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The aim of this study was to quantify the seroprevalence of hare treponematosis in European brown hare (Lepus europaeus) populations in the Czech Republic and to test for an association between treponematosis prevalence and the altitude of the areas in which hares were sampled. We tested 289 serum samples of brown hares collected between 2015 and 2017. The sampling areas included 12 districts (73 villages) distributed throughout the Czech Republic. Serum samples were tested for the presence of antibodies against the causative agent of hare treponematosis (Treponema paraluisleporidarum ecovar Lepus, TPeL) using two serological tests for human syphilis that cross-react with TPeL: the Treponema pallidum hemagglutination assay (TPHA) and the fluorescent treponemal antibody absorption (FTA-ABS) test. To account for the imperfect diagnostic sensitivity and specificity of each test, apparent prevalence estimates of TPeL were converted to true prevalence estimates using the Rogan Gladen estimator. The correlation between TPeL true seroprevalence and altitude of sampling areas was analyzed using Pearson's correlation coefficient at three levels of spatial resolution: (1) four groups, each composed of two merged districts, with ≥20 samples collected, differing in their altitude median (206, 348, 495, and 522 m above sea level); (2) separately tested eight districts, where ≥20 samples were collected per district; and (3) 27 groups composed of villages of the same altitude level distributed across the whole dataset. RESULTS One hundred and seven of the 289 samples were seropositive to both tests, the FTA-ABS test was positive for an additional 47 samples. Seropositive samples were found in all 12 districts. True seroprevalence of TPeL in the sampled hares was 52% (95% confidence interval 46 to 58%). A statistically significant negative correlation between TPeL seroprevalence and altitude was identified at the district level (Pearson's r = - 0.722, p = 0.043). CONCLUSIONS Between 2015 and 2017 hare treponematosis was present at a relatively high prevalence in brown hares in all 12 districts in the Czech Republic where sampling was carried out. The seroprevalence of TPeL in brown hares was negatively correlated with the altitude of the areas in which hares were sampled.
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Affiliation(s)
- Markéta Nováková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic
| | - David Najt
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic.,Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic
| | | | - Eliška Vrbová
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic
| | - Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic
| | - Annika Posautz
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany.,Division of Microbiology and Animal Hygiene, Georg-August-University of Goettingen, Goettingen, Germany
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic.
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35
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Hallmaier-Wacker LK, Lüert S, Gronow S, Spröer C, Overmann J, Buller N, Vaughan-Higgins RJ, Knauf S. A Metataxonomic Tool to Investigate the Diversity of Treponema. Front Microbiol 2019; 10:2094. [PMID: 31552004 PMCID: PMC6746968 DOI: 10.3389/fmicb.2019.02094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 06/13/2019] [Accepted: 08/26/2019] [Indexed: 12/11/2022] Open
Abstract
The genus Treponema contains a number of human and animal pathogenic as well as symbiotic bacteria that are found in vastly different anatomical and environmental habitats. Our understanding of the species range, evolution, and biology of these important bacteria is still limited. To explore the diversity of treponemes, we established, validated, and tested a novel metataxonomic approach. As the informative nature of the hypervariable regions of the 16S rRNA gene differ, we first analyzed each variable region independently. Considering the in silico results obtained, we established and validated the sequencing of the V4-region of the 16S rRNA gene using known mixtures of Treponema species as well as a selected number of clinical samples. The metataxonomic approach was able to identify Treponema to a near-species level. We demonstrate that using a spirochete-specific enrichment, our method is applicable to complex microbial communities and large variety of biological samples. The metataxonomic approach described provides a useful method to unravel the full diversity and range of Treponema in various ecosystems.
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Affiliation(s)
- Luisa K Hallmaier-Wacker
- Neglected Tropical Diseases Work Group, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Simone Lüert
- Neglected Tropical Diseases Work Group, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Department of Microbiology, Braunschweig University of Technology, Braunschweig, Germany
| | - Nicky Buller
- Animal Pathology - Bacteriology Laboratory, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Rebecca J Vaughan-Higgins
- Department of Conservation Medicine, College of Veterinary Medicine, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Sascha Knauf
- Neglected Tropical Diseases Work Group, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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36
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Chuma IS, Batamuzi EK, Collins DA, Fyumagwa RD, Hallmaier-Wacker LK, Kazwala RR, Keyyu JD, Lejora IA, Lipende IF, Lüert S, Paciência FMD, Piel A, Stewart FA, Zinner D, Roos C, Knauf S. Widespread Treponema pallidum Infection in Nonhuman Primates, Tanzania. Emerg Infect Dis 2019; 24:1002-1009. [PMID: 29774840 PMCID: PMC6004850 DOI: 10.3201/eid2406.180037] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We investigated Treponema pallidum infection in 8 nonhuman primate species (289 animals) in Tanzania during 2015-2017. We used a serologic treponemal test to detect antibodies against the bacterium. Infection was further confirmed from tissue samples of skin-ulcerated animals by 3 independent PCRs (polA, tp47, and TP_0619). Our findings indicate that T. pallidum infection is geographically widespread in Tanzania and occurs in several species (olive baboons, yellow baboons, vervet monkeys, and blue monkeys). We found the bacterium at 11 of 14 investigated geographic locations. Anogenital ulceration was the most common clinical manifestation; orofacial lesions also were observed. Molecular data show that nonhuman primates in Tanzania are most likely infected with T. pallidum subsp. pertenue-like strains, which could have implications for human yaws eradication.
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37
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Knauf Y, Köhler K, Knauf S, Wehrend A. Histological classification of canine ovarian cyst types with reference to medical history. J Vet Sci 2019; 19:725-734. [PMID: 30304884 PMCID: PMC6265583 DOI: 10.4142/jvs.2018.19.6.725] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 05/10/2018] [Revised: 08/30/2018] [Accepted: 09/17/2018] [Indexed: 12/25/2022] Open
Abstract
Ovaries of 21 bitches presented with gynecopathies were surgically removed and histologically examined. Standard histological, as well as immunohistochemical, classification of 193 cystic structures resulted in the classification of 72 cysts of subsurface epithelial structures (SES), 61 follicular cysts (FCs), 38 cystic rete ovarii (CRO), 13 lutein cysts (LCs), and 9 non-classifiable cysts (NCCs). In addition to the histological classification, results were interpreted according to subject medical history, clinical examination outcome, and macroscopic observations during ovariohysterectomy. Dogs with ovarian cysts (OCs) and associated reproductive perturbations were mostly nulliparous, of large breed, and had an average of 9.5 ± 3 years. Prolonged or shortened inter-estrus intervals of past heats, however, seemed to be relatively low-risk factors for the development of OCs in dogs. Furthermore, we provide histological observations of a rarely seen canine LC including a degenerated oocyte in the central cavity.
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Affiliation(s)
- Yvonne Knauf
- Clinic for Obstetrics, Gynecology and Andrology of Large and Small Animals with Veterinary Ambulance, Justus-Liebig-University, D 35392 Giessen, Germany.,Department of Animal Sciences, Georg-August-University, D 37077 Goettingen, Germany
| | - Kernt Köhler
- Institute of Veterinary Pathology, Justus-Liebig-University, D 35392 Giessen, Germany
| | - Sascha Knauf
- Department of Infection Biology, Work Group Neglected Tropical Diseases, German Primate Center, Leibniz-Institute for Primate Research, D 37077 Goettingen, Germany
| | - Axel Wehrend
- Clinic for Obstetrics, Gynecology and Andrology of Large and Small Animals with Veterinary Ambulance, Justus-Liebig-University, D 35392 Giessen, Germany
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38
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Zinner D, Chuma IS, Knauf S, Roos C. Inverted intergeneric introgression between critically endangered kipunjis and yellow baboons in two disjunct populations. Biol Lett 2018; 14:rsbl.2017.0729. [PMID: 29343565 DOI: 10.1098/rsbl.2017.0729] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 11/27/2017] [Accepted: 12/20/2017] [Indexed: 11/12/2022] Open
Abstract
Intergeneric hybridization and introgression was reported from one of two populations of the recently discovered kipunji (Rungwecebus kipunji), a critically endangered African monkey species of southern Tanzania. Kipunjis of the introgressed population (from Mount Rungwe) carry a mitochondrial DNA (mtDNA) haplotype closely related to those of parapatric yellow baboons (Papio cynocephalus), whereas the second kipunji population, in the Udzungwa Mountains, carries the original kipunji mtDNA haplotypes, which diverged from the baboon lineage about 3 million years ago. Interestingly, in our study of yellow baboons in Tanzania, we found that baboons from the southeastern boundary of the Udzungwa Mountains carry mtDNA haplotypes closely related to the original kipunji haplotype, whereas baboons from the northern boundary, as expected, carry mtDNA haplotypes of the northern yellow baboon clade. These findings provide evidence for a case of inverted intergeneric admixture in primates: (i) a baboon mtDNA haplotype introgressed the Mount Rungwe kipunji population by mitochondrial capture and (ii) an Udzungwa Mountains kipunji mtDNA haplotype introgressed a small subpopulation of yellow baboons by either mitochondrial capture or nuclear swamping. The baboon-kipunji example therefore constitutes an interesting system for further studies of the effects of genetic admixture on fitness and speciation.
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Affiliation(s)
- Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Göttingen, Germany
| | - Idrissa S Chuma
- Work Group Neglected Tropical Diseases, German Primate Center, Göttingen, Germany.,Primate Genetics Laboratory, German Primate Center, Göttingen, Germany.,Sokoine University of Agriculture, Morogoro, Tanzania
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, German Primate Center, Göttingen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Göttingen, Germany
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39
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Strouhal M, Mikalová L, Haviernik J, Knauf S, Bruisten S, Noordhoek GT, Oppelt J, Čejková D, Šmajs D. Complete genome sequences of two strains of Treponema pallidum subsp. pertenue from Indonesia: Modular structure of several treponemal genes. PLoS Negl Trop Dis 2018; 12:e0006867. [PMID: 30303967 PMCID: PMC6197692 DOI: 10.1371/journal.pntd.0006867] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 06/19/2018] [Revised: 10/22/2018] [Accepted: 09/24/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Treponema pallidum subsp. pertenue (TPE) is the causative agent of yaws, a multistage disease endemic in tropical regions in Africa, Asia, Oceania, and South America. To date, seven TPE strains have been completely sequenced and analyzed including five TPE strains of human origin (CDC-2, CDC 2575, Gauthier, Ghana-051, and Samoa D) and two TPE strains isolated from the baboons (Fribourg-Blanc and LMNP-1). This study revealed the complete genome sequences of two TPE strains, Kampung Dalan K363 and Sei Geringging K403, isolated in 1990 from villages in the Pariaman region of Sumatra, Indonesia and compared these genome sequences with other known TPE genomes. METHODOLOGY/PRINCIPAL FINDINGS The genomes were determined using the pooled segment genome sequencing method combined with the Illumina sequencing platform resulting in an average coverage depth of 1,021x and 644x for the TPE Kampung Dalan K363 and TPE Sei Geringging K403 genomes, respectively. Both Indonesian TPE strains were genetically related to each other and were more distantly related to other, previously characterized TPE strains. The modular character of several genes, including TP0136 and TP0858 gene orthologs, was identified by analysis of the corresponding sequences. To systematically detect genes potentially having a modular genetic structure, we performed a whole genome analysis-of-occurrence of direct or inverted repeats of 17 or more nucleotides in length. Besides in tpr genes, a frequent presence of repeats was found in the genetic regions spanning TP0126-TP0136, TP0856-TP0858, and TP0896 genes. CONCLUSIONS/SIGNIFICANCE Comparisons of genome sequences of TPE Kampung Dalan K363 and Sei Geringging K403 with other TPE strains revealed a modular structure of several genomic loci including the TP0136, TP0856, and TP0858 genes. Diversification of TPE genomes appears to be facilitated by intra-strain genome recombination events.
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Affiliation(s)
- Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jan Haviernik
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Sylvia Bruisten
- Public Health Laboratory, Department of Infectious Diseases GGD Amsterdam, WT Amsterdam, the Netherlands
| | - Gerda T. Noordhoek
- Izore, Centrum Infectieziekten Friesland, EN Leeuwarden, the Netherlands
| | - Jan Oppelt
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Darina Čejková
- Department of Immunology, Veterinary Research Institute, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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40
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Zinner D, Atickem A, Beehner JC, Bekele A, Bergman TJ, Burke R, Dolotovskaya S, Fashing PJ, Gippoliti S, Knauf S, Knauf Y, Mekonnen A, Moges A, Nguyen N, Stenseth NC, Roos C. Phylogeography, mitochondrial DNA diversity, and demographic history of geladas (Theropithecus gelada). PLoS One 2018; 13:e0202303. [PMID: 30138418 PMCID: PMC6107150 DOI: 10.1371/journal.pone.0202303] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 04/30/2018] [Accepted: 07/31/2018] [Indexed: 11/18/2022] Open
Abstract
The large-bodied, terrestrial primates in the tribe Papionini are among the most intensely studied animals in the world, yet for some members of this tribe we know comparatively little about their evolutionary history and phylogeography. Geladas (Theropithecus gelada Rüppell, 1835), endemic primates of the Ethiopian highlands, are largely unstudied both in genetic diversity and intrageneric phylogeny. Currently, a northern and central subspecies and one isolated southern population are recognized, of which the central is classified as Least Concern, the northern as Vulnerable, and the southern is not yet assessed. The distribution and taxonomy of the subspecies remain poorly defined. Here, we estimate the mitochondrial DNA (mtDNA) diversity and phylogenetic relationships among gelada mtDNA lineages based on samples across the entire species range. We analysed 1.7 kb-long sequences of the mtDNA genome, spanning the cytochrome b gene and the hypervariable region I of the D-loop, derived from 162 faecal samples. We detected five major haplogroups or clades (south, central-1, central-2, north-1, north-2) which diverged between 0.67 and 0.43 million years ago, thus suggesting a rapid radiation, resulting in largely unresolved intrageneric phylogenetic relationships. Both, the northern and central demes contain two similarly valid haplogroups, each with little or no geographic segregation among respective haplogroups. Effective population sizes of the northern and central demes decreased during and after the last glacial maximum but remained stable for the southern deme, although on a very low level. The distribution of haplogroups within the geographic ranges of the putative gelada subspecies indicates that mtDNA sequence information does not allow reliable taxonomic inferences and thus is not sufficient for solving the taxonomic rank of the three demic populations, with the possible exception of the southern population. Nevertheless, due to the genetic differences all three populations deserve conservation efforts, in particular the smallest southern population.
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Affiliation(s)
- Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, Kellnerweg 4, Göttingen, Germany
- * E-mail: (DZ); (CR)
| | - Anagaw Atickem
- Cognitive Ethology Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, Kellnerweg 4, Göttingen, Germany
- Primate Genetics Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, Kellnerweg 4, Göttingen, Germany
| | - Jacinta C. Beehner
- Department of Psychology, University of Michigan, Ann Arbor, MI, United States of America
- Department of Anthropology, University of Michigan, Ann Arbor, MI, United States of America
| | - Afework Bekele
- Department of Zoological Sciences, College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Thore J. Bergman
- Department of Psychology, University of Michigan, Ann Arbor, MI, United States of America
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Ryan Burke
- Long-Term Ecology Laboratory, Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Sofya Dolotovskaya
- Primate Genetics Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, Kellnerweg 4, Göttingen, Germany
| | - Peter J. Fashing
- Department of Anthropology & Environmental Studies Program, California State University Fullerton, Fullerton, CA, United States of America
| | - Spartaco Gippoliti
- Società Italiana per la Storia della Fauna “G. Altobello”, Viale Liegi 48A, Roma, Italy
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Infection Biology Unit, German Primate Center, Leibniz-Institute for Primate Research, Kellnerweg 4, Göttingen, Germany
| | - Yvonne Knauf
- Work Group Neglected Tropical Diseases, Infection Biology Unit, German Primate Center, Leibniz-Institute for Primate Research, Kellnerweg 4, Göttingen, Germany
- Department of Animal Sciences, University of Göttingen, Burckhardtweg 2, Göttingen, Germany
| | - Addisu Mekonnen
- Department of Zoological Sciences, College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Blindern, Oslo, Norway
| | - Amera Moges
- Department of Biology, College of Natural Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Nga Nguyen
- Department of Anthropology & Environmental Studies Program, California State University Fullerton, Fullerton, CA, United States of America
| | - Nils Chr. Stenseth
- Department of Zoological Sciences, College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Blindern, Oslo, Norway
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, Kellnerweg 4, Göttingen, Germany
- Gene Bank of Primates, German Primate Center (DPZ), Leibniz Institute for Primate Research, Kellnerweg 4, Göttingen, Germany
- * E-mail: (DZ); (CR)
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Knauf S, Bast RC. Tumor Antigen Nb/70K and Ca 125 Levels in the Blood of Preoperative Ovarian Cancer Patients and Controls: A Preliminary Report of the use of the Nb12123 and Ca 125 Radioimmunoassays Alone and in Combination. Int J Biol Markers 2018; 3:75-81. [PMID: 3243980 DOI: 10.1177/172460088800300201] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The NB12123 and CA125 radioimmunoassays, murine monoclonal antibody assays for measuring circulating levels of human ovarian tumor associated antigens NB/70K and CA 125, respectively, have been previously described. In the present study, preoperative serum samples were obtained from patients undergoing laparotomy for benign neoplastic ovarian tumors (N = 16), cancer of the cervix (N = 22), cancer of the uterus (N = 20), and cancer of the ovary (N = 47). Controls (N = 50) were obtained from healthy blood bank donors. No correlation was observed between the levels of NB/70K and CA 125 in these samples (r2 = .079, linear regression analysis). In general, increasing levels of both antigens were present with increasing tumor burden and higher histological grade. In addition, both markers were most elevated in the serum of ovarian cancer patients with serous and unclassified adenocarcinomas. Using 40 AU and 35 unit cut-offs for the NB/70K and CA 125 assay, respectively, overall specificity for healthy controls and patients with benign diseases approaches 100%. The combined sensitivity of the assays for ovarian cancer patient sera in this study indicates that the assays may be helpful in establishing a pre operative diagnosis of ovarian cancer. Complementarity of the NB/70K and CA 125 assays has been demonstrated, indicating that one or both assays may be used to monitor as many as 85% of ovarian cancer patients.
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Affiliation(s)
- S Knauf
- University of Rochester Cancer Center, N.Y
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Knauf S, Lüert S, Šmajs D, Strouhal M, Chuma IS, Frischmann S, Bakheit M. Gene target selection for loop-mediated isothermal amplification for rapid discrimination of Treponema pallidum subspecies. PLoS Negl Trop Dis 2018; 12:e0006396. [PMID: 29649256 PMCID: PMC5978989 DOI: 10.1371/journal.pntd.0006396] [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: 12/31/2017] [Revised: 04/24/2018] [Accepted: 03/21/2018] [Indexed: 11/19/2022] Open
Abstract
We show proof of concept for gene targets (polA, tprL, and TP_0619) that can be used in loop-mediated isothermal amplification (LAMP) assays to rapidly differentiate infection with any of the three Treponema pallidum subspecies (pallidum (TPA), pertenue (TPE), and endemicum (TEN)) and which are known to infect humans and nonhuman primates (NHPs). Four TPA, six human, and two NHP TPE strains, as well as two human TEN strains were used to establish and validate the LAMP assays. All three LAMP assays were highly specific for the target DNA. Amplification was rapid (5-15 min) and within a range of 10E+6 to 10E+2 of target DNA molecules. Performance in NHP clinical samples was similar to the one seen in human TPE strains. The newly designed LAMP assays provide proof of concept for a diagnostic tool that enhances yaws clinical diagnosis. It is highly specific for the target DNA and does not require expensive laboratory equipment. Test results can potentially be interpreted with the naked eye, which makes it suitable for the use in remote clinical settings.
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Affiliation(s)
- Sascha Knauf
- Work Group Neglected Tropical Diseases, Infection Biology Unit, German Primate Center, Leibniz- Institute for Primate Research, Göttingen, Germany
| | - Simone Lüert
- Work Group Neglected Tropical Diseases, Infection Biology Unit, German Primate Center, Leibniz- Institute for Primate Research, Göttingen, Germany
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Idrissa S. Chuma
- Work Group Neglected Tropical Diseases, Infection Biology Unit, German Primate Center, Leibniz- Institute for Primate Research, Göttingen, Germany
- Sokoine University of Agriculture, Faculty of Veterinary Medicine, Morogoro, Tanzania
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Šmajs D, Strouhal M, Knauf S. Genetics of human and animal uncultivable treponemal pathogens. Infect Genet Evol 2018; 61:92-107. [PMID: 29578082 DOI: 10.1016/j.meegid.2018.03.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 03/16/2018] [Accepted: 03/20/2018] [Indexed: 10/17/2022]
Abstract
Treponema pallidum is an uncultivable bacterium and the causative agent of syphilis (subsp. pallidum [TPA]), human yaws (subsp. pertenue [TPE]), and bejel (subsp. endemicum). Several species of nonhuman primates in Africa are infected by treponemes genetically undistinguishable from known human TPE strains. Besides Treponema pallidum, the equally uncultivable Treponema carateum causes pinta in humans. In lagomorphs, Treponema paraluisleporidarum ecovar Cuniculus and ecovar Lepus are the causative agents of rabbit and hare syphilis, respectively. All uncultivable pathogenic treponemes harbor a relatively small chromosome (1.1334-1.1405 Mbp) and show gene synteny with minimal genetic differences (>98% identity at the DNA level) between subspecies and species. While uncultivable pathogenic treponemes contain a highly conserved core genome, there are a number of highly variable and/or recombinant chromosomal loci. This is also reflected in the occurrence of intrastrain heterogeneity (genetic diversity within an infecting bacterial population). Molecular differences at several different chromosomal loci identified among TPA strains or isolates have been used for molecular typing and the epidemiological characterization of syphilis isolates. This review summarizes genome structure of uncultivable pathogenic treponemes including genetically variable regions.
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Affiliation(s)
- David Šmajs
- Department of Biology, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic.
| | - Michal Strouhal
- Department of Biology, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic.
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Pathology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany,.
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Roos C, Chuma IS, Collins DA, Knauf S, Zinner D. Complete mitochondrial genome of an olive baboon ( Papio anubis) from Gombe National Park, Tanzania. Mitochondrial DNA B Resour 2018; 3:177-178. [PMID: 33474109 PMCID: PMC7800945 DOI: 10.1080/23802359.2018.1437813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The olive baboon (Papio anubis) is the most widely distributed baboon species. We report here on the complete mitochondrial genome of an olive baboon from the south-eastern edge of the species' range from Gombe National Park (NP), Tanzania. The genome (GenBank accession number MG787545) has a length of 16,490 bp and exhibits the typical structure of mammalian mitochondrial genomes. Phylogenetically, the olive baboon from Gombe NP is most closely related to eastern P. anubis, northern P. cynocephalus and P. hamadryas. The data are an important addition to further clarify the phylogeography of baboons and phylogeny of papionins in general.
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Affiliation(s)
- Christian Roos
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany.,Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Idrissa S Chuma
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany.,Department of Veterinary Medicine and Public Health, College of Veterinary and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania.,Work Group Neglected Tropical Diseases, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - D Anthony Collins
- Gombe Stream Research Centre, Jane Goodall Institute, Kigoma, Tanzania
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
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Hallmaier-Wacker LK, Munster VJ, Knauf S. Disease reservoirs: from conceptual frameworks to applicable criteria. Emerg Microbes Infect 2017; 6:e79. [PMID: 28874791 PMCID: PMC5625316 DOI: 10.1038/emi.2017.65] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 03/21/2017] [Revised: 06/20/2017] [Accepted: 06/28/2017] [Indexed: 11/25/2022]
Abstract
Central to the One Health approach and any disease eradication program is the question of whether a pathogen has a non-human reservoir. Despite well-established conceptual frameworks that define a reservoir of infection, empirical characterization of reservoirs often remains controversial, challenging and sometimes misleading. What is essentially missing are applicable requirements that standardize the use of the term ‘reservoir of infection’ across multiple disciplines. We propose an empirical framework, considering maintenance and feasible transmission of a pathogen, to standardize the acceptance of a disease reservoir across multiple disciplines. We demonstrate the intended use of these requirements by applying them to different diseases that are known to infect both humans and animals.
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Affiliation(s)
- Luisa K Hallmaier-Wacker
- Work Group Neglected Tropical Diseases, Pathology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, Göttingen 37077, Germany.,Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, Göttingen 37077, Germany
| | - Vincent J Munster
- Virus Ecology Unit, Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT 59840, USA
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Pathology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, Göttingen 37077, Germany
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Klegarth AR, Ezeonwu CA, Rompis A, Lee BPYH, Aggimarangsee N, Chalise M, Cortes J, Feeroz M, Molini BJ, Godornes BC, Marks M, Schillaci M, Engel G, Knauf S, Lukehart SA, Jones-Engel L. Survey of Treponemal Infections in Free-Ranging and Captive Macaques, 1999-2012. Emerg Infect Dis 2017; 23:816-819. [PMID: 28418297 PMCID: PMC5403046 DOI: 10.3201/eid2305.161838] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Survey results showed treponemal infection among pet macaques in Southeast Asia, a region with a high prevalence of human yaws. This finding, along with studies showing treponemal infection in nonhuman primates in Africa, should encourage a One Health approach to yaws eradication and surveillance activities, possibly including monitoring of nonhuman primates in yaws-endemic regions.
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Paciência F, Baluya D, Mbaryo P, Knauf S, Zinner D. Olive baboons' ( Papio anubis) response towards crowned eagles ( Stephanoaetus coronatus) at Lake Manyara National Park. Primate Biol 2017; 4:101-106. [PMID: 32110697 PMCID: PMC7041538 DOI: 10.5194/pb-4-101-2017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 03/10/2017] [Accepted: 04/25/2017] [Indexed: 11/11/2022] Open
Abstract
In this paper we report on two encounters between olive baboons (Papio anubis) and crowned eagles (Stephanoaetus coronatus) at Lake Manyara National Park, northern Tanzania. During these encounters olive baboons responded by giving alarm calls and all infants and juveniles rushed down from trees seeking cover under bushes or close proximity to adult conspecifics. In one of the events, alarm calls from banded mongoose (Mungos mungo) and rock hyraxes (Procavia capensis) most likely triggered alarm calling of vervet monkeys (Chlorocebus pygerythrus) which in turn prompted baboons to respond with alarm calls as well. In both observations, adult male baboons took the lead in climbing trees, threatening the eagle (staring, yawning, ground slapping) and chasing it away. The reaction of the baboons suggests that crowned eagles pose a threat at least for juvenile baboons at Lake Manyara National Park.
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Affiliation(s)
- Filipa M. D. Paciência
- Cognitive Ethology Laboratory, German Primate Center, Leibniz
Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | | | - Pay Mbaryo
- Tanzania National Parks, P.O. Box 3134, Arusha, Tanzania
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Pathology Unit, German Primate
Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077
Göttingen, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz
Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
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Houinei W, Godornes C, Kapa A, Knauf S, Mooring EQ, González-Beiras C, Watup R, Paru R, Advent P, Bieb S, Sanz S, Bassat Q, Spinola SM, Lukehart SA, Mitjà O. Haemophilus ducreyi DNA is detectable on the skin of asymptomatic children, flies and fomites in villages of Papua New Guinea. PLoS Negl Trop Dis 2017; 11:e0004958. [PMID: 28489855 PMCID: PMC5425006 DOI: 10.1371/journal.pntd.0004958] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 12/25/2015] [Accepted: 08/08/2016] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Haemophilus ducreyi and Treponema pallidum subsp. pertenue are major causes of leg ulcers in children in Africa and the Pacific Region. We investigated the presence of DNA (PCR positivity) from these bacteria on asymptomatic people, flies, and household linens in an endemic setting. METHODOLOGY/PRINCIPAL FINDINGS We performed a cross-sectional study in rural villages of Lihir Island, Papua New Guinea during a yaws elimination campaign. Participants were asymptomatic subjects recruited from households with cases of leg ulcers, and from households without cases of leg ulcers. We rubbed swabs on the intact skin of the leg of asymptomatic individuals, and collected flies and swabs of environmental surfaces. All specimens were tested by PCR for H. ducreyi and T. p. pertenue DNA. Of 78 asymptomatic participants that had an adequate specimen for DNA detection, H. ducreyi-PCR positivity was identified in 16 (21%) and T. p. pertenue-PCR positivity in 1 (1%). In subgroup analyses, H. ducreyi-PCR positivity did not differ in participants exposed or not exposed to a case of H. ducreyi ulcer in the household (24% vs 18%; p = 0.76). Of 17 cultures obtained from asymptomatic participants, 2 (12%) yielded a definitive diagnosis of H. ducreyi, proving skin colonization. Of 10 flies tested, 9 (90%) had H. ducreyi DNA and 5 (50%) had T. p. pertenue DNA. Of 6 bed sheets sampled, 2 (33%) had H. ducreyi DNA and 1 (17%) had T. p. pertenue DNA. CONCLUSIONS/SIGNIFICANCE This is the first time that H. ducreyi DNA and colonization has been demonstrated on the skin of asymptomatic children and that H. ducreyi DNA and T. p. pertenue DNA has been identified in flies and on fomites. The ubiquity of H. ducreyi in the environment is a contributing factor to the spread of the organism.
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Affiliation(s)
- Wendy Houinei
- Disease Control Branch, National Department of Health, Port Moresby, Papua New Guinea
| | - Charmie Godornes
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - August Kapa
- Lihir Medical Centre– International SOS, Newcrest Mining, Lihir Island, Papua New Guinea
| | - Sascha Knauf
- German Primate Center, Leibniz-Institute for Primate Research, Pathology Unit, Working Group Neglected Tropical Diseases, Göttingen, Germany
| | - Eric Q. Mooring
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | | | - Ronald Watup
- Lihir Medical Centre– International SOS, Newcrest Mining, Lihir Island, Papua New Guinea
| | - Raymond Paru
- Lihir Medical Centre– International SOS, Newcrest Mining, Lihir Island, Papua New Guinea
| | - Paul Advent
- Lihir Medical Centre– International SOS, Newcrest Mining, Lihir Island, Papua New Guinea
| | - Sivauk Bieb
- Disease Control Branch, National Department of Health, Port Moresby, Papua New Guinea
| | - Sergi Sanz
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic-University of Barcelona, Barcelona, Spain
| | - Quique Bassat
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic-University of Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Stanley M. Spinola
- Departments of Microbiology and Immunology, Medicine, and Pathology and Laboratory Medicine Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Sheila A. Lukehart
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Oriol Mitjà
- Lihir Medical Centre– International SOS, Newcrest Mining, Lihir Island, Papua New Guinea
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic-University of Barcelona, Barcelona, Spain
- Division of Public Health, School of Medicine and Health Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
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Richard M, Knauf S, Lawrence P, Mather AE, Munster VJ, Müller MA, Smith D, Kuiken T. Factors determining human-to-human transmissibility of zoonotic pathogens via contact. Curr Opin Virol 2016; 22:7-12. [PMID: 27907884 PMCID: PMC5346033 DOI: 10.1016/j.coviro.2016.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 09/22/2016] [Revised: 11/02/2016] [Accepted: 11/11/2016] [Indexed: 01/25/2023]
Abstract
There are several modes of contact transmission of pathogens amongst humans. Factors promoting contact transmission act at the pathogen, host or environmental levels. Common pathogen factors are immune evasion, high viral load and low infectious dose. Common host factors are crowding, promiscuity and the presence of co-infections.
The pandemic potential of zoonotic pathogens lies in their ability to become efficiently transmissible amongst humans. Here, we focus on contact-transmitted pathogens and discuss the factors, at the pathogen, host and environmental levels that promote or hinder their human-to-human transmissibility via the following modes of contact transmission: skin contact, sexual contact, respiratory contact and multiple route contact. Factors common to several modes of transmission were immune evasion, high viral load, low infectious dose, crowding, promiscuity, and co-infections; other factors were specific for a pathogen or mode of contact transmission. The identification of such factors will lead to a better understanding of the requirements for human-to-human spread of pathogens, as well as improving risk assessment of newly emerging pathogens.
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Affiliation(s)
- Mathilde Richard
- Department of Viroscience, Postgraduate School Molecular Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, German Primate Center, Leibniz-Institute for Primate Research, Göttingen, Germany
| | - Philip Lawrence
- Université de Lyon, UMRS 449, Laboratoire de Biologie Générale, Université Catholique de Lyon - EPHE, Lyon 69288, France; Molecular Basis of Viral Pathogenicity, International Centre for Research in Infectiology (CIRI), INSERM U1111 - CNRS UMR5308, Université Lyon 1, Ecole Normale Supérieure de Lyon, Lyon 69007, France
| | - Alison E Mather
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Vincent J Munster
- Virus Ecology Unit, Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT, USA
| | - Marcel A Müller
- Institute of Virology, University of Bonn Medical Center, Bonn, Germany
| | - Derek Smith
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Thijs Kuiken
- Department of Viroscience, Postgraduate School Molecular Medicine, Erasmus MC, Rotterdam, The Netherlands.
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Knauf S, Raphael J, Mitjà O, Lejora IAV, Chuma IS, Batamuzi EK, Keyyu JD, Fyumagwa R, Lüert S, Godornes C, Liu H, Schwarz C, Šmajs D, Grange P, Zinner D, Roos C, Lukehart SA. Isolation of Treponema DNA from Necrophagous Flies in a Natural Ecosystem. EBioMedicine 2016; 11:85-90. [PMID: 27488881 PMCID: PMC5049926 DOI: 10.1016/j.ebiom.2016.07.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 06/16/2016] [Revised: 07/26/2016] [Accepted: 07/27/2016] [Indexed: 11/19/2022] Open
Abstract
Background Recently, the World Health Organization launched a campaign to eradicate the tropical disease yaws, caused by the bacterium Treponema pallidum subsp. pertenue; however, for decades researchers have questioned whether flies act as a vector for the pathogen that could facilitate transmission. Methods A total of 207 fly specimens were trapped in areas of Africa in which T. pallidum-induced skin ulcerations are common in wild baboons; 88 flies from Tarangire National Park and 119 from Lake Manyara National Park in Tanzania were analyzed by PCR for the presence of T. pallidum DNA. Findings We report that in the two study areas, T. pallidum DNA was found in 17–24% of wild-caught flies of the order Diptera. Treponemal DNA sequences obtained from many of the flies match sequences derived from nearby baboon T. pallidum strains, and one of the fly species with an especially high prevalence of T. pallidum DNA, Musca sorbens, has previously been shown to transmit yaws in an experimental setting. Interpretation Our results raise the possibility that flies play a role in yaws transmission; further research is warranted, given how important understanding transmission is for the eradication of this disfiguring disease. Treponema pallidum DNA was found in 17–24% of wild-caught flies in the Manyara region of Tanzania. Results further support the possibility that flies play a role in yaws transmission. New theoretic route of inter-species transmission for Treponema
The discovery of Treponema pallidum DNA on necrophagous flies in Africa supports historical reports on possible transmission of the bacterium by flies as a mechanical vector. The bacterium (subsp. pertenue) causes human yaws, which is currently subject to eradication efforts. It has been shown that African nonhuman primates are also found to be infected with T. pallidum strains that are closely related to human yaws causing strains. The ecology of T. pallidum infection in primates is not yet fully understood and intra- and interspecies transmission pathways, apart from skin-to-skin contact in humans, are largely unknown.
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Affiliation(s)
- Sascha Knauf
- Work Group Neglected Tropical Diseases, Pathology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany.
| | - Jane Raphael
- Ecology Monitoring Department, Tanzania National Parks, P.O. Box 3134, Arusha, Tanzania
| | - Oriol Mitjà
- ISGlobal, Barcelona Centre for International Health Research, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Inyasi A V Lejora
- Ecology Monitoring Department, Tanzania National Parks, P.O. Box 3134, Arusha, Tanzania
| | - Idrissa S Chuma
- Ecology Monitoring Department, Tanzania National Parks, P.O. Box 3134, Arusha, Tanzania
| | - Emmanuel K Batamuzi
- Department of Surgery and Theriogenology, Faculty of Veterinary Medicine, Sokoine University of Agriculture, P.O. Box 3020, Morogoro, Tanzania
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute, P.O. Box. 661, Arusha, Tanzania
| | - Robert Fyumagwa
- Tanzania Wildlife Research Institute, P.O. Box. 661, Arusha, Tanzania
| | - Simone Lüert
- Work Group Neglected Tropical Diseases, Pathology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany; Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Charmie Godornes
- Department of Medicine, University of Washington, Harborview Medical Center, 325 Ninth Avenue, Seattle, WA 98104, USA
| | - Hsi Liu
- National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Diseases Control and Prevention, Atlanta, GA 30333, USA
| | - Christiane Schwarz
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Philippe Grange
- Laboratoire de Dermatologie, Centre National de Reference de la Syphilis, 75014 Paris, France
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany; Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Sheila A Lukehart
- Department of Medicine, University of Washington, Harborview Medical Center, 325 Ninth Avenue, Seattle, WA 98104, USA
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