Clinical metagenomics bioinformatics pipeline for the identification of hospital-acquired pneumonia pathogens antibiotic resistance genes from bronchoalveolar lavage samples

Autor: Stéphane Schicklin, Jacques Schrenzel, Levrat A, Lazarevic, Etienne Ruppé, Hauser S, Gaspard Gervasi, Pierre Mahé, Louis K, Perrin G, Ghislaine Guigon, Maud Tournoud, Mirande C

BackgroundShortening the time-to-result for pathogen detection and identification and antibiotic susceptibility testing for patients with Hospital-Acquired and Ventilator-Associated pneumonia (HAP-VAP) is of great interest. For this purpose, clinical

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::50a1d9b88eefb748a1976f2efbdb13d3
https://doi.org/10.1101/2020.02.26.966309

Testing a global standard for quantifying species recovery and assessing conservation impact.

Autor: Grace MK; Department of Zoology, University of Oxford, Oxford, UK.; IUCN Species Survival Commission, Caracas, Venezuela., Akçakaya HR; IUCN Species Survival Commission, Caracas, Venezuela.; Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA., Bennett EL; Wildlife Conservation Society, Bronx, New York, USA., Brooks TM; International Union for Conservation of Nature (IUCN), Gland, Switzerland.; World Agroforestry Center (ICRAF), University of the Philippines, Los Baños, Philippines.; Institute for Marine & Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia., Heath A; Synchronicity Earth, London, UK., Hedges S; Wildlife Conservation Society, Bronx, New York, USA.; IUCN SSC Asian Elephant Specialist Group, Noida, India.; IUCN SSC Asian Wild Cattle Specialist Group, Chester, UK., Hilton-Taylor C; IUCN Red List Unit, Cambridge, UK., Hoffmann M; IUCN Species Survival Commission, Caracas, Venezuela.; Conservation Programmes, Zoological Society of London, London, UK., Hochkirch A; Department of Biogeography, Trier University, Trier, Germany., Jenkins R; IUCN Global Species Programme, Cambridge, UK., Keith DA; IUCN Species Survival Commission, Caracas, Venezuela.; Centre for Ecosystem Sciences, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.; NSW Office of Environment and Heritage, Hurstville, New South Wales, Australia., Long B; Re:wild, Washington, DC, USA., Mallon DP; Division of Biology and Conservation Ecology, Manchester Metropolitan University, Manchester, UK.; IUCN SSC Antelope Specialist Group, Manchester, UK., Meijaard E; IUCN SSC Wild Pig Specialist Group and Centre of Excellence for Environmental Decisions, University of Queensland, Brisbane, Queensland, Australia., Milner-Gulland EJ; Merton College, University of Oxford, Oxford, UK., Rodriguez JP; IUCN Species Survival Commission, Caracas, Venezuela.; Instituto Venezolano de Investigaciones Científicas, and Provita, Caracas, Venezuela., Stephenson PJ; IUCN SSC Species Monitoring Specialist Group, Gingins, Switzerland.; Laboratory for Conservation Biology, Department of Ecology & Evolution, UNIL - University of Lausanne, Lausanne, Switzerland., Stuart SN; IUCN Species Survival Commission, Caracas, Venezuela.; Synchronicity Earth, London, UK., Young RP; Durrell Wildlife Conservation Trust, Trinity, UK., Acebes P; Centro de Investigación en Biodiversidad y Cambio Global, Departamento de Ecología, Universidad Autónoma de Madrid, Madrid, Spain., Alfaro-Shigueto J; Carrera de Biologia Marina, Universidad Cientifica del Sur, Lima, Peru., Alvarez-Clare S; The Morton Arboretum, Lisle, Illinois, USA., Andriantsimanarilafy RR; Madagasikara Voakajy, Antananarivo, Madagasikara., Arbetman M; Grupo Ecología de la Polinización, INIBIOMA, Universidad Nacional del Comahue, CONICET, Bariloche, Argentina., Azat C; Sustainability Research Centre & PhD Programme in Conservation Medicine, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile., Bacchetta G; Centre for Conservation of Biodiversity, University of Cagliari, Cagliari, Italy., Badola R; Wildlife Institute of India, Dehradun, India., Barcelos LMD; Azorean Biodiversity Group, Centre for Ecology, Evolution, and Environmental Changes, Faculty of Agricultural and Environmental Sciences, University of the Azores, Angra do Heroísmo, Portugal., Barreiros JP; Universidade dos Açores, Faculdade de Ciências Agrárias e do Ambiente, Rua Capitão João d'Ávila, Angra do Heroísmo, Portugal., Basak S; Wildlife Institute of India, Dehradun, India., Berger DJ; School of Natural Resources, University of Nebraska-Lincoln, Lincoln, Nebraska, USA., Bhattacharyya S; Centre for Ecological Sciences, Indian Institute of Sciences, Bangalore, India., Bino G; University of New South Wales, Centre for Ecosystem Science, School of Biological, Earth & Environmental Sciences, University of New South Wales, Randwick, New South Wales, Australia., Borges PAV; Departamento de Ciências e Engenharia do Ambiente Universidade dos Açores, Azores, Portugal., Boughton RK; Range Cattle Research and Education Center, University of Florida, Gainesville, Florida, USA., Brockmann HJ; Department of Biology, University of Florida, Gainesville, Florida, USA., Buckley HL; Auckland University of Technology, Auckland, New Zealand., Burfield IJ; BirdLife International, Cambridge, UK., Burton J; IUCN SSC Asian Wild Cattle Specialist Group, Cedar House, Chester, UK., Camacho-Badani T; Museo de Historia Natural Alcide d' Orbigny, Cochabamba, Bolivia., Cano-Alonso LS; Department of Zoology and Physical Anthropology, Complutense University of Madrid, Madrid, Spain., Carmichael RH; Dauphin Island Sea Lab, Dauphin Island, Alabama, USA., Carrero C; The Morton Arboretum, Lisle, Illinois, USA., Carroll JP; University of Nebraska, School of Natural Resources, Lincoln, Nebraska, USA., Catsadorakis G; Society for the Protection of Prespa, Agios Germanos, Greece., Chapple DG; School of Biological Sciences, Monash University, Clayton, Victoria, Australia., Chapron G; Department of Ecology, Swedish University of Agricultural Sciences, Riddarhyttan, Sweden., Chowdhury GW; Department of Zoology, University of Dhaka, Dhaka, Bangladesh., Claassens L; Rhodes University, Grahamstown, South Africa., Cogoni D; Dipartimento di Scienze della Vita e dell'Ambiente, Centro Conservazione Biodiversità, Università degli Studi di Cagliari, Cagliari, Italy., Constantine R; School of Biological Sciences & Institute of Marine Science, University of Auckland, Auckland, New Zealand., Craig CA; Endangered Wildlife Trust, Office 8 & 9, Centre for Biodiversity Conservation, Cape Town, South Africa., Cunningham AA; Institute of Zoology, Zoological Society of London, London, UK., Dahal N; CSIR-Institute of Himalayan Bioresource Technology, Palampur, India., Daltry JC; Fauna & Flora International, Cambridge, UK., Das GC; Wildlife Institute of India, Dehradun, India., Dasgupta N; Wildlife Institute of India, Dehradun, India., Davey A; Fauna & Flora International, Cambridge, UK., Davies K; Botanic Gardens Conservation International, Richmond, UK., Develey P; BirdLife/SAVE Brasil, Fernão Dias, Brazil., Elangovan V; University of Otago, Dunedin, New Zealand., Fairclough D; Department of Primary Industries and Regional Development, Department of Fisheries, Hillarys, Western Australia, Australia., Febbraro MD; University of Molise, Pesche, Italy., Fenu G; Dipartimento di Scienze della Vita e dell'Ambiente, Centro Conservazione Biodiversità, Università degli Studi di Cagliari, Cagliari, Italy., Fernandes FM; Sociedade de Amigos da Fundação Zoobotânica de Belo Horizonte, (Pampulha), Belo Horizonte, Brazil., Fernandez EP; Brazilian National Centre for Flora Conservation, Rio de Janeiro, Brazil., Finucci B; National Institute of Water and Atmospheric Research, Wellington, New Zealand., Földesi R; Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany., Foley CM; Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kaneohe, Hawai'i, USA., Ford M; Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany., Forstner MRJ; Texas State University, San Marcos, Texas, USA., García N; Pontificia Universidad Javeriana, Bogotá, Colombia., Garcia-Sandoval R; Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito exterior s/n, Ciudad Universitaria, Coyoacán, Mexico., Gardner PC; Danau Girang Field Centre, c/o Sabah Wildlife Department, Kota Kinabalu, Malaysia., Garibay-Orijel R; Instituto de Biología, Universidad Nacional Autonoma de Mexico, Tercer Circuito s/n, Ciudad Universitaria, Ciudad de México, México., Gatan-Balbas M; Mabuwaya Foundation Inc., ISU Garita, Cabagan, Philippines., Gauto I; Asociación Etnobotánica Paraguaya, Lambaré, Paraguay., Ghazi MGU; Wildlife Institute of India, Dehradun, India., Godfrey SS; Department of Zoology, University of Otago, Dunedin, New Zealand., Gollock M; Zoological Society of London, London, UK., González BA; Laboratorio de Ecología de Vida Silvestre, Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile., Grant TD; San Diego Zoo Institute for Conservation Research, San Diego, California, USA., Gray T; Wildlife Alliance, Phnom Penh, Cambodia., Gregory AJ; Bowling Green State University, School of Earth Environment and Society, Bowling Green, Ohio, USA., van Grunsven RHA; Dutch Butterfly Conservation, Wageningen, the Netherlands., Gryzenhout M; Department of Genetics, University of the Free State, Bloemfontein, South Africa., Guernsey NC; World Wildlife Fund Inc., Northern Great Plains Program, Bozeman, Montana, USA., Gupta G; School of Natural and Environmental Sciences, Newcastle University, Newcastle, UK., Hagen C; BirdLife South Africa, Roggebaai, South Africa., Hagen CA; Department of Fisheries & Wildlife, Oregon State University, Corvallis, Oregon, USA., Hall MB; Department of Biology, University of Central Florida, Orlando, Florida, USA., Hallerman E; Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA., Hare K; Urban Wildlife Trust, Wellington/Hamilton, New Zealand., Hart T; Department of Zoology, Oxford University, Oxford, UK., Hartdegen R; Dallas Zoo, Dallas, Texas, USA., Harvey-Brown Y; Botanic Gardens Conservation International, Richmond, UK., Hatfield R; The Xerces Society for Invertebrate Conservation, Portland, Oregon, USA., Hawke T; University of New South Wales, Centre for Ecosystem Science, School of Biological, Earth & Environmental Sciences, University of New South Wales, Randwick, New South Wales, Australia., Hermes C; BirdLife International, Cambridge, UK., Hitchmough R; Department of Conservation-Te Papa Atawhai, Wellington, New Zealand., Hoffmann PM; Sociedade Chauá, Rua Julio Gorski, Paraná, Brazil., Howarth C; Durrell Wildlife Conservation Trust, Trinity, UK., Hudson MA; Durrell Wildlife Conservation Trust, Trinity, UK., Hussain SA; Wildlife Institute of India, Dehradun, India., Huveneers C; Southern Shark Ecology Group, Flinders University, Adelaide, South Australia, Australia., Jacques H; IUCN Otter Specialist Group, Brie et Angonnesù, France., Jorgensen D; World Wildlife Fund Inc., Northern Great Plains Program, Bozeman, Montana, USA., Katdare S; Wildlife Institute of India, Dehradun, India., Katsis LKD; Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Abingdon, UK., Kaul R; Wildlife Trust of India, Noida, India., Kaunda-Arara B; Department of Fisheries and Aquatic Sciences, University of Eldoret, Eldoret, Kenya., Keith-Diagne L; African Aquatic Conservation Fund, Thies, Senegal., Kraus DT; University of Waterloo, School of Environment, Resources and Sustainability, Waterloo, Ontario, Canada., de Lima TM; Federal University of Rio de Janeiro, Rio de Janeiro, Brazil., Lindeman K; Florida Institute of Technology, Program in Sustainability Studies, Melbourne, Florida, USA., Linsky J; Botanic Gardens Conservation International, Richmond, UK., Louis E Jr; Omaha's Henry Doorly Zoo and Aquarium, Omaha, Nebraska, USA., Loy A; Department of Biosciences and Territory, University of Molise, Pesche, Italy., Lughadha EN; Royal Botanic Gardens, Richmond, Surrey, UK., Mangel JC; Carrera de Biologia Marina, Universidad Cientifica del Sur, Lima, Peru., Marinari PE; Smithsonian Conservation Biology Institute, Front Royal, Virginia, USA., Martin GM; Centro de Investigación Esquel de Montaña y Estepa Patagónica, CONICET, Buenos Aires, Argentina., Martinelli G; National Center for Flora Conservation (CNCFlora), Rio de Janeiro, Brazil., McGowan PJK; School of Natural and Environmental Sciences, Newcastle University, Newcastle, UK., McInnes A; Seabird Conservation Programme, BirdLife South Africa, Foreshore, South Africa., Teles Barbosa Mendes E; Federal University of Rio de Janeiro, Rio de Janeiro, Brazil., Millard MJ; U.S. Fish and Wildlife Service, Lamar, Pennsylvania, USA., Mirande C; International Crane Foundation, Baraboo, Wisconsin, USA., Money D; Department of Zoology, University of Cambridge, Cambridge, UK., Monks JM; Department of Conservation, Dunedin, New Zealand., Morales CL; Grupo Ecología de la Polinización, INIBIOMA, Universidad Nacional del Comahue, CONICET, Bariloche, Argentina., Mumu NN; Center for Natural Resource Studies, Dhaka, Bangladesh., Negrao R; Royal Botanic Gardens, Richmond, Surrey, UK., Nguyen AH; Fauna & Flora International - Vietnam Programme, Hanoi, Vietnam., Niloy MNH; Department of Zoology, University of Dhaka, Dhaka, Bangladesh., Norbury GL; Manaaki Whenua Landcare Research, Alexandra, New Zealand., Nordmeyer C; Minnesota Zoo, Apple Valley, Minnesota, USA., Norris D; School of Environmental Sciences, Federal University of Amapá, Macapá, Brazil., O'Brien M; BirdLife International Pacific Regional Office, Suva, Fiji., Oda GA; Federal Rural University of Rio de Janeiro - UFRRJ, Department of Environmental Sciences, Forestry Institute, Seropédica, Rio de Janeiro, Brazil., Orsenigo S; Dipartimento di Scienze della Terra e dell'Ambiente, Università di Pavia; Dipartimento di Scienze della Vita e dell'Ambiente, Centro Conservazione Biodiversità, Università degli Studi di Cagliari, Cagliari, Italy., Outerbridge ME; Bermuda Government, Department of Environment and Natural Resources, Paget, Bermuda., Pasachnik S; International Iguana Foundation, Fort Worth, Texas, USA., Pérez-Jiménez JC; El Colegio de la Frontera Sur, Lerma, Campeche, Mexico., Pike C; Zoological Society of London, London, UK., Pilkington F; Fauna & Flora International, Cambridge, UK., Plumb G; US National Park Service, Livingston, Montana, USA., Portela RCQ; Ecology Department, Biology Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil., Prohaska A; GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Quintana MG; Division of Invertebrates, Argentine Museum of Natural Sciences, Buenos Aires, Argentina., Rakotondrasoa EF; Madagasikara Voakajy, Antananarivo, Madagasikara., Ranglack DH; University of Nebraska Kearney, Kearney, Nebraska, USA., Rankou H; IUCN SSC Orchid Specialist Group, Royal Botanic Gardens, Richmond, Surrey, UK., Rawat AP; Wildlife Institute of India, Dehradun, India., Reardon JT; Department of Conservation, New Zealand, Fiordland District Office, Te Anau, New Zealand., Rheingantz ML; Universidade Federal do Rio de Janeiro, Laboratório de Ecologia e Conservação de Populações, Centro de Ciências da Saúde - Instituto de Biologia, Rio de Janeiro, RJ, Brazil., Richter SC; Division of Natural Areas and Department of Biological Sciences, Eastern Kentucky University, Richmond, Kentucky, USA., Rivers MC; Botanic Gardens Conservation International, Richmond, UK., Rogers LR; University of Nebraska Kearney, Kearney, Nebraska, USA., da Rosa P; National Center for Flora Conservation (CNCFlora), Rio de Janeiro, Brazil., Rose P; University of Exeter, Exeter, UK., Royer E; Minnesota Zoo, Apple Valley, Minnesota, USA., Ryan C; Auckland University of Technology, School of Science, Auckland City, New Zealand., de Mitcheson YJS; Swire Institute of Marine Science, University of Hong Kong, Hong Kong., Salmon L; Nottingham Trent University, Brackenhurst Campus, Southwell, Nottinghamshire, UK., Salvador CH; Cooperative Caipora, Florianópolis, Brazil., Samways MJ; Department of Conservation Ecology & Entomology, Stellenbosch University, Stellenbosch, South Africa., Sanjuan T; Grupo Micologos Colombia, Calle, Colmbia., Souza Dos Santos A; Universidade Federal do Rio de Janeiro, Health Science Centre, Biology Institute, Plant Ecology Laboratory, Rio de Janeiro, Brazil., Sasaki H; Chikushi Jogakuen University, Dazaifu, Japan., Schutz E; D'ABOVILLE Foundation and Demo Farm Inc, Makati, Philippines., Scott HA; Namibia Crane Working Group, Swakopmund, Namibia., Scott RM; Namibia Crane Working Group, Swakopmund, Namibia., Serena F; Institute for Biological Resources and Marine Biotechnology, National Research Council-(CNR -IRBIM), Mazara del Vallo, Italy., Sharma SP; Wildlife Institute of India, Dehradun, India., Shuey JA; The Nature Conservancy, Indianapolis, Indiana, USA., Silva CJP; Facultad de Ciencias Naturales e Ingeniería, Universidad de Bogotá Jorge Tadeo Lozano, Bogotá, Colombia., Simaika JP; Department of Water Resources and Ecosystems, IHE Delft Institute for Water Education, Delft, The Netherlands., Smith DR; U.S. Geological Survey, Kearneysville, West Virginia, USA., Spaet JLY; Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge, UK., Sultana S; Department of Zoology, University of Dhaka, Dhaka, Bangladesh., Talukdar BK; IUCN Asian Rhino Specialist Group, Guwahati, India., Tatayah V; Mauritian Wildlife Foundation, Vacoas, Mauritius., Thomas P; Royal Botanic Garden, Edinburgh, UK., Tringali A; Archbold Biological Station, Venus, Florida, USA., Trinh-Dinh H; Fauna & Flora International - Vietnam Programme, Hanoi, Vietnam., Tuboi C; Wildlife Institute of India, Dehradun, India., Usmani AA; Wildlife Institute of India, Dehradun, India., Vasco-Palacios AM; Grupo de Microbiología Ambiental - BioMicro, Escuela de Microbiología, Universidad de Antioquia, UdeA, Medellín, Colombia.; Fundación Biodiversa Colombia, FBC, Bogotá, Colombia., Vié JC; Fondation Franklinia, Genève, Switzerland., Virens J; University of Otago, Dunedin, New Zealand., Walker A; Centre for Environment, Fisheries & Aquaculture Science, Lowestoft, Suffolk, UK., Wallace B; Ecolibrium Inc, Boulder, Colorado, USA., Waller LJ; Southern African Foundation for the Conservation of Coastal Birds, Cape Town, South Africa.; Department of Biodiversity and Conservation Biology, University of the Western Cape, Belville, South Africa., Wang H; Northeast Forestry University, Harbin City, China., Wearn OR; Fauna & Flora International - Vietnam Programme, Hanoi, Vietnam., van Weerd M; Institute of Environmental Sciences (CML), Leiden University, Leiden, the Netherlands., Weigmann S; Elasmo-Lab, Elasmobranch Research Laboratory, Hamburg, Germany.; Center of Natural History, University of Hamburg, Hamburg, Germany., Willcox D; Save Vietnam's Wildlife, Cuc Phuong National Park, Ninh Bình Province, Vietnam., Woinarski J; Charles Darwin University, Casuarina, Northern Territory, Australia., Yong JWH; Department of Biosystems and Technology, Swedish University of Agricultural Sciences, Alnarp, Sweden., Young S; IUCN SSC Asian Wild Cattle Specialist Group, Cedar House, Chester, UK.

Publikováno v: Conservation biology : the journal of the Society for Conservation Biology [Conserv Biol] 2021 Dec; Vol. 35 (6), pp. 1833-1849. Date of Electronic Publication: 2021 Jul 21.

Corrigendum: Genomic evolution and local epidemiology of Klebsiella pneumoniae from a major hospital in Beijing, China, over a 15 year period: dissemination of known and novel high-risk clones.

Autor: Palmieri M; bioMérieux, Data Analytics Unit, La Balme Les Grottes, France., Wyres KL; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia., Mirande C; bioMérieux, R&D Microbiology, La Balme Les Grottes, France., Qiang Z; Center for Clinical Laboratory Medicine, First Medical Center of Chinese PLA General Hospital, Beijing, PR China., Liyan Y; Center for Clinical Laboratory Medicine, First Medical Center of Chinese PLA General Hospital, Beijing, PR China., Gang C; Center for Clinical Laboratory Medicine, First Medical Center of Chinese PLA General Hospital, Beijing, PR China., Goossens H; Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Belgium., Belkum AV; bioMérieux, Data Analytics Unit, La Balme Les Grottes, France., Ping LY; Center for Clinical Laboratory Medicine, First Medical Center of Chinese PLA General Hospital, Beijing, PR China.

Publikováno v: Microbial genomics [Microb Genom] 2021 Aug; Vol. 7 (8).

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Bayesian accuracy estimates for diagnostic tests to detect tuberculosis in captive sun bears (Helarctos malayanus) and Asiatic black bears (Ursus thibetanus) in Cambodia and Vietnam.

Autor: Officer, Kirsty^1,2 (AUTHOR) kirsty.officer@murdoch.edu.au, Arango-Sabogal, Juan Carlos³ (AUTHOR), Dufour, Simon³ (AUTHOR), Lyashchenko, Konstantin P.⁴ (AUTHOR), Cracknell, Jonathan^2,5 (AUTHOR), Thomson, Shaun⁶ (AUTHOR), Cheng, Sokleaph⁷ (AUTHOR), Warren, Kris^1,8 (AUTHOR), Jackson, Bethany^1,8 (AUTHOR)

Publikováno v: PLoS ONE. 11/13/2024, Vol. 19 Issue 11, p1-22. 22p.