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A global metagenomic map of urban microbiomes and antimicrobial resistance.
Danko, David; Bezdan, Daniela; Afshin, Evan E; Ahsanuddin, Sofia; Bhattacharya, Chandrima; Butler, Daniel J; Chng, Kern Rei; Donnellan, Daisy; Hecht, Jochen; Jackson, Katelyn; Kuchin, Katerina; Karasikov, Mikhail; Lyons, Abigail; Mak, Lauren; Meleshko, Dmitry; Mustafa, Harun; Mutai, Beth; Neches, Russell Y; Ng, Amanda; Nikolayeva, Olga; Nikolayeva, Tatyana; Png, Eileen; Ryon, Krista A; Sanchez, Jorge L; Shaaban, Heba; Sierra, Maria A; Thomas, Dominique; Young, Ben; Abudayyeh, Omar O; Alicea, Josue; Bhattacharyya, Malay; Blekhman, Ran; Castro-Nallar, Eduardo; Cañas, Ana M; Chatziefthimiou, Aspassia D; Crawford, Robert W; De Filippis, Francesca; Deng, Youping; Desnues, Christelle; Dias-Neto, Emmanuel; Dybwad, Marius; Elhaik, Eran; Ercolini, Danilo; Frolova, Alina; Gankin, Dennis; Gootenberg, Jonathan S; Graf, Alexandra B; Green, David C; Hajirasouliha, Iman; Hastings, Jaden J A.
Affiliation
  • Danko D; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Bezdan D; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübi
  • Afshin EE; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Ahsanuddin S; Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  • Bhattacharya C; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Butler DJ; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Chng KR; Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore.
  • Donnellan D; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Hecht J; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
  • Jackson K; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Kuchin K; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Karasikov M; ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
  • Lyons A; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Mak L; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Meleshko D; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Mustafa H; ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
  • Mutai B; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Kenya Medical Research Institute - Kisumu, Kisumu, Kenya.
  • Neches RY; Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Ng A; Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore.
  • Nikolayeva O; Independent Researcher, Zurich, Switzerland.
  • Nikolayeva T; Independent Researcher, Zurich, Switzerland.
  • Png E; Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore.
  • Ryon KA; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Sanchez JL; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Shaaban H; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Sierra MA; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Thomas D; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Young B; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Abudayyeh OO; Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA.
  • Alicea J; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Bhattacharyya M; Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India; Centre for Artificial Intelligence and Machine Learning, Indian Statistical Institute, Kolkata, India.
  • Blekhman R; University of Minnesota, Minneapolis, MN, USA.
  • Castro-Nallar E; Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Santiago, Chile.
  • Cañas AM; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Chatziefthimiou AD; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Crawford RW; California State University, Sacramento, Sacramento, CA, USA.
  • De Filippis F; Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
  • Deng Y; University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA.
  • Desnues C; Aix-Marseille Université, Mediterranean Institute of Oceanology, Université de Toulon, CNRS, IRD, UM 110, Marseille, France.
  • Dias-Neto E; Medical Genomics group, A.C.Camargo Cancer Center, São Paulo - SP, Brazil.
  • Dybwad M; Norwegian Defence Research Establishment FFI, Kjeller, Norway.
  • Elhaik E; Department of Biology, Lund University, Lund, Sweden.
  • Ercolini D; Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
  • Frolova A; Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, Kyiv, Ukraine; Kyiv Academic University, Kyiv, Ukraine.
  • Gankin D; Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA.
  • Gootenberg JS; Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA.
  • Graf AB; University of Applied Sciences Vienna, Vienna, Austria.
  • Green DC; Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK.
  • Hajirasouliha I; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
  • Hastings JJA; Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Cell ; 184(13): 3376-3393.e17, 2021 06 24.
Article in En | MEDLINE | ID: mdl-34043940
ABSTRACT
We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Urban Population / Drug Resistance, Bacterial / Metagenomics / Microbiota Type of study: Prognostic_studies Limits: Humans Language: En Journal: Cell Year: 2021 Type: Article Affiliation country: United States
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Urban Population / Drug Resistance, Bacterial / Metagenomics / Microbiota Type of study: Prognostic_studies Limits: Humans Language: En Journal: Cell Year: 2021 Type: Article Affiliation country: United States