Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach

• Rene S. Hendriksen ,

  Roles Conceptualization, Formal analysis, Investigation, Project administration, Supervision, Writing – original draft, Writing – review & editing

  * E-mail: rshe@food.dtu.dk

  Affiliation National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark

  http://orcid.org/0000-0003-2934-8214

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• Oksana Lukjancenko,

  Roles Formal analysis, Methodology, Visualization, Writing – review & editing

  Affiliation National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark

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• Patrick Munk,

  Roles Formal analysis, Methodology, Visualization, Writing – review & editing

  Affiliation National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark

  http://orcid.org/0000-0001-8813-4019

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• Mathis H. Hjelmsø,

  Roles Formal analysis, Methodology, Visualization, Writing – review & editing

  Affiliation National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark

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• Jennifer R. Verani,

  Roles Conceptualization, Data curation, Formal analysis, Investigation, Resources, Supervision, Writing – review & editing

  Affiliations Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Nairobi, Kenya, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, United States of America

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• Eric Ng’eno,

  Roles Conceptualization, Data curation, Formal analysis, Investigation, Resources, Writing – review & editing

  Affiliation Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Nairobi, Kenya

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• Godfrey Bigogo,

  Roles Data curation, Resources

  Affiliation Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Nairobi, Kenya

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• Samuel Kiplangat,

  Roles Data curation, Resources

  Affiliation Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Nairobi, Kenya

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• Traoré Oumar,

  Roles Data curation, Resources

  Affiliation Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Nairobi, Kenya

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• Lasse Bergmark,

  Roles Methodology

  Affiliation National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark

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• Timo Röder,

  Roles Visualization

  Affiliation National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark

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• John C. Neatherlin,

  Roles Resources

  Affiliation Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Nairobi, Kenya

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• Onyango Clayton,

  Roles Data curation, Resources

  Affiliation Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Nairobi, Kenya

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• Tine Hald,

  Roles Formal analysis

  Affiliation National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark

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• Susanne Karlsmose,

  Roles Resources

  Affiliation National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark

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• Sünje J. Pamp,

  Roles Resources, Supervision, Writing – review & editing

  Affiliation National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark

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• Barry Fields,

  Roles Resources, Supervision, Writing – review & editing

  Affiliations Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Nairobi, Kenya, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, United States of America

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• Joel M. Montgomery,

  Roles Resources, Supervision, Writing – review & editing

  Affiliations Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Nairobi, Kenya, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, United States of America

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•  [ ... ],
• Frank M. Aarestrup

  Roles Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Supervision, Writing – review & editing

  Affiliation National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark

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