Methods for cost-efficient, whole genome sequencing surveillance for enhanced detection of outbreaks in a hospital setting

• Kady D. Waggle,

  Roles Conceptualization, Data curation, Formal analysis, Methodology, Visualization, Writing – original draft, Writing – review & editing

  Affiliations Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America, Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America

  https://orcid.org/0009-0001-9237-9964

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• Marissa Pacey Griffith,

  Roles Formal analysis, Methodology, Resources, Validation, Writing – original draft, Writing – review & editing

  Affiliations Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America

  https://orcid.org/0000-0003-0677-8203

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• Alecia B. Rokes,

  Roles Data curation, Methodology, Writing – review & editing

  Affiliations Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America, Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America

  https://orcid.org/0000-0001-9496-0296

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• Vatsala Rangachar Srinivasa,

  Roles Data curation, Writing – review & editing

  Affiliations Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America, Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America

  https://orcid.org/0000-0001-7376-8764

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• Erin M. Nawrocki,

  Roles Data curation, Methodology, Writing – review & editing

  Affiliations Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America, Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America

  https://orcid.org/0000-0002-7610-7117

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• Deena Ereifej,

  Roles Data curation, Investigation, Methodology, Writing – review & editing

  Affiliations Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America, Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America

  https://orcid.org/0009-0002-2984-3784

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• Rose Patrick,

  Roles Data curation, Investigation, Writing – review & editing

  Affiliations Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America

  https://orcid.org/0009-0003-3541-5513

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• Hunter Coyle,

  Roles Data curation, Methodology, Writing – review & editing

  Affiliations Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America

  https://orcid.org/0009-0006-0463-4168

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• Shurmin Chaudhary,

  Roles Data curation, Methodology, Writing – review & editing

  Affiliations Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America

  https://orcid.org/0009-0009-1640-7132

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• Nathan J. Raabe,

  Roles Data curation, Formal analysis, Investigation, Methodology, Visualization, Writing – review & editing

  Affiliations Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America, Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America

  https://orcid.org/0000-0002-3258-9003

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• Kathleen Shutt,

  Roles Data curation, Formal analysis, Writing – review & editing

  Affiliations Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America

  https://orcid.org/0000-0003-3376-6152

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• Alexander J. Sundermann,

  Roles Data curation, Formal analysis, Investigation, Methodology, Validation, Visualization, Writing – review & editing

  Affiliations Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America

  https://orcid.org/0000-0002-2439-6287

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• Vaughn S. Cooper,

  Roles Data curation, Project administration, Supervision, Writing – review & editing

  Affiliations Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America, Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America

  https://orcid.org/0000-0001-7726-0765

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• Lee H. Harrison,

  Roles Conceptualization, Funding acquisition, Investigation, Methodology, Resources, Supervision, Writing – original draft, Writing – review & editing

  Affiliations Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America, Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America

  https://orcid.org/0000-0002-3787-2705

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• Lora Lee Pless

  Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Project administration, Resources, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing

  * E-mail: lora.pless@pitt.edu

  Affiliations Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America

  https://orcid.org/0000-0003-0163-3689

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