About the Authors

Krystal L. Ching

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

Affiliation Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, New York, United States of America

Maren de Vries

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

Affiliation Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America

Juan Gago

Roles Formal analysis, Investigation, Writing – review & editing

Affiliations Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America, Division of Epidemiology, Department of Population Health, New York University Grossman School of Medicine, New York, New York, United States of America

Kristen Dancel-Manning

Roles Formal analysis, Methodology, Writing – review & editing

Affiliations Division of Advanced Research Technologies, New York University Langone Health, New York, New York, United States of America, The Microscopy Laboratory at New York University Langone Health, New York, New York, United States of America

Joseph Sall

Roles Formal analysis, Methodology, Writing – review & editing

Affiliations Division of Advanced Research Technologies, New York University Langone Health, New York, New York, United States of America, The Microscopy Laboratory at New York University Langone Health, New York, New York, United States of America

William J. Rice

Roles Formal analysis, Methodology, Writing – review & editing

Affiliations Division of Advanced Research Technologies, New York University Langone Health, New York, New York, United States of America, The Cryo–Electron Microscopy Laboratory at New York University Langone Health, New York, New York, United States of America

Clea Barnett

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

Affiliation Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, New York, New York, United States of America

Alireza Khodadadi-Jamayran

Roles Data curation, Formal analysis, Resources, Validation

Affiliations Department of Pathology, New York University School of Medicine, New York, New York, United States of America, Applied Bioinformatics Laboratories, NYU School of Medicine, New York, New York, United States of America

Aristotelis Tsirigos

Roles Resources, Supervision

Affiliations Department of Pathology, New York University School of Medicine, New York, New York, United States of America, Applied Bioinformatics Laboratories, NYU School of Medicine, New York, New York, United States of America, Perlmutter Cancer Center, NYU Langone Health, New York, New York, United States of America

Feng-Xia Liang

Roles Formal analysis, Methodology, Writing – review & editing

Affiliations Division of Advanced Research Technologies, New York University Langone Health, New York, New York, United States of America, The Microscopy Laboratory at New York University Langone Health, New York, New York, United States of America

Lorna E. Thorpe

Roles Supervision, Writing – review & editing

Affiliation Division of Epidemiology, Department of Population Health, New York University Grossman School of Medicine, New York, New York, United States of America

Bo Shopsin

Roles Formal analysis, Supervision, Writing – review & editing

Affiliations Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America, Division of Infectious Diseases and Immunology, Department of Medicine, New York University Grossman School of Medicine, New York, New York, United States of America, Antimicrobial-Resistant Pathogens Program, NYU Langone Health, New York, New York, United States of America

Leopoldo N. Segal

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

Affiliation Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, New York, New York, United States of America

Meike Dittmann

Roles Conceptualization, Supervision, Writing – review & editing

Meike.Dittmann@nyulangone.org (MD); Victor.torres@nyulangone.org (VJT); ken.cadwell@nyulangone.org (KC)

Affiliation Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America

Victor J. Torres

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

Meike.Dittmann@nyulangone.org (MD); Victor.torres@nyulangone.org (VJT); ken.cadwell@nyulangone.org (KC)

Affiliations Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America, Antimicrobial-Resistant Pathogens Program, NYU Langone Health, New York, New York, United States of America

Ken Cadwell

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

Meike.Dittmann@nyulangone.org (MD); Victor.torres@nyulangone.org (VJT); ken.cadwell@nyulangone.org (KC)

Affiliations Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, New York, United States of America, Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America, Division of Gastroenterology and Hepatology, Department of Medicine, New York University Grossman School of Medicine, New York, New York, United States of America

Competing Interests

I have read the journal’s policy and the authors of this manuscript have the following competing interests: K.C. has received research support from Pfizer, Takeda, Pacific Biosciences, Genentech, and Abbvie. K.C. has consulted for or received honoraria from Vedanta, Genentech, and Abbvie. K.C. is an inventor on U.S. patent 10,722,600 and provisional patent 62/935,035 and 63/157,225. V.J.T. receives research support from Janssen Biotech Inc. V.J.T has consulted for Janssen Research & Development, LLC and have or received honoraria from Genentech and Medimmune. V.J.T. is an inventor on patents and patent applications filed by New York University, which are currently under commercial license to Janssen Biotech Inc. provides research funding and other payments associated with a licensing agreement.