Author Contributions: Dr Pallen had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis. Drs Loman, Constantinidou, and Christner contributed equally to this work. Drs Aepfelbacher and Pallen contributed equally to this work.
Study concept and design: Loman, Rohde, Aepfelbacher, Pallen.
Acquisition of data: Loman, Constantinidou, Christner, Rohde, Chan, Quick, Weir, Smith, Betley, Aepfelbacher.
Analysis and interpretation of data: Loman, Rohde, Chan, Quince, Pallen.
Drafting of the manuscript: Loman, Constantinidou, Chan, Quick, Smith, Aepfelbacher, Pallen.
Critical revision of the manuscript for important intellectual content: Loman, Christner, Rohde, Weir, Quince, Betley, Aepfelbacher.
Statistical analysis: Loman, Quince.
Obtained funding: Loman, Pallen.
Administrative, technical, or material support: Loman, Constantinidou, Christner, Rohde, Chan, Quick, Weir, Smith, Betley, Aepfelbacher.
Study supervision: Rohde, Aepfelbacher, Pallen.
Conflict of Interest Disclosures: The authors have completed and submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Dr Rohde reported receiving speakers fees from Novartis and Gilead; and receiving travel reimbursement from Novartis and Merck Sharp Dohme. Ms Weir and Drs Smith and Betley are employees of and own stock in Illumina Inc, which manufactures the MiSeq and HiSeq 2500 instruments. No other authors reported disclosures.
Funding/Support: This work was supported in Germany by the Medical Faculty of the University Medical Center Hamburg–Eppendorf. Work in Birmingham, England, was supported by a grant from the UK's Biotechnology and Biological Sciences Research Council supporting the xBASE project, by a grant from the UK's National Institute for Health Research awarded to the Surgical Reconstruction and Microbiology Research Centre (MRC), and by an MRC Special Training Fellowship in Biomedical Informatics to Dr Loman. The HiSeq2500 sequencing was supported by Illumina Inc.
Role of the Sponsor: Neither the UK's Biotechnology and Biological Sciences Research Council, the MRC, nor the UK's National Institute for Health Research had any role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; and preparation, review, or approval of the manuscript.
Additional Contributions: We are indebted to the laboratory staff in the clinical microbiology laboratory at the University Medical Centre Hamburg-Eppendorf who performed conventional microbiological analyses as part of routine management of patients, to Richard Brown, BSc, and Gemma Kay, PhD, for technical support in the laboratory at University of Birmingham, and to Holly Duckworth, BSc, and Peter Saffrey, PhD, for technical support in the sequencing laboratory at Illumina. The persons listed were not compensated for their contributions beyond their normal salaries.