@article{445cd8ebe4c2478dbb4863f28cfc07af,
title = "Core genome multilocus sequence typing and prediction of antimicrobial susceptibility using whole-genome sequences of Escherichia coli bloodstream infection isolates",
abstract = "In total, 50 Escherichia coli bloodstream isolates from the clinical laboratory and 12 E. coli isolates referred for pulsed-field gel electrophoresis (PFGE) were sequenced, assessed for clonality using core genome multilocus sequence typing (cgMLST), and evaluated for genomic susceptibility predictions using ARESdb. Results of sequence typing using whole-genome sequencing (WGS)-based MLST and sequence type (ST)-specific PCR were identical. Overall categorical agreement between genotypic (ARESdb) and phenotypic susceptibility testing for 62 isolates and 11 antimicrobial agents was 91%. Among the referred isolates, high major error rates were found for ceftazidime, cefepime, and piperacillin-tazobactam.",
keywords = "Antibiotic susceptibility prediction, Escherichia coli, Molecular typing, Whole-genome sequencing",
author = "Ritu Banerjee and Cunningham, {Scott A.} and Stephan Beisken and Posch, {Andreas E.} and Brian Johnston and Johnson, {James R.} and Robin Patel",
note = "Funding Information: R. Patel reports grants from ContraFect, TenNor Therapeutics Limited, Hylomorph, and Shionogi. R. Patel is a consultant to Curetis, Specific Technologies, Next Gen Diagnostics, PathoQuest, Selux Diagnostics, 1928 Diagnostics, PhAST, and Qvella; monies are paid to Mayo Clinic. R. Patel is also a consultant to Netflix. In addition, R. Patel has a patent on Bordetella pertussis/B. parapertussis PCR issued, a patent on a device/method for sonication with royalties paid by Samsung to Mayo Clinic, and a patent on an antibiofilm substance issued. R. Patel receives an editor{\textquoteright}s stipend from IDSA and honoraria from the NBME, Up-to-Date, and the Infectious Diseases Board Review Course. J. R. Johnson has had grants and/or consultancies from Allergan, Cipla/Achaogen, Crucell/Janssen, Melinta, Merck, Shionogi, and Tetraphase. Funding Information: R. Patel and R. Banerjee and the collection of the original isolates were supported, in part, by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award number UM1AI104681. Funding Information: R. Patel reports grants from ContraFect, TenNor Therapeutics Limited, Hylomorph, and Shionogi. R. Patel is a consultant to Curetis, Specific Technologies, Next Gen Diagnostics, PathoQuest, Selux Diagnostics, 1928 Diagnostics, PhAST, and Qvella; monies are paid to Mayo Clinic. R. Patel is also a consultant to Netflix. In addition, R. Patel has a patent on Bordetella pertussis/B. parapertussis PCR issued, a patent on a device/method for sonication with royalties paid by Samsung to Mayo Clinic, and a patent on an antibiofilm substance issued. R. Patel receives an editor's stipend from IDSA and honoraria from the NBME, Up-to-Date, and the Infectious Diseases Board Review Course. J. R. Johnson has had grants and/or consultancies from Allergan, Cipla/Achaogen, Crucell/Janssen, Melinta, Merck, Shionogi, and Tetraphase. Publisher Copyright: {\textcopyright} 2021 American Society for Microbiology",
year = "2021",
month = nov,
doi = "10.1128/AAC.01139-21",
language = "English (US)",
volume = "65",
journal = "Antimicrobial Agents and Chemotherapy",
issn = "0066-4804",
publisher = "American Society for Microbiology",
number = "11",
}