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Rapid pathogen-specific phenotypic antibiotic susceptibility testing using digital LAMP quantification in clinical samples

Schoepp, Nathan G. and Schlappi, Travis S. and Curtis, Matthew S. and Butkovich, Slava S. and Miller, Shelley and Humphries, Romney M. and Ismagilov, Rustem F. (2017) Rapid pathogen-specific phenotypic antibiotic susceptibility testing using digital LAMP quantification in clinical samples. Science Translational Medicine, 9 (410). Art. No. eaal3693. ISSN 1946-6234. http://resolver.caltech.edu/CaltechAUTHORS:20161213-131157930

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Abstract

Rapid antimicrobial susceptibility testing (AST) is urgently needed for informing treatment decisions and preventing the spread of antimicrobial resistance resulting from the misuse and overuse of antibiotics. To date, no phenotypic AST exists that can be performed within a single patient visit (30 min) directly from clinical samples. We show that AST results can be obtained by using digital nucleic acid quantification to measure the phenotypic response of Escherichia coli present within clinical urine samples exposed to an antibiotic for 15 min. We performed this rapid AST using our ultrafast (~7 min) digital real-time loop-mediated isothermal amplification (dLAMP) assay [area under the curve (AUC), 0.96] and compared the results to a commercial (~2 hours) digital polymerase chain reaction assay (AUC, 0.98). The rapid dLAMP assay can be used with SlipChip microfluidic devices to determine the phenotypic antibiotic susceptibility of E. coli directly from clinical urine samples in less than 30 min. With further development for additional pathogens, antibiotics, and sample types, rapid digital AST (dAST) could enable rapid clinical decision-making, improve management of infectious diseases, and facilitate antimicrobial stewardship.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1126/scitranslmed.aal3693 DOIArticle
http://stm.sciencemag.org/content/9/410/eaal3693PublisherArticle
http://www.sciencetranslationalmedicine.org/cgi/content/full/9/410/eaal3693/DC1?_ga=2.93566111.307320353.1507216798-2046127699.1503951604PublisherSupplementary Materials
ORCID:
AuthorORCID
Ismagilov, Rustem F.0000-0002-3680-4399
Alternate Title:Thirty minute Pathogen-specific Phenotypic Antibiotic Susceptibility Test Directly from Clinical Samples Using Digital LAMP Quantification, 30 min Pathogen-specific Phenotypic Antibiotic Susceptibility Test Directly from Clinical Samples Using Digital LAMP Quantification
Additional Information:© 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Submitted 16 December 2016; Resubmitted 30 June 2017; Accepted 5 September 2017; Published 4 October 2017. We thank N. Shelby for contributions to manuscript writing and editing, M. Lee at the Clinical Microbiology Laboratory at UCLA for assistance with clinical sample and data acquisition, SlipChip Corp. for providing injection-molded SlipChips for dLAMP quantification, and W. Liu and D. Capule of SlipChip Corp. for providing technical assistance and expertise. Funding: This research was supported by the Defense Advanced Research Projects Agency (DARPA) Cooperative Agreement HR0011-11-2-0006, NIH grant R01EB012946, a Burroughs Wellcome Fund Innovation in Regulatory Science award, an NIH National Research Service Award (NRSA) (5T32GM07616NSF) to N.G.S., and a grant from the Joseph J. Jacobs Institute for Molecular Engineering for Medicine. Author contributions: The order of co-first authors was determined by coin toss. T.S.S., N.G.S., and R.F.I. contributed to the design and/or interpretation of the reported experiments or results. T.S.S., N.G.S., M.S.C., S.S.B., and R.F.I. contributed to the acquisition and/or analysis of the data. T.S.S., N.G.S., R.M.H., and R.F.I. contributed to the drafting and/or revising of the manuscript. M.S.C. was primarily responsible for real-time imaging acquisition and analysis. S.M. and R.M.H. were primarily responsible for acquiring clinical samples and performing gold standard broth microdilution ASTs. R.F.I. and R.M.H. contributed administrative, technical, and supervisory support. Competing interests: R.F.I., T.S.S., M.S.C., and N.G.S. are inventors on a patent (PCT/US2015/059344) filed by Caltech and SlipChip Corp. and on provisional patent applications 62/399,196 and 62/460,625 filed by Caltech that cover devices and methods for rapid digital antibiotic susceptibility testing. R.F.I. has a financial interest in SlipChip Corp. and is a consultant for SlipChip Corp. Data and materials availability: Requests for additional information should be addressed to R.F.I. (rustem.admin@caltech.edu).
Funders:
Funding AgencyGrant Number
Defense Advanced Research Projects Agency (DARPA)HR0011-11-2-0006
NIHR01EB012946
Burroughs Wellcome FundUNSPECIFIED
NIH5T32GM07616NSF
Joseph J. Jacobs Institute for Molecular Engineering for MedicineUNSPECIFIED
Record Number:CaltechAUTHORS:20161213-131157930
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20161213-131157930
Official Citation:N. G. Schoepp, T. S. Schlappi, M. S. Curtis, S. S. Butkovich, S. Miller, R. M. Humphries, R. F. Ismagilov, Rapid pathogen-specific phenotypic antibiotic susceptibility testing using digital LAMP quantification in clinical samples. Sci. Transl. Med. 9, eaal3693 (2017)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:72778
Collection:CaltechAUTHORS
Deposited By: Katherine Johnson
Deposited On:05 Oct 2017 16:04
Last Modified:05 Oct 2017 16:04

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