title: Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility after only 15 Minutes of Antibiotic Exposure.
abstract: Rapid antimicrobial susceptibility testing (AST) would decrease misuse and overuse of antibiotics. The "holy grail" of AST is a phenotype-based test that can be performed within a doctor visit. Such a test requires the ability to determine a pathogen's susceptibility after only a short antibiotic exposure. Herein, digital PCR (dPCR) was employed to test whether measuring DNA replication of the target pathogen through digital single-molecule counting would shorten the required time of antibiotic exposure. Partitioning bacterial chromosomal DNA into many small volumes during dPCR enabled AST results after short exposure times by 1) precise quantification and 2) a measurement of how antibiotics affect the states of macromolecular assembly of bacterial chromosomes. This digital AST (dAST) determined susceptibility of clinical isolates from urinary tract infections (UTIs) after 15 min of exposure for all four antibiotic classes relevant to UTIs. This work lays the foundation to develop a rapid, point-of-care AST and strengthen global antibiotic stewardship.
authors.affiliation: Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA.
authors.forename: Nathan G
authors.identifier: 0000-0002-2406-3693
authors.initials: NG
authors.lastname: Schoepp
authors.affiliation: Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA.
authors.forename: Eugenia M
authors.identifier: 0000-0003-3620-4884
authors.initials: EM
authors.lastname: Khorosheva
authors.affiliation: Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA.
authors.forename: Travis S
authors.initials: TS
authors.lastname: Schlappi
authors.affiliation: Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA.
authors.forename: Matthew S
authors.identifier: 0000-0002-9662-3266
authors.initials: MS
authors.lastname: Curtis
authors.affiliation: Pathology and Laboratory Medicine, University of California, Los Angeles, 10888 Le Conte Avenue, Brentwood Annex, Los Angeles, CA, 90095, USA.
authors.forename: Romney M
authors.initials: RM
authors.lastname: Humphries
authors.affiliation: Pathology and Laboratory Medicine, University of California, Los Angeles, 10888 Le Conte Avenue, Brentwood Annex, Los Angeles, CA, 90095, USA.
authors.forename: Janet A
authors.initials: JA
authors.lastname: Hindler
authors.affiliation: Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA. rustem.admin@caltech.edu.
authors.forename: Rustem F
authors.identifier: 0000-0002-3680-4399
authors.initials: RF
authors.lastname: Ismagilov
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D020090:Chromosome Segregation / Q000187:drug effects*; D004261:DNA Replication / Q000187:drug effects*; D004269:DNA, Bacterial / Q000187:drug effects* / Q000235:genetics; D016133:Polymerase Chain Reaction
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial
keywords: DNA replication; analytical methods; antibiotics; polymerase chain reaction; susceptibility