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

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Science Translational Medicine  04 Oct 2017:
Vol. 9, Issue 410, eaal3693
DOI: 10.1126/scitranslmed.aal3693

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Rapidly recognizing resistance

Reducing the time required to determine whether a bacterial sample is resistant to an antibiotic could hasten proper treatment of infections. Toward this goal, Schoepp et al. developed an antibiotic susceptibility test that could be performed within 30 min using clinical urine samples. The test uses digital loop-mediated isothermal amplification to measure the amount of nucleic acid markers of antibiotic susceptibility produced by bacteria present within a clinical sample after a brief incubation with an antibiotic. Performing the test on a microfluidic platform enabled single-molecule amplification and quantification in real time, determining Escherichia coli susceptibility comparably to gold standard methods, but in less time.


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.

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