microfluidic antibiotic susceptibility test

Microfluidic-assisted analysis of antibiotic susceptibility for mixed samples


“Antimicrobial resistance is an increasing problem on a global scale. Rapid antibiotic susceptibility testing (AST) is urgently needed in the clinic to enable personalized prescriptions in high-resistance environments and to limit the use of broad-spectrum drugs. Current rapid phenotypic AST methods do not include species identification (ID), leaving time-consuming plating or culturing as the only available option when ID is needed to make the sensitivity call. Here we describe a method to perform phenotypic AST at the single-cell level in a microfluidic chip that allows subsequent genotyping by in situ FISH. By stratifying the phenotypic AST response on the species of individual cells, it is possible to determine the susceptibility profile for each species in a mixed sample in 2 h. In this proof-of-principle study, we demonstrate the operation with four antibiotics and mixed samples with combinations of seven species.

a A cartoon of the microfluidics setup with the mixed species loaded on the chip. b Time-lapse phase-contrast images of the cells in the traps when grown in media with (top) and without (bottom) antibiotics. c Fluorescence images of the bacteria with ssDNA probes targeting the ribosomal RNA of specific bacteria for species identification. d Analysis of time-lapse stacks and species ID using deep learning for segmenting and tracking cells. e Detection of AST profiles for individual pathogens at a given antibiotic concentration. Part of Fig. 1a created using www.biorender.com.” Reproduced under a Creative Commons Attribution 4.0 International License from Kandavalli, V., Karempudi, P., Larsson, J. et al. Rapid antibiotic susceptibility testing and species identification for mixed samples. Nat Commun 13, 6215 (2022). https://doi.org/10.1038/s41467-022-33659-1.


Figures and the abstract are reproduced from N. Pacocha, M. Zapotoczna, K. Makuch, J. Bogusławski and P. Garstecki, Lab Chip, 2022, Advance Article , DOI: 10.1039/D2LC00234E under a Creative Commons Attribution 4.0 International License.

Read the original article: Rapid antibiotic susceptibility testing and species identification for mixed samples