Microfluidics for single-cell study of antibiotic tolerance and persistence induced by nutrient limitation

TL;DR

This paper introduces two innovative microfluidic devices to investigate how spatial and temporal nutrient variations influence bacterial survival and antibiotic tolerance at the single-cell level.

Contribution

The study presents novel microfluidic setups that mimic natural nutrient fluctuations to analyze bacterial responses and tolerance mechanisms.

Findings

Spatial nutrient gradients increase antibiotic tolerance in biofilm-like conditions.

Feast-and-famine cycles promote phenotypic heterogeneity in growth resumption.

Single-cell measurements reveal mechanisms of tolerance induced by nutrient variation.

Abstract

Nutrient limitation is one of the most common triggers of antibiotic tolerance and persistence. Here, we present two microfluidic setups to study how spatial and temporal variation in nutrient availability lead to increased survival of bacteria to antibiotics. The first setup is designed to mimic the growth dynamics of bacteria in spatially structured populations (e.g. biofilms) and can be used to study how spatial gradients in nutrient availability, created by the collective metabolic activity of a population, increase antibiotic tolerance. The second setup captures the dynamics of feast-and-famine cycles that bacteria recurrently encounter in nature, and can be used to study how phenotypic heterogeneity in growth resumption after starvation increases survival of clonal bacterial populations. In both setups, the growth rates and metabolic activity of bacteria can be measured at the single-cell level. This is useful to build a mechanistic understanding of how spatiotemporal variation in nutrient availability triggers bacteria to enter phenotypic states that increase their tolerance to antibiotics.