Phenotypic Antibiotic Susceptibility Testing at the limit of one bacterial cell

Abstract

The blood of a patient with bacteremia contains only a few bacteria per milliliter. Recently, techniques have been developed for extracting these few bacteria from whole blood. Here, we evaluate if a phenotypic Antibiotic Susceptibility Test (AST) can be performed on a single bacterial cell by monitoring changes in its phenotypic distributions sampled over time rather than across populations, while also accounting for experimental noise and cell-to-cell variability. We use the method to estimate the time required to correctly classify single susceptible or resistant bacteria when treated with antibiotics that affect growth, cell division, or cause lysis. We find that due to heterogeneous single cell responses, it is necessary to consider all bacteria close to the susceptibility breakpoint as resistant. However, it is possible to follow up resistance calls by sequentially exposing the cell or its lineage to new antibiotics until a susceptible phenotype is detected.