Phenotypic Antibiotic Susceptibility Testing at the limit of one bacterial cell

The blood of a septic patient contains only a few bacteria per milliliter. Recently, various techniques have been developed for extracting these few bacteria from a blood sample. Independent of how these bacteria are separated from the blood cells, we want to learn from them how to treat the infection. Here, we describe how a phenotypic Antibiotic Susceptibility Test can be executed with a single bacterial cell by making averages over time instead of populations, if we account for the experimental noise and cell-to-cell variability. We use the method to make preliminary estimates for how long it takes to distinguish a single susceptible from a resistant cell with statistical confidence. We also exemplify how it is possible to sequentially test different antibiotics, or different concentrations of the same antibiotic, on one cell lineage until a susceptible phenotype is detected. The assay can be followed by single-cell species identification using FISH probes.