Digital microbiology

A method for rapidly assaying a target microorganism for a minimum inhibitory concentration of a test antimicrobial, the method comprising:

• i) encapsulating a plurality of the target microorganisms in a plurality of water-in-oil emulsion droplets,
• wherein the water-in-oil emulsion droplets further encapsulate a microbiological growth medium;
• wherein:
• a) a first portion of the water-in-oil droplets encapsulate the test antimicrobial at a first concentration, or do not encapsulate the test antimicrobial;
• b) a second portion of the water-in-oil droplets encapsulate the test antimicrobial at a second concentration different than the first concentration;
• wherein the target microorganism is a bacterium or a yeast;
• and
• ii) incubating the plurality of water-in-oil emulsion droplets at a temperature permissive of microbiological growth in an absence of the test antimicrobial, and for a period of time sufficient to allow the target microorganisms, if not inhibited by the test antimicrobial, to divide from 5 to 20 times, or more;
• and
• iii) determining from the incubated water-in-oil emulsion droplets by measuring autofluorescence:
• a number of water-in-oil emulsion droplets that have an increase in microorganisms that results in increased autofluorescence, thereby determining a number of positive droplets;
• and
• a number of water-in-oil emulsion droplets that have no increase in microorganisms and no increase in autofluorescence, thereby determining a number of negative droplets;
• iv) determining the number of positive droplets and negative droplets at the tested antimicrobial concentrations;
• thereby assaying the minimum inhibitory concentration of the test antimicrobial.