Digital microbiology

A method for determining the presence or absence of a microorganism in a sample, the method comprising:

• i) encapsulating a sample in a plurality of water-in-oil emulsion droplets wherein the water-in-oil emulsion droplets further encapsulate a microbiological growth medium;
• ii) incubating the plurality of water-in-oil emulsion droplets at a temperature permissive of microbiological growth, and for a period of time sufficient to allow the target microorganisms to go through 5 to 45 doubling times;
• iii) measuring autofluorescence, turbidity, an amount of a labeled microorganism binding agent and/or an intercalating dye in each of the water-in-oil emulsion droplets and identifying water-in-oil emulsion droplets comprising target microorganisms on the basis of autofluorescence, turbidity, signal of binding agent bound to the microorganism, and/or the presence of intercalating dye in the nucleic acids of the microorganism;
• and
• iv) responsive to identifying the target microorganism in at least one water-in-oil emulsion droplet, determining that the target microorganism is present in the sample, wherein the target microorganisms are selected from bacteria, yeasts and molds and wherein the incubating step is performed for a period of time corresponding to:
• at least about 4 hours and no more than about 16 hours when the target microorganisms are bacteria;
• at least about 6 hours and no more than about 12 hours when the target microorganisms are yeasts;
• and
• at least about 8 hours and no more than about 36 hours when the target microorganisms are molds.