Digital microbiology

1. 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.

2. The method of claim 1 , wherein the incubation is performed for a period of time corresponding to:

at least about 2 hours and no more than about 8 hours when the plurality of target microorganisms are bacteria; or

at least about 4 hours and no more than about 12 hours when the plurality of target microorganisms are yeasts.

3. The method of claim 1 , wherein:

a) a third portion of the water-in-oil droplets encapsulate the test antimicrobial at a third concentration;

b) a fourth portion of the water-in-oil droplets encapsulate the test antimicrobial at a fourth concentration;

c) a fifth portion of the water-in-oil droplets encapsulate the test antimicrobial at a fifth concentration; and

d) a sixth portion of the water-in-oil droplets encapsulate the test antimicrobial at a sixth concentration,

wherein the first, second, third, fourth, fifth, and sixth concentrations of the test antimicrobial in the water-in-oil droplets span a concentration range that is both above and below the minimum inhibitory concentration of the test antimicrobial.

4. The method of claim 1 , wherein the test antimicrobial is a β-lactam antibiotic, aminoglycoside antibiotic, glycopeptide antibiotic, macrolide antibiotic, quinolone antibiotic, a fluoroquinolone antibiotic, polyene antifungal, an imidazole antifungal, a triazole antifungal, a thiazole antifungal, an allylamine antifungal, an echinocandins antifungal or a 5-fluorocytosine antifungal.

5. The method of claim 1 , wherein the determining the concentrations of antimicrobial in each water-in-oil droplet is determined according to a gradient.

6. The method of claim 1 , wherein the water-in-oil emulsion droplets have a volume of about 100 pL to about 10 nL.

7. The method of claim 1 , wherein substantially all water-in-oil emulsion droplets contain no more than one microorganism.

8. The method of claim 7 , wherein the water-in-oil emulsion droplets have a volume of about 100 pL to about 10 nL.

9. The method of claim 6 , wherein substantially all water-in-oil emulsion droplets contain no more than one microorganism.