Method for microfluidic quantification, growth monitoring and separation of microorganisms in droplets

A method for detecting and/or quantifying at least one microorganism in a sample, the method comprising the following steps:

• (i) encapsulating the sample into a plurality of water-in-oil emulsion droplets using a microfluidic device, said water-in-oil emulsion droplets comprising a growth medium, a fluorescent dye and a fraction of the sample,
• wherein the fluorescent dye is non-exchangeable between the droplets and does not interact with the microorganism, and the fluorescent dye is not affected by the growth of the microorganism;
• (ii) incubating the plurality of droplets at a temperature and for a period of time sufficient to allow at least one microorganism to grow for at least two doubling times;
• (iii) measuring the fluorescence in each individual droplet, wherein droplets comprising no microorganism have a basal fluorescence intensity and droplets comprising a microorganism have a fluorescence intensity at least equal to 1.001 times the basal fluorescence intensity;
• (iv) detecting and/or quantifying at least one population of droplets comprising a microorganism, thereby determining the presence and/or the amount of at least one microorganism in the sample.