Compositions and methods for disease diagnosis using single cell analysis

A method for detecting and characterizing microbes in a sample, the method comprising:

• (a) contacting a sample containing microbes with at least one reporter forming a sample mixture, wherein optical emissions of the reporter indicate microbial cell viability;
• (b) dividing the sample mixture into at least two portions, wherein a first portion is treated with an antimicrobial drug forming a test portion and the second portion is a control portion;
• (c) partitioning the test portion and the control portion into two-dimensional arrays of sub-nanoliter droplets, wherein a portion of the droplets have one microbe or one natural microbe aggregate per droplet;
• (d) incubating the sub-nanoliter droplets for a period of time at a specified temperature or series of temperatures;
• (e) monitoring optical emissions of the sub-nanoliter droplets during the incubation time;
• (f) constructing an optical emission waveform for each sub-nanoliter droplet based on the optical emissions of the sub-nanoliter droplet over time resulting in a sub-nanoliter droplet waveform;
• (g) identifying the microbes in the sample using the sub-nanoliter droplet waveforms;
• and
• (h) determining susceptibility of the microbes in the sample to the antimicrobial drug by comparing waveforms for sub-nanoliter droplets of the treated portion to waveforms of the sub-nanoliter droplets of the control portion, wherein differences in the sub-nanoliter droplet waveforms between the droplets of the treated portion to droplets of the control portion indicates susceptibility to the antimicrobial.