Microfluidic measurements of the response of an organism to a drug

1. A method, comprising:

providing a first sample comprising a target molecule from a first portion of a population of bacteria and a second sample comprising a target molecule from a second portion of said population of bacteria, wherein the first portion has been treated with an antibiotic for a period of no more than 2 hours, and wherein the second portion has not been treated with the antibiotic;

distributing said first sample among a plurality of first analysis regions;

distributing said second sample among a plurality of second analysis regions;

contacting each of the first and second analysis regions with a reagent for performing a reaction to detect the presence or absence of a threshold number of target molecules in each of the first and second analysis regions, wherein the target molecules comprise a segment of a bacterial chromosome or plasmid, wherein the segment of the bacterial chromosome or plasmid is contacted with the reagent in at least some of the first and second analysis regions; and

detecting the presence or absence of the threshold number of target molecules in each of the first and second analysis regions, wherein the distribution of each sample among the analysis regions is effected such that the threshold number of target molecules is detected in some of the first and second analysis regions and is not detected in some of the first and second analysis regions after said reaction.

2. The method of claim 1 , wherein the threshold number is greater than zero, one, two, three, four, or five.

3. The method of claim 1 , wherein the distribution of each sample among the analysis regions is effected such that at least some of the analysis regions do not have the target molecule, and at least some of the analysis regions have only one target molecule.

4. The method of claim 1 , wherein the distribution of each sample among the analysis regions is effected such that at least one of the analysis regions contains only one target molecule.

5. The method of claim 1 , wherein the first sample comprises said reagent, and wherein contacting the plurality of first analysis regions with the reagent comprises said step of distributing said first sample among said plurality of first analysis regions.

6. The method of claim 1 , wherein the second sample comprises said reagent, and wherein contacting the plurality of second analysis regions with the reagent comprises said step of distributing said second sample among said plurality of second analysis regions.

7. The method of claim 1 , wherein said reaction comprises nucleic acid amplification.

8. The method of claim 1 , wherein the reagent is disposed in a plurality of reagent regions.

9. The method of claim 8 , wherein contacting is effected by placing the plurality of reagent regions in fluid communication with the first or second plurality of analysis regions.

10. The method of claim 9 , wherein contacting comprises effecting relative motion between a substrate comprising the reagent regions with a substrate comprising the first and second plurality of analysis regions.

11. The method of claim 1 , further comprising analyzing the detection of the presence or the absence of the threshold number of target molecules in each plurality of analysis regions to determine a resistance or susceptibility to an antibiotic in the population of bacteria.

12. The method of claim 1 , wherein said detection of the presence or absence of the threshold number of target molecules in each of the first and second analysis regions is performed less than 3 hours, 2 hours, or one hour after the end of exposure of the first sample to the antibiotic.

13. The method of claim 12 , wherein said detection of the presence or absence of the threshold number of target molecules in each of the first and second analysis regions is performed less than 45 minutes, 30 minutes, 15 minutes, or 10 minutes after the end of exposure of the first sample to the antibiotic.

14. The method of claim 1 , wherein said bacteria from said first sample have been treated with antibiotic for a period of no more than 1 hour, no more than 45 minutes, no more than 30 minutes, no more than 15 minutes, or no more than 10 minutes.

15. A method of determining a resistance or susceptibility to an antibiotic in a population of bacteria, comprising:

providing a first sample comprising a target molecule from a first portion of a population of bacteria and a second sample comprising a target molecule from a second portion of said population of bacteria, wherein the first portion has been treated with an antibiotic for a period of no more than 2 hours, and wherein the second portion has not been treated with the antibiotic;

distributing said first sample among a plurality of first analysis regions;

distributing said second sample among a plurality of second analysis regions;

contacting each of the first and second analysis regions with a reagent for performing a reaction to detect the presence or absence of a threshold number of target molecules in each of the first and second analysis regions, wherein the target molecules comprise a segment of a bacterial chromosome or plasmid, wherein the segment of the bacterial chromosome or plasmid is contacted with the reagent in at least some of the first and second analysis regions;

detecting the presence or absence of the threshold number of target molecules in each of the first and second analysis regions, wherein the distribution of each sample among the analysis regions is effected such that the threshold number of target molecules is detected in some of the first and second analysis regions and is not detected in some of the first and second analysis regions after said reaction; and

determining a resistance or susceptibility to said antibiotic in the population of bacteria from the results of said detection in each of the first and second analysis regions.

16. The method of claim 15 , wherein said bacteria from said first sample have been treated with antibiotic for a period of no more than 1 hour, no more than 45 minutes, no more than 30 minutes, no more than 15 minutes, or no more than 10 minutes.

17. The method of claim 15 , wherein said reaction comprises nucleic acid amplification.

18. A method, comprising:

providing a first sample comprising a target analyte from a first portion of a population of cells and a second sample comprising a target analyte from a second portion of said population of cells, wherein the first portion has been treated with a drug for a period of no more than 2 hours, and wherein the second portion has not been treated with the drug;

distributing said first sample among a plurality of first analysis regions;

distributing said second sample among a plurality of second analysis regions;

contacting each of the first and second analysis regions with a reagent for performing a reaction to detect the presence or absence of a threshold number of target analytes in each of the first and second analysis regions, wherein the target analytes comprise a segment of a bacterial chromosome or plasmid, wherein the segment of the bacterial chromosome or plasmid is contacted with the reagent in at least some of the first and second analysis regions; and

detecting the presence or absence of the threshold number of target analytes in each of the first and second analysis regions, wherein the distribution of each sample among the analysis regions is effected such that the threshold number of target analytes is detected in some of the first and second analysis regions and is not detected in some of the first and second analysis regions after said reaction.

19. The method of claim 18 , wherein said cells from said first sample have been treated with said drug for a period of no more than 1 hour, no more than 45 minutes, no more than 30 minutes, no more than 15 minutes, or no more than 10 minutes.

20. The method of claim 18 , wherein said reaction comprises nucleic acid amplification.