Instrument and system for rapid microorganism identification and antimicrobial agent susceptibility testing
A system for automated microorganism identification and antibiotic susceptibility testing comprising a reagent cartridge, a reagent stage, a cassette, a cassette, stage, a pipettor assembly, an optical detection system, and a controller is disclosed. The system is designed to dynamically adjust motor idle torque to control heat load and employs a fast focus process for determining the true focus position of an individual microorganism. The system also may quantify the relative abundance of viable microorganisms in a sample using dynamic dilution, and facilitate growth of microorganisms in customized media for rapid, accurate antimicrobial susceptibility testing.
1. A system comprising:
a system controller comprising:
a processor; and
a computer-readable storage medium storing instructions that, when executed by the processor, cause the system controller to perform operations comprising:
extracting three or more subsamples from a sample comprising cells of a species of microorganism;
diluting each subsample using a distinct dilution factor for each subsample;
determining a cell concentration of each diluted subsample;
approximating a non-linear effective dilution curve for the sample using the subsample cell concentrations and the distinct dilution factors;
determining from the non-linear effective dilution curve a target dilution factor usable in diluting the sample to a target cell concentration; and
diluting a portion of the sample using the determined target dilution factor.
2. The system of claim 1 , wherein the determining a cell concentration of each diluted subsample further comprises a counting of a number of cells present in each diluted sub sample.
3. The system of claim 1 , wherein approximating a non-linear effective dilution curve for the sample further comprises determining an average subsample cell concentration by multiplying each subsample cell concentration by its corresponding sample dilution factor raised to a power of a proportionality constant to obtain a mathematical product, summing the mathematical products to obtain a sum, and dividing the sum by the number of sub samples.
4. The system of claim 1 , wherein the operations performed by the system controller further comprise adjusting the determined target dilution factor with a growth factor associated with the species of microorganism prior to diluting a portion of the sample to the target cell concentration.
5. The system of claim 4 , wherein the growth factor accounts for the rate of growth of the species of microorganism and a rate of nonviable cells in the sample.
6. The system of claim 4 , wherein the growth factor is determined empirically for each microorganism.
7. The system of claim 1 , wherein approximating a non-linear effective dilution curve for the sample comprises plotting dilution test points on an x/y plot, wherein each dilution test point comprises a subsample cell concentration and a corresponding sample dilution factor used to dilute the subsample.
8. The system of claim 7 , wherein approximating a non-linear effective dilution curve for the sample further comprises interpolating between the dilution test points by performing at least one of multiple linear interpolations or multiple spline interpolations between the dilution test points, and creating a model of the non-linear effective dilution curve using the multiple interpolations.
9. The system of claim 8 , wherein interpolating between multiple dilution test points comprises identifying a first of the dilution test points with a subsample cell concentration that, when adjusted by a growth factor associated with the species of microorganism, is less than the target cell concentration; identifying a second of the dilution test points with a subsample cell concentration that, when adjusted by the growth factor, is greater than or equal to the target cell concentration, and using an interpolation between the first and second identified dilution test points to determine the target dilution factor.