HIGH CONFIDENCE IN POSITIVE STATUS DETERMINATION

• US 20110029252A1
• Filed: 02/19/2008
• Published: 02/03/2011
• Est. Priority Date: 02/19/2008
• Status: Active Grant

• Current Assignee: Becton, Dickinson & Co
• Original Assignee: Becton, Dickinson & Co
• Inventors: Beaty, Patrick Shawn
• Granted Patent: US 10,337,046 B2
• Time in Patent Office: Days
• US Class Current: 702/19
• CPC Class Codes: C12Q 1/04 Determining presence or kind of microorganism; Use of selective media for testing antibiotics or bacteriocides; Compositions containing a chemical indicator therefor C12Q1/6897 takes precedence

Abstract

Systems, methods, and apparatus for determining whether a culture in a vessel contains a plurality of microorganisms are provided. A normalization relative value is calculated for each respective measurement of a biological state of the culture between (i) the respective measurement and (ii) an initial biological state. For each fixed interval of time points, a derivative of the normalization relative values in the interval of time points is calculated, thereby forming a plurality of rate transformation values. For each set of rate transformation values in the plurality of rate transformation values, a measure of central tendency of the values in the set is computed, thereby forming a plurality of average relative transformation values. A determination whether the culture contains the microorganisms is made based on whether any calculated average relative transformation value exceeds a first threshold or whether an extent of growth exhibited by the culture exceeds a second threshold.

Claims

1. A method of determining whether a culture in a vessel contains a plurality of microorganisms, the method comprising:

(A) calculating a normalization relative value for each respective measurement in a plurality of measurements of a biological state of the culture in the vessel, taken at different time points between a first time point and a second time point, between (i) the respective measurement and (ii) an initial biological state of the culture taken at an initial time point, thereby forming a plurality of normalization relative values;

(B) determining, for each respective predetermined fixed interval of time points between the first time point and the second time point, a first derivative of the normalization relative values for measurements of the biological state in the respective predetermined fixed interval of time points, thereby forming a plurality of rate transformation values, wherein the plurality of rate transformation values comprises a plurality of sets of rate transformation values, wherein each respective set of rate transformation values in the plurality of sets of rate transformation values is for a different set of contiguous time points between the first time point and the second time point;

(C) computing, for each respective set of rate transformation values in the plurality of sets of rate transformation values, an average relative transformation value as a measure of central tendency of each of the rate transformation values in the respective set of rate transformation values, thereby computing a plurality of average relative transformation values;

(D) obtaining (i) a first result based on a determination of whether any average relative transformation value in the plurality of average relative transformation values exceeds a first threshold value or (ii) a second result based on a determination of whether an extent of growth exhibited by the culture exceeds a second threshold value; and

(E) using the first result or the second result to determine whether the culture in the vessel contains the plurality of microorganisms.

2. The method of claim 1, the method further comprising:

(F) outputting the first result, the second result, or a determination of whether the culture in the vessel contains the plurality of microorganisms to a user interface device, a monitor, a computer-readable storage medium, a computer-readable memory, or a local or remote computer system;

or displaying the first result, the second result, or the determination of whether the culture in the vessel contains the plurality of microorganisms.

3. The method of claim 1, wherein the first time point is five or more minutes after the initial time point and the final time point is thirty or more hours after the initial time point.

4. The method of claim 1, wherein the first time point is between 0.5 hours and 3 hours after the initial time point and the final time point is between 4.5 hours and twenty hours after the initial time point.

5. The method of claim 1, wherein the measure of central tendency of the rate transformation values in a first set of rate transformation values in the plurality of sets of rate transformation values comprises:

a geometric mean of each of the rate transformation values in the first set of rate transformation values,

an arithmetic mean of each of the rate transformation values in the first set of rate transformation values,

a median of each of the rate transformation values in the first set of rate transformation values, or

a mode of each of the rate transformation values in the first set of rate transformation values.

6. The method of claim 1, wherein the measurements in the plurality of measurements of the biological state of the culture are each taken of the culture at a periodic time interval between the first time point and the second time point.

7. The method of claim 6, wherein the periodic time interval is an amount of time between one minute and twenty minutes.

8. The method of claim 6, wherein the periodic time interval is an amount of time between five minutes and fifteen minutes.

9. The method of claim 1, wherein the initial biological state of the culture is determined by a fluorescence output of a sensor that is in contact with the culture.

10. The method of claim 9, wherein the amount of fluorescence output of the sensor is affected by CO₂ concentration, O₂ concentration, or pH.

11. The method of claim 1, wherein between 10 and 50,000 measurements of the biological state of the culture in the vessel are in the plurality of measurements of the biological state of the culture.

12. The method of claim 1, wherein between 100 and 10,000 measurements of the biological state of the culture in the vessel are in the plurality of measurements of the biological state of the culture.

13. The method of claim 1, wherein between 150 and 5,000 measurements of the biological state of the culture in the vessel are in the plurality of measurements of the biological state of the culture.

14. The method of claim 1, wherein each respective predetermined fixed interval of time points of step (B) consists of each of the rate transformation values for time points in a time window between the first time point and the second time point, and wherein the time window is a period of time that is between twenty minutes and ten hours.

15. The method of claim 1, wherein each respective predetermined fixed interval of time points of step (B) consists of the rate transformation values for all time points in a time window between the first time point and the second time point in which a biological state of the culture in the vessel was measured, and wherein a duration of the time window is a period of time that is between twenty minutes and two hours.

16. The method of claim 1, wherein each respective predetermined fixed interval of time points of step (B) consists of the rate transformation values for all time points in a time window between the first time point and the second time point in which a biological state of the culture in the vessel was measured, and wherein a duration of the time window is a period of time that is between thirty minutes and ninety minutes.

17. The method of claim 1, wherein each set of rate transformation values in the plurality of rate transformation values consists of between four and twenty contiguous rate transformation values.

18. The method of claim 1, wherein each set of rate transformation values in the plurality of rate transformation values consists of between five and fifteen contiguous rate transformation values.

19. The method of claim 1, wherein there are between five and five hundred average relative transformation values in the plurality of average relative transformation values.

20. The method of claim 1, wherein there are between twenty and one hundred average relative transformation values in the plurality of average relative transformation values.

21. The method of claim 1, wherein a volume of the culture is between 1 ml and 40 ml.

22. The method of claim 1, wherein a volume of the culture is between 2 ml and 10 ml.

23. The method of claim 1, wherein the vessel contains a sensor composition in fluid communication with the culture, wherein the sensor composition comprises a luminescent compound that exhibits a change in luminescent property, when irradiated with light containing wavelengths that cause said luminescent compound to luminesce, upon exposure to oxygen, wherein the presence of the sensor composition is non-destructive to the culture and wherein the initial biological state of the culture is measured by

irradiating said sensor composition with light containing wavelengths that cause said luminescent compound to luminesce;

and

observing the luminescent light intensity from said luminescent compound while irradiating said sensor composition with said light.

24. The method of claim 23, wherein said luminescent compound is contained within a matrix that is relatively impermeable to water and non-gaseous solutes, but which has a high permeability to oxygen.

25. The method of claim 24, wherein said matrix comprises rubber or plastic.

26. The method of claim 1, wherein the extent of growth (EG) is the maximum normalization relative value in the plurality of normalization relative values.

27. The method of claim 1, wherein the extent of growth is determined by the equation:

EG=NR<sub>after—

growth</sub>−

NR<sub>minimum—

growth</sub>

wherein,

NR<sub>after—

growth</sub> is a normalization relative value in the plurality of normalization relative values that was used in the calculation of (i) the first average relative transformation value following a maximum average relative transformation value, (ii) a maximum average relative transformation value, or (iii) a first average relative transformation value preceding the maximum average relative transformation value in the plurality of average relative transformation values; and

NR<sub>minimum—

growth</sub> is a normalization relative value in the plurality of normalization relative values that was used in the calculation of the first average relative transformation value to achieve a third threshold value.

28. The method of claim 27, wherein the third threshold value is a value between 5 and 100.

29. The method of claim 27, wherein the third threshold value is a value between 25 and 75.

30. The method of claim 1, wherein the culture in the vessel is deemed to contain the plurality of microorganisms when an average relative transformation value in the plurality of average relative transformation values exceeds said first threshold value.

31. The method of claim 1, wherein the culture in the vessel is deemed to contain the plurality of microorganisms when the extent of growth exhibited by the culture exceeds said second threshold value.

32. The method of claim 1, wherein the using step (E) determines that the culture is contains the plurality of microorganisms, and wherein the plurality of microorganisms is bacteria in the Enterobacteriaceae family.

33. The method of claim 1, wherein the using step (E) determines that the culture contains the plurality of microorganisms, and wherein the plurality of microorganisms is (i) Enterobacteriaceae, (ii) Staphylococcaceae, (iii) Streptococcus, or (iv) Acinetobacter.

34. The method of claim 1, wherein the using step (E) determines that the culture contains the plurality of microorganisms, and wherein the plurality of microorganisms is Alishewanella, Alterococcus, Aquamonas, Aranicola, Arsenophonus, Azotivirga, Blochmannia, Brenneria, Buchnera, Budvicia, Buttiauxella, Cedecea, Citrobacter, Dickeya, Edwardsiella, Enterobacter, Erwinia, Escherichia, Ewingella, Griimontella, Hafnia, Klebsiella, Kluyvera, Leclercia, Leminorella, Moellerella, Morganella, Obesumbacterium, Pantoea, Pectobacterium, Candidatus Phlomobacter, Photorhabdus, Plesiomonas, Pragia, Proteus, Providencia, Rahnella, Raoultella, Salmonella, Samsonia, Serratia, Shigella, Sodalis, Tatumella, Trabulsiella, Wigglesworthia, Xenorhabdus, Yersinia, or Yokenella.

35. The method of claim 1, wherein the using step (E) determines that the culture contains the plurality of microorganisms, and wherein the plurality of microorganisms is a single species of Staphylococcaceae selected from the group consisting of Staphylococcus aureus, Staphylococcus caprae, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus lugdunensis, Staphylococcus pettenkoferi, Staphylococcus saprophyticus, Staphylococcus warneri, and Staphylococcus xylosus.

36. The method of claim 1, wherein the using step (E) determines that the culture contains the plurality of microorganisms, and wherein the plurality of microorganisms is Staphylococcus aureus or coagulase negative staphylococci.

37. The method of claim 1, wherein the using step (E) determines that the culture contains the plurality of microorganisms, and wherein the plurality of microorganisms are a single species of Streptococcus selected from the group consisting of S. agalactiae, S. bovis, S. mutans, S. pneumoniae, S. pyogenes, S. salivarius, S. sanguinis, S. suis, Streptococcus viridans, and Streptococcus uberis.

38. The method of claim 1, wherein the using step (E) determines that the culture contains the plurality of microorganisms, and wherein the plurality of microorganisms is aerobic.

39. The method of claim 1, wherein the using step (E) determines that the culture contains the plurality of microorganisms, and wherein the plurality of microorganisms is anaerobic.

40. The method of claim 1, wherein the initial biological state of the culture is measured by a colorimetric means, a fluorometric means, a nephelometric means, or an infrared means.

41. The method of claim 1, wherein each biological state in the plurality of measurements of the biological state is determined by a colorimetric means, a fluorometric means, a nephelometric means, or an infrared means.

42. The method of claim 1, wherein the culture is a blood culture from a subject.

43. The method of claim 1, wherein the obtaining step (D) obtains the first result and the using step (E) uses the first result to determine whether the culture contains the plurality of organisms.

44. The method of claim 1, wherein the obtaining step (D) obtains the second result and the using step (E) uses the second result to determine whether the culture contains the plurality of organisms.

45. The method of claim 1, wherein the obtaining step (D) obtains the first result and the second result and the using step (E) uses the first result and the second result to determine whether the culture contains the plurality of organisms.

46. The method of claim 1, wherein the first threshold value is a value between 50 and 200.

47. The method of claim 1, wherein the first threshold value is a value between 75 and 125.

48. The method of claim 1, wherein the second threshold value is a value between 112 and 140.

49. The method of claim 1, wherein the second threshold value is a value between 113 and 118.

50. The method of claim 1, wherein the extent of growth is determined by the equation:

EG=NR_max−

NR_initial

wherein,

NR_max is the maximum normalization relative value in the plurality of normalization relative values; and

NR_initial is a measurement of the initial biological state.

51. The method of claim 50, wherein the second threshold value is a value between 12 and 40.

52. The method of claim 50, wherein the second threshold value is a value between 13 and 18.

53. An apparatus for determining whether a culture in a vessel contains a plurality of microrganisms, the apparatus comprising a processor and a memory, coupled to the processor, the memory comprising:

a first threshold value;

a second threshold value; and

a culture determination module comprising;

(A) electronically encoded instructions for calculating a normalization relative value for each respective measurement in a plurality of measurements of a biological state of the culture in the vessel, taken at different time points between a first time point and a second time point, between (i) the respective measurement and (ii) an initial biological state of the culture taken at an initial time point, thereby forming a plurality of normalization relative values;

(B) electronically encoded instructions for determining, for each respective predetermined fixed interval of time points between the first time point and the second time point, a first derivative of the normalization relative values for measurements of the biological state in the respective predetermined fixed interval of time points, thereby forming a plurality of rate transformation values, wherein the plurality of rate transformation values comprises a plurality of sets of rate transformation values, wherein each respective set of rate transformation values in the plurality of sets of rate transformation values is for a different set of contiguous time points between the first time point and the second time point;

(C) electronically encoded instructions for computing, for each respective set of rate transformation values in the plurality of sets of rate transformation values, an average relative transformation value as a measure of central tendency of each of the rate transformation values in the respective set of rate transformation values, thereby computing a plurality of average relative transformation values;

(D) electronically encoded instructions for obtaining (i) a first result based on a determination of whether any average relative transformation value in the plurality of average relative transformation values exceeds a first threshold value or (ii) a second result based on a determination of whether an extent of growth exhibited by the culture exceeds a second threshold value; and

(E) electronically encoded instructions for using the first result or the second result to determine whether the culture in the vessel contains the plurality of microorganisms.

54. A computer-readable medium storing a computer program product for determining whether a culture in a vessel contains a plurality of microorganisms, executable by a computer, wherein the computer program product comprises:

a first threshold value;

a second threshold value; and

a culture determination module comprising;

(A) electronically encoded instructions for calculating a normalization relative value for each respective measurement in a plurality of measurements of a biological state of the culture in the vessel, taken at different time points between a first time point and a second time point, between (i) the respective measurement and (ii) an initial biological state of the culture taken at an initial time point, thereby forming a plurality of normalization relative values;

(B) electronically encoded instructions for determining, for each respective predetermined fixed interval of time points between the first time point and the second time point, a first derivative of the normalization relative values for measurements of the biological state in the respective predetermined fixed interval of time points, thereby forming a plurality of rate transformation values, wherein the plurality of rate transformation values comprises a plurality of sets of rate transformation values, wherein each respective set of rate transformation values in the plurality of sets of rate transformation values is for a different set of contiguous time points between the first time point and the second time point;

(C) electronically encoded instructions for computing, for each respective set of rate transformation values in the plurality of sets of rate transformation values, an average relative transformation value as a measure of central tendency of each of the rate transformation values in the respective set of rate transformation values, thereby computing a plurality of average relative transformation values;

(D) electronically encoded instructions for obtaining (i) a first result based on a determination of whether any average relative transformation value in the plurality of average relative transformation values exceeds a first threshold value or (ii) a second result based on a determination of whether an extent of growth exhibited by the culture exceeds a second threshold value; and

(E) electronically encoded instructions for using the first result or the second result to determine whether the culture in the vessel contains the plurality of microorganisms.

55. A method of determining whether a culture in a vessel contains a plurality of microorganisms, the method comprising:

(A) obtaining a plurality of measurements of the biological state of the culture, each measurement in the plurality of measurements taken at a different time point between a first time point and a second time point;

(B) determining, for each respective predetermined fixed interval of time points between the first time point and the second time point, a first derivative of the measurements of the biological state in the respective predetermined fixed interval of time points, thereby forming a plurality of rate transformation values, wherein the plurality of rate transformation values comprises a plurality of sets of rate transformation values, wherein each respective set of rate transformation values in the plurality of sets of rate transformation values is for a different set of contiguous time points between the first time point and the second time point;

(C) computing, for each respective set of rate transformation values in the plurality of sets of rate transformation values, an average relative transformation value as a measure of central tendency of each of the rate transformation values in the respective set of rate transformation values, thereby computing a plurality of average relative transformation values;

(D) obtaining (i) a first result based on a determination of whether any average relative transformation value in the plurality of average relative transformation values exceeds a first threshold value or (ii) a second result based on a determination of whether an extent of growth exhibited by the culture exceeds a second threshold value; and

(E) using the first result or the second result to determine whether the culture in the vessel contains the plurality of microorganisms.