(WO2019222227) Methods for estimating microbial density in specimens by measurement of ribosomal rna 机翻标题: 暂无翻译,请尝试点击翻译按钮。

源语言标题
(WO2019222227) Methods for estimating microbial density in specimens by measurement of ribosomal rna
公开号/公开日
WO2019/222227 / 2019-11-21
申请号/申请日
WOUS2019/032235 / 2019-05-14
发明人
CHURCHILL BERNARDCHURCHMAN SCOTT ADAMHAAKE DAVID ARNOLDHALFORD COLIN WYNNKNAUF ROGERMONTI GABRIELSCOTT VICTORIA;
申请人
MICROBIOTIX UNIVERSITY OF CALIFORNIA;
主分类号
IPC分类号
C07H-021/04 C12Q-001/04 C12Q-001/06 C12Q-001/18 C12Q-001/68 C12Q-001/6888 C12Q-001/689
摘要
(WO2019/222227) A method of determining a bacterial density in a specimen may include the steps of: (a) conducting an RNA assay on the specimen to determine a microbial rRNA concentration, wherein the microbial rRNA concentration is defined as the number of rRNA molecules per volume of the specimen; and (b) converting the rRNA concentration to a bacterial density value.
机翻摘要
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地址
代理人
(WO2019222227) TOMSA, Michael S. ([US])
代理机构
;
优先权号
2018US-62671380
主权利要求
(WO2019/222227) CLAIMS What is claimed is: 1. A method of determining a bacterial density in a specimen, the method comprising:   (a) conducting an RNA assay on the specimen to determine a bacterial rRNA concentration, wherein the bacterial rRNA concentration is defined as the number of rRNA molecules per volume of the specimen; and   (b) converting the rRNA concentration to a bacterial density value. 2. The method described in claim 1 , wherein a pre-determined translation function is used to convert the rRNA concentration to a bacterial density value. 3. The method of claim 1 or 2, the method comprising the further step of:   outputting the bacterial density value in a format that is useful for determining the dilution factor for a phenotypic antimicrobial susceptibility test. 4. The method described in any of claims 1 to 3, wherein the method is free of culturing the specimen. 5. The method described in any of claims 1 to 3, wherein the specimen comprises at least one of a biological material and a culture of biological material. 6. The method described in any one of claims 1 to 5, wherein the rRNA assay produces an assay signal and wherein the bacterial rRNA concentration is based on a linear log-log correlation between the assay signal and an rRNA analyte concentration. 7. The method of any one of claims 1 to 6, wherein the bacterial rRNA concentration is determined by steps comprising:   (a) processing the bacterial rRNA to obtain an rRNA signal;   (b) taking the log of the rRNA signal to obtain an rRNA signakoG; and (c) comparing the rRNA signa oc with a positive control to determine the rRNA concentration of the specimen. 8. The method of claim 7, wherein the rRNA signal is determined using an electrochemical sensor platform, an optical platform, or qRT-PCR. 9. The method of claim 8, wherein the optical platform is an ELISA, magnetic beads, or capture probe array. 10. The method of any of claims 1 -9, wherein the rRNA is processed by steps comprising (a) lysing the specimen to release bacterial rRNA; (b) if necessary, neutralizing the released rRNA; (c) hybridizing the rRNA with capture and detector probes to form one or more capture probe-rRNA-detector probe complexes; and (d) detecting the resulting capture probe-rRNA-detector probe complexes.   1 1. The method of claim 10, wherein the lysis of the bacteria comprises at least one of mechanical lysis, chemical lysis, and a combination of mechanical and chemical lysis. 12. The method of any one of claims 1 to 1 1 , wherein a pre-determined correlation is used to convert the bacterial rRNA concentration to a bacterial density value. 13. The method of claim 12, wherein a slope of a regression line from the pre-determined correlation is used to convert the bacterial rRNA concentration to a bacterial density value. 14. The method of claim 13, wherein the slope of the regression line is a linear function. 15. The method of claim 14, wherein the linear function has a formula y=mx+b, and wherein x in the formula is the bacterial rRNA concentration and y in the formula is the bacterial density value. 16. The method of claim 15, wherein the slope of the regression line is represented by the formula: y=1 79x+3.5. 17. The method of any one of claims 1 to 16, wherein the steps (a) and (b) are completed in less than four (4) hours from the commencement of step (a). 18. The method of any one of claims 1 to 16, wherein the steps (a) and (b) are completed in less than three (3) hours from the commencement of step (a). 19. The method of any one of claims 1 to 16, wherein the steps (a) and (b) are completed in less than two (2) hours from the commencement of step (a). 20. The method of any one of claims 1 to 16, wherein the steps (a) and (b) are completed in less than one (1 ) hour from the commencement of step (a).   21 . The method of any one of claims 1 to 16, wherein the steps (a) and (b) are completed in less than thirty (30) minutes from the commencement of step (a). 22. The method of any one of claims 1 to 16, wherein the steps (a) and (b) are completed in less than fifteen (15) minutes from the commencement of step (a). 23. The method of any one of claims 1 to 22, wherein the specimen contains one bacterial species. 24. The method of any one of claims 1 to 22, wherein the specimen contains more than one bacterial species. 25. The method of any one of claims 1 to 24, wherein bacteria in the specimen have between about 1000 and about 100,000 rRNA copies each. 26. The method of any one of claims 1 to 24, wherein bacteria in the specimen have between about 5000 and about 45,000 rRNA copies each. 27. The method of any one of claims 1 to 26, wherein the bacterial density value is equal to the actual concentration of bacteria in the specimen. 28. The method of any one of claims 1 to 26, wherein the bacterial density value is not equal to the actual concentration of bacteria in the specimen. 29. The method of any one of claims 1 to 28, wherein the specimen is provided by or taken from a mammal. 30. The method of claim 29, wherein the mammal is a human, dog, cat, murine, simian, farm animal, sport animal, or companion animal.   31 . The method of any one of claims 1 to 28, wherein the specimen is a clinical specimen. 32. The method of claim 31 , wherein steps 1 a) and 1 b) are conducted directly on the clinical specimen. 33. The method of claim 32, wherein the clinical specimen comprises a biological material. 34. The method of claim 33, wherein the biological material comprises at least one of urine, blood, blood culture, serum, plasma, saliva, tears, gastric fluids, digestive fluids, stool, mucus, sputum, sweat, earwax, oil, semen, vaginal fluid, glandular secretion, breast milk, synovial fluid, pleural fluid, lymph fluid, amniotic fluid, feces, cerebrospinal fluid, wounds, burns, tissue homogenates and an inoculum derived therefrom that is generated during conventional laboratory testing procedures. 35. A method of determining a relationship between bacterial rRNA concentration and bacterial density in a group of specimens, the method comprising:   (a) conducting a rRNA assay to determine a bacterial rRNA concentration in one or more specimens of a group of specimens, wherein the bacterial rRNA concentration is defined as the number of rRNA molecules per volume of the specimen;   (b) converting the rRNA concentration in each specimen in the group to a bacterial density value; and   (c) correlating the bacterial rRNA concentrations from (a) with the bacterial densities from (b). 36. The method of claim 35, wherein each specimen in the group contains one bacterial specie. 37. The method of claim 35, wherein at least one specimen in the group contains more than one bacterial species. 38. The method of any one of claims 35 to 37, wherein the specimens are provided by or taken from mammals. 39. The method of claim 38, wherein the mammals are humans, dogs, cats, murines, simians, farm animals, sport animals, or companion animals. 40. The method of any one of claims 35 to 39, wherein each specimen in the group comprises a clinical specimens.   41 . The method of claim 40, wherein the clinical specimens are biological material. 42. The method of claim 41 , wherein the biological material comprises at least one of urine, blood, blood culture, serum, plasma, saliva, tears, gastric fluids, digestive fluids, stool, mucus, sputum, sweat, earwax, oil, semen, vaginal fluid, glandular secretion, breast milk, synovial fluid, pleural fluid, lymph fluid, amniotic fluid, feces, cerebrospinal fluid, wounds, burns, tissue homogenates and an inoculum derived therefrom that is generated during conventional laboratory testing procedures. 43. The method of any one of claims 35 to 42, a linear log-log correlation between an assay signal and an rRNA analyte concentration. 44. The method of any one of claims 35 to 43, wherein the bacterial rRNA concentration is determined for each specimen by steps comprising:   (a) processing the bacterial rRNA to obtain an rRNA signal;   (b) taking the log of the rRNA signal to obtain an rRNA signakoG; and   (c) comparing the rRNA signaLoc with a positive control to determine the rRNA concentration. 45. The method of claim 44, wherein the rRNA signal is determined using an electrochemical sensor platform, an optical platform, or a qRT-PCR. 46. The method of claim 45, wherein the optical platform is an ELISA, magnetic beads, or capture probe array. 47. The method of claim 46, wherein the rRNA is processed by steps comprising (a) lysing the specimen to release bacterial rRNA; (b) neutralizing the released rRNA; (c) hybridizing the rRNA with capture and detector probes to form one or more capture probe-rRNA- detector probe complexes; and (d) detecting the resulting capture probe-rRNA-detector probe complexes. 48. The method of claim 47, wherein the lysis of the bacteria is mechanical, chemical, or both mechanical and chemical. 49. The method of any one of claims 35 to 48, wherein the bacterial density of each specimen is determined by plate counts or microscopy. 50. The method of any one of claims 35 to 49, wherein the correlation between the bacterial rRNA concentrations and the bacterial densities is determined by plotting the log 10 of the bacterial rRNA concentration of each specimen against the log 10 of the bacterial density of each specimen.   51 . The method of claim 50, wherein the correlation between the bacterial rRNA concentrations and the bacterial densities has a linear relationship. 52. The method of claim 51 , wherein the linear relationship is represented by the formula: y=1 .79x+3.5, wherein x in the formula is the bacterial rRNA concentration and y in the formula is the bacterial density. 53. A method of determining if a subject has an infection, comprising   (a) conducting a rRNA assay on a clinical specimen to determine a bacterial rRNA concentration, wherein the bacterial rRNA concentration is defined as the number of rRNA molecules per volume of the specimen;   (b) converting the rRNA concentration to a bacterial density value; and   (c) determining a likelihood of infection by comparing the bacterial density value with a predetermined infection threshold value. 54. The method described in claim 53, wherein a pre-determined translation function is used to convert the rRNA concentration to a bacterial density value. 55. The method of claim 53 or 54, the method comprising the further step of: outputting the bacterial density value in a format that is useful for determining the dilution factor for a phenotypic antimicrobial susceptibility test. 56. The method of any one of claims claim 53-55, wherein the method is free of culturing the clinical specimen. 57. The method of any one of claims 53 to 55, wherein the specimen comprises at least one of a biological material and a culture of biological material. 58. The method of any one of claims 53 to 57, wherein a known correlation between actual rRNA concentration and bacterial density is used to convert the bacterial rRNA concentration to a bacterial density value. 59. The method of claim 58, wherein a slope of a regression line from the known correlation between actual rRNA concentration and bacterial density is used to convert the bacterial rRNA concentration to a bacterial density value. 60. The method of claim 59, wherein the slope of the regression line is a linear function.   61 . The method of claim 60, wherein the slope of the regression line has a formula y=mx+b, and wherein x in the formula is the bacterial rRNA concentration and y in the formula is the bacterial density value. 62. The method of any one of claims 60 to 61 , wherein the slope of the regression line is represented by the formula: y=1 79x+3.5. 63. The method of any one of claims 53 to claim 62, wherein an infection is likely if the bacterial density value is greater than or equal to the infection threshold value. 64. The method of any one of claims 53 to 62, wherein an infection is not likely if the bacterial density value is less than the infection threshold value. 65. The method of any one of claims 53 to claim 64, wherein the infection threshold value is 2 standard deviations above background. 66. The method of any one of claims 53 to 65, wherein the infection threshold value is 10,000 CFU/ml. 67. The method of any one of claims 53 to 66, wherein the steps (a) and (b) are completed in less than four (4) hours from the commencement of step (a). 68. The method of any one of claims 53 to 66, wherein the steps (a) and (b) are completed in less than three (3) hours from the commencement of step (a). 69. The method of any one of claims 53 to 66, wherein the steps (a) and (b) are completed in less than two (2) hours from the commencement of step (a). 70. The method of any one of claims 53 to 66, wherein the steps (a) and (b) are completed in less than one (1 ) hour from the commencement of step (a).   71 . The method of any one of claims 53 to 66, wherein the steps (a) and (b) are completed in less than thirty (30) minutes from the commencement of step (a). 72. The method of any one of claims 53 to 66, wherein the steps (a) and (b) are completed in less than fifteen (15) minutes from the commencement of step (a). 73. The method of any one of claims 53 to 72, wherein the clinical specimen contains one bacterial species. 74. The method of any one of claims 53 to 72, wherein the clinical specimen contains more than one bacterial species. 75. The method of any one of claims 53 to 77 wherein bacteria in the specimen have between about 100 and about 100,000 rRNA copies each. 76. The method of any one of claims 53 to 77, wherein bacteria in the specimen have between about 5000 and about 45,000 rRNA copies each. 77. The method of any one of claims 53 to 74, wherein the bacterial density value is equal to the actual concentration of bacteria in the specimen 78. The method of any one of claims 53 to 74, the bacterial density value is not equal to the actual concentration of bacteria in the specimen. 79. The method of any one of claims 53 to 78, wherein the clinical specimen is obtained from a mammal. 80. The method of claim 79, wherein the mammal is at least one of a human, dog, cat, murine, simian, farm animal, sport animal, and a companion animal.   81 . The method of any one of claims 53 to 80, wherein the clinical specimen comprises at least one of urine, blood, blood culture, serum, plasma, saliva, tears, gastric fluids, digestive fluids, stool, mucus, sputum, sweat, earwax, oil, semen, vaginal fluid, glandular secretion, breast milk, synovial fluid, pleural fluid, lymph fluid, amniotic fluid, feces, cerebrospinal fluid, wounds, burns, tissue homogenates and an inoculum derived therefrom that is generated during conventional laboratory testing procedures. 82. The method of any one of claims 53 to 81 , wherein the bacterial rRNA concentration is based on a linear log-log correlation between an assay signal and an rRNA analyte concentration. 83. The method of any one of claims 53 to 82, wherein the bacterial rRNA concentration is determined by steps comprising:   (a) processing the bacterial rRNA to obtain an rRNA signal;   (b) taking the log of the rRNA signal to obtain an rRNA signakoG; and   (c) comparing the rRNA signa oc with a positive control to determine the rRNA concentration. 84. The method of claim 83, wherein the rRNA signal is determined using an electrochemical sensor platform, an optical platform, or a qRT-PCR. 85. The method of claim 84, wherein the optical platform is an ELISA, magnetic beads, or capture probe array. 86. The method of any of claims 53 to 85, wherein the rRNA is processed by steps comprising (a) lysing the specimen to release bacterial rRNA; (b) neutralizing the released rRNA; (c) hybridizing the rRNA with capture and detector probes to form one or more capture probe- rRNA-detector probe complexes; and (d) detecting the resulting capture probe-rRNA- detector probe complexes. 87. The method of claim 86, wherein the lysis of the bacteria is mechanical, chemical, or both mechanical and chemical. 88. A method of determining a dilution factor of a clinical specimen to use in a direct-from- specimen phenotypic antimicrobial susceptibility test, the method comprising:   (a) conducting a rRNA assay on the clinical specimen to determine a bacterial rRNA concentration, wherein the bacterial rRNA concentration is defined as the number of rRNA molecules per volume of the specimen; and   (b) converting the rRNA concentration to a bacterial density value; and.   (c) comparing the bacterial density value to a target inoculation concentration for use in a phenotypic antimicrobial susceptibility test. 89. The method described in claim 88, wherein a pre-determined translation function is used to convert the rRNA concentration to a bacterial density value. 90. The method of claim 88 or 89, wherein when the bacterial density value is greater than the target inoculation concentration.   91 . The method of claim 90, the method comprising the further step of diluting the clinical specimen until the bacterial density value is equal to or less than the target inoculation concentration. 92. The method of claim 88 or 89, wherein when the bacterial density value is equal to or less than the target inoculation concentration. 93. The method of claim 92, comprising the further step of preparing the inoculation. 94. The method of any one of claims 88 to 93, wherein the target inoculation concentration is between about 1x105CFU/ml to about 5x106CFU/ml. 95. The method of any one of claims 88 to 94, wherein the target inoculation concentration is about 5x105CFU/ml. 96. The method of any one of claims 88 to 95, wherein the clinical specimen is diluted with a growth medium. 97. The method of any one of claims 88 to 96, wherein a pre-determined correlation is used to convert the bacterial rRNA concentration to a bacterial density value. 98. The method of claim 12, wherein a slope of a regression line from the pre-determined correlation is used to convert the bacterial rRNA concentration to a bacterial density value 99. The method of claim 98, wherein the slope of the regression line is a linear function. 100. The method of claim 99, wherein the slope of the regression line has a formula y=mx+b, and wherein x in the formula is the bacterial rRNA concentration in the specimen and y in the formula is the bacterial density value. 101. The method of any one of claims 99 to 100, wherein the slope of the regression line is represented by the formula: y=1 79x+3.5. 102. The method of any one of claims 88 to 101 , wherein the steps (a) and (b) are completed in less than four (4) hours from the commencement of step (a). 103. The method of any one of claims 88 to 101 , wherein the steps (a) and (b) are completed in less than three (3) hours from the commencement of step (a). 104. The method of any one of claims 88 to 101 , wherein the steps (a) and (b) are completed in less than two (2) hours from the commencement of step (a). 105. The method of any one of claims 88 to 101 , wherein the steps (a) and (b) are completed in less than one (1 ) hour from the commencement of step (a). 106. The method of any one of claims 88 to 101 , wherein the steps (a) and (b) are completed in less than thirty (30) minutes from the commencement of step (a). 107. The method of any one of claims 88 to 101 , wherein the steps (a) and (b) are completed in less than fifteen (15) minutes from the commencement of step (a). 108. The method of any one of claims 88 to 107, wherein the clinical specimen contains one bacterial species. 109. The method of any one of claims 88 to 107, wherein the clinical specimen contains more than one bacterial species.   1 10. The method of any one of claims 88 to 109, wherein bacteria in the clinical specimen have between about 1000 and about 100,000 rRNA copies each.   1 1 1. The method of any one of claims 88 to 109, wherein bacteria in the clinical specimen have between about 5000 and about 45,000 rRNA copies each.   1 12. The method of any one of claims 88 to 1 1 1 , wherein the bacterial density value is equal to the actual concentration of bacteria in the specimen.   1 13. The method of any one of claims 88 to 1 1 1 , wherein the bacterial density value is not equal to the actual concentration of bacteria in the specimen.   1 14. The method of any one of claims 88 to 1 13, wherein the clinical specimen is provided by or taken from a mammal.   1 15. The method of claim 1 14, wherein the mammal is a human, dog, cat, murine, simian, farm animal, sport animal, or companion animal.   1 16. The method of claim 1 15, wherein the clinical specimen comprises a biological material.   1 17. The method of claim 1 16, wherein the biological material comprises at least one of urine, blood, serum, plasma, saliva, tears, gastric fluids, digestive fluids, stool, mucus, sputum, sweat, earwax, oil, semen, vaginal fluid, glandular secretion, breast milk, synovial fluid, pleural fluid, lymph fluid, amniotic fluid, feces, cerebrospinal fluid, wounds, burns, tissue homogenates and an inoculum derived therefrom that is generated during conventional laboratory testing procedures.   1 18. The method of any one of claims 88 to 1 17, wherein the bacterial rRNA concentration is based on a linear log-log correlation between an assay signal and an rRNA analyte concentration.   1 19. The method of any one of claims 88 to 1 18, wherein the bacterial rRNA concentration is determined by steps comprising:   (a) processing the bacterial rRNA to obtain an rRNA signal;   (b) taking the log of the rRNA signal to obtain an rRNA signakoG; and   (c) comparing the rRNA signaLoc with a positive control to determine the bacterial rRNA concentration. 120. The method of claim 1 19, wherein the rRNA signal is determined using an electrochemical sensor platform, an optical platform, or qRT-PCR. 121. The method of claim 120, wherein the optical platform is an ELISA, magnetic beads, or capture probe array. 122. The method of claim 121 , wherein the rRNA is processed by steps comprising (a) lysing the specimen to release bacterial rRNA; (b) neutralizing the released rRNA; (c) hybridizing the rRNA with capture and detector probes to form one or more capture probe-rRNA- detector probe complexes; and (d) detecting the resulting capture probe-rRNA-detector probe complexes. 123. The method of claim 1222, wherein the lysis of the bacteria comprises at least one of mechanical lysis, chemical lysis and a combination of both mechanical and chemical lysis. 124. A method of determining a microbial density in a specimen, the method comprising:   (a) conducting an RNA assay on the specimen to determine a microbial rRNA concentration, wherein the microbial rRNA concentration is defined as the number of rRNA molecules per volume of the specimen; and   (b) converting the rRNA concentration to a microbial density value. 125. The method described in claim 124, wherein a pre-determined translation function is used to convert the rRNA concentration to a microbial density value. 126. The method of claim 124 or 125, the method comprising the further sept of: outputting the microbial density value in a format that is useful for determining the dilution factor for a direct-from-specimen phenotypic antimicrobial susceptibility test. 127. The method of any of claims 124 to126, wherein the method is free of culturing the specimen. 128. The method of any one of claims 124 to 126, wherein the specimen comprises at least one of a biological material and a culture of biological material. 129. The method of any one of claims 124 to 128, wherein the RNA assay produces an assay signal and wherein the microbial rRNA concentration is based on a linear log-log correlation between the assay signal and an rRNA analyte concentration. 130. The method of any one of claims 124 to 129, wherein the microbial rRNA concentration is determined by steps comprising:   (a) processing the microbial rRNA to obtain an rRNA signal;   (b) taking the log of the rRNA signal to obtain an rRNA signaLoG; and   (c) comparing the rRNA signaLoGwith a positive control to determine the rRNA concentration. 131. The method of claim 130, wherein the rRNA signal is determined using an electrochemical sensor platform, an optical platform, or qRT-PCR. 132. The method of claim 131 , wherein the optical platform is an ELISA, magnetic beads, or capture probe array. 133. The method of any of claims 124 to 132, wherein the rRNA is processed by steps comprising (a) lysing the specimen to release bacterial rRNA; (b) neutralizing the released rRNA; (c) hybridizing the rRNA with capture and detector probes to form one or more capture probe-rRNA-detector probe complexes; and (d) detecting the resulting capture probe-rRNA-detector probe complexes. 134. The method of claim 133, wherein the lysis of the microbes comprises at least one of mechanical lysis, chemical lysis, and a combination of mechanical and chemical lysis. 135. The method of any one of claims 124 to 134, wherein a pre-determined correlation is used to convert the microbial rRNA concentration to a microbial density value. 136. The method of claim 135, wherein a slope of a regression line from the pre-determined correlation is used to convert the microbial rRNA concentration to a microbial density value. 137. The method of claim 136, wherein the slope of the regression line is a linear function. 138. The method of claim 137, wherein the linear function has a formula y=mx+b, and wherein x in the formula is the microbial rRNA concentration and y in the formula is the microbial density value. 139. The method of claim 138, wherein the slope of the regression line is represented by the formula: y=1 79x+3.5. 140. The method of any one of claims 124 to 139, wherein the steps (a) and (b) are completed in less than four (4) hours from the commencement of step (a). 141. The method of any one of claims 124 to 139, wherein the steps (a) and (b) are completed in less than three (3) hours from the commencement of step (a). 142. The method of any one of claims 124 to 139, wherein the steps (a) and (b) are completed in less than two (2) hours from the commencement of step (a). 143. The method of any one of claims 124 to 139, wherein the steps (a) and (b) are completed in less than one (1 ) hour from the commencement of step (a). 144. The method of any one of claims 124 to 139, wherein the steps (a) and (b) are completed in less than thirty (30) minutes from the commencement of step (a) 145. The method of any one of claims 124 to 139, wherein the steps (a) and (b) are completed in less than fifteen (15) minutes from the commencement of step (a). 146. The method of any one of claims 124 to 145, wherein the specimen contains one microbial species. 147. The method of any one of claims 124 to 145, wherein the specimen contains more than one microbial species. 148. The method of any one of claims 124 to 147, wherein microbes in the specimen have between about 1000 and about 100,000 rRNA copies each. 149. The method of any one of claims 124 to 147, wherein microbes in the specimen have between about 5000 and about 45,000 rRNA copies each. 150. The method of any one of claims 124 to 149, wherein the microbial density value is equal to the actual concentration of microbes in the specimen. 151. The method of any one of claims 124 to 149, wherein the microbial density value is not equal to the actual concentration of microbes in the specimen. 152. The method of any one of claims 124 to 151 , wherein the specimen is provided by or taken from a mammal. 153. The method of claim 152, wherein the mammal is a human, dog, cat, murine, simian, farm animal, sport animal, or companion animal. 154. The method of any one of claims 124 to 153, wherein the specimen is a clinical specimen. 155. The method of claim 154, wherein steps 124(a) and 124(b) are conducted directly on the clinical specimen. 156. The method of claim 155, wherein the clinical specimen comprises a biological material. 157. The method of claim 156, wherein the biological material comprises at least one of urine, blood, blood culture, serum, plasma, saliva, tears, gastric fluids, digestive fluids, stool, mucus, sputum, sweat, earwax, oil, semen, vaginal fluid, glandular secretion, breast milk, synovial fluid, pleural fluid, lymph fluid, amniotic fluid, feces, cerebrospinal fluid, wounds, burns, or tissue homogenates and an inoculum derived therefrom that is generated during conventional laboratory testing procedures.
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