METHODS FOR IDENTIFICATION OF SEPSIS-CAUSING BACTERIA

• US 20080146455A1
• Filed: 05/25/2007
• Published: 06/19/2008
• Est. Priority Date: 09/11/2003
• Status: Abandoned Application

• Current Assignee: Ibis Biosciences Incorporated
• Original Assignee: Ibis Biosciences Incorporated
• Inventors: Hofstadler, Steven A., Sampath, Rangarajan, Hall, Thomas A., Jiang, Yun, Harpin, Vanessa
• Application Number:
  US11/754,169
• Publication Number:
  US 20080146455A1
• Time in Patent Office: Days
• US Class Current: 506/8
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: G16B 35/00 ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• CPC Class Codes: G16B 35/20 Screening of libraries
• CPC Class Codes: G16C 20/60 In silico combinatorial chemistry

Abstract

The present invention provides compositions, kits and methods for rapid identification and quantification of sepsis-causing bacteria by molecular mass and base composition analysis.

Claims

1-55. -55. (canceled)

56. A purified oligonucleotide primer pair comprising a forward primer and a reverse primer, each independently between 13 and 35 linked nucleotides in length, said primer pair configured to generate an amplification product between 45 and 200 linked nucleotides in length, said forward primer configured to hybridize with at least 70% complementarity to a first portion of a region defined by nucleotides 649 to 783 of the reverse complement of nucleotide residues 3448565 to 3449386 of Genbank gi number:

49175990, and said reverse primer configured to hybridize with at least 70% complementarity to said second portion of said region.

57. The purified oligonucleotide primer pair of claim 56, wherein said forward primer has at least 70% sequence identity with SEQ ID NO:

309.

58. The purified oligonucleotide primer pair of claim 57, wherein said forward primer comprises at least 80% sequence identity with SEQ ID NO:

309.

59. The purified oligonucleotide primer pair of claim 58, wherein said forward primer comprises at least 90% sequence identity with SEQ ID NO:

309.

60. The purified oligonucleotide primer pair of claim 56, wherein said forward primer comprises 100% sequence identity with SEQ ID NO:

309.

61. The purified oligonucleotide primer pair of claim 56, wherein said reverse primer comprises at least 70% sequence identity with SEQ ID NO:

1458.

62. The purified oligonucleotide primer pair of claim 61, wherein said reverse primer comprises at least 80% sequence identity with SEQ ID NO:

1458.

63. The purified oligonucleotide primer pair of claim 62, wherein said reverse primer comprises at least 90% sequence identity with SEQ ID NO:

1458.

64. The purified oligonucleotide primer pair of claim 56, wherein said reverse primer is SEQ ID NO:

1458.

65. The purified oligonucleotide primer pair of claim 56, wherein at least one of said forward primer and said reverse primer comprises at least one modified nucleobase.

66. The purified oligonucleotide primer pair of claim 65, wherein at least one of said at least one modified nucleobases is a mass modified nucleobase.

67. The purified oligonucleotide primer pair of claim 66, wherein said mass modified nucleobase is 5-Iodo-C.

68. The composition of claim 66, wherein said mass modified nucleobase comprises a molecular mass modifying tag.

69. The purified oligonucleotide primer pair of claim 65, wherein at least one of said at least one modified nucleobases is a universal nucleobase.

70. The purified oligonucleotide primer pair of claim 69, wherein said universal nucleobase is inosine.

71. The purified oligonucleotide primer pair of claim 56, wherein at least one of said forward primer and said reverse primer comprises a non-templated T residue at its 5′

end.

101. A method for identifying at least one sepsis causing bacteria from a sample comprising the steps of:

a. obtaining a sample;

b. contacting at least one nucleic acid from said sample with at least one purified oligonucleotide primer pair from claim 56;

c. performing an amplification reaction, thereby generating at least one amplification product and;

d. analyzing at least one amplification product from step c to identify at least one sepsis causing bacteria in said sample.

102. The method of claim 101 wherein said analyzing step is selected from the group consisting of mass spectrometry analysis, Real Time PCR analysis, sequencing analysis, hybridization analysis, hybridization protection assay analysis and mass array analysis.

103. The method of claim 102 wherein said mass spectrometry analysis is ESI TOF mass spectrometry.

104. The method of claim 102 wherein said mass spectrometry analysis comprises generating molecular mass data for said amplification product.

105. The method of claim 104 further comprising calculating a base composition from said generated molecular mass data.

106. The method of claim 104 further comprising comparing said molecular mass data to a plurality of molecular masses in a database, wherein said plurality of molecular masses are indexed to said oligonucleotide primer pairs and to a plurality of known sepsis causing bacteria, and wherein a match between said generated molecular masses and a member of said plurality of molecular masses identifies at least one sepsis causing bacteria in said sample.

107. The method of claim 105 further comprising comparing said base composition to a plurality of base compositions in a database, wherein said plurality of base compositions are indexed to said primer pairs and to a plurality of known sepsis causing bacteria, and wherein a match between said base composition and a member of said plurality of base compositions identifies at least one sepsis causing bacteria in said sample.

108. The method of claim 106 wherein said at least one sepsis causing bacteria is identified by genus, species, sub-species, serotype or genotype.

109. The method of claim 107 wherein said at least one sepsis causing bacteria is identified by genus, species, sub-species, serotype or genotype.

110. The method of claim 101 wherein said at least one amplification product in step d is substantially purified before analysis.

111. The method of claim 110 wherein said at least one amplification product is substantially purified using a magnetic bead covalently linked with an ion exchange resin.

72. A purified oligonucleotide primer pair comprising a forward primer and a reverse primer, wherein

a. said primers individually comprise between 13 and 35 linked nucleotides,

b. said forward primer has at least 70% sequence identity with SEQ ID NO:

309 and

c. said reverse primer has at least 70% sequence identity with SEQ ID NO;

1458.

73. The purified oligonucleotide primer pair of claim 72, wherein said forward primer comprises at least 80% sequence identity with SEQ ID NO:

309.

74. The purified oligonucleotide primer pair of claim 73, wherein said forward primer comprises at least 90% sequence identity with SEQ ID NO:

309.

75. The purified oligonucleotide primer pair of claim 72, wherein said forward primer comprises 100% sequence identity with SEQ ID NO:

309.

76. The purified oligonucleotide primer pair of claim 72, wherein said reverse primer comprises at least 80% sequence identity with SEQ ID NO:

1458.

77. The purified oligonucleotide primer pair of claim 76, wherein said reverse primer comprises at least 90% sequence identity with SEQ ID NO:

1458.

78. The purified oligonucleotide primer pair of claim 72, wherein said reverse primer is SEQ ID NO:

1458.

79. The purified oligonucleotide primer pair of claim 72, wherein at least one of said forward primer and said reverse primer comprises at least one modified nucleobase.

80. The purified oligonucleotide primer pair of claim 79, wherein at least one of said at least one modified nucleobases is a mass modified nucleobase.

81. The purified oligonucleotide primer pair of claim 80, wherein said mass modified nucleobase is 5-Iodo-C.

82. The oligonucleotide primer of claim 80, wherein said mass modified nucleobase comprises a molecular mass modifying tag.

83. The purified oligonucleotide primer pair of claim 72, wherein at least one of said at least one modified nucleobases is a universal nucleobase.

84. The purified oligonucleotide primer pair of claim 83, wherein said universal nucleobase is inosine.

85. The purified oligonucleotide primer pair of claim 72, wherein at least one of said forward primer and said reverse primer comprises a non-templated T residue at its 5′

end.

86. A kit for identifying a sepsis-causing bacterium, comprising:

i) a first purified oligonucleotide primer pair comprising a forward primer and a reverse primer, each independently between 13 and 35 linked nucleotides in length, said primer pair configured to generate an amplification product that is between 45 and 200 linked nucleotides in length, said forward primer configured to hybridize with at least 70% complementarity to a first portion of a region defined by nucleotides 649 to 783 of the reverse complement of nucleotide residues 3448565 to 3449386 of Genbank gi number;

49175990, and said reverse primer configured to hybridize with at least 70% complementarity to a second portion of said region; and

ii) at least one additional purified primer pair configured to hybridize to a bacterial gene selected from the group consisting of;

16S rRNA, 23S rRNA, tufB, rpoB, valS, rplB, and gyrB.

87. The kit of claim 86, wherein each of said at least one additional primer pairs is a primer pair comprising a forward primer and a reverse primer, said forward primer and said reverse primer each independently between 13 to 35 linked nucleotides in length and each independently having at least 70% sequence identity with the corresponding forward or reverse primers, respectively, of primer pair numbers selected from the group consisting of:

346 (SEQ ID NOs;

202;

1110), 347 (SEQ ID NOs;

560;

1278), 348 (SEQ ID NOs;

706;

895), 349 (SEQ ID NOs;

401;

1156), 360 (SEQ ID NOs;

409;

1434), 361 (SEQ ID NOs;

697;

1398), 2249 (SEQ ID NOs;

430;

1321), 3361 (SEQ ID NOs;

1454;

1468), 354 (SEQ ID NOs;

405;

1072), 358 (SEQ ID NOs;

385;

1093), 359 (SEQ ID NOs;

659;

1250), 449 (SEQ ID NOs;

309;

1336), and 3346 (SEQ ID NOs;

1448;

1461).

88. The kit of claim 86, wherein said first oligonucleotide primer pair comprises a forward primer and a reverse primer, said forward primer and said reverse primer each independently between 13 to 35 linked nucleotides in length and each independently having at least 70% sequence identity with the corresponding forward or reverse primers, respectively, of primer pair number 3350 (SEQ ID NOs:

309;

1458); and

said at least one additional primer pair consists of at least three additional oligonucleotide primer pairs, each of said three oligonucleotide primer pairs comprising a forward primer and a reverse primer, said forward primer and said reverse primer each independently between 13 to 35 linked nucleotides in length and each independently having at least 70% sequence identity with the corresponding forward and reverse primers of primer pair numbers, 346 (SEQ ID NOs;

202;

1110), 348 (SEQ ID NOs;

706;

895), and 349 (SEQ ID NOs;

401;

1156).

89. The kit of claim 88, further comprising one or more additional primer pairs, said additional primer pairs comprising a forward primer and a reverse primer, said forward primer and said reverse primer each independently between 13 to 35 linked nucleotides in length and each independently having at least 70% sequence identity with corresponding forward or reverse primers, respectively, selected from the group consisting of primer pair numbers:

3360 (SEQ ID NOs;

1444;

1457), 3350 (SEQ ID NO;

309;

1458), 3351 (SEQ ID NOs;

309;

1460), 3354 (SEQ ID NO;

309;

1459), 3355 (SEQ ID NOs;

1446;

1458), 3353 (SEQ ID NOs;

1447;

1460), 3352 (SEQ ID NOs;

1445;

1458), 3347 (SEQ ID NOs;

1448;

1464), 3348 (SEQ ID NOs;

1451;

1464), 3349 (SEQ ID NOs;

1450;

1463), 3359 (SEQ ID NOs;

1449;

1462), 3358 (SEQ ID NOs;

1453;

1466), 3356 (SEQ ID NOs;

1452;

1467), 3357 (SEQ ID NOs;

1452;

1465), 3361 (SEQ ID NOs;

1454;

1468), 3362 (SEQ ID NOs;

1455;

1469), and 3363 (SEQ ID NOs;

1456;

1470).

90. The kit of claim 86 wherein two or more of said first purified oligonucleotide primer pair and said at least one additional purified primer pair are in the same vial and wherein said vial is free from other oligonucleotides.

91. A method for identifying a sepsis-causing bacterium in a sample, comprising:

a) amplifying a nucleic acid from said sample using an oligonucleotide primer pair comprising a forward primer and a reverse primer, each independently between 13 and 35 linked nucleotides in length, said primer pair configured to generate an amplification product that is between 45 and 200 linked nucleotides in length, said forward primer configured to hybridize with at least 70% complementarity to a first portion of a region defined by nucleotides 649 to 783 of the reverse complement of nucleotide residues 3448565 to 3449386 of Genbank gi number;

49175990, and said reverse primer configured to hybridize with at least 70% complementarity to a second portion of said region; and

b) determining the molecular mass of said at least one amplification product by mass spectrometry.

92. The method of claim 91, further comprising comparing said molecular mass to a database comprising a plurality of molecular masses of bioagent identifying amplicons, wherein a match between said determined molecular mass and a molecular mass in said database identifies said sepsis-causing bacterium in said sample.

93. The method of claim 91, further comprising calculating a base composition of said at least one amplification product using said molecular mass.

94. The method of claim 93, further comprising comparing said calculated base composition to a database comprising a plurality of base compositions of bioagent identifying amplicons, wherein a match between said calculated base composition and a base composition included in said database identifies said sepsis-causing bacterium in said sample.

95. The method of claim 91, wherein said forward primer has at least 70% sequence identity with SEQ ID NO:

309.

96. The method of claim 91, wherein said reverse primer comprises at least 70% sequence identity with SEQ ID NO:

1458.

97. The method of claim 91, further comprising repeating said amplifying and determining steps using at least one additional oligonucleotide primer pair wherein the primers of each of said at least one additional primer pair are designed to hybridize to a bacterial gene selected from the group consisting of 16S rRNA, 23S rRNA, tufB rpoB, valS, rplB, and gyrB.

98. The method of claim 91, wherein said molecular mass identifies the presence of said sepsis-causing bacterium in said sample.

99. The method of claim 98, further comprising determining either sensitivity or resistance of said sepsis-causing bacterium in said sample to one or more antibiotics.

100. The method of claim 91, wherein said molecular mass identifies a sub-species characteristic, strain, or genotype of said sepsis-causing bacterium in said sample.