Method for the detection of the antibiotic resistance spectrum of Mycobacterium species

A composition comprising at least one isolated oligonucleotide selected from the group consisting of:

• S1,
• (SEQ ID NO:
• 1)
• S33,
• (SEQ ID NO:
• 5)
• S4,
• (SEQ ID NO:
• 6)
• S44,
• (SEQ ID NO:
• 7)
• S444,
• (SEQ ID NO:
• 43)
• S55,
• (SEQ ID NO:
• 10)
• S555,
• (SEQ ID NO:
• 39)
• S5555,
• (SEQ ID NO:
• 40)
• S6,
• (SEQ ID NO:
• 11)
• S66, and
• (SEQ ID NO:
• 12)
• the RNA form of said SEQ ID NOs wherein T is replaced by U, and the complementary form of said SEQ ID NOs.

A kit for the detection of the resistance to rifampicin of Mycobacterium tuberculosis present in a biological sample comprising the following components:

• (i) at least one rpoB gene fragment selected from the group consisting of:
• S1,
• (SEQ ID NO:
• 1)
• S33,
• (SEQ ID NO:
• 5)
• S4,
• (SEQ ID NO:
• 6)
• S44,
• (SEQ ID NO:
• 7)
• S444,
• (SEQ ID NO:
• 43)
• S55,
• (SEQ ID NO:
• 10)
• S555,
• (SEQ ID NO:
• 39)
• S5555,
• (SEQ ID NO:
• 40)
• S6,
• (SEQ ID NO:
• 11)
• S66, and
• (SEQ ID NO:
• 12)
• the RNA form of said SEQ ID NOs wherein T is replaced by U, and the complementary form of said SEQ ID NOs;
• (ii) a hybridization buffer, or components necessary for producing said buffer;
• and
• (iii) a wash solution, or components necessary for producing said solution.

A method for the identification of a mycobacterial species and the simultaneous detection of its resistance to rifampicin, comprising

• (i) optionally releasing, isolating or concentrating the polynucleotides present in the sample;
• (ii) optionally amplifying the relevant part of the rpoB gene with at least one suitable primer pair;
• (iii) simultaneously hybridizing the polynucleotides of steps (i) or (ii) with at least two rpoB gene fragments, wherein the first rpoB gene fragment is selected from the group consisting of:
• S1,
• (SEQ ID NO:
• 1)
• S33,
• (SEQ ID NO:
• 5)
• S4,
• (SEQ ID NO:
• 6)
• S44,
• (SEQ ID NO:
• 7)
• S444,
• (SEQ ID NO:
• 43)
• S55,
• (SEQ ID NO:
• 10)
• S555,
• (SEQ ID NO:
• 39)
• S5555,
• (SEQ ID NO:
• 40)
• S6,
• (SEQ ID NO:
• 11)
• S66, and
• (SEQ ID NO:
• 12)
• the RNA form of said SEQ ID NOs wherein T is replaced by U, and the complementary form of said SEQ ID NOs;
• and wherein the second rpoB gene fragment is selected from the group consisting of:
• MT-POL-2,
• (SEQ ID NO:
• 24)
• MT-POL-3,
• (SEQ ID NO:
• 25)
• MT-POL-4,
• (SEQ ID NO:
• 26)
• MT-POL-5,
• (SEQ ID NO:
• 27)
• MP-POL-1,
• (SEQ ID NO:
• 28)
• MA-POL-1,
• (SEQ ID NO:
• 29)
• MS-POL-1,
• (SEQ ID NO:
• 38)
• MK-POL-1,
• (SEQ ID NO:
• 55)
• MI-POL-1,
• (SEQ ID NO:
• 68)
• ML-POL-1,
• (SEQ ID NO:
• 57)
• ML-S1,
• (SEQ ID NO:
• 58)
• ML-S2,
• (SEQ ID NO:
• 59)
• ML-S3,
• (SEQ ID NO:
• 60)
• ML-S4,
• (SEQ ID NO:
• 61)
• ML-S5,
• (SEQ ID NO:
• 62)
• ML-S6, and
• (SEQ ID NO:
• 63)
• the RNA form of said SEQ ID NOs wherein T is replaced by U, and the complementary form of said SEQ ID NOs;
• (iv) detecting the hybrids formed in step (iii);
• and
• (v) inferring the identification of a mycobacterial species and its resistance to rifampicin from the differential hybridization signal(s) obtained in step (iv).