Patent ID: 8486638

Claim:
A method for determining the presence of micro-organisms in a sample and identifying and characterizing said micro-organisms if present, comprising the steps of: (a) extracting nucleic acids from micro-organisms, said nucleic acids comprising target nucleic acids, (b) performing a ligase detection reaction (LDR) on said target nucleic acids, comprising: (b1) providing a pair of a first nucleic acid probe and a second nucleic acid probe, said first nucleic acid probe comprising a 3′ located target-specific sequence I complementary to a distinct part of said target nucleic acid and said second nucleic acid probe comprising a 5′ located target-specific sequence II complementary to a second part of said target nucleic acid located adjacent to and 3′ from said target-specific sequence I, wherein said first nucleic acid probe further comprises a 5′ located primer binding section I (PBS(I)), and said second nucleic acid probe comprises a 3′ located primer binding section II (PBS(II)); (b2) incubating said target nucleic acid with said first nucleic acid probe and said second nucleic acid probe under conditions allowing hybridisation of complementary nucleic acids, (b3) connecting any adjacent probes, (b4) providing at least one set of two primers, wherein a first primer (primer I) is substantially identical to primer binding section I, and the second primer (primer II) is substantially complementary to primer binding section II, and (b5) amplifying any connected probe nucleic acid of step (b3), wherein amplification is initiated by binding of nucleic acid primer specific for a primer binding section, thereby providing amplified target nucleic acids, wherein one or more detector molecules that detect the amplified target nucleic acids, are present in step (b5), (c) monitoring the signal of said detector molecule and/or the modulation of the signal of said detector molecule, wherein modulation in the signal of said detector molecule indicates the presence of said target sequence whereby the presence of a microorganism is determined, (d) whereby step (c) determines that a microorganism is present, hybridizing the amplified target nucleic acids of step (c) to a capture probe, and, (e) detecting the hybridized target nucleic acids of step (d), whereby the micro-organism is identified.