The present invention relates to a method of identifying a microorganism in a sample, based upon sequencing, and analysing, using a sequencing-by-synthesis procedure, short stretches, or fragments of a gene. ;Accordingly, the present invention provides a method of identifying a microorganism in a sample, said method comprising: ;determining the sequence of a region of up to 50 nucleotides in a predetermined site in a gene of said microorganism, thereby to obtain a signature sequence; and ;analysing sequencing information in said signature sequence to identify said microorganism, ;wherein said sequence is determined by detecting the nucleotides incorporated in a primer extension reaction performed using a primer binding at a pre-determined site in said gene.
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