Fingerprinting bacterial strains using repetitive DNA sequence amplification

A method for differentiating a strain in the same species of bacteria, comprising the steps of:

• amplifying DNA between interspersed, non-coding BOX repetitive sequences in a sample containing said bacteria by adding a pair of outwardly-directed BOX primers to said sample, said primers hybridizing to BOX repetitive DNA sequences in the bacterial DNA and extending outwardly from one hybridizable BOX repetitive sequence to another hybridizable BOX repetitive sequence;
• separating the extension products generated in the amplification step by size;
• and
• determining the specific strain of bacteria by measuring the pattern of sized extension products.

A method for identifying a species of bacteria, comprising the steps of:

• amplifying DNA between interspersed, non-coding repetitive sequences in a sample containing said bacteria by adding to said sample a BOX primer selected from the group consisting of SEQ. ID. NOs. 61, 62 and 63, wherein said primer hybridizes to the interspersed, non-coding repetitive sequence in either of the complementary strands of the DNA and wherein the hybridized primer extends from one interspersed, non-coding repetitive sequence across non-repetitive DNA to another interspersed, non-coding repetitive sequence and wherein said extension product hybridizes to the primer for generations of further extension products;
• separating the extension products by size;
• and
• determining the specific strain of bacteria by measuring the pattern of sized extension products.