Many bacteria have the capability to rearrange their genomic structure whether it be adding, deleting, or altering base pair sequences. NAAT detection methods are dependent upon known DNA sequences in order to commercially produce primers and probes for the assay.
Specific DNA sequences called insertion sequences are transposable DNA elements that are anywhere from 700-2,500 base pairs (bp) in length, which can be inserted into multiple locations of the same chromosome. These insertion sequences are usually present in multiple copies within a single bacterial genome. They can move around and insert into different locations on the genome, changing the overall genetic sequence of the bacteria. However, the bp sequence of the actual insertion sequence remains unchanged. Because the insertion sequences remain pure and unaltered, they are the target regions for NAAT detection. The long-term success of the assay requires that a constant in the genetic area is amplified and detected.
For Bordetella pertussis, the most well-described insertion sequence that serves as a NAAT target is IS481. It is common to find more than 50 copies of IS481 in each B. pertussis genome. One problem with using IS481 is that it is not specific to B. pertussis. It is also present in other species of Bordetella such as B. holmesii and B. bronchiseptica.
Other insertion sequences for Bordetella have been identified, including IS1001, hIS1001, and IS1002.