Hi,
I am studying genes for the resistance to the antibiotics in Klebsiella and I am analysing an outbreak of carbapenem-resistant isolates. The gene I am analysing is OXA-48 and it is known to be located on a transposon made of two copies of the insertion sequence IS1999. According to my results, all strains of mine, except one, carry that gene in the insertion sequence, in agreement with what it is reported in literature. I don't understand what happens to the only one strain that has the resistance gene but not the insertion sequence. I tried to repeat the PCR more times and I have always the same result. Is there a genetic explanation to this?What do you suggest?
Thanks
Hi Silvia,
This is depends on the resources you have available. IS sequences are not the most stable genetic elements, If feasible you might want to sequence the genome of the isolate and determine the location of the OXA-48 gene.
Frank
Hi Frank,
thank you for your answer. So, you suggest that maybe OXA-48 is not associated to a IS1999 sequence? and What could it be happened to it? Because even if I imagined that it moved to another genetic location, I would suppose that it brings with it also the sequence insertion..so I don't understand why I don't find IS1999 in this case...
Hi Silva,
As with other transposable elements, Insertion sequences can excise from the genome (and be lost) as well as insert into it.
You could try a few primer sets to see if the entire IS is gone, or perhaps the specific region targeted by you PCR is mutated or missing.
Is this transposon in the same site in all the other Klebsiella ? if so you can use primers to see if the genetic elements flanking the transposn have rejoined. I have put in reference for a paper where they used this approach for excising of prophage.
J Bacteriol. 2003 Jun; 185(12): 3596–3605.
If you have the option I would go straight to sequencing as it will answer the question.
Regards,
Frank
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