Each Molecular tools and typing technique have their own advantages as well as limitations, However the following articles may useful while designing your experiments.

http://aac.asm.org/content/57/10/5162.long

http://www.ijmm.org/article.asp?issn=0255-0857;year=2013;volume=31;issue=4;spage=385;epage=389;aulast=Chen 

It is frequent to have more than one class 1 integron in clinical samples. So, you need to elute all amplicons (usually there are 2 or 3) and the you send each amplicon to sequence.