Dear Ranjith. For electrroporation procol, did you recover cells in SOC medium at 30 °C before platting?

 Thanks Victor Antonio Garcia-Angulo  for the input.

i am adding LB media instead of SOC.

Have you done the proper controls to show that your DNA prep of pKD46 is good and can transform a control strain, and that your competent cells are good and control plasmid can transform them well. The problem is likely one or the other and it would help to determine which is the problem first. There is no special protocol other than transforming at 30 degrees, so it should be fine if your reagents are good.

What Michael said would definitely be the place to start.

How long are you recovering for anyway? I usually give a 30° recovery at least 3 hours because of the slowed growth time. 

EDIT: I just noticed that one of the topic tags for this is "kanamycin." You aren't using kan to select for pKD46 right? It's an AmpR plasmid.

Alternative possibilities: 

Restriction systems in your clinical strain not present in your cloning strain targeting the plasmid. (or a target for a CRISPR-Cas system on pKD46 but that's a bit less likely I think)

A physical barrier, such as a capsule, which gives it low transformation efficiency. 

The suggestions from MIcheal and Alexendra a totally valid an i would like to add a little to that.

We had a similar problem of pKD46 transformation where we were able to transform but could not get the transformed cells to grow properly. To check the overall integrity of the vector, We did a restriction mapping with the plasmid and found something fishy with the plasmid. We requested a new copy of the vector and the system worked fine then.

I suggest you do a similar check with the vector and follow the suggestions stated above. 

Ranjith , were you able to fix the problem. I am facing the same problem right now with the same plasmid and i mad all the proper controls but it did not work as well