What strain are you using? The small ones does not look like E.coli to me. We had similar contamination in our E.coli cultures. Yet the small ones where Gramm+ in a simple KOH test. Maybe you could check it?

http://wiki.bugwood.org/KOH_test

It's non-pathogenic E. coli O157:H7.

On plate count agar 50-300 discrete colonies can be counted easily. You can also use an image analysing software.

Sorry  i am confused here . Is there such organism as non pathogenic E.coli 0157:H7? . I dont think there is . Please educate me 

Yes. http://www.atcc.org/products/all/25922.aspx

Sauer, Anne, and Carmen I. Moraru. "Inactivation of Escherichia coli ATCC 25922 and Escherichia coli O157: H7 in apple juice and apple cider, using pulsed light treatment." Journal of Food Protection® 72, no. 5 (2009): 937-944.

It's something which u can work with in BSL 1.

 Harikrishnan did you find out which colonies to count?I am having the same problem. 

Nope...

But I would say count all of them and do it consistently for all samples. Also the method is valid only for 30-300 CFUs according to standards. I would also suggest using an alternative method to enumerate CFUs once (as a calibration) to make sure the number is not off by much.

Thank you so much for the response!

In nature there is nothing like none pathogenic E. coli 0157:H7 but you can make it none pathogenic when treated to be such foe experimental purpose only