I have fiddled with it enough to know the solution will be complicated. I do not have time to chase it down, but I think one solution would be to do something like have Shorthand expand to "E coli" (without the period), then put in commands to go back to the "E" and insert a period, and then have a command to have the cursor go back to end of the word "coli"
I have other entries that do that kind of thing, so I am familiar with how to get Shorthand to do that; so that is the route I would personally go with first. Using the Field Code (Ctl+F9 in Word 2010) is what I use to get the cursor back to the end of the word "coli".