Hello, LA
I did some googling and found a site that does say that Lyme Disease can cause bowel incontinence. "Many LD patients will experience a spastic (irritable) colon and that diagnosis should spark a search for LD. ... Fecal incontinence due to impaired rectal sphincter tone can occur."
I'm quite aware that Lyme, untreated, is a very serious thing. I'm glad that you found out you have it before it got any worse. I had a friend in college who got a tick bite when she was a girl staying in a cabin in the woods. She came down with all sorts of health problems and years later was finally diagnosed LD. By that time it has started attacking her heart.
Here's something you might research on the internet. I've heard that some people have had success with taking oregano oil, the kind that health food stores have as a supplement. You might do some googling and ask your doctor about it. Wild oregano oil is an antiviral, antifungal and antibiotic and one drop will purify 1000 times as much water. It's strong stuff, so if your doctor says it's ok to try, dilute the oil in a teaspoon of olive oil before you take it orally.
A couple of years ago I got a MRSA infection in my leg that the doctor said wasn't "totally" invulnerable to antibiotics but very close to it. It started with an infected chigger bite. It turned into a huge oozing sore above my ankle. The infection spread to both legs, chest, back and neck and I was in danger of losing my leg, and maybe my life.
Nothing the doctor gave me helped. But then I got some oregano oil and rubbed it on the open sore. It stopped weeping within an hour. Within 3 days the infection was disappearing all over and I kept my leg. So I will admit to being a fan. 
I need to add you need to talk to your doctors about anything you're taking. You never know when something natural might interfere with a medication you're on, so it never hurts to double-check.
Anyway, it's just a suggestion.
Lyme isn't the unbeatable killer that many people think it is. I don't believe in the unbeatable bug... there's something out there that will beat it.
Don't stop looking till you find it.
And keep your chin up! Smiling rarely heals anything but it never hurts.
Kendal