This is also a reason I tell people don't use shared hosting if you can avoid it. No matter how good the hosting is, any customer that doesn't know what they're doing, which is the majority, can allow the server to be compromised by running outdated software that has known vulnerabilities.
I found a host a couple of years ago that had 50% of their shared hosting clients index pages infected on at least 20 servers that I tested. It was nearly a thousand domains involved, maybe more.
Bottom line, even if you clean up your account it can get infected over and over if you remain on that server so I agree with Tedster that moving to a new host is probably the best strategy.