1)Make sure all libraries,  modules and applications are fully updated. 

2)**Stop using FTP**.  There are worms that spread by sniffing for FTP Logins. 

3) Run [PHPSecInfo][1]

4)Consider using a Web Application Firewall (WAF) like mod_security.

5) If by chance you can get an IP address of the attacker or someone accessing the backdoor.  **REPORT THEM TO THE FBI**.  (A WAF helps with this)


(Bonus points:  replace the backdoor with a simple .php script that logs the ip address.  If anyone hits it you'll have an ip for the fbi)


  [1]: http://phpsec.org/projects/phpsecinfo/