All our servers are tuned to the highest security levels, keep all software up-to-date and install all necessary security patches.
On all ours shared servers ConfigServer eXploit Scanner is installed.
CXS allows to perform on-demand scanning of files, directories and user accounts for suspected exploits, viruses and suspicious resources (files, directories, symlinks, sockets).
CXS prevents the exploitation of an account by malware by deleting or moving suspicious files to quarantine. Also CXS isolates the server from PHP and perl shell scripts, commonly used to launch more malicious attacks and for sending spam.
So, from your side you need timely update your scripts to the latest stable and secure versions and upload your content from trusted sources.