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Just want to provide an update that I have managed to rebuild the DB server and malware is gone. Thanks again for all the information provided. Cheers!
Here the only approach is to set up a new server, harden it properly and then migrate data but only after thorough inspection.
I agree with this assessment. The more pressing matter is active logins. I recommend blocking all network access to the server. Right now it serves as a jump box to further hack and infect your network. If you can't block network access then shut it down.
EDIT: never mind I didn't realize this thread was three pages deep.
I have also checked with the vendors who provided my company this DB server. They said there are only a few ways to harden this server; create administration portal to act as a proxy, and to change root password. They further mentioned that they only use root account on the server.
Either way, I have since left that company, but it was a good learning experience. I will definitely read up more on Linux!
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