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Whatever vulnerability must have been on the server to allowed this infection in the first place might still be present. You will need to find the security hole and patch it. If these sites are on a shared hosting platform they could easily be infecting each other.

You need to review the log files on your server which correspond to the activity at the exact time of the infections. You can get all the infection times from the Anti-malware Quarantine page in your wp-admin. The activity in your log files at those times should lean you to the vulnerability that needs to be patched.