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Certain spyware programs either log your keystrokes (keyloggers) or look for specific files with passwords and send them out to the attacker to use maliciously. I've had this happen to me with FTP passwords and the end result was not pleasant at all as not only did my websites become infected, they infected others as well. So my advice is to immediately change your passwords once you've realized you have some sort of infection, just don't do it on the same computer that's infected for obvious reasons.
Also, in the event that your websites do get infected, block all access to them immediately until you've removed the malicious code to prevent others from getting affected. As for other accounts, especially financial stuff, monitor them closely to see if you see anything suspicious and contact support ASAP.
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