It appears everything began from a spear phishing attack in which employees of HVAC company Fazio Mechanical Services targeted with an email containing a piece of malware.
Sources have told Krebs that the malware used in the attack is Citadel- a notorious banking trojan capable of stealing login credentials and other information. However, Krebs isn't able to confirm the information.
The reason why the company didn't get chance to identify the malware is because it is using a free version of Malwarebytes Anti-malware to protect is internal systems.
Malwarebytes is one of good tool capable of scanning and removing threats from infected machines. However, unlike the Pro version(just $25), it doesn't offer any real-time protection.
Furthermore, the free version is meant for individuals not for companies, also the license for free version prohibits corporate use.