Design of optional control system design for detect-to-alarm, detect-to-isolate, and detect-to-treat systems are available on request. Using particle detection technology and/or air sampling procedural programs, building and ventilation systems can be configured for system or building isolation, emergency system operation, and continuous air monitoring. Alarms and secondary protective systems can be engaged by particle detectors located downstream of filter banks. Protocols for continuous or periodic air monitoring can be developed for each building’s unique operating conditions or requirements using air sampling of ventilation supply air. Systems are designed to be cost-effective.