Healthcare ecosystems form a critical type of infrastructures that provide valuable services in today societies. However, the underlying sensitive information is also of interest of malicious entities around the globe, with the attack volume being continuously increasing. Safeguarding this complex computerized setting constitutes a major challenge for the involved organizations. This paper presents an incident handling system for healthcare organizations and their supply-chain. The proposed approach utilizes swarm intelligence in order to assess the current security posture in a continuous basis and respond to attacks in real-time. The overall solution is based on the related NIST 800.61 standard and implements the operations of i) preparation, ii) detection and analysis, iii) containment, eradication, and recovery, and iv) post-incident activity. The system is developed under the EU funded project AI4HEALTHSEC and is applied in the relevant healthcare pilots.