Strengthening Indonesia’s Emerging Infectious Disease Surveillance to Care Ecosystem: A Mixed-Methods Study of Challenges and Facilitators

Background Effective surveillance systems are critical for early detection of emerging infectious diseases (EIDs). Challenges and facilitators can impact surveillance performance at the individual, social, policy, and community levels. This study aimed to identify barriers and enablers to strengthen the surveillance ecosystem across these levels. Methods A mixed-methods study was conducted across 21 public health centers in Bali, Indonesia. Quantitative analysis was conducted using mixed-effects linear regression on data from 349 participants to examine factors associated with the surveillance score. Qualitative data from 18 in-depth interviews and 20 focus group discussions, involving 38 participants, were thematically analyzed to explore barriers and facilitators to surveillance implementation. Results In the adjusted model, knowledge of surveillance was significantly associated with surveillance score (β = −0.328; 95% CI: −0.589 to − 0.067; p = 0.014). Facility readiness, community engagement, and interaction terms were not statistically significant. Qualitative findings identified key barriers, including limited human resources, fragmented reporting systems, logistical constraints, reagent shortages, weak coordination, and misinformation within communities. Bureaucratic procurement processes and inadequate digital infrastructure further delayed reporting and specimen transport. Facilitators included rapid response teams, digital reporting systems, routine cross-sector meetings, training for staff, and active involvement of community leaders and health cadres. Conclusions Surveillance performance is influenced by both individual knowledge and systemic health system factors. Strengthening referral coordination, workforce capacity, digital integration, and community engagement is essential to enhance EID surveillance effectiveness.