Chikim Nguyen, Chelsea Reitzel, Arjun Sukumaran, Kristina A. Ganzinger, Jennifer Geddes-McAlister
Dissecting host-pathogen interactions is challenging due to heterogeneous co-cultures and limited separation methods. Here, we developed a label-free microfluidic chip enabling reproducible separation of Klebsiella pneumoniae and murine macrophages during co-culture for high-resolution proteomic analysis. Using an optimized 1.4 μm filter, the platform preserved cell viability while improving host protein identification and enriching immune-associated proteins compared to traditional scraping and supernatant collection. Chip-isolated non-phagocytosed bacteria displayed distinct proteome profiles, including reduced metabolic enzymes and increased biosynthetic and iron-binding proteins. Iron-associated proteins were uniquely enriched in this population, and functional assays confirmed that iron promotes macrophage evasion and bacterial survival. Together, these results establish a microfluidic-proteomic workflow for resolving complex host-pathogen dynamics and propose an iron-dependent mechanism of immune evasion. This approach reduces sample handling and cross-contamination while preserving cellular structure, providing a powerful framework for studying infection biology and identifying therapeutic targets.