Cytomics, the high-dimensional profiling of immune cells, provides a systems-level view of host responses to infection. Unlike traditional diagnostics focused on pathogen detection or early immune activation, cytomics captures rare and functionally specialized immune subsets linked to disease severity and clinical outcome. In this review, we explore how advances in spectral cytometry, mass cytometry, and multimodal single-cell platforms enable unprecedented resolution of immune complexity during infection by summarizing cytomics evolution, high-dimensional single-cell and multimodal technologies, as well as their roles in defining immune heterogeneity and host–pathogen interactions across infectious diseases. Several single-cell technologies rely on antibodies conjugated to fluorochromes or non-radioactive isotopes, generating high-dimensional datasets processed with advanced computational tools, enabling unprecedented precision in defining cell populations and supporting diagnostic advances. During infections, cytomic approaches map immune architecture, identify dysfunctional or protective cell states, and monitor therapeutic responses. In viral infections, it detects hyperinflammatory monocytes and exhausted T-cell subsets; in bacterial diseases, it reveals immunosuppressive monocytes and disrupted neutrophil networks; in parasitic infections, it clarifies mechanisms of persistence and clearance. Integrated with complementary omics technologies, cytomics informs personalized immunomodulatory strategies and rational vaccine design. This review provides a unified framework for applying cytomics to precision diagnostics, therapeutic decision-making, vaccine development, and population-level preparedness, positioning high-dimensional immune profiling as a cornerstone of modern infectious-disease management.

This dialogue explores the transformative potential of spatiotemporal omics in reshaping the future of infectious disease research. Experts Zhihua Ou, Ziqing Deng, George Fu Gao, Andrea Cossarizza, Wenhong Zhang, and Aldo Tagliabue discussed the integration of multi-omics technologies to obtain high-resolution, dynamic, and spatiotemporal insights into disease pathogenesis. The conversation highlighted the key technical barriers that must be addressed for the broad application of spatiotemporal omics. Strategic research priorities were outlined, with a focus on diseases with high global burden and an emphasis on a “One Health” framework. The dialogue underscored the need to prioritize omics technologies based on specific biological questions and clinical goals. Major challenges in translating basic discoveries into clinical applications, such as data standardization, interdisciplinary collaboration, and ethical considerations, were also examined. Finally, the experts proposed strategies for the newly established SpatioTemporal Omics Consortium (STOC) Infection Working Group to foster international collaboration through cultivating a shared vision, developing interoperable platforms, and securing sustainable funding to effectively integrate global scientific talent and resources for substantive innovations.