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Preventing future outbreaks and developing efficient mitigation protocols can benefit from advanced computational modeling approaches. Here, we developed an agent-based modeling approach to study the spatiotemporal dynamics of an infection outbreak in a confined environment caused by a specific pathogen, and to determine effective containment protocols. The approach integrates the 3D geographic information system of a confined environment, behavior of the hosts, key biological parameters about the pathogen obtained from the experimental data, and the general mechanics of host\u2013pathogen and pathogen\u2013fomite interactions. To assess our approach, we applied it to the historical data of infectious outbreaks caused by norovirus, H1N1 influenza A, and SARS-CoV-2 viruses. Our AI-GIS Infection Dynamics (AGID) model accurately predicted daily infection numbers, correctly identified the day when the CDC vessel sanitation protocol would be triggered, singled out key biological parameters affecting the infection spread, and propose pathogen-specific changes to existing containment protocols. Our work advances the understanding of infection spread on cruise ships while offering insights applicable to other similar confined settings, such as nursing homes, schools, and hospitals. By providing a robust framework for real-time outbreak modeling, this study proposes more effective containment protocols and enhances our preparedness for managing infectious diseases and emerging pathogens in confined environments.<\/jats:p>","DOI":"10.1073\/pnas.2422574123","type":"journal-article","created":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T18:59:25Z","timestamp":1768935565000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":0,"title":["Real-time spatiotemporal tracking of infectious outbreaks in confined environments with a host\u2013pathogen agent-based system"],"prefix":"10.1073","volume":"123","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8309-9648","authenticated-orcid":false,"given":"Suhas","family":"Srinivasan","sequence":"first","affiliation":[{"name":"Data Science Program, Worcester Polytechnic Institute","place":["Worcester"]},{"name":"Program in Epithelial Biology, Stanford School of Medicine","place":["Stanford"]},{"name":"Center for Personal Dynamic Regulomes, Stanford School of Medicine","place":["Stanford"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey","family":"King","sequence":"additional","affiliation":[{"name":"Earthshot Labs","place":["Mill Valley"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1662-0987","authenticated-orcid":false,"given":"Jacob M.","family":"Collins","sequence":"additional","affiliation":[{"name":"Department of Genomics and Computational Biology, UMass Chan Medical School","place":["Worcester"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5559-9661","authenticated-orcid":false,"given":"Andres","family":"Colubri","sequence":"additional","affiliation":[{"name":"Department of Genomics and Computational Biology, UMass Chan Medical School","place":["Worcester"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3875-9085","authenticated-orcid":false,"given":"Dmitry","family":"Korkin","sequence":"additional","affiliation":[{"name":"Data Science Program, Worcester Polytechnic Institute","place":["Worcester"]},{"name":"Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute","place":["Worcester"]},{"name":"Department of Computer Science, Worcester Polytechnic Institute","place":["Worcester"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2026,1,20]]},"reference":[{"key":"e_1_3_4_1_2","first-page":"1015","article-title":"The transmission of tuberculosis in confined spaces: An analytical review of alternative epidemiological models","volume":"7","author":"Beggs C.","year":"2003","unstructured":"C. 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