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Joint profiling is limited by fundamental technical mismatches between host- and pathogen-derived material, particularly differences in cell wall structure, lysis requirements, and molecular abundance. Here we introduce a lysis-independent strategy that enables unified measurement of intracellular bacterial presence and state alongside host single-cell profiles. We repurpose bacterial surface display to encode promoter activity and bacterial identity as antibody-detectable signals, rendering bacterial features compatible with existing antibody-based single-cell assays. This approach is modular across promoters, epitope tags, display scaffolds, and bacterial species, including\n                  <jats:italic>Escherichia coli<\/jats:italic>\n                  and\n                  <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                  . Surface-displayed reporters are detectable during intracellular infection and can be read out by flow cytometry and droplet-based single-cell RNA sequencing without pathogen-specific lysis optimization or pre-sorting on pathogen signal. Applying this method to infected macrophages, we link heterogeneous bacterial uptake to heterogeneous expression of phagocytosis-associated host programs. This strategy enables scalable, joint host\u2013pathogen single-cell measurements and expands the range of pathogens and states accessible to high-throughput single-cell analysis.\n                <\/jats:p>","DOI":"10.64898\/2026.07.21.739887","type":"posted-content","created":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T22:40:16Z","timestamp":1784760016000},"source":"Crossref","is-referenced-by-count":0,"title":["Bacterial surface display enables lysis-independent joint host\u2013pathogen single-cell profiling"],"prefix":"10.64898","author":[{"given":"Cal","family":"Gunnarsson","sequence":"first","affiliation":[{"name":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA"},{"name":"Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeff C.","family":"Hsiao","sequence":"additional","affiliation":[{"name":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA"},{"name":"Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob B.","family":"Hochfelder","sequence":"additional","affiliation":[{"name":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA"},{"name":"Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sydney L.","family":"Solomon","sequence":"additional","affiliation":[{"name":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA"},{"name":"Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bianca A.","family":"Lepe","sequence":"additional","affiliation":[{"name":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA"},{"name":"Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharon","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA"},{"name":"Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA"},{"name":"Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8417-5606","authenticated-orcid":false,"given":"Hattie A.","family":"Chung","sequence":"additional","affiliation":[{"name":"Department of Medicine, Cardiovascular Research Center, Yale School of Medicine, New Haven, CT, USA"},{"name":"Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA"},{"name":"Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA"},{"name":"Yale Center for Research on Aging, Yale School of Medicine, New Haven, CT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1716-6712","authenticated-orcid":false,"given":"Bryan D.","family":"Bryson","sequence":"additional","affiliation":[{"name":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA"},{"name":"Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026072415300923000_2026.07.21.739887v1.1","doi-asserted-by":"publisher","DOI":"10.1111\/tra.12752"},{"key":"2026072415300923000_2026.07.21.739887v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-10065-8"},{"key":"2026072415300923000_2026.07.21.739887v1.3","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1003902"},{"key":"2026072415300923000_2026.07.21.739887v1.4","doi-asserted-by":"crossref","unstructured":"Saliba, A.-E. et al. 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