Engineered probiotics target granulomas to treat mycobacterial infection

Chen, Y.-Y.; Harimoto, T.; Makafe, G. G.; Coker, C.; Kim, H.; Im, J.; Jing, Y.; Jin, H.; Hu, X.; Zutshi, S.; Raneri, M. R.; Weinrick, B.; Danino, T.

doi:10.64898/2026.10.27.762313

bioRxiv · 10.64898/2026.10.27.762313

Engineered probiotics target granulomas to treat mycobacterial infection

Chen, Y.-Y.·Harimoto, T.·Makafe, G. G.·Coker, C.·Kim, H.·Im, J.·Jing, Y.·Jin, H.·Hu, X.·Zutshi, S.·Raneri, M. R.·Weinrick, B.·Danino, T.

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Abstract

Granulomas are a pathological niche for mycobacteria that remain difficult to access with conventional therapies. Here we show that probiotic Escherichia coli Nissle 1917 (EcN) infiltrates and colonizes granulomas and can be engineered as a delivery system that senses the local microenvironment and releases antimycobacterial payloads. Specifically, we leveraged the hypoxic microenvironment of necrotic granulomas to restrict bacterial growth, and developed a dual-mode lysis circuit combining intracellular and extracellular killing for sustained payload release with limited evolutionary escape. We further engineered EcN to express a mycobacteriophage-derived enzyme, generating a strain that suppressed drug-sensitive and drug-resistant mycobacteria in vitro and potentiated conventional antibiotic activity. Engineered probiotics also reduced mycobacterial burden in vivo, and in a murine model of rifampicin-resistant infection, combination treatment with pretomanid achieved greater bacterial reduction than either monotherapy. Together, these results establish a synthetic biology framework for targeting granulomatous infections with programmable living microbes.

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Chen, Y.-Y., Harimoto, T., Makafe, G. G., Coker, C., Kim, H., Im, J., Jing, Y., Jin, H., Hu, X., Zutshi, S., Raneri, M. R., Weinrick, B., Danino, T.. 2026-10-29. Engineered probiotics target granulomas to treat mycobacterial infection. https://doi.org/10.64898/2026.10.27.762313

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