Microcin MccI47 reduces Klebsiella pneumoniae colonization in vivo when administered via an engineered live biotherapeutic with no effect on resident microbiota

The gastrointestinal (GI) tract acts a reservoir for multi-drug resistant pathogens, specifically carbapenem-resistant (CR) Klebsiella pneumoniae and other CR Enterobacteriaceae, which often lead to severe extraintestinal infections and lethal outcomes in vulnerable populations1. To combat this, selective decolonization of these bacteria from the GI tract has been proposed as a new strategy for preventing transmission to other body sites and minimizing spreading to susceptible individuals2. Towards this goal, we first purify the previously uncharacterized bacteriocin, microcin I47 (MccI47), and demonstrate its potent inhibition of multiple Enterobacteriaceae strains in vitro at concentrations resembling those of commonly prescribed antibiotics. We then engineer the probiotic bacterium Escherichia coli Nissle 1917 (EcN) to constitutively express MccI47-producing genes from a stably retained multicopy plasmid, while rendering provisions for inducible gene expression and plasmid selection unnecessary. We then explore the in vivo applicability of the MccI47-producing EcN in a murine model of CR K. pneumoniae GI colonization and demonstrate significant MccI47-dependent reduction of CR K. pneumoniae GI colonization after seven days of daily oral live biotherapeutic administration with no significant disruption of the resident microbiota.