Engineered gut symbionts mediate cross-phylum antagonism to suppress uropathogenic Escherichia coli colonization

Urinary tract infections (UTIs) are among the most common bacterial infections globally and create a large burden on the healthcare system. Uropathogenic Escherichia coli (UPEC) account for the majority of UTIs and increase the risk of recurrence. The standard treatment is antibiotics and, with the rise of multi-drug resistant UPEC lineages, there is a need for alternative treatments and prevention. Colicins, bacteriocins targeting and produced by E. coli, have previously been shown to inhibit the growth of pathogenic E. coli and are a promising alternative. Here, we engineer commensal Bacteroidaceae to secrete colicins via outer membrane vesicle (OMV) targeting signal peptides to suppress E. coli in the mouse gut. Secreted colicins were assessed for their ability to kill primary clinical isolate UPEC strains, including epidemic multi-drug resistant ST131 strains, along with other pathogenic and type strains. Specifically, secreted colicin E7, from Phocaeicola vulgatus fully eliminated of several UPEC strains in culture. In mice, P. vulgatus secreting colicin E7 prevented the extended colonization of two clinical UPEC strains and restored microbiome diversity. Together, this work shows the viability of secreted, heterologous antimicrobials from P. vulgatus as prophylactic treatment against the colonization of pathogenic E. coli utilizing cross-phylum antagonism in the gut.