Engineering probiotic Escherichia coli Nissle 1917 to block transfer of multiple antibiotic resistance genes by exploiting a type I CRISPR-Cas system

Many multidrug-resistant (MDR) bacteria evolved through accumulation of antibiotic-resistance genes (ARGs). Although the potential risk of probiotics as reservoirs of ARGs has been recognized, strategies for blocking transfer of ARGs while using probiotics have rarely been explored. The probiotic Escherichia coli Nissle 1917 (EcN) has long been used for treating intestinal diseases. Here, we showed frequent transfer of ARGs into EcN both in vitro and in vivo, raising its potential risk of accumulating antibiotic resistance. Given that no CRISPR-Cas system is found in natural EcN, we integrated the endogenous type I-E CRISPR-Cas system derived from E. coli BW25113 into EcN, and showed that the engineered EcN was able to efficiently cleave multiple ARGs (i.e., mcr-1, blaNDM-1 and tet(X)). By co-incubation of EcN expressing Cas3-Cascade and that expressing Cas9, we showed that the growth of the former strain outcompeted the latter strain, demonstrating better clinical application prospect of EcN expressing the type I-E CRISPR-Cas system. Finally, the engineered EcN exhibited immunity against transfer of targeted ARGs in the intestine of a model animal (i.e. zebrafish). Our work provides a new strategy for restricting transfer of ARGs in EcN, paving the way for safe use of this probiotic and development of probiotics as living therapeutics.