Specific exclusion of conjugative plasmids from the gut microflora
The rise of dangerous antimicrobial resistance (AMR), especially to the newer carbapenem antibiotics, is largely driven by the spread of conjugative plasmids between bacteria. These plasmids rapidly disseminate among common gut organisms like Escherichia coli and Klebsiella pneumoniae, which together account for around half of lethal sepsis and septic shock. Current AMR control measures, such as surveillance and isolation, are often ineffective, and AMR is often detected for the first time when infection is well established. Natural plasmid entry-exclusion systems (EES) protect bacterial populations from repeated entry by plasmids that are already established, or indeed by any plasmid with a related cognate EES, and we demonstrate here the exploitation of this mechanism for therapeutic purposes. We combined exclusion genes from three major AMR plasmid types (IncM, IncL, and IncC) into an efficient conjugative plasmid backbone and showed that this engineered ‘probiotic plasmid’ prevents invasive AMR plasmids from entering bacterial populations in vitro and in vivo, in the mouse gut. This offers a promising new strategy to control invasive AMR plasmids and prevent AMR acquisition in high-risk settings, such as in hospitals or AMR-endemic regions. Graphical abstract