The Resistance-Nodulation-Division efflux pump EefABC is highly conserved within lineages of E. coli commonly associated with infection.

Resistance-nodulation-division (RND) efflux pumps confer multidrug resistance in Gram-negative bacteria and are critical for many physiological functions including virulence and biofilm formation. The common Escherichia coli laboratory strain, K-12 MG1655, has six recognized RND transporters (AcrB, AcrD, AcrF, CusA, MdtBC and MdtF). However, by studying >20,000 E. coli assemblies, we show that E. coli belonging to phylogroups B2, D, E, F and G, which are commonly associated with infection, possess an additional, seventh RND transporter, EefB. It is found in a five-gene operon, eefRABCD, which also encodes a TetR family transcription factor, a periplasmic adapter protein, an outer membrane factor and major facilitator superfamily pump. In contrast, E. coli from phylogroups A, B1 and C, generally containing environmental/commensal strains, do not encode the operon. Where the eefRABCD operon is present, it was highly conserved. In fact, conservation levels were comparable to that of the major RND efflux system AcrAB-TolC, suggesting an important biological function. Protein modelling shows that this pump is distinct from endogenous E. coli RND systems with unique structural features. However, unlike other RND efflux systems, EefABC does not appear to transport antimicrobials and instead may be important for infection or survival in the host environment.