E. coli ST11 (O157:H7) does not encode a functional AcrF efflux pump

Escherichia coli is a facultative anaerobe found in a wide range of environments. Commonly described as the laboratory work-horse, E. coli is one of the best characterized bacterial species to date, however much of our understanding comes from studies involving the laboratory strain E. coli K-12. Resistance- nodulation-division efflux pumps are found in Gram-negative bacteria and can export a diverse range of substrates, including antibiotics. E. coli K-12 has six RND pumps; AcrB, AcrD, AcrF, CusA, MdtBC and MdtF, and it is frequently reported that all E. coli strains possess these six pumps. However, this is not true of E. coli ST11, a lineage of E. coli, which is primarily composed of the highly virulent important human pathogen, E. coli O157:H7. Here we show that acrF is absent from the pangenome of ST11 and that this lineage of E. coli has a highly conserved insertion within the acrF gene, which when translated encodes 13 amino acids and two stop codons. This insertion was found to be present in 97.59 % of 1787 ST11 genome assemblies. Non-function of AcrF in ST11 was confirmed in the laboratory as complementation with acrF from ST11 was unable to restore AcrF function in E. coli K-12 substr. MG1655 Delta acrB Delta acrF. This shows that the com-plement of RND efflux pumps present in laboratory bacterial strains may not reflect the situation in virulent strains of bacterial pathogens.

Automated summary

Escherichia coli is a facultative anaerobe commonly found in various environments. This study shows that the presence of resistance-nodulation-division (RND) efflux pumps in laboratory bacterial strains may not reflect the situation in virulent strains of bacterial pathogens, using E. coli ST11 as an example. The absence of acrF and the conserved insertion in its gene were observed in 97.59% of ST11 genome assemblies, and the non-functionality of AcrF in ST11 was confirmed in laboratory experiments.