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

Abstract

<i>Escherichia coli</i> is a facultative anaerobe found in a wide range of environments. Commonly described as the laboratory workhorse, <i>E. coli</i> is one of the best characterized bacterial species to date, however much of our understanding comes from studies involving the laboratory strain <i>E. coli</i> K-12. Resistance-nodulation-division efflux pumps are found in Gram-negative bacteria and can export a diverse range of substrates, including antibiotics. <i>E. coli</i> K-12 has six RND pumps; AcrB, AcrD, AcrF, CusA, MdtBC and MdtF, and it is frequently reported that all <i>E. coli</i> strains possess these six pumps. However, this is not true of <i>E. coli</i> ST11, a lineage of <i>E. coli</i>, which is primarily composed of the highly virulent important human pathogen, <i>E. coli</i> O157:H7. Here we show that <i>acrF</i> is absent from the pangenome of ST11 and that this lineage of <i>E. coli</i> has a highly conserved insertion within the <i>acrF</i> 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 <i>acrF</i> from ST11 was unable to restore AcrF function in <i>E. coli</i> K-12 substr. MG1655 Δ<i>acrB</i> Δ<i>acrF</i>. This shows that the complement of RND efflux pumps present in laboratory bacterial strains may not reflect the situation in virulent strains of bacterial pathogens.