Loss of type VI secretion systems in multi-drug resistant Escherichia coli clones

The repeated emergence of pandemic multi-drug resistant (MDR) Escherichia coli clones is a threat to public health globally. In recent work, drug resistant E. coli were shown to be capable of displacing commensal E. coli in the human gut. We hypothesise that there are three factors potentially responsible for the apparent competitive advantage of drug resistant E. coli clones: enhanced metabolic capabilities; production of lytic phage or bacteriocins; or the presence of a type VI secretion system (T6SS). We employed genomic and experimental approaches to investigate. First, we searched for T6SS apparatus genes across a curated dataset of over 20,000 genomes representing the full phylogenetic diversity of E. coli. This revealed large, non-phylogenetic variation in the presence of T6SS genes. No association was found between T6SS gene presence and MDR clones. However, multiple MDR clones have lost essential T6SS genes. We have shown that the pandemic MDR clone ST131-H30Rx lost the essential T6SS gene tssM when it was interrupted by insertion of ISEc12. To investigate the importance of this, a three-way competition assay was designed to assess the contact-killing capabilities of three strains - ST131-H30Rx, its drug-susceptible TssM-producing ancestor, and laboratory strain K-12 MG1655. Our results confirmed the competitive advantage of ST131-H30Rx in the absence of antibiotics, but its success was not due to the presence of phage, secreted proteins or contact-dependent killing. Our findings suggest that metabolic advantages are therefore likely a key component in the success of ST131-H30Rx. ### Competing Interest Statement The authors have declared no competing interest.