Parallel loss of type VI secretion systems in two multi-drug resistantEscherichia colilineages

Abstract

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.

Multidrug-resistant E. coli encoding high genetic diversity in carbohydrate metabolism genes displace commensal E. coli from the intestinal tract

“…Both F084 and F016 strains out-competed the commensal 822-E8 strain achieving 96.1% and 80.7% of the total It is possible that F084 and MDR F016 are out-competing the commensal 822-E8 strain due to phage or production of a secreted toxin. Previous data from our group has shown that an ST131 strain retards growth of both ST73 and ST10 strains in LB broth [16]. Therefore, we grew each strain in LB broth overnight, filter sterilised the spent medium before mixing in a 1:1 ratio with fresh LB, and investigated the growth kinetics of all strains in the presence of supernatant from a competing strain.…”