Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131

Abstract

Escherichia coli associated with urinary tract infections and bacteremia has been intensively investigated, including recent work focusing on the virulent, globally disseminated, multidrug-resistant lineage ST131. To contextualize ST131 within the broader E. coli population associated with disease, we used genomics to analyze a systematic 11-yr hospital-based survey of E. coli associated with bacteremia using isolates collected from across England by the British Society for Antimicrobial Chemotherapy and from the Cambridge University Hospitals NHS Foundation Trust. Population dynamics analysis of the most successful lineages identified the emergence of ST131 and ST69 and their establishment as two of the five most common lineages along with ST73, ST95, and ST12. The most frequently identified lineage was ST73. Compared to ST131, ST73 was susceptible to most antibiotics, indicating that multidrug resistance was not the dominant reason for prevalence of E. coli lineages in this population. Temporal phylogenetic analysis of the emergence of ST69 and ST131 identified differences in the dynamics of emergence and showed that expansion of ST131 in this population was not driven by sequential emergence of increasingly resistant subclades. We showed that over time, the E. coli population was only transiently disturbed by the introduction of new lineages before a new equilibrium was rapidly achieved. Together, these findings suggest that the frequency of E. coli lineages in invasive disease is driven by negative frequency-dependent selection occurring outside of the hospital, most probably in the commensal niche, and that drug resistance is not a primary determinant of success in this niche.

Characterization and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential

“…When the complete genomes of these strains were subsequently analyzed, they were placed between phylogroups F and B2 in the E. coli phylogeny. Similar data were obtained by other groups, one of them proposing a new phylogroup called G to describe these strains (Lu et al ., ; Kallonen et al ., ). In this work, we have described the diversity of this new phylogroup and proposed an easy assay to identify these strains.…”

“…Recently, it has been shown in the East of England that ST117 represents 8% and 20% of livestock (poultry and pigs) and poultry meat E. coli isolates respectively (Ludden et al, 2019). In humans, phylogroup G strains represent around 1% of the E. coli isolates and are found both in commensal and extra-intestinal pathogenic conditions, including septicaemia (Table 2) (Kallonen et al, 2017). Interestingly, these ExPEC human strains belong mainly to STc117 and exhibit O24:H4/O33:H4/O143:H4 serotypes.…”

“…Recently, this method has been adapted in silico to allow E. coli phylotyping using WGS data (Beghain et al, 2018). With the accumulation of WGS data, it is clear that some strains belong to a group intermediate between phylogroups F and B2 (Lu et al, 2016;Kallonen et al, 2017). These strains are closely related to, but distinct from, the phylogroup B2 strains and are assigned to phylogroup F with both in vitro and in silico Clermont methods (Beghain et al, 2018).…”

Genomic epidemiology of multidrug‐resistant Gram‐negative organisms

“…It has been hypothesized that these capsular switching events are important for immune evasion and persistence in hosts. Recombination events altering antigenic molecules have also been observed in E. coli and A. baumannii , with recombinant switching of lipopolysaccharide (LPS) loci reported in both species . In addition to altering putative antigenic determinants, horizontal transfer events have also been observed that have the potential to modify interactions with the host environment in other ways.…”

“…Recombination events altering antigenic molecules have also been observed in E. coli and A. baumannii, with recombinant switching of lipopolysaccharide (LPS) loci reported in both species. 28,88,89 In addition to altering putative antigenic determinants, horizontal transfer events have also been observed that have the potential to modify interactions with the host environment in other ways. Studies in ST131 and ST258 have both found horizontal transfer events affecting fimbriae and pili, which may provide advantages in host colonization.…”