A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58

Abstract

Escherichia coli ST58 has recently emerged as a globally disseminated uropathogen that often progresses to sepsis. Unlike most pandemic extra-intestinal pathogenic E. coli (ExPEC), which belong to pathogenic phylogroup B2, ST58 belongs to the environmental/commensal phylogroup B1. Here, we present a pan-genomic analysis of a global collection of 752 ST58 isolates from diverse sources. We identify a large ST58 sub-lineage characterized by near ubiquitous carriage of ColV plasmids, which carry genes encoding virulence factors, and by a distinct accessory genome including genes typical of the Yersiniabactin High Pathogenicity Island. This sub-lineage includes three-quarters of all ExPEC sequences in our study and has a broad host range, although poultry and porcine sources predominate. By contrast, strains isolated from cattle often lack ColV plasmids. Our data indicate that ColV plasmid acquisition contributed to the divergence of the major ST58 sub-lineage, and different sub-lineages inhabit poultry, swine and cattle.

Genomic and Temporal Trends in Canine ExPEC Reflect Those of Human ExPEC

“…In the canine collection, 56 isolates (14.9%) carried a ColV plasmid and these sequences were identified across all phylogroups. ExPEC ColV carriage in our canine collection was similar to the estimated human ExPEC carriage rate of 16% ( 25 ). ColV plasmids were particularly dominant in phylogroups C (ST88) and G (ST117), but a significant proportion of phylogroup B1 (ST58) and a small number of B2 (numerous STs) isolates also carried a ColV plasmid.…”

“…The major human ExPEC STs, particularly ST95 ( 22 ), ST131 ( 23 , 26 ), and ST73 ( 45 ), comprise sublineages that are often discernible by serotype and fimH allele variation. Lineage subdivision is also often accompanied by carriage of different F plasmid replicon sequence types belonging to ColV (various replicon types) and pUTI89-like (ColIa + /F29:A-:B10) genotypes ( 22 , 25 , 26 ). In the canine collection, 56 isolates (14.9%) carried a ColV plasmid and these sequences were identified across all phylogroups.…”

“…ST88 is a major ColV plasmid-carrying ST causing extraintestinal disease and has also been identified in store-bought produce ( 36 , 46 – 48 ). ST58 is a multihost pathogen with a major sublineage rich in ColV plasmids and is frequently identified in poultry and pigs ( 25 ). ST117 is a noted avian pathogenic E. coli (APEC) lineage rich in ColV plasmids and is dominant in both commensal and pathogenic E. coli populations from poultry in Australia and abroad ( 49 , 50 ).…”

“…Despite the variety of plasmids that are found in E. coli , F plasmids dominate among a proportion of major and emerging ExPEC STs. For example, carriage of F plasmids is very common in ST131, ST95, ST58, and ST127, with separate plasmid lineages found to be characteristic of ST sublineages ( 7 , 22 , 23 , 25 ). F plasmids can be categorized genotypically by their accessory gene content, and plasmid lineages within those genotypes can be approximated by their F replicon sequence types (RSTs).…”

Distribution of ESBL/AmpC-Escherichia coli on a Dairy Farm

“…Despite recent reports of this ST in healthy cattle at the slaughterhouse [ 34 , 35 ], there are nevertheless reports of involvement of this ST in clinical processes in humans and animals (bloodstream infections [ 36 ]) and cattle (mastitis [ 37 , 38 ]). According to a recent publication, this ST is assigned to the group of extraintestinal pathogenic E. coli (ExPEC) and is described as novel and globally spreading [ 39 ]. Additionally, ST58 is thought to occur in multidrug-resistant variants [ 36 ].…”