Insights into the acquisition of the pks island and production of colibactin in the Escherichia coli population.

Frédéric Auvray,Jean-Philippe Nougayrède,Alexandre Perrat,Clémence Massip,Camille V Chagneau,Nadège Bossuet-Greif,Hubert Brugère,Eric Oswald,Yoshitoshi Ogura,Priscilla Branchu,Yoko Arimizu,Tetsuya Hayashi

doi:10.1099/mgen.0.000579

Abstract

The pks island codes for the enzymes necessary for synthesis of the genotoxin colibactin, which contributes to the virulence of Escherichia coli strains and is suspected of promoting colorectal cancer. From a collection of 785 human and bovine E. coli isolates, we identified 109 strains carrying a highly conserved pks island, mostly from phylogroup B2, but also from phylogroups A, B1 and D. Different scenarios of pks acquisition were deduced from whole genome sequence and phylogenetic analysis. In the main scenario, pks was introduced and stabilized into certain sequence types (STs) of the B2 phylogroup, such as ST73 and ST95, at the asnW tRNA locus located in the vicinity of the yersiniabactin-encoding High Pathogenicity Island (HPI). In a few B2 strains, pks inserted at the asnU or asnV tRNA loci close to the HPI and occasionally was located next to the remnant of an integrative and conjugative element. In a last scenario specific to B1/A strains, pks was acquired, independently of the HPI, at a non-tRNA locus. All the pks-positive strains except 18 produced colibactin. Sixteen strains contained mutations in clbB or clbD, or a fusion of clbJ and clbK and were no longer genotoxic but most of them still produced low amounts of potentially active metabolites associated with the pks island. One strain was fully metabolically inactive without pks alteration, but colibactin production was restored by overexpressing the ClbR regulator. In conclusion, the pks island is not restricted to human pathogenic B2 strains and is more widely distributed in the E. coli population, while preserving its functionality.

Highlights

Escherichia coli is a commensal resident of the human and animal gut, and a pathogen responsible for intestinal or extra-intestinal infections
This island exhibits typical features of horizontally acquired genomic elements: (i) it is a large (i.e. 54 kb) region with a distinct GC content compared to that of the chromosomal backbone, (ii) it is physically associated with a phage-t ype integrase gene that probably mediated its insertion into the chromosome and (iii) it is located at a tRNA locus and is flanked by two short (i.e. 17 bp) direct repeats (DRs) reminiscent of those generated upon integrase-mediated insertion of mobile genetic elements [5, 6]
These pks-positive and pks-negative sequence types (STs) are found in distinct clusters in the core-genomebased phylogenetic tree (Fig. 1), suggesting that pks acquisition occurred after the divergence of these clusters from a common ancestor

Summary

Introduction

Escherichia coli is a commensal resident of the human and animal gut, and a pathogen responsible for intestinal or extra-intestinal infections. The E. coli pks pathogenicity island consists of a clbA-clbS gene cluster enabling the biosynthesis of a polyketide (PK) – non-ribosomal peptide (NRP) hybrid genotoxin known as colibactin [5] This island exhibits typical features of horizontally acquired genomic elements: (i) it is a large (i.e. 54 kb) region with a distinct GC content compared to that of the chromosomal backbone, (ii) it is physically associated with a phage-t ype integrase gene that probably mediated its insertion into the chromosome and (iii) it is located at a tRNA locus and is flanked by two short (i.e. 17 bp) direct repeats (DRs) reminiscent of those generated upon integrase-mediated insertion of mobile genetic elements [5, 6]. The pks island can be found in other members of the Enterobacteriaceae such as Klebsiella pneumoniae, Citrobacter koseri and Enterobacter aerogenes [6], and in the honeybee gut commensal Frischella perrara [7] and the marine sponge commensal Pseudovibrio sp. [8]

Methods

Results

Conclusion