Insights into the acquisition of thepksisland and production of colibactin in theEscherichia colipopulation
Authors: Auvray Frédéric , Perrat Alexandre , Arimizu Yoko , Chagneau Camille V. , Bossuet-Greif Nadège , Massip Clémence , Brugère Hubert , Nougayrède Jean-Philippe , Hayashi Tetsuya , Branchu Priscilla , Ogura Yoshitoshi , Oswald Eric 
Published: April 2021

Thepksisland codes for the enzymes necessary for synthesis of the genotoxin colibactin, which contributes to the virulence ofEscherichia colistrains and is suspected of promoting colorectal cancer. From a collection of 785 human and bovineE. coliisolates, we identified 109 strains carrying a highly conservedpksisland, mostly from the phylogroup B2, but also from phylogroups A, B1 and D. Different scenarios ofpksacquisition were deduced from whole genome sequence and phylogenetic analysis. In the main scenario,pkswas introduced and stabilized into certain sequence types (ST) of the B2 phylogroup, such as ST73 and ST95, at theasnWtRNA locus located in the vicinity of the yersiniabactin-encoding High Pathogenicity Island (HPI). In a few B2 strains,pksinserted at theasnUorasnVtRNAlociclose 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,pkswas acquired, independently of the HPI, at a non-tRNAlocus. All thepks-positive strains except 18 produced colibactin. Sixteen strains contained mutations inclbBorclbD, or a fusion ofclbJandclbKand were no longer genotoxic but most of them still produced low amount of potentially active metabolites associated with thepksisland. One strain was fully metabolically inactive withoutpksalteration, but colibactin production was restored by overexpressing the ClbR regulator. In conclusion, thepksisland is not restricted to human pathogenic B2 strains and is more widely distributed in theE. colipopulation, while preserving its functionality.

IMPACT STATEMENT

Colibactin, a genotoxin associated with the carcinogenicity of certain strains ofE. coli, is encoded by a pathogenicity island calledpks. We took advantage of a large collection of non-clinicalE. colistrains originating from human and bovine hosts to explore the distribution, conservation and functionality of thepksisland. We found that thepksisland was not only present in the phylogroup B2 (and more specifically to certain B2 sublineages), but also in other genetic phylogroups, highlighting its capacity to disseminate though horizontal gene transfer. We identified various geneticpksconfigurations indicative of an introduction of thepksisland intoE. colion multiple independent occasions. Despite the existence of various acquisition scenarios, we found that thepkssequences were highly conserved andpks-carrying strains were overwhelmingly capable of producing colibactin, suggesting that thepksisland is under selective pressure, through the production of colibactin or other secondary metabolites. Future implications include the identification of such metabolites and their biological activities that could be advantageous toE. coliand enable its adaptation to various ecological niches.

DATA SUMMARY

All sequence data of the 785E. coliused in this study are freely available from the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/) under the accession number PRJDB5579. This database was updated to include the sequence data obtained using ONT MinION for theE. colireference strain SP15 and forE. colistrains ECSC054, JML285, KS-NP019, NS-NP030 and SI-NP020. The sequence data ofE. colistrain UPEC129 obtained using PacBio instrument were deposited in the NCBI BioProject database and are available athttps://www.ncbi.nlm.nih.gov/Traces/study/under the accession number PRJNA669570. Hybrid MinION-Illumina and PacBio-Illumina assemblies are available at the NCBI nucleotide database. The genome sequences of 36 otherE. colireference strains and 7 non-E. colistrains were retrieved from NCBI.