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

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 the 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 (ST) 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 amount 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. IMPACT STATEMENT Colibactin, a genotoxin associated with the carcinogenicity of certain strains of E. coli, is encoded by a pathogenicity island called pks. We took advantage of a large collection of non-clinical E. coli strains originating from human and bovine hosts to explore the distribution, conservation and functionality of the pks island. We found that the pks island 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 genetic pks configurations indicative of an introduction of the pks island into E. coli on multiple independent occasions. Despite the existence of various acquisition scenarios, we found that the pks sequences were highly conserved and pks-carrying strains were overwhelmingly capable of producing colibactin, suggesting that the pks island 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 to E. coli and enable its adaptation to various ecological niches. DATA SUMMARY All sequence data of the 785 E. coli used 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 the E. coli reference strain SP15 and for E. coli strains ECSC054, JML285, KS-NP019, NS-NP030 and SI-NP020. The sequence data of E. coli strain UPEC129 obtained using PacBio instrument were deposited in the NCBI BioProject database and are available at https://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 other E. coli reference strains and 7 non-E. coli strains were retrieved from NCBI.