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Genomic analysis of the PAI I_CL3 locus in pathogenic LEE-negative Shiga toxin-producing Escherichia coli and Citrobacter rodentium

INRA, UR454 Unité de Microbiologie, F-63122 Saint-Genès Champanelle, France

Correspondence
Christine Martin
cmartin{at}clermont.inra.fr

Shiga toxin-producing Escherichia coli (STEC) causes a spectrum of human illnesses such as haemorrhagic colitis and haemolytic–uraemic syndrome. Although the locus of enterocyte effacement (LEE) seems to confer enhanced virulence, LEE-negative STEC strains are also associated with severe human disease, suggesting that other unknown factors enhance the virulence potential of STEC strains. A novel hybrid pathogenicity island, termed PAI I_CL3, has been previously characterized in the LEE-negative O113 : H21 STEC strain CL3. Screening for the presence of PAI I_CL3 elements in 469 strains of E. coli, including attaching and effacing (A/E) pathogens [enteropathogenic E. coli (EPEC) and enterohaemorrhagic E. coli (EHEC)], non-A/E pathogens [LEE-negative STEC, extra-intestinal pathogenic E. coli (ExPEC), enterotoxigenic E. coli (ETEC) and enteroaggregative E. coli (EAEC)] and commensal E. coli isolates, showed that PAI I_CL3 is unique to LEE-negative STEC strains linked to disease, providing a new marker for these strains. We also showed that a PAI I_CL3-equivalent gene cluster is present in the genome of Citrobacter rodentium, on a 53 kb genomic island inserted into the pheV tRNA locus. While the C. rodentium PAI I_CL3 shows high similarities at the nucleotide level and in organization with the E. coli PAI I_CL3, the genetic context of the integration differs completely. In addition, BLAST searches revealed that other E. coli pathotypes (O157 : H7 EHEC, ExPEC, EPEC and EAEC) possess incomplete PAI I_CL3 elements that contain only the genes located at the extremities of the island. Six of the 16 sequenced E. coli genomes showed deleted PAI I_CL3 gene clusters which are carried on mobile genetic elements inserted into pheV, selC or serW tRNA loci, which is compatible with the idea that the PAI I_CL3 gene cluster entered E. coli and C. rodentium at multiple times through independent events. The phylogenetic distribution of the PAI I_CL3 variants suggests that a B1 genetic background is necessary for the maintenance of the full complement of PAI I_CL3 genes in E. coli.

A supplementary table listing genetic features of the identified GlpheV-CR_ICC168 ORFs is available with the online version of this paper.