Identification of regions of the Escherichia coli chromosome specific for neonatal meningitis-associated strains

Specific virulence factors associated with the pathogenesis of Escherichia coli strains causing neonatal meningitis (ECNM), such as the K1 capsular po lysaccharide, the S fimbriae, and the Ibe10 protein, have been previously i dentified. However, some other yet unidentified factors are likely to be in volved in the pathogenesis of ECNM. To identify specialized unique DNA regi ons associated with ECNM virulence, we used the representational difference analysis technique. The genomes of two strains belonging to nonpathogenic phylogenetic group A of the ECOR reference collection were subtracted from E. coli strain C5, isolated from a case of neonatal meningitis. Strain C5 b elongs to the phylogenetic group B2 as do the majority of ECNM, We have iso lated and mapped 64 DNA fragments which are specific for strain C5 and not found in nonpathogenic strains. Of these clones, 44 were clustered in six d istinct regions on the chromosome. The sfa and ibe10 genes were located in regions 2 and 6, respectively, A group of genes (cnf1, hra, hly, and prs) k nown to be present in a pathogenicity island of the uropathogenic strain E. coli J96 colocalized with region 6. The occurrence of these DNA regions wa s tested in a set of meningitis-associated strains and in a central group c omposed of non-meningitis-associated strains belonging to the same B2 group . Regions 1, 3, and 4 were present in 91, 82, and 81%, respectively, of the meningitis strains and in 40, 13, and 47% of the control strains. Together , these data suggest that regions 1, 3, and 4 code for factors associated w ith the ability of E. coli to invade the meninges of neonates.