Insights from the Whole Genome Sequence of Escherichia coli RS218 in Identifying Potential Virulence Traits Common to E. coli Causing Neonatal Meningitis and Other Extra-intestinal Diseases

Abstract

Escherichia coli RS218 is the prototypic strain of neonatal meningitis causing E. coli (NMEC) that has been used in many studies relevant to NMEC pathogenesis. In the present study, the whole genome of E. coli RS218 was sequenced and compared with the genomes of eight other extraintestinal pathogenic E. coli (ExPEC) as well as with the laboratory strain of E. coli K-12. Analysis of E. coli RS218 genome revealed that it consists of a circular chromosome of 5.087 Mb in size and a 114-Kbp plasmid with an average G+C content of 50.6%. The chromosome contains 4,658 coding sequences, 88 transfer RNAs, 22 ribosomal RNAs, one clustered regularly interspaced short palindromic repeats array, and five noncoding RNAs. Escherichia coli RS218 genome demonstrated 98% nucleotide similarity to cystitis causing E. coli strain UTI89. Comparative genomic analysis identified a total of 51 genomic islands (GIs) in E. coli RS218 which were not present in the E. coli K-12 genome. Of these GIs, 16 were common to all NMEC strains studied whereas two GIs were common to all ExPEC. The GIs common to all NMEC encode for several sugar uptake pathways, arginine/ornithine metabolism, iron uptake systems, and putative adhesins and invasins, which may contribute to NMEC pathogenesis. This study also identified NMEC-specific traits that might play a role in initial colonization of mucosal epithelia and penetration of the intestinal and blood brain barriers by NMEC. Overall, these data will facilitate a better understanding of the genetic bases of virulence and adaptation mechanisms of ExPEC.