Abstract: Objective To study the prevalence of virulent gene of invasin of brain endothelial cells C (ibeC) of neonatal meningitis Escherichia coli. Methods The genome data of 1620 E. coli strains were downloaded from GenBank to establish a local database. The ibeC gene was analyzed for all the strains by using BLAST program. Multiple Sequences alignment was conducted for ibeC from representative E. coli strains by clustalx software. Additionally, a multilocus sequence typing (MLST) was performed for the 1620 E. coli strains. For the further analysis, 72 ECOR strains were collected from MLST database. Minimum spanning tree of MLST of released E. coli strains were conducted by BioNumerics V4.0 software to analyze the species structure. Results All the strains were found to carry ibeC gene. The 1620 E. coli strains belonged to 261 sequence types, and ECOR strains had 49 sequence types. The origination and pathogenicity of E. coli strains had no significance relationship in its phylogeny grouping. Conclusion The ibeC gene was widely distributed in various E. coli strains. The difference in ibeC gene carriage between meningitis related E. coli strains and other pathogenic E. coli strains was small. MLST indicated that all the strains were widely distributed and the origins were complex, suggesting that the ibeC gene is very conservative, and the hypothesis of the ibeC gene is the related with the invasion of neonatal meningitis E. coli to cerebral microvascular endothelial cell needs further confirmation.