Semi-automated rep-PCR for rapid differentiation of major clonal groups of Escherichia coli meningitis strains

DiversiLab, a semi-automated repetitive-sequence-based PCR (rep-PCR) device, is a highly integrated platform designed for rapid bacterial genotyping. Here, we evaluated the capacity of the DiversiLab system to determine the genetic relatedness of Escherichia coli neonatal meningitis (ECNM) strains and to identify clonal groups. We analyzed 80 isolates representative of the diversity of ECNM strains in Europe and North America and 52 E. coli reference (ECOR) strains belonging to phylogenetic groups A, D, and B2. All the strains had previously been characterized by means of multilocus sequence typing (MLST). The DiversiLab dendrogram clustered all but 8 of the strains according to their phylogenetic groups. After defining a rep-PCR type complex (RPTc) based on an average similarity threshold of 95% between rep-PCR types, we observed excellent agreement between RPTc and sequence type complexes (STc) in groups D and B2. In group A, rep-PCR typing was more discriminative than MLST, dividing the 25 ECOR group A strains into 19 RPTc, compared to only 10 STc. In the highly virulent clonal group B21, mainly composed of O1, O2, O18, and O45:K1 strains, the DiversiLab system individualized a particular subgroup of O2:K1 strains. In addition, among O18:K1 strains the system identified a particular genetic background associated with pathogenicity island IIJ96-like domains. Thus, the DiversiLab system is a rapid and powerful tool for identifying and discriminating clonal groups among ECNM strains.