Classification of and other using O- antigen virulence gene: -Typing and hypothesis for pathogenic vs. probiotic strain differentiation.

() is the type species for the new genus, and a gut commensal of the phylum. Emerging reports (primarily based on reference strain/ATCC-8503) concerningly propose that long-known opportunistic pathogen is a probiotic. We posit there is an urgent need to characterize the pathogenicity of strain-strain variability. Unfortunately, no methods/insights exist to classify for this purpose. Herein, we developed a virulence gene-based classification system for and to facilitate pathogenic-vs-probiotic characterization. We used DNA methods to develop a system based on the virulence (lipopolysaccharide/bacterial wall) ' O-antigen-synthesis gene'. We then performed phylogenetic analysis of from fourteen complete genomes (21 genes), other , and ; and proposed a PCR-based Restriction-Fragment Length Polymorphism method. Cluster analysis revealed that can be classified into four lineages (based on gene gaps/insertions) which we designated -Types I, II, III, and IV. In context, we found 14 additional -types (I-XVIII) interspersed with numerous and pathogenic forming three major "-superclusters." For laboratory -Typing implementation, we developed a PCR-primer strategy to amplify genes (100%-specificity) to conduct MboII-RFLP and sub-classify primers for other are proposed/discussed. Comparative analysis of lipopolysaccharide/lipid-A gene confirmed as highly discriminant. In conclusion, -Typing classifies into unique clusters/superclusters given copy/sequence variability. Analysis revealed that most pathogenic  strains are single-copy -Type I . The relevance of the strain variability in disease might depend on their hypothetical modulatory interactions with other O-antigens/lipopolysaccharides and TLR4 lipopolysaccharide-receptors in human/animal cells.