Selection and Validation of a Multilocus Variable-Number Tandem-Repeat Analysis Panel for Typing Shigellaspp

ABSTRACTThe Shigellagenus has historically been separated into four species, based on biochemical assays. The classification within each species relies on serotyping. Recently, genome sequencing and DNA assays, in particular the multilocus sequence typing (MLST) approach, greatly improved the current knowledge of the origin and phylogenetic evolution of Shigellaspp. The Shigellaand Escherichiagenera are now considered to belong to a unique genomospecies. Multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) provides valuable polymorphic markers for genotyping and performing phylogenetic analyses of highly homogeneous bacterial pathogens. Here, we assess the capability of MLVA for Shigellatyping. Thirty-two potentially polymorphic VNTRs were selected by analyzing in silico five Shigellagenomic sequences and subsequently evaluated. Eventually, a panel of 15 VNTRs was selected (i.e., MLVA15 analysis). MLVA15 analysis of 78 strains or genome sequences of Shigellaspp. and 11 strains or genome sequences of Escherichia colidistinguished 83 genotypes. Shigellapopulation cluster analysis gave consistent results compared to MLST. MLVA15 analysis showed capabilities for E. colityping, providing classification among pathogenic and nonpathogenic E. colistrains included in the study. The resulting data can be queried on our genotyping webpage (http://mlva.u-psud.fr). The MLVA15 assay is rapid, highly discriminatory, and reproducible for Shigellaand Escherichiastrains, suggesting that it could significantly contribute to epidemiological trace-back analysis of Shigellainfections and pathogenic Escherichiaoutbreaks. Typing was performed on strains obtained mostly from collections. Further studies should include strains of much more diverse origins, including all pathogenic E. colitypes.