Refinement of whole-genome multilocus sequence typing analysis by addressing gene paralogy

We developed a user-friendly program, Genome Profiler (GeP), to refine whole-genome multilocus sequence typing analysis by addressing gene paralogy with conserved gene neighborhoods. In comparison to similar programs, GeP produced overall the best results in terms of accuracy and is thus a useful alternative to resolve relationships of bacterial isolates. Whole-genome multilocus sequence typing (wgMLST) is apowerful tool to resolve the relationship of especially closely related bacterial isolates by indexing allele differences in the shared loci in the whole-genome sequencing (WGS) data (1–3). However, if gene paralogy is not adequately addressed, multicopy genes that are commonly observed in the bacterial genome might mislead the inferences of the genetic relationships (4). In closely related bacterial isolates, orthologs have a tendency to retain the same genome context, and synteny has been successfully used for automated clustering of orthologous genes in the pangenomic analysis of bacterial isolates (5, 6). Therefore, we hypothesized that conserved gene neighborhoods (CGN) can be used in the wgMLST to differentiate orthologs from recently duplicated para