Shigella EIEC Cluster Enhanced Serotyper Finder
Shigella EIEC Cluster Enhanced Serotype Finder (ShigEiFinder) is a cluster-specific gene marker based in silico pipeline for differentiation of Shigella and EIEC and for serotyping of Shigella and EIEC using either paired end Illumina sequencing reads or assembled genomes.
The differentiation of Shigella and EIEC from each other is determined by the presence of gene markers that are only found within a single Shigella/EIEC cluster. Where more than one gene is used to identify a cluster, all genes must be present for a cluster to be called. The serotype is then predicted based on the presence of established Shigella serotype specific O antigen genes and modification genes or E. coli O and H antigen genes. ShigEiFinder also uses 38 virulence genes from the pINV invasive plasmid to determine whether the plasmid is present in the genome. When more than 25 of these genes are detected, the isolate is deemed to be pINV positive.
For online analysis, assembled genome upload is preferable as it may take a long time to upload the paired end Illumina sequencing reads to our server (depending on your internet connectivity). You are required to register to use the online tool and results will be sent back by email. Data are not retained on the server. Only metadata regarding number of isolates processed is recorded to assess server usage.
The package is available at https://github.com/LanLab/ShigEiFinder for download.