In silico serotyping pipeline workflow. Schematic of in silico serotyping of
Shigella
and EIEC (enteroinvasive
E. coli
) by cluster-specific genes combined with the ipaH gene, O antigen and modification genes and H antigen genes, implemented in ShigEiFinder. Both assembled genomes and raw reads are accepted as data input. The dotted arrows show the cutoff value applied for initial gene filtering. WGS, whole-genome sequencing; HK, housekeeping; SS, SF, SB and SD,
S. sonnei
,
S. flexneri
,
S. boydii
and
S. dysenteriae
respectively. The abbreviated ‘species’ name plus the serotype number is the designation of a
Shigella
serotype (e.g.
S. dysenteriae
serotype 1 is abbreviated as SD1). For SB11, there were two sequence types (STs) with ST5475 and ST1765 located within clusters C1 and C2 respectively.