Imported from Food Pathogen Team Kwan Lab CUHK: Outbreak strains have EAEC secreted proteins but not EHEC secreted proteins

Introduction: In our first blog, we find the outbreak strains actually have the similarity pathogenicity as EAEC E.coli Ec55989 strain based on alignment with virulence factors from VFDB.  Two questions remain: Whether the outbreak strains are really  "EAEC" intrinsically, and only acquiring Stx2 gene to become a EAEC/EHEC hybrid?  Whether these outbreak strains also maintain other EHEC features such as secretion systems? Methods: We used datasets of genome sequences of the three outbreak strains (TY2482, LB226692 and H112180280), the EAEC strain 55989,  and the EHEC strain O157:H7 Sakai. We use EHEC strain O157:H7 and EAEC strain 55989 as central reference sequences to align with the three outbreak strain genome sequences to identify the presence or absence of EHEC-specific and EAEC-specific secretary proteins using BRIG. Results: 1. The Type III secretion system (T3SS) and related translocated proteins of EHEC are missing in all outbreak strains. Figure 1 shows general features of EHEC E.coli O157:H7 strain and its homology to HPA strain (H112180280), BGI TY2482 strain, Life technology (LB226692), and E.coli 55989 strain, ordered from inner to outside rings. The three inner rings showed high sequence similarities among the outbreak strains. The two EHEC-specific gene clusters encoding T3SS (shown in left and colored in red), are missing in the outbreak strains and EAEC 55989 strains. Figure 1 2. The outbreak strains harbor the EAEC secretion system and its translocated proteins. Figure 2 is a plot of EAEC strain 55989 strain and its homology to HPA sequence (H112180280), BGI sequence (TY2482), Life technology seqeuence (LB226692), and E.coli O157:H7 sequence, respectively.  All the EAEC-specific secretory genes (shown in the outside ring and colored in black) are present in the outbreak strains as well as in EAEC 55989 strain. Figure 2 Analysed by Lei Li, edited by Billy Cheng and HS Kwan