Location: Meat Safety and QualityTitle: Closed genomes of Escherichia coli O55:H7 and O157:H7 add new insight into working STEC O157:H7 evolution model
Submitted to: Genome Biology and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/23/2022
Publication Date: N/A
Interpretive Summary: Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a foodborne pathogen that can cause mild to severe foodborne illness in humans. To better understand how STEC O157:H7 came to be, we evaluated complete closed genomes with its most common related bacteria; E. coli O55:H7. We found that while these two close relatives share many of the same genes, there is also sequence variation in some key areas as well as differences in overall genome architecture. Finally, we proposed a new step in the current proposed evolution of STEC O157:H7 from E. coli O55:H7. These newly publicly released genomes will allow a more complete understanding of the evolution of STEC O157:H7 from E. coli O55:H7 and help us better understand and control this foodborne pathogen.
Technical Abstract: The evolution and propagation of Shiga toxin-producing Escherichia coli (STEC) O157:H7 has resulted in many foodborne outbreaks resulting in mild to severe patient illness. Evolutionary knowledge of STEC O157:H7 points to E. coli O55:H7 as the progenitor to STEC O157:H7 strains. While several models have been constructed to explain this evolutionary process, closed genomes of E. coli O55:H7 and evolutionary important STEC O157:H7 strains are needed to gain a more robust understanding. Here, we publish six E. coli O55:H7 strains as well as four STEC O157:H7 strains that contribute to the understanding of this pathogen’s evolution. All strains underwent both long and short read sequencing resulting in closed chromosomes and plasmids. Sequencing of multiple DEC5 E. coli O55:H7 clones provided a greater understanding of the diversity of this group not previously described, such as variations in prophage, insertion sequence and plasmid content, core genome structure, and chromosomal architecture. Furthermore, through pangenome and phylogenic comparison we propose an earlier strain in the evolution process prior to the A1 clonal complex. The DEC5E isolate appears to be the oldest ancestor having diverged much earlier than other E. coli O55:H7 strains such as TB182A and DEC5A from the A1 clonal complex. The release of these closed genomes to NCBI provides new insight into STEC O157:H7 evolution and will allow for more robust complete models moving forward.