Escherichia coli O157:H7 tir 255 T > A allele strains differ in chromosomal and plasmid composition

Abstract

Shiga toxin-producing Escherichia coli (STEC) O157:H7 strains with the T allele in the translocated intimin receptor polymorphism (tir) 255 A > T gene associate with human disease more than strains with an A allele; however, the allele is not thought to be the direct cause of this difference. We sequenced a diverse set of STEC O157:H7 strains (26% A allele, 74% T allele) to identify linked differences that might underlie disease association. The average chromosome and pO157 plasmid size and gene content were significantly greater within the tir 255 A allele strains. Eighteen coding sequences were unique to tir 255 A allele chromosomes, and three were unique to tir 255 T allele chromosomes. There also were non-pO157 plasmids that were unique to each tir 255 allele variant. The overall average number of prophages did not differ between tir 255 allele strains; however, there were different types between the strains. Genomic and mobile element variation linked to the tir 255 polymorphism may account for the increased frequency of the T allele isolates in human disease.

Keywords: Bacteriophage; Plasmids; STEC; Translocated Intimin Receptor; bacterial genomics; comparative genomics; whole genome sequencing (WGS).

Figure 1

Phylogenetic tree of all STEC O157:H7 chromosomes included in the study. Leaf text colors indicate the source of the isolate as human (blue) or non-human (green). Leaf decorations and labels are based on previously published SNP-based phylogeny (¹Manning et al., 2008, ²Bono et al., 2012), tir 255 allele genotype (³Bono et al., 2007), and Shiga toxin subtype and variant as determined by VirulenceFinder (Camacho et al., 2009; Joensen et al., 2014; Malberg Tetzschner et al., 2020). N.D. abbreviation is for not determined. The non-pO157 plasmids are separated into plasmid groups across the top of the columns. The black boxes beneath the group name indicate that the plasmid was found in the corresponding strain. The red asterisk indicates strains that were not found to contain the mdfA gene by CARD because of a missense mutation resulting in a truncated and presumably inactive protein.

Figure 2

Genetic map showing the apparent scarring left by excision of a phage. The region from an ancestral Escherichia coli O55:H7 chromosome (CP038389) (top) did not have an insertion of a stx2_c containing prophage at the sbcB gene. The intact stx2_c contains prophage from strain Gim1-1 (CP038344) (bottom), and the genes left behind from the excision of the prophage containing the stx2_c gene from strain DEC4E (CP038398) (middle) has some scarring associated with a prophage insertion and subsequent excision. The genes are represented by arrows with the red arrow representing the flanking chromosome genes and the purple arrow representing the genes shared by all three chromosomes. The green and orange arrows represent prophage genes. The shaded areas between the genetic map represent the percent similarly of the regions to each other.

Figure 3

Genetic map showing an 80 kb integrated region in the chromosome from three STEC O157:H7 strains contains antibiotic resistance genes. Each colored arrow represents a different gene, except the green color which represents different genes in the inserted region. Gene names are located either above or below their respective gene. The shaded areas between the genetic map represent the percent similarly of the insertion regions to each other.

Figure 4

Tanglegram of pO157 plasmids (numbered with their chromosome’s GenBank accession number for ease of reading) and their STEC O157:H7 chromosome. The accession numbers boxed in green are tir 255 A allele strains. The accession numbers from the remaining non-highlighted strains are tir 255 T allele strains. The intermediate ancestral strains 493/89 and LSU 61 were not used in this analysis due to their pO157 plasmid being approximately 20 kb larger than the pO157 plasmids in other STEC O157:H7 strains.