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Additional file 5.

Additional file 2. Phylogenic tree visualized in FigTree and constructed via Parsnp of only chromosomes of the 36 strains subjected to long-read (PacBio) sequencing. Coloring indicates previously delineated clade structure and confirms clade membership was not due to plasmid presence.

Additional file 1. Phylogenic tree 181 strains sequenced. Parsnp was used to generate the phylogenetic relationship and the tree was visualized in FigTree. The strain’s names in red indicates the strains that have complete closed genomes.

Additional file 6. Number of strains collected by year. Note that a 2007 study met the inclusion criteria for this study and as a result a larger number of strains are included in that year.

Additional file 1.

Additional file 2.

Additional file 3 Variants found to be in r2 = 1 linkage disequilibrium with at least three other variants (and a minimum of 5% MAF) across all samples (inclusive of both the chromosome and associated plasmids). Variant locations are described in context to reference genome CP038428.

Additional file 5. Phylogenic tree visualized in FigTree and constructed via Parsnp of all samples in the study with both the long read (FLT_*) and short read (FLT_SR_*) samples from the same DNA pool. Coloring is by sample pair with the number to the right indicating the number of informative SNP differences found between each pair (with the average being 1.47 between pairs).

Additional file 4. Summary of the results from each SNP cluster detected in the study via the Pathogen Detection database. Organization is first by clade identify within this study then the pathogen detection database SNP cluster membership. Sub-branch information is only associated with samples from this study and overall SNP cluster is inclusive of all strains in the SNP cluster inclusive of study strains.

The human zoonotic pathogen Escherichia coli O157:H7 is defined by its extensive prophage repertoire including those that encode Shiga toxin, the factor responsible for inducing life-threatening pathology in humans. As well as introducing genes that can contribute to the virulence of a strain, prophage can enable the generation of large-chromosomal rearrangements (LCRs) by homologous recombination. This work examines the types and frequencies of LCRs across the major lineages of the O157:H7 serotype. We demonstrate that LCRs are a major source of genomic variation across all lineages of E. coli O157:H7 and by using both optical mapping and Oxford Nanopore long-read sequencing prove that LCRs are generated in laboratory cultures started from a single colony and that these variants can be recovered from colonized cattle. LCRs are biased towards the terminus region of the genome and are bounded by specific prophages that share large regions of sequence homology associated with the recombinational activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that important virulence phenotypes such as Shiga-toxin production, type-3 secretion and motility can be affected by LCRs. In summary, E. coli O157:H7 has acquired multiple prophage regions over time that act to continually produce structural variants of the genome. These findings raise important questions about the significance of this prophage-mediated genome contingency to enhance adaptability between environments.

Additional file 9: Figure S4. Alignment of genotype 2 AOMB-BP-CP proteins flagged as specific to genotype 2 M. haemolytica with genotype 1 peptidase S6 protein and genotype 2 S6 family IgA-specific metalloendopeptidase protein. The alignment contains peptidase S6 protein sequence from five genotype 1 strains of different subtypes, S6 family IgA-specific metalloendopeptidase protein sequence from four genotype 2 strains of different subtypes, and AOMB-BP-CP protein sequence from four genotype 2 strains of different subtypes. The AOMB-BP-CP proteins flagged by EDGAR as specific to genotype 2 M. haemolytica are denoted by an asterisk. The alignment additionally contains translated nucleotides immediately upstream of, in-frame, and concatenated to the AOMB-BP-CP protein sequence for each of the genotype 2 strains representing different subtypes. The black arrow highlights the location of a stop codon in the concatenated sequences. Areas of greater than 51% chemical identity are indicated with grey boxes.

Additional file 10: Figure S5. Alignment of all annotated porin-like proteins in five genotype 1 and four genotype 2 M. haemolytica strains that are each of a different subtype. The proteins flagged by EDGAR as specific to genotype 2 M. haemolytica are indicated within the alignment with an asterisk. The site of premature stop codons within proteins encoded by a pseudogene homolog of the genotype 2 specific porin is highlighted with an arrow. Areas of 51% chemical identity or greater are indicated with grey boxes.

Additional file 7: Figure S2. Alignment of all detected isoforms of the peptidase S6 gene specific to genotype 2 M. haemolytica and those encoded by a homologous pseudogene in genotype 1 M. haemolytica. The alignment shows all five isoforms of the peptidase S6 specific to genotype 2 M. haemolytica that were detected, and all four of the peptidase S6 homologs in genotype 1 M. haemolytica which all contained a premature stop codon. Isoform numbers in this figure correspond to the isoform numbers listed in Additional file 1: Table S1. *184 iso 1 is an abbreviation for USDA-ARS-USMARC-184 isoform 1. Areas of 51% chemical identity or greater are indicated with grey boxes.

Additional file 6: Figure S1. Alignment of genotypes 1 and 2 peptidase S6 and S6 family IgA-specific metalloendopeptidase gene and pseudogene encoded proteins. Represented in the alignment are four peptidase S6 proteins from five genotype 1 strains that are each of a different subtype, two peptidase S6 proteins from four genotype 2 strains that are each of a different subtype, and two proteins from the same four genotype 2 strains that originated from genes annotated as S6 family IgA-specific metalloendopeptidase proteins. Areas of 51% chemical identity or greater are indicated with grey boxes within the alignment. The peptidase S6 proteins originating from a gene flagged for specificity to genotype 2 M. haemolytica by EDGAR software is annotated as “Genotype 2 specific*”. The most closely related genotype 1 protein to the genotype 2 specific peptidase S6, encoded by a pseudogene, is annotated within the alignment. Regarding the closely related genotype 1 protein, the end of the peptide, which does not contain a corresponding gene sequence stop codon, is denoted with an arrow in the alignment. Extended translation to a stop codon is shown with sequence above the alignment.

Additional file 8: Figure S3.. Alignment of autotransporter outer membrane beta-barrel domain-containing protein (AOMB-BP-CP) isoforms. The alignment contains all annotated AOMB-BP-CP proteins from five genotype 1 and four genotype 2 M. haemolytica strains that are each of a different subtype. The AOMB-BP-CP proteins flagged by EDGAR as specific to genotype 2 M. haemolytica are indicated with an asterisk. Areas of 51% chemical identity or greater are indicated with grey boxes.