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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Meat Safety and Quality » Research » Publications at this Location » Publication #386875

Research Project: Identification, Genomic Characterization, and Metabolic Modeling of Foodborne Pathogens in the Meat Production Continuum

Location: Meat Safety and Quality

Title: Rates of evolutionary change of resident Escherichia coli O157:H7 differ within the same ecological niche

item Weinroth, Margaret - Maggie
item Clawson, Michael - Mike
item Arthur, Terrance
item Wells, James - Jim
item Harhay, Dayna
item STRACHAN, NORVAL - University Of Aberdeen
item Bono, James - Jim

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/31/2022
Publication Date: 4/7/2022
Citation: Weinroth, M.D., Clawson, M.L., Arthur, T.M., Wells, J., Harhay, D.M., Strachan, N., Bono, J.L. 2022. Rates of evolutionary change of resident Escherichia coli O157:H7 differ within the same ecological niche. BMC Genomics. 23. Article 275.

Interpretive Summary: Escherichia coli O157:H7 is a bacterium that causes foodborne illness and is naturally occurring in cattle. Over time, bacteria can change at the genome level, these small changes can provide information on where the bacteria might have come from when compared to the genomes of other bacteria. While there are many studies on E. coli O157:H7’s genome changes over a short amount of time in the laboratory, there was no information on long-term changes in a cattle feedlot environment. In this study, we compared the changes in the genome of E. coli O157:H7 from a single feedlot over more than two decades. This study, demonstrated that the genomes of different groups of E. coli O157:H7 in the same place did not change at the same rate. Additionally, some parts of E. coli O157:H7’s genetic code that was thought to be highly variable was more conserved than previously thought. These findings demonstrate how quickly E. coli O157:H7 strains evolve over time which will improve foodborne outbreak investigations that depend on relatedness of different strains.

Technical Abstract: Background: Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a pathogen known to reside in cattle feedlots. This retrospective study examined 181 STEC O157:H7 strains collected over 23 years from a closed-system feedlot. All strains were subjected to short-read sequencing, with a subset of 36 also subjected to long-read sequencing. Results: Over 96% of the strains fell into four phylogenetically distinct clades. Clade membership was associated with multiple factors including stx composition and the alleles of a well-characterized polymorphism (tir 255 T>A). Small plasmids (2.7 to 40kb) were found to be primarily clade specific. Within each clade, chromosomal rearrangements were observed along with a core phageome and clade specific phages. Across both core and mobile elements of the genome, multiple SNP alleles were in complete linkage disequilibrium across all strains within specific clades. Clade evolutionary rates varied between 0.9 and 2.8 SNP/chromosome/year with two tir A allele clades having the lowest evolutionary rates. Investigation into possible causes of the differing rates was not conclusive but revealed a synonymous based mutation in the DNA polymerase III of the fastest evolving clade. Phylogenetic trees generated through our bioinformatic pipeline versus the NCBI’s pathogen detection project were similar, with the two tir A allele clades matching individual NCBI SNP clusters, and the two tir T allele clades assigned to multiple closely-related SNP clusters. Conclusions: In one ecological niche, a diverse STEC O157:H7 population exhibited different rates of evolution that associated with SNP alleles in linkage disequilibrium in the core genome and mobile elements, including tir 255 T>A.