Skip to main content
ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Meat Safety & Quality Research » Research » Publications at this Location » Publication #370919

Research Project: Genomic and Metagenomic Differences in Foodborne Pathogens and Determination of Ecological Niches and Reservoirs

Location: Meat Safety & Quality Research

Title: Pathogenomes of atypical non-Shigatoxigenic Escherichia coli NSF/SF O157:H7/NM: Comprehensive phylogenomic analysis using closed genomes

item NYONG, EMMANUEL - University Of Texas At San Antonio
item ZAIA, SAM - University Of Texas At San Antonio
item ALLUE-GUARDIA, ANNA - University Of Texas At San Antonio
item RODRIGUEZ, ARMANDO - University Of Texas At San Antonio
item IRION-BYRD, ZAYNA - University Of Texas At San Antonio
item KOENIG, SARA - University Of Texas At San Antonio
item FENG, PETER - Food And Drug Administration(FDA)
item Bono, James - Jim
item EPPINGER, MARK - University Of Texas At San Antonio

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/19/2020
Publication Date: 5/15/2020
Citation: Nyong, E.C., Zaia, S.R., Allue-Guardia, A., Rodriguez, A.L., Irion-Byrd, Z., Koenig, S.S.K., Feng, P., Bono, J.L., Eppinger, M. 2020. Pathogenomes of atypical non-Shigatoxigenic Escherichia coli NSF/SF O157:H7/NM: Comprehensive phylogenomic analysis using closed genomes. Frontiers in Microbiology. 11:619.

Interpretive Summary: Enterohemorrhagic E. coli O157:H7 is a foodborne pathogen that can cause serious disease in humans. One of the main reasons it is able to cause disease is due to a toxin. This toxin is located on a mobile piece of the genome that can be transferred between bacteria. We wanted to looked at the genome of strains without toxin to better understand what allows these toxin containing mobile elements to transfer between strains. We determined that if a bacterial strain loses the mobile element with the toxin that the mobile element is not allow back into the strain. Understanding the resistance to transferring this toxin is foundational to improve risk assessment, biosurveillance, and the development of alternative toxin prevention strategies.

Technical Abstract: The toxigenic conversion of Escherichia coli strains by Shiga toxin-converting (Stx) bacteriophages were prominent and recurring events in the stepwise evolution of enterohemorrhagic E. coli (EHEC) O157:H7 from an enteropathogenic (EPEC) O55:H7 ancestor. Atypical, attenuated isolates have been described for both non- orbitol fermenting (NSF) O157:H7 and SF O157:NM serotypes, which are distinguished by the absence of Stx, the characteristic virulence hallmark of Stx-producing E. coli (STEC). Such atypical isolates either never acquired Stx-phages or may have secondarily lost stx during the course of infection, isolation, or routine subculture; the latter are commonly referred to as LST (Lost Shiga Toxin)-isolates. In this study we analyzed the genomes of 15 NSF O157:H7 and SF O157:NM strains from North America, Europe, and Asia that are characterized by the absence of stx, the virulence hallmark of STEC. The individual genomic basis of the Stx (-) phenotype has remained largely undetermined as the majority of STEC genomes in public genome repositories were generated using short read technology and are in draft stage, posing a major obstacle for the high-resolution whole genome sequence typing (WGST). The application of LRT (longread technology) sequencing provided us with closed genomes, which proved critical to put the atypical non-shigatoxigenic NSF O157:H7 and SF O157:NM strains into the phylogenomic context of the stepwise evolutionary model. Availability of closed chromosomes for representative Stx (-) NSF O157:H7 and SF O157:NM strains allowed to describe the genomic basis and individual evolutionary trajectories underlying the absence of Stx at high accuracy and resolution. The ability of LRT to recover and accurately assemble plasmids revealed a strong correlation between the strains’ featured plasmid genotype and chromosomally inferred clade, which suggests the coevolution of the chromosome and accessory plasmids. The identified ancestral traits n the pSFO157 plasmid of NSF O157:H7 strain LSU-61 provided additional evidence for its intermediate status. Taken together, these observations highlight the utility of LRTs for advancing our understanding of EHEC O157:H7/NM pathogenome evolution. Insights into the genomic and phenotypic plasticity of STEC on a lineage- and genomewide scale are foundational to improve and inform risk assessment, biosurveillance, and prevention strategies.