Reoccurring Escherichia coli O157:H7 Strain Linked to Leafy Greens-Associated Outbreaks, 2016-2019

Abstract

Genomic characterization of an Escherichia coli O157:H7 strain linked to leafy greens-associated outbreaks dates its emergence to late 2015. One clade has notable accessory genomic content and a previously described mutation putatively associated with increased arsenic tolerance. This strain is a reoccurring, emerging, or persistent strain causing illness over an extended period.

Keywords: Escherichia coli O157:H7; United States; bacteria; enteric infections; foodborne disease; sequence analysis.

Figure 1

Tip-dated maximum clade credibility tree of 245 isolates of reoccurring Escherichia coli O157:H7 strain REPEXH02 linked to leafy greens–associated outbreaks, 2016–2019, generated in BEAST2 (https://www.beast2.org). Tips are aligned with the date of collection; calendar year is shown on the x-axis. Tips are colored according to the outbreak to which each isolate belonged; the shape corresponds to sample type (e.g., human, animal, environmental, or food). A horizontal black line segregates the two identified clades. Clade 1 contains outbreak B2 where some illness was traced back to Santa Maria, California, USA, as well as environmental samples collected in that region. Clade 2 contains outbreak A, which was traced back to the Salinas Valley, California. The presence/absence matrix to the right of the tree displays accessory genome content identified using Roary/scoary with 90% sensitivity and specificity to a subset of clade 1 isolates. A legend for accessory genome feature labels is included in Appendix 1 Table 5.

Figure 2

Annotated plasmids of reference genome 2019C-3201 of Escherichia coli O157:H7 containing clade-specific genomic features. A) p2019C-3201_1 annotated with prokka version 1.14.5 (yellow annotations) (11). Mapped list of Roary features (pan_genome_references.fa) onto plasmid (95% nucleotide identity; gray annotations) (14). Features highlighted had >90 sensitivity and >90 specificity to a subset of clade 1 isolates (pink annotations). The region with specific/sensitive features covers a large portion of the plasmid and predominately contains genes encoding hypothetical proteins with unknown functions and common plasmid-associated genes. Three features did not map in Geneious because they were either below 95% identity (2 features) or were identified as partial copy (1 feature). B) p2019C-3201_2 annotated with prokka v1.14.5 (yellow annotations). Mapped list of Roary features (pan_genome_references.fa) onto plasmid (100% nucleotide identity; gray annotations). Features highlighted had >90 sensitivity and >97 specificity (blue annotations) to a subset of clade 1 isolates. The region with specific/sensitive features covers a large portion of the plasmid and is associated with conjugation. Image was generated using Geneious version 2021.2 (https://www.geneious.com).