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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Produce Safety and Microbiology Research » Research » Publications at this Location » Publication #381479

Research Project: Ecology and Detection of Human Pathogens in the Produce Production Continuum

Location: Produce Safety and Microbiology Research

Title: Genomic insights into divergent evolution of virulence and fitness traits in Shiga toxin-producing Escherichia coli O121

item Carter, Michelle
item Pham, Antares

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 3/26/2021
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Shiga toxin-producing Escherichia coli (STEC) serotype O121:H19 is among the top six non-O157 serotypes that are frequently associated with human disease. We previously reported that, although clinical STEC O121:H19 strains are indistinguishable from the environmental ones based solely upon virulence gene content or MLST typing, they differ in carbon utilization profiles and other fitness traits. In this study we identified molecular determinants underlying phenotypic divergence between clinical and environmental STEC O121:H19 isolates and evaluated pathogenicity potential of other O121 serotypes. STEC O121 strains were sequenced using SMRT technology on a PacBio RSII instrument. The genomes were assembled with RS_HGAP_Assembly.3 and annotated using Prokaryotic Genome Annotation Pipelines. Comparative genomics were carried out in Edgar. Virulence genes and antibiotic resistance genes were identified by searching VFDB and CARD, respectively. Pan genome analysis revealed 3760 core CDSs, 1708 dispensable CDSs, and 1441 singletons. This large set of cloud genes were mainly attributed to environmental strains RM8082 (O121:H7) and RM10740 (O121:H10). The environmental isolate RM8352 (O121:H19) exhibited the highest similarity with 16-9255, a clinical isolate linked to the large 2016 outbreak associated with flour in Canada. All O121:H19 strains carry key virulence genes of enterohemorrhagic E. coli and genes encoding TTSS, TTSS effectors, and T6SS. Both non-O121:H19 strains lack LEE and possess a few TTSS effector genes. RM8082 lacks the chromosome-bore hemolysin gene hlyE, T6SS genes, and paa, but carries K88 and P fimbriae genes. RM10740 carries an additional 14 SCI-1 T6SS genes and a homolog of Yersinia virulence gene ail. Analyses of the O121:H19 strain-specific genes revealed that they mainly encode functions related to antibiotic resistance, carbon and energy metabolism, transport, and stress resistance. These data revealed genetic loci determining strain specific traits in STEC O121:H19 and demonstrated distinct evolutionary linages and pathogenicity potential among serotypes O121:H19, O121:H7, and O121:H10.