Comparative genomic and phenotypic analyses of virulence potential in Shiga toxin-producing Escherichia coli O121:H7 and O121:H10

Authors: Carter, Michelle; Laniohan, Nicole; PHAM, ANTARES - Former ARS Employee; Quinones, Beatriz

Submitted to: Frontiers in Cellular and Infection Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/3/2022
Publication Date: 11/24/2022
Citation: Carter, M.Q., Laniohan, N.S., Pham, A., Quinones, B. 2022. Comparative genomic and phenotypic analyses of virulence potential in Shiga toxin-producing Escherichia coli O121:H7 and O121:H10. Frontiers in Cellular and Infection Microbiology. 12. Article 1043726. https://doi.org/10.3389/fcimb.2022.1043726.
DOI: https://doi.org/10.3389/fcimb.2022.1043726

Interpretive Summary: Shiga toxin-producing Escherichia coli (STEC) consists of a group of genetically and phenotypically diverse E. coli strains that differ greatly in pathogenicity. O121:H19 is the predominant serotype in STEC O121 population and can cause severe disease in humans. Other O121 serotype, such as O121:H7 and O121:H10, have been frequently isolated from diverse environmental and food samples, but their virulence potential and pathogenicity are not well understood. In this study, we sequenced the compete genomes of two environmental isolates, one from cattle feces (O121:H7) and the other one from feral pig feces (O121:H10), collected at an agricultural region in California, and performed comparative genomic analyses with O121:H19 to assess the pathogenicity potential and public health risk of STEC strains belonging to the above two serotypes. Both O121:H7 and O121:H10 strains carry a much lower number of virulence genes than any of the O121:H19 strains examined, which was mainly due to the reduction in number of genes encoding adherence factors, the major players in biofilm formation, and the genes related to biosynthesis of the Type Three Secretion System, the major machinery to deliver bacterial toxins to host cells. However, compared with O121:H19 strains, the O121:H10 carries genes encoding cytolethal distending toxin and the O121:H10 strains carries a second set of gene cluster encoding Type Six Secretion System, which can deliver bacterial toxins to both animal hosts and other prokaryotic cells thus contributing to bacterial pathogenesis and environmental survival. Our data reveal reduced pathogenicity in both O121:H7 and O121:H10 strains compared with O121:H19 strains as both strains lack the large pathogenicity island (PAIs) LEE, however, both strains have potential to evolve to be much more virulent considering that the integration sites for several PAIs and fitness islands are unoccupied in both genomes of O121:H7 and O121:H10 strains.

Technical Abstract: Shiga toxin-producing Escherichia coli (STEC) O121 is among the top six non-O157 serogroups that are most frequently associated with severe disease in humans. While serotype O121:H19 is predominant, other O121 serotypes have been frequently isolated from environmental samples, but their virulence repertoire is poorly characterized. Here, we sequenced the complete genomes of two environmental isolates, one of serotype O121:H7 and the other of serotype O121:H10 and performed comparative genomic analysis with O121:H19 to assess their virulence potential and fitness traits. Both O121:H7 and O121:H10 strains carry a genome comparable in size with the O121:H19 genomes and belong to phylogroup B1. However, both strains appear to have evolved from a different lineage than the O121:H19 strains as demonstrated by the core genome-based phylogenetic analysis and Multi Locus Sequence Typing. A systematic search of over 300 E. coli virulence genes listed in the Virulence Factor DataBase revealed a total of 73 and 71 in O121:H7 and O121:H10 strains, respectively, in comparison with an average of 135 in the O121:H19 strains. This variation in the virulence genes repertoire was mainly attributed to the reduction in the number of genes related to the Type Three Secretion System in the O121:H7 and O121:H10 strains. Furthermore, compared to the O121:H19 strains, the O121:H7 strain carries more adherence and toxin genes while the O121:H10 strain carries more genes related to the Type Six Secretion System. Although both O121:H7 and O121:H10 strains carry the large virulence plasmid pEHEC, they do not harbor all the virulence genes located on the O121:H19 pEHEC. Comparative analyses of pathogenicity islands (PAIs) and fitness islands among the O121 strains revealed that, unlike the O121:H19 strains, neither the O121:H7 nor O121:H10 strain carried the locus of enterocyte effacement, PAI OI-122, or the tellurite resistance island. Although an incomplete Locus of Adhesion and Autoaggregation (LAA) was identified in the O121:H7 and O121:H10 strains, a limited number of virulence genes were in the LAAs. Consistent with the genomic analyses, both O121:H7 and O121:H10 strains exhibited reduced cytotoxicity compared with the O121:H19 strain. Our study demonstrated distinct evolutionary lineages among the strains of serotypes O121:H19, O121:H10, and O121:H7 and suggested reduced virulence potential in strains of STEC O121:H10 and O121:H7.