Comparative genomics applied to systematically assess pathogenicity potential in Shiga toxin-producing Escherichia coli O145:H28

Authors: Carter, Michelle; Laniohan, Nicole; LO, CHIEN-CHI - Los Alamos National Research Laboratory; CHAIN, PATRICK S. - Los Alamos National Research Laboratory

Submitted to: Microorganisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/19/2022
Publication Date: 4/19/2022
Citation: Carter, M.Q., Laniohan, N.S., Lo, C., Chain, P.G. 2022. Comparative genomics applied to systematically assess pathogenicity potential in Shiga toxin-producing Escherichia coli O145:H28. Microorganisms. 10(5). Article 866. https://doi.org/10.3390/microorganisms10050866.
DOI: https://doi.org/10.3390/microorganisms10050866

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. STEC naturally reside in ruminant animals, especially cattle, and can be transmitted to humans by direct contact or via contaminated food or water. We previously reported the complete genome sequences of 12 environmental STEC O145:H28 strains isolated from different environmental samples near a leafy green growing region in California. In this study, we performed comparative genomic analyses between the environmental isolates and clinical strains to reveal if clinical strains carry a specific set of genes enhancing their survival fitness and/or pathogenicity. Strain relatedness analysis based on the genes shared by all strains (core gene) separated STEC strains belonging to different serotypes successfully but failed to separate clinical strains from the environmental isolates. In contrast, strain relatedness analysis based on the dispensable genes (genes not shared by all strains) grouped all clinical strains in the same cluster, suggesting clinical strains carry a common set of dispensable genes that confer STEC fitness traits in infected humans. Examining the 333 virulence genes in STEC revealed a high mutation rate in genes encoding protein adhesins, fimbrial structures, transporter proteins, and proteins secreted from bacterial pathogens to host cells, implying presence of selection pressures for these mutations in STEC’s natural habitats. Loss-of-function mutation is likely a mechanism that pathogens adopt to cope with host defense and other antimicrobial compounds including antibiotics. Therefore, understanding the interactions between STEC and their indigenous community members would shed light on factors driving emergence of hypervirulent STEC variants.

Technical Abstract: Shiga toxin-producing Escherichia coli (STEC) O145:H28 can cause severe disease in humans and is a predominant serotype in STEC O145 environmental isolates. Here, comparative genomics was applied to a set of clinical and environmental strains to systematically evaluate the pathogenicity potential in environmental strains. While the core genes-based tree separated all O145:H28 strains from the non O145:H28 reference strains, it failed to segregate environmental strains from the clinical. In contrast, the accessory genes-based tree placed all clinical strains in the same clade regardless of their genotypes or serotypes, apart from the environmental strains. Loss-of-function mutations were common in the virulence genes examined, with a high frequency in genes related to adherence, autotransporters, and the type three secretion system. Distinct differences in pathogenicity islands LEE, OI-122, and OI-57, the acid fitness island, and the tellurite resistance island were detected between the O145:H28 and reference strains. A great amount of genetic variation was detected in O145:H28, which was mainly attributed to deletions, insertions, and gene acquisition at several chromosomal “hot spots”. Our study demonstrated a distinct virulence gene repertoire among the STEC O145:H28 strains originating from the same geographical region and revealed unforeseen contributions of loss-of-function mutations to virulence evolution and genetic diversification in STEC.