Genomic analysis of shiga toxin-containing Escherichia coli O157:H7 isolated from Argentinean cattle

Authors: AMADIO, ARIEL - Instituto Nacional De Tecnologia Agropecuaria; Bono, James - Jim; IRAZOQUI, MATIAS - Instituto Nacional Tecnologia Agropecuaria; LARZABAL, MARIANO - Instituto Nacional Tecnologia Agropecuaria; MARQUES DA SILIVA, WANDERSON - Instituto Nacional Tecnologia Agropecuaria; EBERHARDT, MARIA - Instituto Nacional Tecnologia Agropecuaria; RIVIERE, NAHUEL - Instituto Nacional Tecnologia Agropecuaria; GALLY, DAVID - Roslin Institute; MANNING, SHANNON - Michigan State University; CATALDI, ANGEL - Instituto Nacional De Tecnologia Agropecuaria

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/4/2021
Publication Date: 10/28/2021
Citation: Amadio, A., Bono, J.L., Irazoqui, M., Larzabal, M., Marques Da Siliva, W., Eberhardt, M.F., Riviere, N.A., Gally, D., Manning, S.D., Cataldi, A. 2021. Genomic analysis of shiga toxin-containing Escherichia coli O157:H7 isolated from Argentinean cattle. PLoS ONE. 16(10). Article e0258753. https://doi.org/10.1371/journal.pone.0258753.
DOI: https://doi.org/10.1371/journal.pone.0258753

Interpretive Summary: Shiga toxin-containing Escherichia coli O157:H7 (STEC O157) is a bacterium that can cause diarrhea, bloody diarrhea, and a potentially fatal kidney failure called hemolytic uremic syndrome (HUS). Argentina has the highest HUS incidence caused by STEC O157 worldwide in children under the age of 5. Cattle are one of the natural reservoirs for STEC O157 strains and infections can occur via ingestion of contaminate food products such as meat, dairy, fruits, vegetables and water sources. To determine why the STEC O157:H7 strains from Argentina are responsible for the high rate of HUS in children, we compared the genomes of these strains with previously published strains not from Argentina. There were no significant differences between the two groups when it came to the structure and genes that make up the genomes. However, the regulators that control production of Shiga toxin, the primary virulence factor responsible for HUS were different between the two groups. Further research is needed to better understand the higher production of Shiga toxin in the Argentinean STEC O157 strains.

Technical Abstract: Cattle are the main reservoir of Enterohemorrhagic Escherichia coli (EHEC), with O157:H7 the distinctive serotype. EHEC is the main causative agent of a severe systemic disease, Hemolytic Uremic Syndrome (HUS). Argentina has the highest pediatric HUS incidence worldwide with 12–14 cases per 100,000 children. Herein, we assessed the genomes of EHEC O157:H7 isolates recovered from cattle in the humid Pampas of Argentina. According to phylogenetic studies, EHEC O157 can be divided into clades. Clade 8 strains that were classified as hypervirulent. Most of the strains of this clade have a Shiga toxin stx2a-stx2c genotype. To better understand the molecular bases related to virulence, pathogenicity and evolution of EHEC O157:H7, we performed a comparative genomic analysis of these isolates through whole genome sequencing. The isolates classified as clade 8 (four strains) and clade 6 (four strains) contained 13 to 16 lambdoid prophages per genome, and the observed variability of prophages was analysed. An inter strain comparison show that while some prophages are highly related and can be grouped into families, other are unique. Prophages encoding for stx2a were highly diverse, while those encoding for stx2c were conserved. A cluster of genes exclusively found in clade 8 contained 13 genes that mostly encoded for DNA binding proteins. In the studied strains, polymorphisms in Q antiterminator, the Q-stx2A intergenic region and the O and P ' alleles of prophage replication proteins are associated with different levels of Stx2a production. As expected, all strains had the pO157 plasmid that was highly conserved, although one strain displayed a transposon interruption in the protease EspP gene. This genomic analysis may contribute to the understanding of the genetic basis of the hypervirulence of EHEC O157:H7 strains circulating in Argentine cattle. This work aligns with other studies of O157 strain variation in other populations that shows key differences in Stx2a-encoding prophages.