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ARS Home » Northeast Area » Wyndmoor, Pennsylvania » Eastern Regional Research Center » Characterization and Interventions for Foodborne Pathogens » Research » Publications at this Location » Publication #308972
Title: Genome sequencing and comparative genomics provides insights on the evolutionary dynamics and pathogenic potential of different H-Types of Shiga toxin-producing Escherichia coli O104

Author
item Yan, Xianghe
item Fratamico, Pina
item Bono, James - Jim
item BARANZONI, GIANMARCO - University Of Bologna, Italy
item Chen, Chinyi

Submitted to: BMC Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/12/2015
Publication Date: 4/3/2015
Citation: Yan, X., Fratamico, P.M., Bono, J.L., Baranzoni, G., Chen, C. 2015. Genome sequencing and comparative genomics provides insights on the evolutionary dynamics and pathogenic potential of different H-Types of Shiga toxin-producing Escherichia coli O104. BMC Microbiology. DOI: 10.1186/s12866-015-0413-9.

Interpretive Summary: A bacterium known as Escherichia coli O104:H4 has been identified recently as an emerging food-borne pathogen, and it caused a large outbreak in Europe in 2011 linked to fenugreek sprouts. In 1994, there was an outbreak in the U.S. linked to milk contaminated with E. coli O104:H21, and there have been many cases of human illness linked to other E. coli strains belonging to serogroup O104. This serogroup is also carried by animals; therefore, animals, including cattle, may serve as a reservoir for this group of pathogens, and food of animal origin can be source of human infection. It is known that one way that pathogens emerge is by acquiring DNA from other bacteria that encodes for proteins that are involved in the disease process, increasing their virulence. To understand the emergence of E. coli O104, the DNA sequence of the genomes of two O104 strains (O104:H7 isolated from cattle and the O104:H21 milk outbreak strain) that produce harmful toxins known as Shiga toxins was determined. The DNA sequence of these strains was compared to publicly available genome sequences of E. coli O104:H4 and to other strains that produce Shiga toxins. Genetic similarities and differences among the different bacterial strains analyzed were observed; however, one major conclusion that can be drawn from this work is that O104 strains may become more pathogenic for humans through the acquisition of genes from other bacteria that are carried on mobile genetic elements. This research enhances the understanding of the evolution and virulence of this important group of emerging pathogens and will help in the design of improved methods for detection of pathogenic E. coli O104 strains.

Technical Abstract: Various Shiga toxin-producing Escherichia coli (STEC) O104 H-types including H4, H7, H21, and H¯ have been associated with sporadic cases of illness and have caused outbreaks globally. In the U.S., STEC O104:H21 caused an outbreak associated with milk in 1994. The aim of this work was to conduct a systematic analysis of whole genome sequences and discuss the key challenges in understanding the evolutionary origins and pathogenesis of E. coli O104 strains. STEC O104:H21 (milk outbreak strain) and O104:H7 (cattle isolate) strains were shot-gun sequenced using the Ion Torrent PGM and PacBio SMRT technology generating two closed genomes. The eae gene involved in the attaching-effacing phenotype of diarrheagenic E. coli, was not found in either strain. However, two “complete” left and right end portions of the locus of enterocyte effacement (LEE) fragments were found in13 O104 strains examined with no strain containing the central portion of LEE, which includes eae. In O104:H4 strains, the missing central portion of the LEE locus was replaced by a pathogenicity island carrying the aidA (adhesin involved in diffuse adherence) gene and antibiotic resistance genes commonly carried on plasmids. Enteroaggregative E. coli-specific virulence genes and European outbreak specific stx2-encoding Escherichia P13374 or Escherichia TL-2011c bacteriophages were not found in all O104:H4 isolates. A phylogenetic tree of various O104 strains and non-O104 STEC whole genomes was constructed based on a progressive global alignment (progressive Mauve). The results showed that the two strains sequenced in this study (O104:H21 and O104:H7) are genetically more similar to each other than to the O104:H4 strains that caused an outbreak in Germany in 2011 and strains found in Central Africa. Interestingly, the plasmids from the two sequenced O104 strains were closely related to STEC O113 plasmids. Also, most of the genomic variation in the strains examined was due to the presence of different mobile genetic elements, including prophage and genomic island regions. The presence of plasmids carrying virulence-associated genes may play a role in the pathogenic potential of O104 strains for humans.