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United States Department of Agriculture

Agricultural Research Service

Research Project: Genomic and Proteomic Analysis of Foodborne Pathogens

Location: Molecular Characterization of Foodborne Pathogens

Title: Complete genome sequence and comparison of two Shiga toxin-producing Escherichia coli O104 isolates

Authors
item Yan, Xianghe
item Fratamico, Pina
item Bono, James
item Baranzoni, Gianmarco -
item Tebbs, Robert -
item O'Connell, Catherine -

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: February 21, 2014
Publication Date: May 18, 2014
Citation: Yan, X., Fratamico, P.M., Bono, J.L., Baranzoni, G., Tebbs, R., O'Connell, C. 2014. Complete genome sequence and comparison of two Shiga toxin-producing Escherichia coli O104 isolates. Meeting Abstract. MA.

Technical Abstract: Shiga toxin-producing Escherichia coli (STEC) O104 strains have been associated with sporadic cases of illness and have caused outbreaks associated with milk and sprouts. E. coli O104:H21 caused an outbreak associated with milk in the U.S. in 1994. In this study, next generation sequencing technology was used to determine the genome sequence of two STEC O104 strains, and genomic differences were identified by comparing the genomes of the two sequenced strains to those of 29 other O104 strains deposited in GenBank. DNA obtained from STEC O104:H21 (milk outbreak strain) and O104:H7 (cattle isolate) strains were shot gun sequenced using the Ion Torrent PGM and PacBio SMRT sequencing technologies generating two closed genomes. Raw PacBio reads were de novo assembled using an adapted Celera Assembler PBcR pipeline. CLC workbench 6.5 was used to assemble Ion Torrent raw data, and the two genome sequences were submitted to RAST for automated annotation followed by manual checking. The comparative analysis of the protein-coding sequences of the O104 genomes was assessed by using NCBI BLAST. A phylogenetic tree of all strains was constructed with the program Mega6. The results showed that the two sequenced strains (O104:H21 and O104:H7) are genetically distinct from the O104:H4 outbreak strain. Also, the analysis of these two genome sequences shows a higher similarity to one another than to the corresponding genomes of sequenced O104:H4 strains. Interestingly, the plasmids from the two sequenced O104 strains are closely related to STEC O113 plasmids. Also, most of the genomic variation in the strains examined was due to the presence of a variety of different mobile genetic elements, including prophage regions. The presence of plasmids carrying virulence-associated genes may play a role in the pathogenic potential of O104 strains for humans.

Last Modified: 10/31/2014
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