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Title: Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7

item Cooper, Kerry
item MANDRELL, ROBERT - US Department Of Agriculture (USDA)
item Louie, Jacqueline
item KORLACH, JONAS - Pacific Biosciences Inc
item CLARK, TYSON - Pacific Biosciences Inc
item Parker, Craig
item Huynh, Steven
item CHAIN, PATRICK - Los Alamos National Research Laboratory
item AHMED, SANAA - Los Alamos National Research Laboratory
item Carter, Michelle

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/18/2013
Publication Date: 1/14/2014
Citation: Cooper, K.K., Mandrell, R.E., Louie, J.W., Korlach, J., Clark, T.A., Parker, C., Huynh, S., Chain, P.S., Ahmed, S., Carter, M.Q. 2014. Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7. Biomed Central (BMC) Genomics. doi: 10.1186/1471-2164-15-17.

Interpretive Summary: We determined the complete genome sequences of two E. coli O145 strains, one linked to a 2010 US lettuce-associated outbreak and the other one linked to a 2007 Belgium ice-cream-associated outbreak. The genomic information obtained in this study facilitates the discovery of genetic markers for detection of enterohemorrhagic Escherichia coli in food and in agricultural environments. Furthermore, comparative genomics analyses of two sequenced O145 strains with other EHEC genomes provide evidences on the important factors contributing to the emergence of this important group of foodborne pathogens.

Technical Abstract: Background Although serotype O157:H7 is the predominant enterohemorrhagic Escherichia coli (EHEC), outbreaks of non-O157 EHEC that cause severe foodborne illness, including hemolytic uremic syndrome have increased worldwide. In fact, non-O157 serotypes are now estimated to cause over half of all the Shiga toxin-producing Escherichia coli (STEC) cases, and outbreaks of non-O157 EHEC infections are frequently associated with serotypes O26, O45, O103, O111, O121 and O145. Currently, there are no complete genomes for O145 in public databases. Results We determined the complete genome sequences of two O145 strains (EcO145), one linked to a US lettuce-associated outbreak (RM13514) and one to a Belgium ice-cream-associated outbreak (RM13516). Both strains contain one chromosome and two large plasmids, with genome sizes of 5,737,294 bp for RM13514 and 5,559,008 bp for RM13516. Comparative analysis of the two EcO145 genomes revealed a large core (5,173 genes) and a considerable amount of strain-specific genes. Additionally, the two EcO145 genomes display distinct chromosomal architecture, virulence gene profile, phylogenetic origin of Stx2a prophage, and methylation profile (methylome). Comparative analysis of EcO145 genomes to other completely sequenced EHEC and other E. coli and Shigella genomes revealed that, unlike any other known non-O157 EHEC strain, EcO145 ascended from a mutual lineage with EcO157/EcO55. This evolutionary relationship was further supported by the pangenome analysis of the 11 EHEC strains. Of the 3,902 EHEC core genes, EcO145 shares more genes with EcO157 than with the any other non-O157 EHEC strains. Conclusions Our data provides evidence that EcO145 and EcO157 evolved from a common lineage, but ultimately each serotype evolves via a lineage-independent nature to EHEC by acquisition of the core set of EHEC virulence factors, including the genes encoding Shiga toxin and the large virulence plasmid. The large variation between the two EcO145 genomes suggests a vast diversity of EcO145. The distinct methylome between the two EcO145 strains is likely due to the presence of a BsuBI/PstI methyltransferase gene cassette in the Stx2a prophage of the strain RM13514, suggesting a role of horizontal gene transfer-mediated epigenetic alteration in evolution of individual EHEC strain.