Genome Sequences of Two Emerging Non-O157 Shiga Toxin-Producing Escherichia coli Strains.

Shiga toxin-producing Escherichia coli (STEC) causes severe illness in humans, including hemorrhagic colitis and hemolytic uremic syndrome. A parallel evolutionary model was proposed in which E. coli strains of distinct phylogenies independently integrate Shiga toxin-encoding genes and evolve into STEC. We report the draft genomes of two emerging non-O157 STEC strains.

GENOME ANNOUNCEMENT

Shiga toxin-producing Escherichia coli (STEC) has become a significant food-borne pathogen since E. coli O157:H7 was first identified as the agent causing food-borne outbreaks in 1982 (1). Non-O157 STEC has been increasingly associated with food-borne illness (2–5) and accounts for approximately 50% of all STEC infections in the United States (4). We selected two STEC strains of serogroups O26 and O111 for whole-genome sequencing (WGS) analysis (6). It was proposed that STEC strains from multiple lineages have acquired Shiga toxin genes (stx) independently, referred to as a parallel evolutionary process (7, 8).

There are approximately 100 genome sequences of STEC that are deposited in GenBank. We report two draft genome sequences of non-O157 STEC strains: E. coli O26:H11 strain CFSAN001629 (host, human; stx gene type, stx1) and E. coli O111:H8 strain CFSAN001632 (host, human; stx gene type, stx1). The genome sequence data bring more clarity to the evolutionary processes and virulence factors of these important pathogens.

The two STEC strains were sequenced using a 454 FLX+ pyrosequencing system (Roche, Branford, CT) to obtain 20 to 24×-coverage draft genome sequences. Genomic DNA from each strain was extracted from overnight Trypticase soy broth (TSB) culture with a DNeasy blood and tissue kit (Qiagen, Valencia, CA). Genomic contigs were assembled (de novo) with the 454 Life Sciences Newbler software package version 2.6 (Roche). The data for each draft genome sequence are as follows: for CFSAN001629, 24× coverage, 275 contigs, genome size of 5,444,981 bp, and contig N50 of 100,856 bp, and for CFSAN001632, 20× coverage, 259 contigs, genome size of 5,303,432 bp, and contig N50 of 99,424 bp. Sequences were annotated with the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (9). Totals of 5,564 and 5,400 genes were identified for strains CFSAN001629 and CFSAN001632, respectively.

A detailed report of the phylogenetic analyses of these two draft sequences will be included in a future publication.

Nucleotide sequence accession numbers.

The draft genome sequences of E. coli O26:H11 CFSAN001629 and E. coli O111:H8 CFSAN001632 are available in GenBank under accession no. AMXO00000000 and AMXQ00000000, respectively.