Genome Sequence of Enterohemorrhagic Escherichia coli NCCP15658

Abstract

Enterohemorrhagic Escherichia coli causes severe food-borne disease in the guts of humans and animals. Here, we report the high-quality draft genome sequence of E. coli NCCP15658 isolated from a patient in the Republic of Korea. Its genome size was determined to be 5.46 Mb, and its genomic features, including genes encoding virulence factors, were analyzed.

GENOME ANNOUNCEMENT

Escherichia coli strains are mainly found in the environment or in the guts of endotherms. Most of the E. coli strains existing in human guts are harmless commensals. However, several serotypes can cause severe food-borne infectious diseases (15). E. coli O157:H7 is one of the representative pathogenic E. coli strains, which are classified as Shiga toxin-producing enterohemorrhagic E. coli (EHEC). So far, the genome sequences of E. coli O157:H7 EDL933 (11), Sakai (7), TW14359 (9), and EC4115 (5) have been reported. Strain NCCP15658 was isolated from a female patient who presented with diarrhea, vomit, and stomach cramps in 2004; the isolate was provided to and deposited at the National Culture Collection for Pathogens, National Institute of Health, Republic of Korea.

The genome sequence of NCCP15658 was determined by using the Illumina/Solexa platforms. A total of 4.6 Gb of reads were produced from a 600-bp paired-end library and a 3-kb mate-pair library that were produced, respectively, in-house and at NICEM in the Republic of Korea. CLC Genomics Workbench version 4.8 (CLC bio, Inc.) was used for sequence trimming, de novo assembly, and read mapping. The contigs from de novo assembly and the consensus sequences from mapping to the E. coli TW14359 genome were adopted for the final assembly. SSPACE version 1.2 (3) was used to construct the scaffolds, and the assembly was improved by gap filling with IMAGE version 2.4 (14). Glimmer 3.02 and GeneMarkS were used for prediction of protein-coding sequences. Functional assignment of the predicted genes, performed through homology-based searches against the MicroScope, GenBank, Pfam, and TIGRFam databases, was complemented with the annotation result from the RAST server (1).

The final draft genome sequence in 51 contigs has 5,462,312 bp with a GC content of 50.45%, and 5,547 protein-coding genes were annotated. The genome sequence showed the highest similarity to E. coli TW14359 and EC4115, with an ANIb value of 99.93% as estimated by Jspecies version 1.2.1 (12). The genome has plasmid-borne sequences similar to the sequence of pO157 that is commonly harbored in O157:H7 strains. Serotypes of E. coli have been classified by specific genes, such as wzx, wzy, and fliC (2). Phylogenetic analysis of these genes in NCCP15658 suggests its identity as O157:H7. NCCP15658 contains effectors and structural proteins associated with type III secretion, most of which are encoded at the locus of enterocyte effacement (LEE) (4, 10, 13). The chromosome and pO157 virulence plasmid contain genes for Shiga toxin and a Shiga toxin-like protein that are related to significant enteric human pathogens (6). NCCP15658 also possesses genes involved in cell attachment and virulence, including intimin/invasion/adhesion, hemolysins, and pertactin. Thus, the NCCP15658 genome presents the genetic features for various virulence factors. This work provides additional genomic information for the O157:H7 type of EHEC, which will be useful to study the genome evolution of pathogenicity through comparative analysis of EHEC genomes.

Nucleotide sequence accession number.

The draft genome sequence was deposited in GenBank under the accession number AJMD00000000. The sequence and annotation are also available from the Genome Encyclopedia of Microbes (GEM; http://www.gem.re.kr) (8).