Whole-Genome Sequence of Escherichia coli Serotype O157:H7 Strain ATCC 43888.

Escherichia coli serotype O157:H7 strain ATCC 43888 is a Shiga toxin-deficient human fecal isolate. Due to its reduced toxicity and its availability from a curated culture collection, the strain has been used extensively in applied research studies. Here, we report the Illumina-corrected PacBio whole-genome sequence of E. coli O157:H7 strain ATCC 43888.

ANNOUNCEMENT

Hemorrhagic diarrhea caused by Shiga toxin (Stx)-producing Escherichia coli (STEC) serotype O157:H7 was first reported in the early 1980s (1, 2), and it remains the leading cause of STEC-related illnesses, deaths, and hospitalizations (3). Strains of serotype O157:H7 are genetically diverse due to variations in horizontally transferred regions (HTRs) that encode virulence factors, secretion systems, and host effector proteins (4, 5) and contribute to niche adaptation in the environment, in the host, and in foods (6, 7). The locus of enterocyte effacement (LEE) and stx genes, both encoded in HTRs, are considered definitive virulence factors. For safety reasons, studies of STEC O157:H7 strains often employ those deficient in different virulence factors, especially Stx. One such strain is B6914-MS1, a Stx-deficient human fecal isolate (8) that is available from the American Type Culture Collection (ATCC) as biosafety level 1 strain ATCC 43888. Due to genetic variability, the genome sequence from a single O157:H7 strain would not be considered representative for the serotype. Therefore, we determined the draft genome sequence of strain ATCC 43888 for use in comparative studies with sequenced genomes of O157:H7 strains whose fitness properties differ from those of ATCC 43888.

Strain ATCC 43888 was purchased from the ATCC and grown overnight in LB at 37°C. Large DNA fragments were extracted from a frozen cell pellet (−80°C) collected from 5 ml of the overnight culture using the Genomic-tip 100/G kit (Qiagen, Valencia, CA) and used for both PacBio and Illumina sequencing. PacBio sequencing and de novo genome assembly were done by the University of Delaware Sequencing Center (Dover, DE) as previously described (9). Illumina sequencing, sequence quality scoring, and sequence trimming were done by ProteinCT Biotechnologies, LLC (Madison, WI), as previously described (10). Default parameters were used for all software tools unless otherwise noted (9, 10). PacBio and Illumina sequencing yielded 111,360 reads with an average length of 8.45 kb (171-fold coverage) and 3.5 million 2 × 250-bp paired-end reads (327-fold coverage), respectively. The PacBio sequence assembly was corrected by mapping the Illumina sequence reads against the PacBio assembled contigs using BWA-MEM version 0.7.12-r1044 (https://github.com/lh3/bwa) to identify high-quality variants that were used to update the consensus sequences.

The closed ATCC 43888 genome consists of the following 3 circular contigs: a 5,375,715 bp chromosome with a G+C content of 49.9% and plasmids of 32,726 bp (51.2% G+C content) and 95,081 bp (48.8% G+C content) with sequence similarity to E. coli O157:H7 plasmids p35K (GenBank accession number CP015845) and pO157, respectively, as determined by BLAST analysis using GenBank. Based on the high-quality PacBio reads, the average sequencing coverage for the 3 contigs was 90×. The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline version 4.8 (11). BLAST searches of individual genes or loci revealed that the genes for Stx1 and Stx2 are not present, and no prophage was present in the stx1 insertion site within mlrA, nor was any prophage present in the stx2 insertion sites within the wrbA, sbcB, yecE, or Z2577 genes. An LEE pathogenicity island with 99.99% identity (100% coverage with no gaps) to the reference outbreak strain Sakai (GenBank accession number NC_002695) (4) was present. The PHAge Search Tool Enhanced Release (PHASTER) prophage locator and annotation tool (12, 13) identified 9 intact, 4 incomplete, and 3 questionable prophage regions, representing approximately 11% of the genome.

Data availability.

The whole-genome sequence was deposited at DDBJ/ENA/GenBank (accession numbers CP041623, CP041624, and CP041625). The versions described in this paper are the first versions. The Illumina and PacBio reads can be found in the SRA under accession numbers SRR9694420 and SRR9694229, respectively.