Abstract
Escherichia fergusonii is a Gram-negative, rod-shaped, non-spore-forming member of the Enterobacteriaceae family and is a bacterium with both biotechnological applications and implication in human clinical disease. Here, we report the draft genome sequences of three isolates of E. fergusonii from beef trim (GTA-EF02), ground beef (GTA-EF03), and chopped kale (GTA-EF04).
GENOME ANNOUNCEMENT
Escherichia fergusonii is ubiquitous in nature, having been isolated from soil, water, plants, and animals. This organism was originally classified as enteric group 10, until it was recognized as a new bacterial species via DNA hybridization in 1985 (1). E. fergusonii is closely related to Escherichia coli, with which it exhibits a similar biochemical profile(s). It is also often misidentified as Salmonella due to a similar appearance on MacConkey agar (2, 3). Clinically, it is an opportunistic pathogen that was originally isolated from human blood samples, and it has since been implicated in human and animal disease (4, 5). Industrial applications include bioremediation (6) and hydrogen production (7).
E. fergusonii strains were recovered from food samples, including beef trim (GTA-EF02), ground beef (GTA-EF03), and chopped kale (GTA-EF04). Genomic DNA was isolated from overnight cultures grown on nutrient agar, using the Maxwell 16 cell DNA purification kit (Promega, Madison, WI). Sequencing libraries were constructed using the Nextera XT DNA sample preparation kit (Illumina, Inc., San Diego, CA), and paired-end sequencing was performed with the Illumina MiSeq platform, using 600-cycle MiSeq reagent kits (version 3). Sequencing errors in reads were corrected using Quake version 0.3, with a k-mer size of 15 (8), and assembled de novo using SPAdes version 3.5 (9). Contigs <1,000 bp were excluded from the analysis. Gene predictions and annotations were performed with the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline (PGAP) (10). The assembly and annotation statistics are shown in Table 1.
TABLE 1 .
Genome assembly and annotation statistics for E. fergusonii isolates
| Strain | Accession no. | Depth of coverage (×) | No. of contigs | Contig N50 (bp) | Assembly size (bp) | G+C content (%) | No. of CDSsa | No. of genes | No. of pseudogenes | No. of rRNAs | No. of tRNAs | Virulence gene(s) | Antimicrobial resistance |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GTA-EF02 | JZWQ00000000 | 114 | 22 | 403,657 | 4,764,067 | 49.85 | 4,470 | 4,691 | 116 | 11 | 75 | gad, iss | Sulfonamide (sul2), aminoglycoside (strA, strB), tetracycline [tet(A)] |
| GTA-EF03 | JZWN00000000 | 132 | 29 | 349,091 | 4,494,663 | 49.96 | 4,223 | 4,418 | 94 | 11 | 77 | gad, iss, prfB | None predicted |
| GTA-EF04 | JZWP00000000 | 164 | 39 | 336,937 | 4,644,753 | 49.86 | 4,443 | 4,641 | 92 | 13 | 77 | gad | Aminoglycoside (strA, strB), tetracycline [tet(B)] |
CDSs, coding sequences.
Antimicrobial resistance (ResFinder [11]) and virulence profiles (VirulenceFinder [12]) were determined using tools freely available at http://cge.cbs.dtu.dk/services/, with the results shown in Table 1. Four resistance genes were found on the same 8.5-kb contig in strain GTA-EF02, which is predicted to be aminoglycoside, tetracycline, and sulfonamide resistant. The virulence genes identified included the iss (increased serum survival) gene in both beef isolates and the prfB (P-related fimbriae regulatory) gene in one of the beef isolates (13).
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession numbers listed in Table 1. The versions described in this paper are the first versions.
ACKNOWLEDGMENTS
This work was funded by the CFIA food pathogen genomics research program under the direction of Burton Blais.
We thank George Huszczynski’s group for isolation and biochemical characterization of the strains.
Footnotes
Citation Manninger P, Koziol A, Carrillo CD. 2016. Draft whole-genome sequences of Escherichia fergusonii strains isolated from beef trim (GTA-EF02), ground beef (GTA-EF03), and chopped kale (GTA-EF04). Genome Announc 4(2):e00185-16. doi:10.1128/genomeA.00185-16.
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