Genome Sequence of an Enterobacter helveticus Strain, 1159/04 (LMG 23733), Isolated from Fruit Powder.

We report the draft genome sequence of Enterobacter helveticus strain LMG 23733, isolated from fruit powder. The draft genome assembly for E. helveticus strain LMG 23733 has a size of 4,635,476 bp and a G+C content of 55.9%.

GENOME ANNOUNCEMENT

Stephan et al. (1) reported the isolation of 12 strains from fruit powder, which were presumptively identified as Enterobacter sakazakii, now Cronobacter, through the use of differential media. Biochemical characterization revealed that these isolates did not belong to the genus Cronobacter. Sequence analysis of the 16S rRNA and rpoB genes and DNA-DNA hybridization confirmed this finding, and Stephan et al. (1) classified two of these 12 strains as belonging to the novel species Enterobacter helveticus.

Recently, Brady et al. (2) proposed that E. helveticus be recognized as a new Cronobacter species. Because the taxonomic position of this species has been questioned, we sequenced E. helveticus strain 1159/04 (LMG 23733) to address this question. A library was constructed using the Nextera XT DNA sample preparation kit (Illumina, San Diego, CA), and whole-genome sequencing was performed on a MiSeq sequencer (Illumina, San Diego, CA), utilizing 500-cycle paired-end version 2 chemistry. Paired-end FASTQ datasets were trimmed and assembled using CLC Genomics Workbench, version 6.0.5 (CLC bio, Aarhus, Denmark). A draft genome sequence of strain 1159/04 was 4,635,476 bp, on 161 contigs (>500 bp in size). Genomic contigs were annotated using the RAST annotation server (3) to identify RNAs and protein-encoding genes. The draft genome sequence of strain 1159/04 is predicted to contain 4,454 coding sequences (CDS).

This strain of E. helveticus is closely related, as revealed by comparative genomics, to the type strain LMG23732 (513/05) as sequenced by Massod et al. (4). Indeed, the average nucleotide identity (ANI) between the two genomes is 99.95%. Both genomes contained a number of noteworthy features, namely, operons for the catabolism of protocatechuate, xylose, xyloside, l-rhamnose, d-galactarate, d-galactonate, malonate, galactitol, putrescine, fructoselysine, and l-idonic acid, as well as the presence of six type I fimbria clusters and one sigma fimbria cluster, genes for curli fimbriae, a transposon harboring copper resistance, redundant zinc transporter operons, a pga biofilm operon, and the lsr autoinducer-2 operon. Strain 513/05T harbors a phosphonate degradation operon. Additionally, there are a number of ATP-binding cassette (ABC)-type transporters of unidentified sugar substrates. The main differences between the two strains were due to the presence of a number of mobile elements. These included a Tn7-like transposon commonly found on plasmids of other Enterobacteriaceae, a transposon-like element harboring mercury resistance, an inovirus bacteriophage, and a large (>190-kbp) IncH1 conjugative plasmid, homologous (97 to 99% identity) to the R478 family of group H conjugative plasmids, in the genome of strain 513/05T (5). Strain 1159/04 harbored a smaller plasmid homologous to IncN2 plasmids shown to carry the New Delhi metallo-β-lactamase gene (6, 7).

Nucleotide sequence accession number.

The whole-genome shotgun project for E. helveticus strain 1159/04 is available in GenBank under accession number AXDL00000000.