Genome Sequence of Cronobacter sakazakii Serogroup O:4, Sequence Type 4 Strain CDC 2009-03746, Isolated from a Fatal Case of Infantile Meningitis.

We report the draft genome sequence of a Cronobacter sakazakii serogroup O:4, sequence type 4 strain, CDC 2009-03746 (=NM1240=2009-06-01), isolated from a fatal case of infantile meningitis. The draft genome has a size of 4,492,904 bp and a G+C% content of 56.7.

GENOME ANNOUNCEMENT

Cronobacter comprise a diverse genus of pathogens that cause life-threatening infantile infections, such as meningitis, necrotizing enterocolitis, and septicemia (1, 2). Baumbach et al. (3) recently reported the isolation of three Cronobacter sakazakii strains, from two infant cases, which belong to the newly described C. sakazakii O:4 molecular serotype (4). One of the three isolates, C. sakazakii strain 2009-03746 (=NM1240=2009-06-01), also belongs to sequence type 4 (ST4; http://pubmlst.org/cronobacter), which is implicated as a major cause of neonatal infections (5). To date, clinical ST4 strains which have been sequenced have been shown to belong to the Csak O:2 molecular serotype (6–8).

To further understand this isolate, whole-genome sequencing was performed on the MiSeq platform (Illumina, San Diego, CA, USA), utilizing 500 cycles of paired-end reads (Illumina). Fastq datasets were de novo assembled with CLC Genomics Workbench version 7.0 (CLC bio, Aarhus, Denmark). The draft genome of 2009-03746 is 4,492,904 bp, on 128 contigs (>200 bp in size) and has a G+C% content of 56.7. Genomic contigs were annotated using the RAST annotation server (9), and predicted to contain 4,170 coding sequences.

Interestingly, the genome of C. sakazakii 2009-03746 has a high nucleotide identity (average nucleotide identity [ANI] of 99.8%) with members of the clonal C. sakazakii O:2 group (10), such as C. sakazakii 2151 and C. sakazakii ES713 (GenBank accession numbers AJKT00000000.1 and AJLB00000000.1, respectively). In comparison, the ANI of 2009-03746 with another Csak O:4 isolate, C. sakazakii E764 (GenBank accession number AJLA00000000.1), is only 98.0%. The overall nucleotide identity with Csak O:2 genomes would be higher, except for the presence of an apparent recombination event(s) involving the 171-kb region located between tRNA-Proline-GGG and tRNA-Asparagine-GTT1. This region contains genes involved in extracellular polysaccharide synthesis, including colanic acid and O-antigen biosynthesis, putative galactose and mannose LPS modification operons, and the yeh osmoprotectant operon. Surprisingly, in C. sakazakii strain 2009-03746, the majority of this region has high nucleotide identity with that of C. sakazakii ATCC BAA-894, a Csak O:1 ST1 isolate, except for the Csak O:4 O-antigen region.

In terms of genome content, C. sakazakii strain 2009-03746 possesses many of the features of the species, as determined previously (11). Of note, this strain possesses genes for nine chaperone-usher fimbriae, cellulose synthesis, and sialic acid utilization operons; a 120-kb pESA3-like virulence plasmid (12); and a CRISPR element. The genome contains an additional 52-kb plasmid, homologous to plasmid pSP291-2 of C. sakazakii strain SP291 (GenBank accession number CP004093.1, ST4, Csak O:2) (7), which encodes copper homeostasis and heavy metal resistance operons.

Pathogen-specific virulence factors have been discovered on a variety of mobile genetic elements, such as plasmids and transposons. The “genomic plasticity” demonstrated by C. sakazakii strain 2009-03746 suggests ongoing genomic rearrangement, and these recombination events will undoubtedly complicate our efforts to classify these organisms into sharply delineated genomo-pathotypes.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JZDO00000000. The version described in this paper is version JZDO00000000.1