Draft Genome Sequences of Three Newly Identified Species in the Genus Cronobacter, C. helveticus LMG23732T, C. pulveris LMG24059, and C. zurichensis LMG23730T.

Cronobacter helveticus, Cronobacter pulveris, and Cronobacter zurichensis are newly described species in the Cronobacter genus, which is associated with serious infections of neonates. This is the first report of draft genome sequences for these species.

GENOME ANNOUNCEMENT

The Cronobacter genus until recently consisted of seven species, C. sakazakii, C. malonaticus, C. turicensis, C. universalis, C. muytjensii, C. dublinensis, and C. condimenti (1). In 2013, three new Cronobacter species were proposed, C. zurichensis, C. pulveris, and C. helveticus (2). Due to the association of Cronobacter with fatal neonatal infections there is an international requirement for powdered infant formula to be microbiologically tested for all members of the Cronobacter genus (Codex Alimentarius Commission, code of hygienic practice for powdered formulae for infants and young children, http://www.codexalimentarius.net/download/standards/11026/CXP_066e.pdf). Therefore, the genome sequencing of these newly described species is warranted for better understanding of the genus diversity and improved detection methodology. This was undertaken using C. helveticus strain LMG23732T, C. zurichensis strain LMG23730T, and C. pulveris strain LMG24059 isolated from powdered infant formula.

Bacterial DNA was extracted from 1-day cultures using a GenElute bacterial genome kit (Sigma-Aldrich) and sequenced using an Illumina HiSeq 2500 sequencing system. De novo assembly was performed using Velvet (3). For further annotation we used the SEED-based automated annotation system provided by the RAST server (4).

C. helveticus LMG23732T, C. pulveris LMG24059, and C. zurichensis LMG23730T generated 8,351,512, 5,000,582, and 6,613,368 high-quality paired-end reads of 150 bp in length, respectively. The genome sizes were 4,530,369 bp, 4,900,556 bp, and 4,246,797 bp with G+C contents of 56%, 56.6%, and 57.8%, respectively. These were in 79, 125, and 103 contigs with 4,315, 4,630, and 3,883 coding sequences (CDS), respectively, and 30-fold coverage. The CDS include traits previously described in Cronobacter (5). These included genes associated with iron acquisition, stress response, heavy metal resistance (arsenic, copper cobalt, zinc and cadmium), and phages. Genes encoding proteins associated with several virulence-associated traits such as adhesion and antibiotic resistance, including fluoroquinolones, fosfomycin, β-lactamases, and multidrug efflux pumps, were also determined.

Nucleotide sequence accession numbers.

The genome sequences of C. helveticus, C. pulveris, and C. zurichensis have been deposited in GenBank under the accession numbers AWFX00000000, AWFY00000000, and AWFZ00000000, respectively.