Draft Genome Sequence of the Serratia rubidaea CIP 103234^T Reference Strain, a Human-Opportunistic Pathogen

Abstract

We provide here the first genome sequence of a Serratia rubidaea isolate, a human-opportunistic pathogen. This reference sequence will permit a comparison of this species with others of the Serratia genus.

GENOME ANNOUNCEMENT

Serratia species are Gram-negative rods responsible for human-opportunistic infections. Despite the fact that Serratia species are widespread in the environment, they are also encountered in human fecal flora. Serratia marcescens, the main representative of Serratia, was discovered in the early 19th century by the Italian microbiologist Bizio (1).

Now, the genus comprises 18 species recovered from environment and clinical specimens (http://www.bacterio.net/). Among pathogenic species, S. marcescens is the most frequently identified, along with Serratia liquefaciens. Infections caused by these organisms are varied, including urinary tract infections (UTIs), endocarditis, and wound and pulmonary infections (1). Serratia rubidaea, although rarely recovered from human specimens, is recognized as the fourth common cause of Serratia-related infections (1). Infections caused by S. rubidaea are mainly reported in patients with severe trauma or with underlying diseases, including sepsis, bacteremia, and UTIs (2–5). Serratia spp. may be a source of difficult-to-treat infections, since many of these strains are resistant to β-lactams mediated by the production of chromosomally encoded β-lactamases of either Ambler class C (AmpC-type of S. marcescens), Ambler class A (FonA and SFC-1 of Serratia fonticola), or Ambler class B (Sfh-I of an environmental S. fonticola) (6, 7).

Genomic DNA was extracted using the UltraClean microbial DNA isolation kit (Mo Bio Laboratories) from overnight cultures in LB agar (Bio-Rad, Marnes-la-Coquette, France). Genomic DNA quantification was performed using a Qubit fluorometer (Life Technologies, Carlsbad, CA) and adjusted to 0.2 ng/µl. Library preparation was performed using the Nextera XT DNA sample preparation kit (Illumina, San Diego, CA). Sequencing was performed on an Illumina MiSeq 2000 sequencer with V3 chemistry using 2 × 75-bp paired-end reads.

Illumina sequencing resulted in 4,367,802 reads of an average length of 74.31 nucleotides, giving a total 324,574,495 nucleotides. These generated reads were assembled using Velvet (8) and computed using CLC Workbench version 8.5. Two hundred forty contigs, giving a genome of 4,929,307 bp with a G+C% of 59.3%, were obtained from these raw data and then annotated using the RAST server (http://rast.nmpdr.org/). The RAST system predicted 4,522 coding sequences involved in essential functions, such as cell wall synthesis or RNA/DNA metabolism. One hundred ninety-eight coding sequences (CDSs) were predicted in cell wall and capsule synthesis, with 106 involved in virulence, disease, and defense; 38 involved in cell division and cell cycle; 153 involved in fatty acid and lipid metabolism; 134 involved in the stress response; and 216 and 231 involved in protein and RNA metabolism, respectively.

We hope that this sequence will help for genomic comparisons of the Serratia genus.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. LJZP00000000. The version described in this paper is version LJZP01000000.