Abstract
We report here the complete genome sequence of C. neteri SSMD04, a strain isolated from pickled mackerel sashimi, sequenced by third-generation sequencing technology. To the best of our knowledge, this is the first documentation that reports the complete genome of Cedecea neteri.
GENOME ANNOUNCEMENT
Cedecea is a genus of Gram-negative rod-shape bacteria that belongs to the Enterobacteriaceae family (1). This genus of bacteria is characterized by lipase positivity and resistance to colistin and cephalothin (2). Isolation of Cedecea is rare, and its discovery was originally from a human source (2). Even though the members of Cedecea have been suspected to be human pathogens, their pathogenicity is largely unknown. This is because most of the Cedecea spp. have been isolated from polymicrobial and severely immunocompromised conditions, making the assessment of their medical importance difficult (3). The first evidence of Cedecea spp. as human pathogens was discovered in the cases of C. neteri infection, in which the patients were diagnosed with possible endocarditis and systemic lupus erythematosus. Complications from bacteremia of the second case even led to the patient’s death (4, 5).
Cedecea strains were mostly isolated from a human source but not exclusively. There were cases in which this bacterium has been isolated from fruit flies (6) and vegetables (7). Here, we report the complete genome of C. neteri strain SSMD04, isolated from pickled mackerel (Shime saba) sashimi.
The whole genome of C. neteri SSMD04 was sequenced with a Pacific Biosciences single-molecule real-time (PacBio SMRT) sequencer (8, 9). A 20-kb SMRTbell library was prepared, and the sequencing was carried out using P5 chemistry on two SMRT cells. De novo assembly of 24,369 reads using the hierarchical genome assembly process (HGAP) algorithm in the SMRT version 2.1.1 portal (10) resulted in a single contig of 4.88 Mb in size. The genome has a GC content of 55.1% with an average coverage of 38.42×. This genome was then annotated by RAST (Rapid Annotation using Subsystem Technology) version 2.0 (11), which successfully identified 4,472 coding sequences, as well as 103 RNA sequences. Of these, 56.64% of the annotated coding sequences fell within 539 subsystems available in the RAST database. Similar to other bacteria, most of the genes are involved in common cell metabolism that sustains the survival of C. neteri SSMD04 itself, where 583 gene counts were attributed to carbohydrates, 502 to amino acids and derivatives, 325 to protein metabolism, as well as 247 to cofactors, vitamins, prosthetic groups, and pigments. We hope that the complete genome sequence of this isolate will facilitate the discovery of various genes and their functions in this isolate.
Nucleotide sequence accession numbers.
This complete genome project has been deposited at DDBJ/EMBL/GenBank under the accession number CP009451. The version described in this paper is the first version, CP009451.1.
ACKNOWLEDGMENTS
This research was financed by the University of Malaya High Impact Research (HIR) (UM-MOHE HIR grant UM.C/625/1/HIR/MOHE/CHAN/01, no. H-50001-A000001) to Kok-Gan Chan, which is gratefully acknowledged.
Footnotes
Citation Chan K-G, Tan K-H, Yin W-F, Tan J-Y. 2014. Complete genome sequence of Cedecea neteri strain SSMD04, a bacterium isolated from pickled mackerel sashimi. Genome Announc. 2(6):e01339-14. doi:10.1128/genomeA.01339-14.
REFERENCES
- 1. Berman JJ. 2012. Taxonomic guide to infectious diseases: understanding the Biologic classes of pathogenic organisms. Elsevier/Academic Press, Amsterdam, the Netherlands. [Google Scholar]
- 2. Grimont P, Grimont F, Farmer J, Asbury M. 1981. Cedecea davisae gen. nov., sp. nov. and Cedecea lapagei sp. nov., new Enterobacteriaceae from clinical specimens. Int. J. Syst. Bacteriol. 31:317–326. 10.1099/00207713-31-3-317. [DOI] [Google Scholar]
- 3. Janda JM. 2006. New members of the family Enterobacteriaceae, p. 5–40 In Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E. (ed), The prokaryotes, vol. 6 Springer, New York. 10.1007/0-387-30746-X_1. [DOI] [Google Scholar]
- 4. Farmer JJ, Sheth NK, Hudzinski JA, Rose HD, Asbury MF. 1982. Bacteremia due to Cedecea neteri sp. nov. J. Clin. Microbiol. 16:775–778. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Aguilera A, Pascual J, Loza E, Lopez J, Garcia G, Liaño F, Quereda C, Ortuño J. 1995. Bacteraemia with Cedecea neteri in a patient with systemic lupus erythematosus. Postgrad. Med. J. 71:179–180. 10.1136/pgmj.71.833.179. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Jang EB, Nishijima KA. 1990. Identification and attractancy of bacteria associated with Dacus dorsalis (Diptera: Tephritidae). Environ. Entomol. 19:1726–1731. [Google Scholar]
- 7. Osterblad M, Pensala O, Peterzéns M, Heleniusc H, Huovinen P. 1999. Antimicrobial susceptibility of Enterobacteriaceae isolated from vegetables. J. Antimicrob. Chemother. 43:503–509. 10.1093/jac/43.4.503. [DOI] [PubMed] [Google Scholar]
- 8. Chan K-G, Yin W-F, Goh S-Y. 2014. Complete genome sequence of Pandoraea pnomenusa 3kgm, a quorum-sensing strain isolated from a former landfill site. Genome Announc. 2(3):e00427-14. 10.1128/genomeA.00427-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Lau YY, Yin W-F, Chan K-G. 2014. Enterobacter asburiae strain L1: complete genome and whole genome optical mapping analysis of a quorum sensing bacterium. Sensors 14:13913–13924. 10.3390/s140813913. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Chan K-G, Yin W-F, Lim YL. 2014. Complete genome sequence of Pseudomonas aeruginosa strain YL84, a quorum-sensing strain isolated from compost. Genome Announc. 2(2):e00246-14. 10.1128/genomeA.00246-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. Aziz RK, Devoid S, Disz T, Edwards RA, Henry CS, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Stevens RL, Vonstein V, Xia F. 2012. SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models. PLoS One 7:e48053. 10.1371/journal.pone.0048053. [DOI] [PMC free article] [PubMed] [Google Scholar]