High quality draft genome sequence of Staphylococcus cohnii subsp. cohnii strain hu-01
© The Author(s) 2014
Published: 15 June 2014
Staphylococcus cohnii subsp. cohnii belongs to the family Staphylococcaceae in the order Bacillales, class Bacilli and phylum Firmicutes. The increasing relevance of S. cohnii to human health prompted us to determine the genomic sequence of Staphylococcus cohnii subsp. cohnii strain hu-01, a multidrug-resistant isolate from a hospital in China. Here we describe the features of S. cohnii subsp. cohnii strain hu-01, together with the genome sequence and its annotation. This is the first genome sequence of the species Staphylococcus cohnii.
KeywordsStaphylococcus cohnii subsp. cohnii genome Hiseq2000
Staphylococcus cohnii belongs to the Coagulase-Negative Staphylococci group. It was described by Schleifer and Kloos (1975) and was named for Ferdinand Cohn, a German botanist and bacteriologist . Recently, more cases of Staphylococcus cohnii infection have been reported in the literature. This organism may be responsible for brain abscess, pneumonia, acute cholecystitis, endocarditis, bacteremia, urinary tract infection and septic arthritis . S. cohnii is comprised of two subspecies that are defined on the basis of their phenotypic characteristics: Staphylococcus cohnii subsp. cohnii and Staphylococcus cohnii subsp. urealyticus . S. cohnii subsp. cohnii is a Gram-positive coccus, coagulase negative and catalase positive, that behaves like a commensal mucocutaneous bacterium . It has more frequently been isolated in hospital than in non-hospital environments . Here we report this draft genome of S. cohnii subsp. cohnii strain hu-01, the first genome of this species to be sequenced.
Classification and features
Classification and general features of S. cohnii subsp. cohnii strain hu-01 according to the MIGS recommendations .
Species Staphylococcus cohnii subsp. cohnii
Tolerates 10% NaCl
D-mannitol, fructose, trehalose
Sample collection time
Biochemical features were tested by using two automated systems, the Vitek2 Compact (bioMérieux, Marcy l’Etoile, France) and Phoenix 100 ID/AST system (Becton Dickinson Company [BD], Sparks, Maryland, USA). Positive reactions were obtained for D-fructose, trehalose, D-gluconic acid and D-mannitol. Negative reactions were observed for glucose, D-trehalose, D-sucrose, maltose, urea, cellobiose, glucoside, D-tagatose and maltotriose. This strain was susceptible to gentamicin, ciprofloxacin, levofloxacin, moxifloxacin, quinupristin, linezolid, vancomycin, tetracycline, tigecycline, nitrofurantoin, rifampicin, trimethoprim and resistant to cefoxitin, benzylpenicillin, oxacillin, erythromycin, clindamycin.
Genome sequencing information
Genome project history
One pair-end 500 bp library
Illumina HiSeq 2000
150×(based on 500 bp library)
Gene calling method
Genbank Date of Release
Jan 06, 2014
Biotechnology, Pathway, Pathogenic
Growth conditions and DNA isolation
S. conhii subsp. cohnii strain hu-01 was grown aerobically on Columbia blood agar base, at 37°C for 24h. Genomic DNA was extracted using the DNeasy blood and tissue kit (Qiagen, Germany), according to the manufacturer’s recommended protocol. The quantity of DNA was measured by the NanoDrop Spectrophotometer and Cubit. Then 10µg of DNA was sent to the State Key Laboratory for Diagnosis and Treatment of Infectious Disease at Zhejiang University for sequencing on a Hiseq2000 (Illumina, CA) sequencer.
Genome sequencing and assembly
One DNA library was generated (500 bp insert size, with the Illumina adapter at both ends, detected by Agilent DNA analyzer 2100), then sequencing was performed by using an Illumina Hieseq 2000 genomic sequencer, with a 2×100 pair end sequencing strategy. A total of 1,103 M bp of sequence data was produced which was assessed for quality by the following criteria: 1) Reads linked to adapters at both end were considered as sequencing artifacts then removed. 2) Bases with a quality index lower than Q20 at both ends were trimmed. 3) Reads with ambiguous bases (N) were removed. 4) Single qualified reads were discarded (In this situation, one read is qualified but its mate is not). A total of 867.94 M clean filtered reads were assembled into scaffolds using the Velvet version 1.2.07 with parameters “-scaffolds no” , then we used a PAGIT flow  to prolong the initial contigs and correct sequencing errors. to arrive at a set of improved scaffolds.
Predict genes were identified using Glimmer version 3.0 , tRNAscan-SE version 1.21  was used to find tRNA genes, whereas ribosomal RNAs were found by using RNAmmer version 1.2 . To annotate predicted genes, we used HMMER version 3.0 , with parameters ‘hmmscan -E 0.01 -domainE 0.01’ to align genes against Pfam version 27.0  (only pfam-A was used) to find genes with conserved domains. The KAAS server  was used to assign translated amino acids (with genetic code table 11) into KEGG Orthology with SBH (single-directional best hit) method. Translated genes were aligned with the COG database using NCBI blastp (hits should have scores no less than 60, e-value is no more than 1e-6). To find genes with hypothetical or putative function, we aligned genes against NCBI nucleotide sequence database (nt database was downloaded at Sep 20, 2013) by using NCBI blastn, only if hits have an identity of no less than 0.95, coverage no less than 0.9, and the reference gene had an annotation of putative or hypothetical. To define genes with signal peptide, we use signalp version 4.1  to identify genes with signal peptide with default parameters except “ -t gram+”. TMHMM2.0  was used to identify genes with transmembrane helices.
Genome statistics of S. cohnii subsp. cohnii strain hu-01
% of totala
Genome size (bp)
DNA coding region (bp)
DNA G+C content (bp)
Genes with function prediction
Genes assigned to COGs
Genes assigned to Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Number of genes associated with the general COG functional categories
Translation, ribosomal structure and biogenesis
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, cell division, chromosome partitioning
Signal transduction mechanisms
Cell wall/membrane/envelope biogenesis
Intracellular trafficking, secretion, and vesicular transport
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not archived in COGs
Staphylococcus cohnii ssp. cohnii are part of the normal flora of human skin and mucous membranes which, in particular conditions, may become opportunistic pathogens . The genome sequence of Staphylococcus cohnii subsp. cohnii strain hu-01 will provide the basis to elucidate the molecular principles of host colonization and insight into the genetic background of this organism’s pathogenesis.
We thank Qiang Ye and Li Liang, Chinese Center of Medical Culture Collections/National Institutes for Food and Drug Control for providing the Biochemical features. This study was supported by the National Basic Research Program of China (973 program) (No. 2013CB531401) and the key Program of the National Natural Science Foundation of China (No. 81330011).
- Schleifer KH, Kloos WE. Isolation and Characterization of Staphylococci from Human Skin I. Amended Descriptions of Staphylococcus epidermidis and Staphylococcus saprophyticus and Descriptions of Three New Species: Staphylococcus cohnii, Staphylococcus haemolyticus, and Staphylococcus xylosus. Int J Syst Bacteriol 1975; 25:50–61. http://dx.doi.org/10.1099/00207713-25-1-50View ArticleGoogle Scholar
- Soldera J, Nedel WL, Cardoso PR, d’Azevedo PA. Bacteremia due to I ssp. urealyticus caused by infected pressure ulcer: case report and review of the literature. Sao Paulo Med J 2013; 131:59–61. PubMedView ArticlePubMedGoogle Scholar
- Kloos WE, Wolfshohl JF. Staphylococcus cohnii subspecies: Staphylococcus cohnii subsp. cohnii subsp. nov. and Staphylococcus cohnii subsp. urealyticum subsp. nov. Int J Syst Bacteriol 1991; 41:284–289. PubMed http://dx.doi.org/10.1099/00207713-41-2-284View ArticlePubMedGoogle Scholar
- Stefano M, Del Rosso A, Saldutto P, Paradiso Galatioto G, Vicentini C. Intrascrotal Abscess, Propionibacterium acnes and Staphylococcus cohnii ssp. cohnii: A Case Report and Review of the Literature. Case Rep Urol 2012;2012:313694.PubMed CentralPubMedGoogle Scholar
- Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL. NCBI BLAST: a better web interface. Nucleic Acids Res 2008;36(Web Server issue):W5–9.PubMed CentralView ArticlePubMedGoogle Scholar
- McGinnis S, Madden TL. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 2004;32(Web Server issue):W20–5.PubMed CentralView ArticlePubMedGoogle Scholar
- Thompson JD, Gibson TJ, Higgins DG. Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics 2002;Chapter 2:Unit 2 3.
- Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739. PubMed http://dx.doi.org/10.1093/molbev/msr121PubMed CentralView ArticlePubMedGoogle Scholar
- Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541–547. PubMed http://dx.doi.org/10.1038/nbt1360PubMed CentralView ArticlePubMedGoogle Scholar
- Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829. PubMed http://dx.doi.org/10.1101/gr.074492.107PubMed CentralView ArticlePubMedGoogle Scholar
- Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD. A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat Protoc 2012; 7:1260–1284. PubMed http://dx.doi.org/10.1038/nprot.2012.068PubMed CentralView ArticlePubMedGoogle Scholar
- Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007; 23:673–679. PubMed http://dx.doi.org/10.1093/bioinformatics/btm009PubMed CentralView ArticlePubMedGoogle Scholar
- Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:0955–964.View ArticleGoogle Scholar
- Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108. PubMed http://dx.doi.org/10.1093/nar/gkm160PubMed CentralView ArticlePubMedGoogle Scholar
- Eddy SR. Accelerated Profile HMM Searches. PLOS Comput Biol 2011; 7:e1002195. PubMed http://dx.doi.org/10.1371/journal.pcbi.1002195PubMed CentralView ArticlePubMedGoogle Scholar
- Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, et al. The Pfam protein families database. Nucleic Acids Res 2012; 40:D290–D301. PubMed http://dx.doi.org/10.1093/nar/gkr1065PubMed CentralView ArticlePubMedGoogle Scholar
- Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007;35(Web Server issue):W182–5.PubMed CentralView ArticlePubMedGoogle Scholar
- Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011; 8:785–786. PubMed http://dx.doi.org/10.1038/nmeth.1701View ArticlePubMedGoogle Scholar
- Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305:567–580. PubMed http://dx.doi.org/10.1006/jmbi.2000.4315View ArticlePubMedGoogle Scholar
- Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576–4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576PubMed CentralView ArticlePubMedGoogle Scholar
- Gibbons NE, Murray RGE. Proposals Concerning the Higher Taxa of Bacteria. Int J Syst Bacteriol 1978; 28:1–6. http://dx.doi.org/10.1099/00207713-28-1-1View ArticleGoogle Scholar
- Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119–169.View ArticleGoogle Scholar
- Murray RGE. The Higher Taxa, or, a Place for Everything…? In: Holt JG (ed), Bergey’s Manual of Systematic Bacteriology, First Edition, Volume 1, The Williams and Wilkins Co., Baltimore, 1984, p. 31–34.Google Scholar
- List of new names and new combinations previously effectively, but not validly, published. List no. 132. Int J Syst Evol Microbiol 2010; 60:469–472. http://dx.doi.org/10.1099/ijs.0.022855-0
- Ludwig W, Schleifer KH, Whitman WB. Class I. Bacilli class nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 3, Springer-Verlag, New York, 2009, p. 19–20.Google Scholar
- Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225–420. http://dx.doi.org/10.1099/00207713-30-1-225View ArticleGoogle Scholar
- Prévot AR. In: Hauderoy P, Ehringer G, Guillot G, Magrou. J., Prévot AR, Rosset D, Urbain A (eds), Dictionnaire des Bactéries Pathogènes, Second Edition, Masson et Cie, Paris, 1953, p. 1–692.Google Scholar
- Schleifer KH, Bell JA. Family VIII. Staphylococcaceae fam. nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 3, Springer-Verlag, New York, 2009, p. 392.Google Scholar
- Rosenbach FJ. In: Bergmann JF (ed), Microorganismen bei den Wund Infections Krankheiten des Menschen., Wiesbaden, 1884, p. 1–122.
- Baird-Parker AC. Genus II. Staphylococcus Rosenbach 1884, 18. In: Buchanan RE, Gibbons NE (eds), Bergey’s Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Baltimore, 1974, p. 483–489.Google Scholar
- Judicial Commission. Opinion 17. Conservation of the Generic name Staphylococcus Rosenbach, Designation of Staphylococcus aureus Rosenbach as the Nomenclatural Type of the Genus Staphylococcus Rosenbach, and Designation of the Neotype culture of Staphylococcus aureus Rosenbach. Int Bull Bacteriol Nomencl Taxon 1958; 8:153–154.Google Scholar
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25–29. PubMed http://dx.doi.org/10.1038/75556PubMed CentralView ArticlePubMedGoogle Scholar