Staphylococcus epidermidis strain ET-024 was isolated from a biofilm on an endotracheal tube of a mechanically ventilated patient. This strain is resistant to methicillin and the draft genome sequence shares some characteristics with other nosocomial S. epidermidis strains (such as S. epidermidis RP62A)

Coenye, Tom

Deforce, Dieter

Nelis, Hans

Van Nieuwerburgh, Filip

Vandecandelaere, Ilse

English

PubMed

ABSTRACT
          
            Staphylococcus epidermidis
            strain ET-024 was isolated from a biofilm on an endotracheal tube of a mechanically ventilated patient. This strain is resistant to methicillin, and the draft genome sequence shares some characteristics with other nosocomial
            S. epidermidis
            strains (such as
            S. epidermidis
            RP62A).
          </jats:p

Ilse Vandecandelaere

Filip Van Nieuwerburgh

Dieter Deforce

Hans J. Nelis

Tom Coenye

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Genome Announcements

Draft Genome Sequence of Methicillin-Resistant Staphylococcus epidermidis Strain ET-024, Isolated from an Endotracheal Tube Biofilm of a Mechanically Ventilated Patient

Ghent University Academic Bibliography

Draft Genome Sequence of Methicillin-Resistant Staphylococcusepidermidis Strain ET-024, Isolated from an Endotracheal TubeBiofilm of a Mechanically Ventilated PatientIlse Vandecandelaere,a Filip Van Nieuwerburgh,b Dieter Deforce,b Hans J. Nelis,a Tom CoenyeaLaboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgiuma; Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, BelgiumbStaphylococcus epidermidis strain ET-024 was isolated from a biofilm on an endotracheal tube of a mechanically ventilated pa-tient. This strain is resistant to methicillin, and the draft genome sequence shares some characteristics with other nosocomialS. epidermidis strains (such as S. epidermidis RP62A).Received 12 May 2014 Accepted 14 May 2014 Published 29 May 2014Citation Vandecandelaere I, Van Nieuwerburgh F, Deforce D, Nelis HJ, Coenye T. 2014. Draft genome sequence of methicillin-resistant Staphylococcus epidermidis strain ET-024,isolated from an endotracheal tube biofilm of a mechanically ventilated patient. Genome Announc. 2(3):e00527-14. doi:10.1128/genomeA.00527-14.Copyright © 2014 Vandecandelaere et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Ilse Vandecandelaere, ilse.vandecandelaere@ugent.be.Staphylococcus epidermidis is a commensal skin bacteriumwhich is also recognized as an opportunistic pathogen (1, 2).The majority of infections caused by S. epidermidis are associatedwith the presence of indwelling medical devices, and these in-fections are related to the ability of S. epidermidis to form bio-films (2, 3).We sequenced the genome of S. epidermidis isolate ET-024,recovered from an endotracheal tube biofilm of a mechanicallyventilated patient (4). This strain is susceptible to vancomycin(MIC, 2 g/ml), erythromycin (MIC, 0.25 g/ml) and tobramy-cin (MIC, 2 g/ml) but resistant to methicillin (MIC, 0.5 g/ml) (5). Sequencing was performed using an Illumina MiSeq andpaired reads (7,865,978) of 250 bp were obtained. The high-quality filtered reads were mapped against the S. epidermidisRP62A genome using CLCGenomicsWorkbench 6.5.2 (CLCBio,Aarhus, Denmark), and in this way the reads were assembled. TheRAST serverwas used to annotate the consensus sequence (6). Thedraft genome consists of 2,616,532 bp, 110 contigs, 2,161 codingsequences, 85 predicted RNAs, and 374 subsystems. The guanine-cytosine content is 32.3% (7).Genome sequence analysis demonstrated the presence ofthe ica operon (icaABCDR). A major component of the matrixof staphylococcal biofilms is a polymer of -1,6-linked N-acetylglucosamine (PIA), which is formed by the products of 4genes (icaABCD) (8). Also, genes encoding proteins involved inbiofilm formation (such as atlE, sasG, epb, aap, and sdrE) wereidentified (2).Strain ET-024 carries a set of genes encoding proteins involvedin stress responses. Proteins which play a role in choline andbetaine uptake (glycine betaine is an efficient osmolyte) and be-taine biosynthesis (betA, betB, betT, and opuD) are encoded in thegenome of ET-024 (9). Protection against oxidative stress (sodAand sodB), heat (dnaJ, dnaK, and grpE), and cold shock (cspA andcspC) (10) is also encoded in the genome of ET-024.Furthermore, proteins conferring resistance to toxic com-pounds such as cobalt-zinc-cadmium (czrB and czrD), mercury(mir and merA), arsenic (arsABCDR), and cadmium (cadC andcadD) are encoded in the ET-024 genome. Also, this strain carriesgenes encoding resistance to antibiotics, including teicoplanin(tcaABR), fosfomycin (fosB), and methicillin (mecR1, mecI, andmecA). In addition, genes encoding multidrug resistance proteinsA and B are present in the genome of ET-024. The exact functionof these proteins in Gram-positive bacteria is still unknown (11).The arcABCD genes, collectively referred to as the argininecatabolic element (ACME) cluster, are also present in the genomeof S. epidermidis ET-024 (12). Although the precise function ofACME in staphylococci has not yet been determined, several stud-ies have shown that ACME improves fitness and the ability tocolonize mucosae (12). The opp gene (oppABCDF) cluster is alsopresent (13).Altogether, the presence of genes involved in biofilm forma-tion and antibiotic resistance in the genome of ET-024 suggeststhat S. epidermidis is more than a harmless commensal bacterium.Nucleotide sequence accessionnumbers.Thiswhole-genomeshotgun project has been deposited at DDBJ/EMBL/GenBank un-der the accession number JGVL00000000. The version describedin this paper is version JGVL01000000.ACKNOWLEDGMENTSThis research has been funded by FWO-Vlaanderen (project 3G001211)and by the Interuniversity Attraction Poles Program initiated by the Bel-gian Science Policy Office.REFERENCES1. Wei W, Cao Z, Zhu YL, Wang X, Ding G, Xu H, Jia P, Qu D, DanchinA, Li Y. 2006. Conserved genes in a path from commensalism topathogenicity: comparative phylogenetic profiles of Staphylococcus epider-midis RP62A and ATCC 12228. BMC Genomics 7:112. http://dx.doi.org/10.1186/1471-2164-7-112.2. Otto M. 2012. Molecular basis of Staphylococcus epidermidis infections.Semin. Immunopathol. 34:201–214. http://dx.doi.org/10.1007/s00281-011-0296-2.3. Ziebuhr W, Hennig S, Eckart M, Kränzler H, Batzilla C, Kozitskaya S. 2006.Nosocomial infections by Staphylococcus epidermidis: how a commensal bacte-rium turns into a pathogen. Int. J. Antimicrob. Agents 28(Suppl 1):S14–S20.http://dx.doi.org/10.1016/j.ijantimicag.2006.05.012.Genome AnnouncementsMay/June 2014 Volume 2 Issue 3 e00527-14 genomea.asm.org 14. Vandecandelaere I, Matthijs N, Van Nieuwerburgh F, Deforce D,Vosters P, De Bus L, Nelis HJ, Depuydt P, Coenye T. 2012. Assessmentofmicrobial diversity in biofilms recovered from endotracheal tubes usingculture dependent and independent approaches. PLoS One 7:e38401.http://dx.doi.org/10.1371/journal.pone.0038401.5. Vandecandelaere I, Matthijs N, Nelis HJ, Depuydt P, Coenye T. 2013.The presence of antibiotic-resistant nosocomial pathogens in endotra-cheal tube biofilms and corresponding surveillance cultures. Pathog. Dis.69:142–148. http://dx.doi.org/10.1111/2049-632X.12100.6. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA,Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, OlsonR, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T,Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V,Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations usingsubsystems technology. BMC Genomics 9:75. http://dx.doi.org/10.1186/1471-2164-9-75.7. Gill SR, Fouts DE, Archer GL, Mongodin EF, Deboy RT, Ravel J,Paulsen IT, Kolonay JF, Brinkac L, Beanan M, Dodson RJ, DaughertySC, Madupu R, Angiuoli SV, Durkin AS, Haft DH, Vamathevan J,Khouri H, Utterback T, Lee C, Dimitrov G, Jiang L, Qin H, WeidmanJ, Tran K, Kang K, Hance IR, Nelson KE, Fraser CM. 2005. Insights onevolution of virulence and resistance from the complete genome analysisof an earlymethicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. J. Bac-teriol. 187:2426 –2438. http://dx.doi.org/10.1128/JB.187.7.2426-2438.2005.8. de Silva GD, Kantzanou M, Justice A, Massey RC, Wilkinson AR, DayNP, Peacock SJ. 2002. The ica operon and biofilm production incoagulase-negative staphylococci associated with carriage and disease in aneonatal intensive care unit. J. Clin. Microbiol. 40:382–388. http://dx.doi.org/10.1128/JCM.40.02.382-388.2002.9. Kimura Y, Kawasaki S, Yoshimoto H, Takegawa K. 2010. Glycinebetaine biosynthesized from glycine provides an osmolyte for cell growthand spore germination during osmotic stress in Myxococcus xanthus. J.Bacteriol. 192:1467–1470. http://dx.doi.org/10.1128/JB.01118-09.10. Takechi S, Nakahara K, Adachi M, Yamaguchi T. 2009. Oxidative stressinduced by a dihydropyrazine derivative. Biol. Pharm. Bull. 32:186–189.http://dx.doi.org/10.1248/bpb.32.186.11. Zgurskaya HI, Nikaido H. 2000. Multidrug resistance mechanisms: drugefflux across two membranes. Mol. Microbiol. 37:219–225. http://dx.doi.org/10.1046/j.1365-2958.2000.01926.x.12. Shore AC, Rossney AS, Brennan OM, Kinnevey PM, Humphreys H,Sullivan DJ, Goering RV, Ehricht R, Monecke S, Coleman DC. 2011.Characterization of a novel arginine catabolic mobile element (ACME)and staphylococcal chromosomal cassettemec composite island with sig-nificant homology to Staphylococcus epidermidis ACME type II inmethicillin-resistant Staphylococcus aureus genotype ST22-MRSA-IV. An-timicrob. Agents Chemother. 55:1896–1905. http://dx.doi.org/10.1128/AAC.01756-10.13. Hiron A, Posteraro B, Carrière M, Remy L, Delporte C, La Sorda M,Sanguinetti M, Juillard V, Borezée-Durant E. 2010. A nickel ABC-transporter of Staphylococcus aureus is involved in urinary tract infection.Mol. Microbiol. 77:1246 –1260. http://dx.doi.org/10.1111/j.1365-2958.2010.07287.x.Vandecandelaere et al.Genome Announcements2 genomea.asm.org May/June 2014 Volume 2 Issue 3 e00527-14

Draft genome sequence of methicillin-resistant Staphylococcus epidermidis strain ET-024, isolated from an endotracheal tube biofilm of a mechanically ventilated patient

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Draft genome sequence of methicillin-resistant Staphylococcus epidermidis strain ET-024, isolated from an endotracheal tube biofilm of a mechanically ventilated patient

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