title: Complete genome sequence of the cystic fibrosis pathogen Achromobacter xylosoxidans NH44784-1996 complies with important pathogenic phenotypes.
abstract: Achromobacter xylosoxidans is an environmental opportunistic pathogen, which infects an increasing number of immunocompromised patients. In this study we combined genomic analysis of a clinical isolated A. xylosoxidans strain with phenotypic investigations of its important pathogenic features. We present a complete assembly of the genome of A. xylosoxidans NH44784-1996, an isolate from a cystic fibrosis patient obtained in 1996. The genome of A. xylosoxidans NH44784-1996 contains approximately 7 million base pairs with 6390 potential protein-coding sequences. We identified several features that render it an opportunistic human pathogen, We found genes involved in anaerobic growth and the pgaABCD operon encoding the biofilm adhesin poly-β-1,6-N-acetyl-D-glucosamin. Furthermore, the genome contains a range of antibiotic resistance genes coding efflux pump systems and antibiotic modifying enzymes. In vitro studies of A. xylosoxidans NH44784-1996 confirmed the genomic evidence for its ability to form biofilms, anaerobic growth via denitrification, and resistance to a broad range of antibiotics. Our investigation enables further studies of the functionality of important identified genes contributing to the pathogenicity of A. xylosoxidans and thereby improves our understanding and ability to treat this emerging pathogen.
authors.affiliation: Costerton Biofilm Center, Department of International Health, Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Tim Holm
authors.initials: TH
authors.lastname: Jakobsen
authors.forename: Martin Asser
authors.initials: MA
authors.lastname: Hansen
authors.forename: Peter Østrup
authors.initials: PØ
authors.lastname: Jensen
authors.forename: Lars
authors.initials: L
authors.lastname: Hansen
authors.forename: Leise
authors.initials: L
authors.lastname: Riber
authors.forename: April
authors.initials: A
authors.lastname: Cockburn
authors.forename: Mette
authors.initials: M
authors.lastname: Kolpen
authors.forename: Christine
authors.initials: C
authors.lastname: Rønne Hansen
authors.forename: Winnie
authors.initials: W
authors.lastname: Ridderberg
authors.forename: Steffen
authors.initials: S
authors.lastname: Eickhardt
authors.forename: Marlene
authors.initials: M
authors.lastname: Hansen
authors.forename: Peter
authors.initials: P
authors.lastname: Kerpedjiev
authors.forename: Morten
authors.initials: M
authors.lastname: Alhede
authors.forename: Klaus
authors.initials: K
authors.lastname: Qvortrup
authors.forename: Mette
authors.initials: M
authors.lastname: Burmølle
authors.forename: Claus
authors.initials: C
authors.lastname: Moser
authors.forename: Michael
authors.initials: M
authors.lastname: Kühl
authors.forename: Oana
authors.initials: O
authors.lastname: Ciofu
authors.forename: Michael
authors.initials: M
authors.lastname: Givskov
authors.forename: Søren J
authors.initials: SJ
authors.lastname: Sørensen
authors.forename: Niels
authors.initials: N
authors.lastname: Høiby
authors.forename: Thomas
authors.initials: T
authors.lastname: Bjarnsholt
mesh_terms: D042441:Achromobacter denitrificans / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism / Q000502:physiology*; D000900:Anti-Bacterial Agents / Q000378:metabolism / Q000494:pharmacology; D001422:Bacterial Adhesion / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D018441:Biofilms / Q000254:growth & development; D003550:Cystic Fibrosis / Q000382:microbiology*; D058440:Denitrification / Q000235:genetics; D024881:Drug Resistance, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D006801:Humans; D058977:Molecular Sequence Annotation; D010100:Oxygen / Q000378:metabolism; D010641:Phenotype; D001618:beta-Lactamases / Q000235:genetics / Q000378:metabolism
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D001618:beta-Lactamases; D010100:Oxygen
references.citation: Pediatr Pulmonol. 2002 Aug;34(2):101-4
references.pmid: 12112775
references.citation: J Bacteriol. 2005 Jul;187(13):4306-14
references.pmid: 15968039
references.citation: Antimicrob Agents Chemother. 2002 Jul;46(7):2124-31
references.pmid: 12069964
references.citation: Eur J Clin Microbiol Infect Dis. 1996 Nov;15(11):876-9
references.pmid: 8997562
references.citation: Trends Microbiol. 2001 Jan;9(1):34-9
references.pmid: 11166241
references.citation: Infect Immun. 1998 Oct;66(10):4711-20
references.pmid: 9746568
references.citation: Nucleic Acids Res. 2005 Oct 07;33(17):5691-702
references.pmid: 16214803
references.citation: Mol Microbiol. 1998 Oct;30(2):295-304
references.pmid: 9791175
references.citation: Eur J Clin Microbiol Infect Dis. 2005 Dec;24(12):854-5
references.pmid: 16333608
references.citation: Diagn Microbiol Infect Dis. 1985 Mar;3(2):149-58
references.pmid: 3979021
references.citation: J Clin Microbiol. 2001 Feb;39(2):808-10
references.pmid: 11158159
references.citation: J Clin Microbiol. 2002 Apr;40(4):1210-3
references.pmid: 11923333
references.citation: J Clin Microbiol. 2001 Nov;39(11):3942-5
references.pmid: 11682511
references.citation: Diagn Microbiol Infect Dis. 2005 Nov;53(3):215-20
references.pmid: 16260111
references.citation: J Bacteriol. 2011 Feb;193(3):791-2
references.pmid: 21097610
references.citation: J Clin Microbiol. 2011 Dec;49(12):4352-5
references.pmid: 22012018
references.citation: Acta Crystallogr D Biol Crystallogr. 1997 Jul 1;53(Pt 4):406-18
references.pmid: 15299906
references.citation: Emerg Infect Dis. 2006 Nov;12(11):1737-9
references.pmid: 17283625
references.citation: Science. 1999 May 21;284(5418):1322-8
references.pmid: 10334981
references.citation: Microbiology (Reading). 2009 Nov;155(Pt 11):3500-3508
references.pmid: 19643762
references.citation: Lancet. 2001 Jul 14;358(9276):135-8
references.pmid: 11463434
references.citation: Ann Otol Rhinol Laryngol. 1995 Feb;104(2):120-6
references.pmid: 7857013
references.citation: Mol Microbiol. 1988 Sep;2(5):615-25
references.pmid: 2846986
references.citation: Scand J Respir Dis. 1977 Apr;58(2):65-79
references.pmid: 404701
references.citation: Mol Microbiol. 1998 May;28(3):449-61
references.pmid: 9632250
references.citation: Antimicrob Agents Chemother. 1988 Feb;32(2):276-8
references.pmid: 3163242
references.citation: Nat Protoc. 2010 Feb;5(2):282-93
references.pmid: 20134428
references.citation: Microbiology (Reading). 2007 May;153(Pt 5):1329-1338
references.pmid: 17464047
references.citation: Trends Microbiol. 2005 Dec;13(12):581-8
references.pmid: 16216510
references.citation: J Clin Microbiol. 1988 Aug;26(8):1580-1
references.pmid: 3170714
references.citation: Methods Enzymol. 1999;310:20-42
references.pmid: 10547780
references.citation: Annu Rev Genet. 2010;44:71-90
references.pmid: 21047256
references.citation: Antimicrob Agents Chemother. 2011 Oct;55(10):4912-4
references.pmid: 21807978
references.citation: Annu Rev Microbiol. 1987;41:435-64
references.pmid: 3318676
references.citation: Arch Microbiol. 1996 Jun;165(6):359-69
references.pmid: 8661929
references.citation: Antimicrob Agents Chemother. 2002 Jun;46(6):2014-6
references.pmid: 12019129
references.citation: J Clin Microbiol. 1978 Feb;7(2):239-41
references.pmid: 632351
references.citation: J Cyst Fibros. 2010 Jan;9(1):51-8
references.pmid: 19939747
references.citation: J Bacteriol. 2009 Jan;191(1):261-77
references.pmid: 18931103
references.citation: Microbiology (Reading). 2005 Feb;151(Pt 2):373-383
references.pmid: 15699188
references.citation: Eur J Clin Microbiol Infect Dis. 2004 Apr;23(4):336-9
references.pmid: 15024624
references.citation: J Antimicrob Chemother. 2005 Jul;56(1):20-51
references.pmid: 15914491
references.citation: J Bacteriol. 1996 Jan;178(1):175-83
references.pmid: 8550413
references.citation: Int J Antimicrob Agents. 2010 Jan;35(1):68-71
references.pmid: 19889520
references.citation: Lancet. 2001 Apr 21;357(9264):1225-40
references.pmid: 11418146
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: J Cyst Fibros. 2006 Dec;5(4):245-51
references.pmid: 16777495
references.citation: Cancer. 2004 Nov 1;101(9):2134-40
references.pmid: 15389476
references.citation: Antimicrob Agents Chemother. 2005 Feb;49(2):479-87
references.pmid: 15673721
references.citation: BMC Genomics. 2008 Feb 08;9:75
references.pmid: 18261238
references.citation: J Cyst Fibros. 2007 Jan;6(1):75-8
references.pmid: 16793350
references.citation: Proc Natl Acad Sci U S A. 2007 Sep 25;104(39):15508-13
references.pmid: 17873062
references.citation: J Bacteriol. 2004 May;186(9):2724-34
references.pmid: 15090514
references.citation: Bioinformatics. 2005 Feb 15;21(4):537-9
references.pmid: 15479716
references.citation: Antimicrob Agents Chemother. 2008 Jun;52(6):1952-6
references.pmid: 18362192
references.citation: Science. 1991 Jul 26;253(5018):438-42
references.pmid: 1862344
references.citation: J Clin Microbiol. 1980 Feb;11(2):141-5
references.pmid: 7358838
references.citation: APMIS. 2009 Jul;117(7):537-46
references.pmid: 19594494
references.citation: Int J Med Microbiol. 2010 Dec;300(8):549-56
references.pmid: 20951638
references.citation: J Clin Microbiol. 2012 Sep;50(9):3010-5
references.pmid: 22785192
references.citation: Nature. 2000 Aug 31;406(6799):959-64
references.pmid: 10984043
references.citation: J Clin Microbiol. 2012 Aug;50(8):2688-94
references.pmid: 22675125
references.citation: APMIS. 2008 Sep;116(9):837-41
references.pmid: 19024606
references.citation: PLoS One. 2011;6(11):e27943
references.pmid: 22132176
references.citation: J Clin Invest. 2002 Feb;109(3):317-25
references.pmid: 11827991
references.citation: Dev Cell. 2002 Oct;3(4):593-603
references.pmid: 12408810
references.citation: J Med Microbiol. 1984 Jun;17(3):283-93
references.pmid: 6327987
references.citation: Eur J Clin Microbiol Infect Dis. 1998 Feb;17(2):132-4
references.pmid: 9629983
references.citation: Pediatr Pulmonol. 2009 Jun;44(6):547-58
references.pmid: 19418571
references.citation: Trends Microbiol. 2001 Feb;9(2):50-2
references.pmid: 11173226
references.citation: FEMS Immunol Med Microbiol. 2010 Aug;59(3):324-36
references.pmid: 20602635
references.citation: Diagn Microbiol Infect Dis. 2011 Jul;70(3):408-11
references.pmid: 21497041
references.citation: Antimicrob Agents Chemother. 1997 Oct;41(10):2188-95
references.pmid: 9333046
references.citation: Arch Microbiol. 1993;160(6):432-9
references.pmid: 8297209
references.citation: Chemioterapia. 1987 Feb;6(1):32-7
references.pmid: 3103930
references.citation: Mol Microbiol. 1998 Oct;30(2):285-93
references.pmid: 9791174
references.citation: Mol Plant Microbe Interact. 1993 May-Jun;6(3):299-308
references.pmid: 8324248
references.citation: Genome Biol. 2008 Apr 17;9(4):R74
references.pmid: 18419807
references.citation: Science. 1995 Jul 28;269(5223):496-512
references.pmid: 7542800
references.citation: J Clin Microbiol. 1999 Jun;37(6):1771-6
references.pmid: 10325322
references.citation: Rinsho Byori. 1973 Jan;21(1):102-8
references.pmid: 4196545
references.citation: Pediatr Pulmonol. 2000 Mar;29(3):177-81
references.pmid: 10686037
references.citation: Eur J Clin Microbiol Infect Dis. 2003 Jun;22(6):360-3
references.pmid: 12750959
references.citation: J Antimicrob Chemother. 1992 Dec;30(6):769-79
references.pmid: 1289351
references.citation: J Clin Microbiol. 1995 Sep;33(9):2233-9
references.pmid: 7494007
references.citation: Science. 1999 May 21;284(5418):1318-22
references.pmid: 10334980
references.citation: Am J Respir Crit Care Med. 2008 May 1;177(9):995-1001
references.pmid: 18263800
references.citation: Clin Microbiol Rev. 2002 Apr;15(2):167-93
references.pmid: 11932229
references.citation: Thorax. 2010 Jan;65(1):57-62
references.pmid: 19846469
references.citation: APMIS. 1991 Jun;99(6):492-8
references.pmid: 1905144
references.citation: J Clin Microbiol. 2005 Jun;43(6):2998-3002
references.pmid: 15956444
references.citation: Int J Antimicrob Agents. 1999 May;11(3-4):217-21; discussion 237-9
references.pmid: 10394973