title: Complete genome sequence and phenotype microarray analysis of Cronobacter sakazakii SP291: a persistent isolate cultured from a powdered infant formula production facility.
abstract: Outbreaks of human infection linked to the powdered infant formula (PIF) food chain and associated with the bacterium Cronobacter, are of concern to public health. These bacteria are regarded as opportunistic pathogens linked to life-threatening infections predominantly in neonates, with an under developed immune system. Monitoring the microbiological ecology of PIF production sites is an important step in attempting to limit the risk of contamination in the finished food product. Cronobacter species, like other microorganisms can adapt to the production environment. These organisms are known for their desiccation tolerance, a phenotype that can aid their survival in the production site and PIF itself. In evaluating the genome data currently available for Cronobacter species, no sequence information has been published describing a Cronobacter sakazakii isolate found to persist in a PIF production facility. Here we report on the complete genome sequence of one such isolate, Cronobacter sakazakii SP291 along with its phenotypic characteristics. The genome of C. sakazakii SP291 consists of a 4.3-Mb chromosome (56.9% GC) and three plasmids, denoted as pSP291-1, [118.1-kb (57.2% GC)], pSP291-2, [52.1-kb (49.2% GC)], and pSP291-3, [4.4-kb (54.0% GC)]. When C. sakazakii SP291 was compared to the reference C. sakazakii ATCC BAA-894, which is also of PIF origin, the annotated genome data identified two interesting functional categories, comprising of genes related to the bacterial stress response and resistance to antimicrobial and toxic compounds. Using a phenotypic microarray (PM), we provided a full metabolic profile comparing C. sakazakii SP291 and the previously sequenced C. sakazakii ATCC BAA-894. These data extend our understanding of the genome of this important neonatal pathogen and provides further insights into the genotypes associated with features that can contribute to its persistence in the PIF environment.
authors.affiliation: UCD Centre for Food Safety, WHO Collaborating Centre for Research, Reference and Training on Cronobacter, School of Public Health, Physiotherapy and Population Science, University College Dublin Dublin, Ireland.
authors.forename: Qiongqiong
authors.initials: Q
authors.lastname: Yan
authors.forename: Karen A
authors.initials: KA
authors.lastname: Power
authors.forename: Shane
authors.initials: S
authors.lastname: Cooney
authors.forename: Edward
authors.initials: E
authors.lastname: Fox
authors.forename: Gopal R
authors.initials: GR
authors.lastname: Gopinath
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Grim
authors.forename: Ben D
authors.initials: BD
authors.lastname: Tall
authors.forename: Matthew P
authors.initials: MP
authors.lastname: McCusker
authors.forename: Séamus
authors.initials: S
authors.lastname: Fanning
keywords: Cronobacter sakazakii; antibiotic resistance; complete genome; plasmid; stress response; toxic compounds
references.citation: J Virol. 2012 Jul;86(14):7713-4
references.pmid: 22733879
references.citation: Appl Environ Microbiol. 2008 Jun;74(12):3783-94
references.pmid: 18441119
references.citation: PLoS One. 2012;7(11):e49455
references.pmid: 23166675
references.citation: JAMA. 2002 May 1;287(17):2204-5
references.pmid: 11987295
references.citation: J Appl Microbiol. 2012 Jul;113(1):1-15
references.pmid: 22420458
references.citation: Genome Announc. 2013 Mar 21;1(2):e0008213
references.pmid: 23516209
references.citation: Appl Environ Microbiol. 2013 Jul;79(14):4376-84
references.pmid: 23666329
references.citation: J Food Sci. 2008 Sep;73(7):M354-9
references.pmid: 18803719
references.citation: J Med Microbiol. 2012 Jul;61(Pt 7):1034-1035
references.pmid: 22466029
references.citation: Nucleic Acids Res. 2005 Oct 07;33(17):5691-702
references.pmid: 16214803
references.citation: Bioeng Bugs. 2011 Sep-Oct;2(5):260-70
references.pmid: 21918371
references.citation: J Bacteriol. 2011 Oct;193(20):5861
references.pmid: 21952538
references.citation: FEMS Microbiol Lett. 2004 Jul 15;236(2):221-6
references.pmid: 15251200
references.citation: Minerva Pediatr. 2007 Apr;59(2):137-48
references.pmid: 17404564
references.citation: Int J Food Microbiol. 2009 Dec 31;136(2):185-8
references.pmid: 19729216
references.citation: J Bacteriol. 2003 Nov;185(22):6600-8
references.pmid: 14594833
references.citation: Clin Microbiol Infect. 2002 Sep;8(9):564-78
references.pmid: 12427217
references.citation: Bioresour Technol. 2011 Feb;102(3):2333-41
references.pmid: 21075615
references.citation: J Clin Microbiol. 2007 Nov;45(11):3814-6
references.pmid: 17881547
references.citation: Nucleic Acids Res. 2010 Mar;38(5):1723-37
references.pmid: 20007596
references.citation: J Bacteriol. 2006 Nov;188(22):7722-30
references.pmid: 17079680
references.citation: Annu Rev Microbiol. 2000;54:799-825
references.pmid: 11018145
references.citation: J Appl Microbiol. 2011 Mar;110(3):697-703
references.pmid: 21255207
references.citation: Lett Appl Microbiol. 2009 Jun;48(6):718-25
references.pmid: 19413805
references.citation: BMC Microbiol. 2009 Feb 02;9:24
references.pmid: 19187534
references.citation: Eur J Intern Med. 2006 May;17(3):185-8
references.pmid: 16618451
references.citation: Antonie Van Leeuwenhoek. 2011 Aug;100(2):279-89
references.pmid: 21567153
references.citation: Surg Infect (Larchmt). 2008 Oct;9(5):533-9
references.pmid: 18687047
references.citation: Int J Syst Evol Microbiol. 2008 Jun;58(Pt 6):1442-7
references.pmid: 18523192
references.citation: PLoS One. 2010 Mar 08;5(3):e9556
references.pmid: 20221447
references.citation: Age Ageing. 2007 Sep;36(5):595-6
references.pmid: 17646217
references.citation: Antimicrob Agents Chemother. 2003 Mar;47(3):883-8
references.pmid: 12604516
references.citation: Appl Environ Microbiol. 2011 May;77(10):3255-67
references.pmid: 21421789
references.citation: J Appl Microbiol. 2009 Nov;107(5):1606-14
references.pmid: 19457042
references.citation: Int J Syst Evol Microbiol. 2012 Jun;62(Pt 6):1277-1283
references.pmid: 22661070
references.citation: Res Microbiol. 2009 Oct;160(8):608-14
references.pmid: 19748571
references.citation: Microbiol Mol Biol Rev. 2002 Jun;66(2):223-49
references.pmid: 12040125
references.citation: FEMS Microbiol Lett. 2007 Feb;267(1):1-8
references.pmid: 17233672
references.citation: J Bacteriol. 2006 Dec;188(24):8360-7
references.pmid: 17041039
references.citation: J Bacteriol. 2012 Aug;194(16):4438-9
references.pmid: 22843579
references.citation: Emerg Infect Dis. 2013 Jan;19(1):167-9
references.pmid: 23260041
references.citation: Appl Environ Microbiol. 2008 Oct;74(19):5913-7
references.pmid: 18641152
references.citation: Bioinformatics. 2009 Jan 1;25(1):119-20
references.pmid: 18990721
references.citation: J Food Sci. 2012 Jul;77(7):M354-8
references.pmid: 22671692
references.citation: Appl Environ Microbiol. 2010 Aug;76(15):5188-98
references.pmid: 20543055
references.citation: Foodborne Pathog Dis. 2010 Jan;7(1):71-6
references.pmid: 19821740
references.citation: Appl Environ Microbiol. 2011 Jun;77(12):4017-26
references.pmid: 21531829
references.citation: Int J Food Microbiol. 2009 Dec 31;136(2):165-8
references.pmid: 19467725
references.citation: J Food Prot. 2013 Jan;76(1):150-72
references.pmid: 23317872
references.citation: BMC Genomics. 2008 Feb 08;9:75
references.pmid: 18261238
references.citation: Foodborne Pathog Dis. 2011 Sep;8(9):975-81
references.pmid: 21542776
references.citation: Eur J Clin Microbiol Infect Dis. 2009 Nov;28(11):1297-304
references.pmid: 19662446
references.citation: Acta Paediatr. 2001 Mar;90(3):356-8
references.pmid: 11332182
references.citation: J Bacteriol. 2012 Aug;194(15):3861-71
references.pmid: 22609924
references.citation: BMC Microbiol. 2009 Oct 27;9:225
references.pmid: 19860874
references.citation: BMC Microbiol. 2006 Jun 26;6:58
references.pmid: 16800879
references.citation: Appl Environ Microbiol. 2012 Sep;78(17):6035-50
references.pmid: 22706064
references.citation: Int J Food Microbiol. 2009 Dec 31;136(2):189-92
references.pmid: 19419789
references.citation: J Clin Microbiol. 2004 Nov;42(11):5368-70
references.pmid: 15528745
references.citation: Mol Microbiol. 1991 May;5(5):1049-64
references.pmid: 1956285
references.citation: J Bacteriol. 1985 Dec;164(3):1224-32
references.pmid: 3905768
references.citation: Proteomics. 2005 Nov;5(16):4161-9
references.pmid: 16196092
references.citation: J Bacteriol. 2011 Jan;193(1):309-10
references.pmid: 21037008
references.citation: BMC Genomics. 2013 May 31;14:366
references.pmid: 23724777
references.citation: Proteomics. 2010 Sep;10(18):3248-61
references.pmid: 20718006
references.citation: Front Microbiol. 2012 Nov 22;3:397
references.pmid: 23189075
references.citation: Genes Dev. 2009 Feb 15;23(4):522-34
references.pmid: 19240136
references.citation: J Basic Microbiol. 2011 Oct;51(5):540-9
references.pmid: 21656805
references.citation: Foodborne Pathog Dis. 2013 Apr;10(4):343-52
references.pmid: 23566272
references.citation: Int J Food Microbiol. 2005 Sep 25;104(1):1-34
references.pmid: 16039742
references.citation: Int J Food Microbiol. 2011 Mar 30;146(2):137-43
references.pmid: 21402424
references.citation: Microbiol Mol Biol Rev. 2000 Sep;64(3):503-14
references.pmid: 10974124
references.citation: Int J Food Microbiol. 2006 Jul 15;110(2):127-34
references.pmid: 16730386
references.citation: J Bacteriol. 2007 Jun;189(11):4070-7
references.pmid: 17416659
references.citation: Emerg Infect Dis. 2006 Aug;12(8):1185-9
references.pmid: 16965695