title: Whole-genome comparison of two Campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage.
abstract: Campylobacter jejuni ST-474 is the most important human enteric pathogen in New Zealand, and yet this genotype is rarely found elsewhere in the world. Insight into the evolution of this organism was gained by a whole genome comparison of two ST-474, flaA SVR-14 isolates and other available C. jejuni isolates and genomes. The two isolates were collected from different sources, human (H22082) and retail poultry (P110b), at the same time and from the same geographical location. Solexa sequencing of each isolate resulted in ~1.659 Mb (H22082) and ~1.656 Mb (P110b) of assembled sequences within 28 (H22082) and 29 (P110b) contigs. We analysed 1502 genes for which we had sequences within both ST-474 isolates and within at least one of 11 C. jejuni reference genomes. Although 94.5% of genes were identical between the two ST-474 isolates, we identified 83 genes that differed by at least one nucleotide, including 55 genes with non-synonymous substitutions. These covered 101 kb and contained 672 point differences. We inferred that 22 (3.3%) of these differences were due to mutation and 650 (96.7%) were imported via recombination. Our analysis estimated 38 recombinant breakpoints within these 83 genes, which correspond to recombination events affecting at least 19 loci regions and gives a tract length estimate of ~2 kb. This includes a ~12 kb region displaying non-homologous recombination in one of the ST-474 genomes, with the insertion of two genes, including ykgC, a putative oxidoreductase, and a conserved hypothetical protein of unknown function. Furthermore, our analysis indicates that the source of this recombined DNA is more likely to have come from C. jejuni strains that are more closely related to ST-474. This suggests that the rates of recombination and mutation are similar in order of magnitude, but that recombination has been much more important for generating divergence between the two ST-474 isolates.
authors.affiliation: Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand. p.biggs@massey.ac.nz
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Biggs
authors.forename: Paul
authors.initials: P
authors.lastname: Fearnhead
authors.forename: Grant
authors.initials: G
authors.lastname: Hotter
authors.forename: Vathsala
authors.initials: V
authors.lastname: Mohan
authors.forename: Julie
authors.initials: J
authors.lastname: Collins-Emerson
authors.forename: Errol
authors.initials: E
authors.lastname: Kwan
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Besser
authors.forename: Adrian
authors.initials: A
authors.lastname: Cookson
authors.forename: Philip E
authors.initials: PE
authors.lastname: Carter
authors.forename: Nigel P
authors.initials: NP
authors.lastname: French
mesh_terms: D016123:Campylobacter jejuni / Q000145:classification / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D059765:Homologous Recombination / Q000235:genetics; D011995:Recombination, Genetic / Q000235:genetics
references.citation: Genome Res. 2001 Oct;11(10):1725-9
references.pmid: 11591649
references.citation: J Bacteriol. 2007 Nov;189(22):8186-95
references.pmid: 17675389
references.citation: Mol Biol Evol. 2006 Feb;23(2):254-67
references.pmid: 16221896
references.citation: J Clin Microbiol. 1997 Nov;35(11):2810-4
references.pmid: 9350739
references.citation: J Bacteriol. 1990 Apr;172(4):1853-60
references.pmid: 2318805
references.citation: Environ Microbiol. 2011 Jun;13(6):1549-60
references.pmid: 21418497
references.citation: Genetics. 2003 Dec;165(4):2213-33
references.pmid: 14704198
references.citation: Genome Res. 2003 Sep;13(9):2178-89
references.pmid: 12952885
references.citation: Genome Res. 2008 Nov;18(11):1851-8
references.pmid: 18714091
references.citation: Int J Food Microbiol. 2007 Jul 15;117(3):237-57
references.pmid: 17368847
references.citation: Infect Genet Evol. 2009 Dec;9(6):1311-9
references.pmid: 19778636
references.citation: Bioinformatics. 2009 Jul 15;25(14):1754-60
references.pmid: 19451168
references.citation: Science. 2008 Apr 11;320(5873):237-9
references.pmid: 18403712
references.citation: Emerg Infect Dis. 2002 Sep;8(9):949-55
references.pmid: 12194772
references.citation: ISME J. 2009 Feb;3(2):199-208
references.pmid: 18830278
references.citation: BMC Genomics. 2009 Aug 19;10:385
references.pmid: 19691844
references.citation: PLoS Genet. 2008 Sep 26;4(9):e1000203
references.pmid: 18818764
references.citation: Bioinformatics. 2007 Mar 15;23(6):673-9
references.pmid: 17237039
references.citation: Nature. 2000 Feb 10;403(6770):665-8
references.pmid: 10688204
references.citation: Mol Ecol. 2011 Aug;20(16):3484-90
references.pmid: 21762392
references.citation: Bioinformatics. 2008 Dec 1;24(23):2672-6
references.pmid: 18845581
references.citation: Nucleic Acids Res. 1998 Jan 15;26(2):544-8
references.pmid: 9421513
references.citation: BMC Bioinformatics. 2010 Jan 12;11:21
references.pmid: 20064276
references.citation: Genome Biol Evol. 2010;2:646-55
references.pmid: 20688752
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22
references.pmid: 19920124
references.citation: Nucleic Acids Res. 1999 Dec 1;27(23):4636-41
references.pmid: 10556321
references.citation: Nat Rev Genet. 2010 Jan;11(1):31-46
references.pmid: 19997069
references.citation: Genetics. 2007 Mar;175(3):1251-66
references.pmid: 17151252
references.citation: Annu Rev Microbiol. 2001;55:561-90
references.pmid: 11544367
references.citation: BMC Bioinformatics. 2005 Feb 15;6:31
references.pmid: 15713233
references.citation: Nucleic Acids Res. 1997 Mar 1;25(5):955-64
references.pmid: 9023104
references.citation: Trends Genet. 2000 Jun;16(6):276-7
references.pmid: 10827456
references.citation: Emerg Infect Dis. 2008 Oct;14(10):1620-2
references.pmid: 18826829
references.citation: Zoonoses Public Health. 2012 Feb;59(1):52-60
references.pmid: 21824372
references.citation: Genome Res. 2008 May;18(5):821-9
references.pmid: 18349386
references.citation: Genome Res. 2009 Sep;19(9):1639-45
references.pmid: 19541911
references.citation: Comput Appl Biosci. 1988 Mar;4(1):11-7
references.pmid: 3382986
references.citation: Epidemiol Infect. 2007 Jan;135(1):163-70
references.pmid: 16753076
references.citation: Mol Biol Evol. 2009 Feb;26(2):385-97
references.pmid: 19008526
references.citation: BMC Bioinformatics. 2007 Feb 26;8:64
references.pmid: 17324286
references.citation: PLoS One. 2010 Dec 15;5(12):e15708
references.pmid: 21179537
references.citation: Prev Vet Med. 2011 Dec 1;102(3):242-53
references.pmid: 21872952
references.citation: Trends Genet. 2009 Mar;25(3):107-10
references.pmid: 19168257
references.citation: Microb Ecol. 2001 Dec;42(4):635-643
references.pmid: 12024246
references.citation: Bioinformatics. 2003 Jan 22;19(2):295-6
references.pmid: 12538257
references.citation: PLoS One. 2010 Aug 26;5(8):e12253
references.pmid: 20865039
references.citation: PLoS Genet. 2009 Oct;5(10):e1000627
references.pmid: 19855823
references.citation: Bioinformatics. 2009 Aug 15;25(16):2078-9
references.pmid: 19505943
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D363-8
references.pmid: 16381887
references.citation: J Mol Evol. 2005 Sep;61(3):333-40
references.pmid: 16044246
references.citation: Bioinformatics. 2000 Oct;16(10):944-5
references.pmid: 11120685
references.citation: BMC Genomics. 2007 Jun 12;8:162
references.pmid: 17565669
references.citation: Genome Res. 2009 Jul;19(7):1224-32
references.pmid: 19304960
references.citation: Microbiology (Reading). 2011 Apr;157(Pt 4):1066-1074
references.pmid: 21212120
references.citation: J Clin Microbiol. 2003 Jan;41(1):15-26
references.pmid: 12517820
references.citation: Epidemiol Infect. 2008 Sep;136(9):1244-52
references.pmid: 18028582
references.citation: Appl Environ Microbiol. 2010 Apr;76(7):2145-54
references.pmid: 20154115
references.citation: Emerg Infect Dis. 2011 Jun;17(6):1007-15
references.pmid: 21749761
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Brief Bioinform. 2004 Sep;5(3):237-48
references.pmid: 15383210
references.citation: Nucleic Acids Res. 2007;35(9):3100-8
references.pmid: 17452365