title: Complete genome analysis of a Haemophilus parasuis serovar 12 strain from China.
abstract: Haemophilus parasuis is the etiological agent of Glässer's disease in pigs and 15 standard serovars were identified. The widespread disease causes great economic loss in the swine industry worldwide. Aiming to investigate the differences in genome composition and functions among various strains, a highly virulent strain ZJ0906 of H. parasuis serovar 12 from China was analyzed and compared with serovar 5 SH0165. Strain ZJ0906 genome is 2,324,740 base pairs with 40.06% genomic GC content. It contains 2,484 open reading frames (ORF) predicted by Glimmer 3.02, of which 2,352 (∼94.7%) were annotated by NCBI nr blast, 1,745 by COG database and 1,829 by KEGG database. 109 potential virulence factors were annotated in strain ZJ0906 and 3 of which are potentially related to antibiotic resistance. Strain ZJ0906 genome is ∼55 kilobases longer than SH0165 genome, with an extra 211 predicted ORFs. VFDB, ARDB, and PAIDB blast searches showed that ZJ0906 and SH0165 shared a nearly identical panel of potential virulence factors, drug resistant genes and four PAI-like regions which showed high homology to Enterococcus, Escherichia and Salmonella. Synteny analysis showed that gene rearrangements are frequent between the two strains, which may lead to variations in pathogenicity and cross-protection among serovars. KEGG pathway analyses showed strain ZJ0906 shared similar metabolic pathways to strain SH0165. Molecular identification of these genomic elements and potential virulence factors pave the way to the better understanding of mechanisms underlying metabolic capabilities and pathogenicity of H. parasuis and prospective vaccine targets besides the widely used method of inactivated bacteria.
authors.affiliation: College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Li
authors.forename: Amy H Y
authors.initials: AH
authors.lastname: Kwok
authors.forename: Jingwei
authors.initials: J
authors.lastname: Jiang
authors.forename: Yao
authors.initials: Y
authors.lastname: Zou
authors.forename: Fangyuan
authors.initials: F
authors.lastname: Zheng
authors.forename: Pan
authors.initials: P
authors.lastname: Chen
authors.forename: Chengcai
authors.initials: C
authors.lastname: Hou
authors.forename: Frederick C
authors.initials: FC
authors.lastname: Leung
authors.forename: Ping
authors.initials: P
authors.lastname: Jiang
mesh_terms: D002681:China; D016680:Genome, Bacterial / Q000235:genetics*; D044137:Haemophilus parasuis / Q000145:classification / Q000235:genetics*; D010802:Phylogeny
references.citation: Stand Genomic Sci. 2011 Oct 15;5(1):61-8
references.pmid: 22180811
references.citation: Bioinformatics. 2007 Mar 15;23(6):673-9
references.pmid: 17237039
references.citation: J Bacteriol. 2004 Jan;186(1):244-7
references.pmid: 14679245
references.citation: Microb Pathog. 2007 Nov-Dec;43(5-6):198-207
references.pmid: 17600669
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14
references.pmid: 22080510
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D45-9
references.pmid: 14681355
references.citation: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D325-8
references.pmid: 15608208
references.citation: Vet Rec. 2002 Oct 26;151(17):502-5
references.pmid: 12430998
references.citation: Vet Microbiol. 2013 Feb 22;162(1):278-84
references.pmid: 22981816
references.citation: Res Vet Sci. 2012 Jun;92(3):366-71
references.pmid: 21529864
references.citation: PLoS One. 2011;6(5):e19631
references.pmid: 21611187
references.citation: Vet Microbiol. 2007 Feb 25;120(1-2):184-91
references.pmid: 17110059
references.citation: Trends Microbiol. 1995 Mar;3(3):87-92
references.pmid: 7773593
references.citation: J Vet Med Sci. 2011 Aug;73(8):1061-5
references.pmid: 21467759
references.citation: BMC Bioinformatics. 2003 Sep 11;4:41
references.pmid: 12969510
references.citation: Mol Microbiol. 1997 Mar;23(6):1089-97
references.pmid: 9106201
references.citation: Curr Microbiol. 2013 Jun;66(6):582-7
references.pmid: 23370732
references.citation: Clin Vaccine Immunol. 2013 Feb;20(2):134-9
references.pmid: 23220998
references.citation: Biochemistry (Mosc). 2001 Sep;66(9):973-8
references.pmid: 11703177
references.citation: Vet J. 2013 Apr;196(1):111-3
references.pmid: 23103218
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D443-7
references.pmid: 18832362
references.citation: Annu Rev Biochem. 2002;71:635-700
references.pmid: 12045108
references.citation: Can J Vet Res. 1991 Jan;55(1):37-41
references.pmid: 1884282
references.citation: Bioinformatics. 2003 Aug 12;19(12):1572-4
references.pmid: 12912839
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D395-400
references.pmid: 17090594
references.citation: Genome Res. 2002 Apr;12(4):656-64
references.pmid: 11932250
references.citation: Appl Environ Microbiol. 2011 Apr;77(7):2303-8
references.pmid: 21317254
references.citation: Vet Microbiol. 2005 Dec 20;111(3-4):231-6
references.pmid: 16271834
references.citation: Aust Vet J. 2000 Mar;78(3):172-4
references.pmid: 10860155
references.citation: Lett Appl Microbiol. 2011 Jun;52(6):589-95
references.pmid: 21507027
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references.pmid: 15034147
references.citation: Vet Microbiol. 2004 Mar 26;99(1):1-12
references.pmid: 15019107
references.citation: J Small Anim Pract. 1997 Jul;38(7):286-91
references.pmid: 9239629
references.citation: J Clin Microbiol. 2003 Feb;41(2):880-2
references.pmid: 12574306
references.citation: J Clin Microbiol. 1992 Apr;30(4):862-5
references.pmid: 1572971