title: Genome analysis and in vivo virulence of porcine extraintestinal pathogenic Escherichia coli strain PCN033.
abstract: BACKGROUND
  Strains of extraintestinal pathogenic Escherichia coli (ExPEC) can invade and colonize extraintestinal sites and cause a wide range of infections. Genomic analysis of ExPEC has mainly focused on isolates of human and avian origins, with porcine ExPEC isolates yet to be sequenced. To better understand the genomic attributes underlying the pathogenicity of porcine ExPEC, we isolated two E. coli strains PCN033 and PCN061 from pigs, assessed their in vivo virulence, and completed and compared their genomes.
  
  
  RESULTS
  Animal experiments demonstrated that strain PCN033, but not PCN061, was pathogenic in a pig model. The chromosome of PCN033 was 384 kb larger than that of PCN061. Among the PCN033-specific sequences, genes encoding adhesins, unique lipopolysaccharide, unique capsular polysaccharide, iron acquisition and transport systems, and metabolism were identified. Additionally, a large plasmid PCN033p3 harboring many typical ExPEC virulence factors was identified in PCN033. Based on the genetic variation between PCN033 and PCN061, corresponding phenotypic differences in flagellum-dependent swarming motility and metabolism were verified. Furthermore, the comparative genomic analyses showed that the PCN033 genome shared many similarities with genomic sequences of human ExPEC strains. Additionally, comparison of PCN033 genome with other nine characteristic E. coli genomes revealed 425 PCN033-special coding sequences. Genes of this subset included those encoding type I restriction-modification (R-M) system, type VI secretion system (T6SS) and membrane-associated proteins.
  
  
  CONCLUSIONS
  The genetic and phenotypic differences between PCN033 and PCN061 could partially explain their differences in virulence, and also provide insight towards the molecular mechanisms of porcine ExPEC infections. Additionally, the similarities between the genomes of PCN033 and human ExPEC strains suggest that some connections between porcine and human ExPEC strains exist. The first completed genomic sequence for porcine ExPEC and the genomic differences identified by comparative analyses provide a baseline understanding of porcine ExPEC genetics and lay the foundation for their further study.
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. liucy3032@163.com.|Department of Veterinary Medicine, Foshan University, Foshan, Guangdong, China. liucy3032@163.com.
authors.forename: Canying
authors.initials: C
authors.lastname: Liu
authors.affiliation: Shanghai-Most Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China. zhenghj@chgc.sh.cn.
authors.forename: Huajun
authors.initials: H
authors.lastname: Zheng
authors.affiliation: Shanghai-Most Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China. yangmj@chgc.sh.cn.
authors.forename: Minjun
authors.initials: M
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. zhuofei.xu@gmail.com.
authors.forename: Zhuofei
authors.initials: Z
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. wangxr228@163.com.
authors.forename: Xiangru
authors.initials: X
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. weiliuya_0913@163.com.
authors.forename: Liuya
authors.initials: L
authors.lastname: Wei
authors.affiliation: Shanghai-Most Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China. tb_411@163.com.|State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China. tb_411@163.com.
authors.forename: Biao
authors.initials: B
authors.lastname: Tang
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. liufeng376711883@163.com.
authors.forename: Feng
authors.initials: F
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. zhangyanyan54219@163.com.
authors.forename: Yanyan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. 279076998@qq.com.
authors.forename: Yi
authors.initials: Y
authors.lastname: Ding
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. tangren77@126.com.
authors.forename: Xibiao
authors.initials: X
authors.lastname: Tang
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. wub@mail.hzau.edu.cn.
authors.forename: Bin
authors.initials: B
authors.lastname: Wu
authors.affiliation: Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA. joh04207@umn.edu.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Johnson
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. chenhch@mail.hzau.edu.cn.
authors.forename: Huanchun
authors.initials: H
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. tanchen@mail.hzau.edu.cn.
authors.forename: Chen
authors.initials: C
authors.lastname: Tan
mesh_terms: D000818:Animals; D058947:Bacterial Secretion Systems; D004251:DNA Transposable Elements; D004926:Escherichia coli / Q000145:classification / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity*; D004927:Escherichia coli Infections / Q000662:veterinary*; D029968:Escherichia coli Proteins / Q000235:genetics; D023061:Gene Order; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D008070:Lipopolysaccharides / Q000096:biosynthesis; D053858:Metabolic Networks and Pathways; D008969:Molecular Sequence Data; D010802:Phylogeny; D013552:Swine; D013553:Swine Diseases / Q000382:microbiology* / Q000401:mortality; D014774:Virulence / Q000235:genetics; D037521:Virulence Factors / Q000235:genetics
chemical_list: D058947:Bacterial Secretion Systems; D004251:DNA Transposable Elements; D029968:Escherichia coli Proteins; D008070:Lipopolysaccharides; D037521:Virulence Factors