title: Genome sequences and phylogenetic analysis of K88- and F18-positive porcine enterotoxigenic Escherichia coli.
abstract: Porcine enterotoxigenic Escherichia coli (ETEC) continues to result in major morbidity and mortality in the swine industry via postweaning diarrhea. The key virulence factors of ETEC strains, their serotypes, and their fimbrial components have been well studied. However, most studies to date have focused on plasmid-encoded traits related to colonization and toxin production, and the chromosomal backgrounds of these strains have been largely understudied. Here, we generated the genomic sequences of K88-positive and F18-positive porcine ETEC strains and examined the phylogenetic distribution of clinical porcine ETEC strains and their plasmid-associated genetic content. The genomes of porcine ETEC strains UMNK88 and UMNF18 were both found to contain remarkable plasmid complements containing known virulence factors, potential novel virulence factors, and antimicrobial resistance-associated elements. The chromosomes of these strains also possessed several unique genomic islands containing hypothetical genes with similarity to classical virulence factors, although phage-associated genomic islands dominated the accessory genomes of these strains. Phylogenetic analysis of 78 clinical isolates associated with neonatal and porcine diarrhea revealed that a limited subset of porcine ETEC lineages exist that generally contain common toxin and fimbrial profiles, with many of the isolates belonging to the ST10, ST23, and ST169 multilocus sequencing types. These lineages were generally distinct from existing human ETEC database isolates. Overall, most porcine ETEC strains appear to have emerged from a limited subset of E. coli lineages that either have an increased propensity to carry plasmid-encoded virulence factors or have the appropriate ETEC core genome required for virulence.
authors.affiliation: Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA.
authors.forename: Sara M
authors.initials: SM
authors.lastname: Shepard
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Danzeisen
authors.forename: Richard E
authors.initials: RE
authors.lastname: Isaacson
authors.forename: Torsten
authors.initials: T
authors.lastname: Seemann
authors.forename: Mark
authors.initials: M
authors.lastname: Achtman
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Johnson
mesh_terms: D000818:Animals; D000942:Antigens, Bacterial / Q000235:genetics / Q000378:metabolism*; D002876:Chromosomes, Bacterial; D054307:Enterotoxigenic Escherichia coli / Q000145:classification / Q000235:genetics*; D004927:Escherichia coli Infections / Q000382:microbiology / Q000662:veterinary*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D036781:Fimbriae Proteins / Q000235:genetics / Q000378:metabolism*; D016680:Genome, Bacterial; D044404:Genomic Islands; D008969:Molecular Sequence Data; D010802:Phylogeny; D013552:Swine; D013553:Swine Diseases / Q000382:microbiology*
chemical_list: D000942:Antigens, Bacterial; D029968:Escherichia coli Proteins; C113053:FedA protein, E coli; C026888:K88 antigen, E coli; D036781:Fimbriae Proteins
references.citation: Nucleic Acids Res. 2005 Oct 07;33(17):5691-702
references.pmid: 16214803
references.citation: Vet Res. 2005 Mar-Apr;36(2):241-56
references.pmid: 15720976
references.citation: Crit Rev Microbiol. 2010 Aug;36(3):212-20
references.pmid: 20367550
references.citation: Vet Res. 1999 Mar-Jun;30(2-3):317-42
references.pmid: 10367361
references.citation: Antimicrob Agents Chemother. 2010 May;54(5):2216-8
references.pmid: 20145079
references.citation: Appl Environ Microbiol. 2000 Oct;66(10):4555-8
references.pmid: 11010916
references.citation: Infect Immun. 2009 Mar;77(3):1222-9
references.pmid: 19103769
references.citation: Appl Environ Microbiol. 2009 Sep;75(18):5779-86
references.pmid: 19633120
references.citation: Int J Med Microbiol. 2005 Oct;295(6-7):443-54
references.pmid: 16238018
references.citation: J Clin Microbiol. 2006 Dec;44(12):4528-36
references.pmid: 17050815
references.citation: Int J Antimicrob Agents. 2009 Aug;34(2):173-6
references.pmid: 19464856
references.citation: J Bacteriol. 2004 Jun;186(11):3547-60
references.pmid: 15150243
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22
references.pmid: 19920124
references.citation: Science. 1997 Sep 5;277(5331):1453-62
references.pmid: 9278503
references.citation: Nucleic Acids Res. 2001 Jun 15;29(12):2607-18
references.pmid: 11410670
references.citation: Vet Microbiol. 1998 Aug 15;62(4):291-301
references.pmid: 9791875
references.citation: DNA Res. 2009 Oct;16(5):299-309
references.pmid: 19767599
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D225-9
references.pmid: 21109532
references.citation: J Antimicrob Chemother. 2011 Sep;66(9):2002-5
references.pmid: 21669947
references.citation: Plasmid. 2003 Nov;50(3):213-29
references.pmid: 14597010
references.citation: Nucleic Acids Res. 1997 Mar 1;25(5):955-64
references.pmid: 9023104
references.citation: J Clin Microbiol. 2006 Sep;44(9):3074-7
references.pmid: 16954229
references.citation: Nat Biotechnol. 2005 Jul;23(7):873-8
references.pmid: 15980861
references.citation: Vet Microbiol. 2002 May 24;86(4):303-11
references.pmid: 11955780
references.citation: J Bacteriol. 2010 Nov;192(21):5822-31
references.pmid: 20802035
references.citation: J Bacteriol. 2008 Oct;190(20):6881-93
references.pmid: 18676672
references.citation: Clin Diagn Lab Immunol. 2001 Jan;8(1):143-9
references.pmid: 11139209
references.citation: Infect Immun. 1978 May;20(2):559-66
references.pmid: 352948
references.citation: Antimicrob Agents Chemother. 2011 May;55(5):2451-7
references.pmid: 21343460
references.citation: J Bacteriol. 2005 Dec;187(23):8164-71
references.pmid: 16291689
references.citation: Adv Exp Med Biol. 1999;473:179-84
references.pmid: 10659356
references.citation: Vet Clin North Am Food Anim Pract. 2000 Mar;16(1):175-85
references.pmid: 10707419
references.citation: J Bacteriol. 2002 Sep;184(17):4690-8
references.pmid: 12169592
references.citation: Plasmid. 2002 Jul;48(1):24-37
references.pmid: 12206753
references.citation: J Gen Microbiol. 1980 Aug;119(2):475-83
references.pmid: 7014768
references.citation: Infect Immun. 2003 Aug;71(8):4516-25
references.pmid: 12874331
references.citation: J Clin Microbiol. 2010 Aug;48(8):2916-24
references.pmid: 20534806
references.citation: Curr Opin Microbiol. 2008 Feb;11(1):3-8
references.pmid: 18289922
references.citation: J Bacteriol. 2004 Nov;186(21):7032-68
references.pmid: 15489417
references.citation: Genomics. 1999 Dec 15;62(3):500-7
references.pmid: 10644449
references.citation: BMC Bioinformatics. 2010 Aug 18;11:431
references.pmid: 20718988
references.citation: Plasmid. 2011 Sep;66(3):144-51
references.pmid: 21843549
references.citation: PLoS One. 2011;6(8):e23415
references.pmid: 21858108
references.citation: Mol Biol Evol. 2007 Aug;24(8):1596-9
references.pmid: 17488738
references.citation: DNA Res. 2008 Dec;15(6):375-86
references.pmid: 18931093
references.citation: Vet Res. 2008 May-Jun;39(3):38
references.pmid: 18316019
references.citation: Anim Health Res Rev. 2001 Dec;2(2):129-40
references.pmid: 11831435
references.citation: Mol Microbiol. 2006 Jun;60(5):1136-51
references.pmid: 16689791
references.citation: Infect Immun. 2009 Jun;77(6):2272-84
references.pmid: 19307211
references.citation: Vet Microbiol. 2002 Mar 22;85(3):275-84
references.pmid: 11852194
references.citation: J Infect Dis. 2000 Jan;181(1):261-72
references.pmid: 10608775
references.citation: Nucleic Acids Res. 2007;35(9):3100-8
references.pmid: 17452365
references.citation: Infect Immun. 2006 Apr;74(4):2102-14
references.pmid: 16552039
references.citation: Infect Immun. 2011 Feb;79(2):950-60
references.pmid: 21078854
references.citation: J Bacteriol. 1997 Sep;179(18):5783-8
references.pmid: 9294435
references.citation: J Bacteriol. 2006 Aug;188(16):5975-83
references.pmid: 16885466