(Patho-)Genomics of Escherichia coli

Allen, 2001, Use of representational difference analysis to identify Escherichia coli O157-specific DNA sequences, FEMS Microbiol. Lett., 197, 195, 10.1111/j.1574-6968.2001.tb10603.x

Ambrozic, 1998, Escherichia coli CoIV plasmid pRK100: genetic organization, stability and conjugal transfer, Microbiology, 144, 343, 10.1099/00221287-144-2-343

Anjum, 2003, Comparative genomic indexing reveals the phylogenomics of Escherichia coli pathogens, Infect. Immun., 71, 4674, 10.1128/IAI.71.8.4674-4683.2003

Bergthorsson, 1998, Distribution of chromosome length variation in natural isolates of Escherichia coli, Mol. Biol. Evol., 15, 6, 10.1093/oxfordjournals.molbev.a025847

Bertin, 1998, Phenotypic expression of K88 adhesion alone or simultaneously with K99 and/or F41 adhesins in the bovine enterotoxigenic Escherichia coli strain B41, Vet. Microbiol., 59, 283, 10.1016/S0378-1135(97)00186-7

Bingen-Bidois, 2002, Phylogenetic analysis and prevalence of urosepsis strains of Escherichia coli bearing pathogenicity island-like domains, Infect. Immun., 70, 3216, 10.1128/IAI.70.6.3216-3226.2002

Blanc-Potard, 2002, Representational difference analysis between Afa/Dr diffusely adhering Escherichia coli and nonpathogenic E. coli K-12, Infect. Immun., 70, 5503, 10.1128/IAI.70.10.5503-5511.2002

Blattner, 1997, The complete genome sequence of Escherichia coli K-12, Science, 277, 1453, 10.1126/science.277.5331.1453

Blum-Oehler, 2003, Development of strain-specific PCR reactions for the detection of the probiotic Escherichia coli strain Nissle 1917 in fecal samples, Res. Microbiol., 154, 59, 10.1016/S0923-2508(02)00007-4

Boerlin, 1998, Evolution of enterohemorrhagic Escherichia coli hemolysin plasmids and the locus for enterocyte effacement in shiga toxin-producing E. coli, Infect. Immun., 66, 2553, 10.1128/IAI.66.6.2553-2561.1998

Bonacorsi, 2000, Identification of regions of the Escherichia coli chromosome specific for neonatal meningitis-associated strains, Infect. Immun., 68, 2096, 10.1128/IAI.68.4.2096-2101.2000

Bonacorsi, 2003, Molecular analysis and experimental virulence of French and North American Escherichia coli neonatal meningitis isolates: identification of a new virulent clone, J. Infect. Dis., 187, 1895, 10.1086/375347

Boyd, 2002, Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved, Trends Microbiol., 10, 521, 10.1016/S0966-842X(02)02459-9

Boyd, 1996, Mosaic structure of plasmids from natural populations of Escherichia coli, Genetics, 143, 1091, 10.1093/genetics/143.3.1091

Boyd, 2001, Bacteriophage–bacteriophage interactions in the evolution of pathogenic bacteria, Trends Microbiol., 9, 137, 10.1016/S0966-842X(01)01960-6

Boyd, 2004, Complete nucleotide sequence of a 92-kilobase plasmid harboring the CTX-M-15 extended-spectrum beta-lactamase involved in an outbreak in long-term-care facilities in Toronto, Canada, Antimicrob. Agents Chemother., 48, 3758, 10.1128/AAC.48.10.3758-3764.2004

Brunder, 1996, KatP, a novel catalase-peroxidase encoded by the large plasmid of enterohaemorrhagic Escherichia coli O157:H7, Microbiology, 142, 3305, 10.1099/13500872-142-11-3305

Brüssow, 2001, Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages, Mol. Microbiol., 39, 213, 10.1046/j.1365-2958.2001.02228.x

Brüssow, 2004, Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion, Microbiol. Mol. Biol. Rev., 68, 560, 10.1128/MMBR.68.3.560-602.2004

Buchrieser, 2000, The virulence plasmid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri, Mol. Microbiol., 38, 760, 10.1046/j.1365-2958.2000.02179.x

Burrus, 2002, Conjugative transposons: the tip of the iceberg, Mol. Microbiol., 46, 601, 10.1046/j.1365-2958.2002.03191.x

Campbell, 1996, Bacteriophages, 2325

Castillo, 2005, A genomic population genetics analysis of the pathogenic enterocyte effacement island in Escherichia coli: the search for the unit of selection, Proc. Natl. Acad. Sci. USA, 102, 1542, 10.1073/pnas.0408633102

Cheetham, 1995, A role for bacteriophages in the evolution and transfer of bacterial virulence determinants, Mol. Microbiol., 18, 201, 10.1111/j.1365-2958.1995.mmi_18020201.x

Delicato, 2003, Virulence-associated genes in Escherichia coli isolates from poultry with colibacillosis, Vet. Microbiol., 94, 97, 10.1016/S0378-1135(03)00076-2

Dobrindt, 2002, Genetic structure and distribution of four pathogenicity islands (PAI I(536) to PAI IV(536)) of uropathogenic Escherichia coli strain 536, Infect. Immun., 70, 6365, 10.1128/IAI.70.11.6365-6372.2002

Dobrindt, 2003, Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays, J. Bacteriol., 185, 1831, 10.1128/JB.185.6.1831-1840.2003

Dobrindt, 2004, Genomic islands in pathogenic and environmental microorganisms, Nat. Rev. Microbiol., 2, 414, 10.1038/nrmicro884

Donnenberg, 1992, A plasmid-encoded type IV fimbrial gene of enteropathogenic Escherichia coli associated with localized adherence, Mol. Microbiol., 6, 3427, 10.1111/j.1365-2958.1992.tb02210.x

Dozois, 1999, Pathogenic diversity of Escherichia coli and the emergence of ‘exotic’ islands in the gene stream, Vet. Res., 30, 157

Dozois, 2003, Identification of pathogen-specific and conserved genes expressed in vivo by an avian pathogenic Escherichia coli strain, Proc. Natl. Acad. Sci. USA, 100, 247, 10.1073/pnas.232686799

Fleischmann, 1995, Whole-genome random sequencing and assembly of Haemophilus influenzae Rd, Science, 269, 496, 10.1126/science.7542800

Fukiya, 2004, Extensive genomic diversity in pathogenic Escherichia coli and Shigella strains revealed by comparative genomic hybridization microarray, J. Bacteriol., 186, 3911, 10.1128/JB.186.12.3911-3921.2004

Gomez-Duarte, 1999, Identification of lngA, the structural gene of longus type IV pilus of enterotoxigenic Escherichia coli, Microbiology, 145, 1809, 10.1099/13500872-145-7-1809

Gomez-Lus, 1998, Evolution of bacterial resistance to antibiotics during the last three decades, Int. Microbiol., 1, 279

Gophna, 2003, A novel ColV plasmid encoding type IV pili, Microbiology, 149, 177, 10.1099/mic.0.25858-0

Grozdanov, 2002, A single nucleotide exchange in the wzy gene is responsible for the semirough O6 lipopolysaccharide phenotype and serum sensitivity of Escherichia coli strain Nissle 1917, J. Bacteriol., 184, 5912, 10.1128/JB.184.21.5912-5925.2002

Grozdanov, 2004, Analysis of the genome structure of the nonpathogenic probiotic Escherichia coli strain Nissle 1917, J. Bacteriol., 186, 5432, 10.1128/JB.186.16.5432-5441.2004

Guyer, 1998, Genomic analysis of a pathogenicity island in uropathogenic Escherichia coli CFT073: distribution of homologous sequences among isolates from patients with pyelonephritis, cystitis, and catheter-associated bacteriuria and from fecal samples, Infect. Immun., 66, 4411, 10.1128/IAI.66.9.4411-4417.1998

Hacker, 2001, Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes, EMBO Rep., 2, 376, 10.1093/embo-reports/kve097

Hacker, J., Kaper, J.B. (Eds.), 2002. Pathogenicity islands and the evolution of pathogenic microbes. Curr. Top. Microbiol. Immunol. 264 (1,2).

Hayashi, 2001, Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12, DNA Res., 8, 11, 10.1093/dnares/8.1.11

Heimer, 2002, Urease of enterohemorrhagic Escherichia coli: evidence for regulation by fur and a trans-acting factor, Infect. Immun., 70, 1027, 10.1128/IAI.70.2.1027-1031.2002

Hejnova, 2005, Characterization of the flexible genome complement of the commensal Escherichia coli strain A0 34/86 (O83:K24:H31), Microbiology, 151, 385, 10.1099/mic.0.27469-0

Hendrix, 1999, Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage, Proc. Natl. Acad. Sci. USA, 96, 2192, 10.1073/pnas.96.5.2192

Herias, 1995, Role of Escherichia coli P fimbriae in intestinal colonization in gnotobiotic rats, Infect. Immun., 63, 4781, 10.1128/IAI.63.12.4781-4789.1995

Herias, 1997, Escherichia coli K5 capsule expression enhances colonization of the large intestine in the gnotobiotic rat, Infect. Immun., 65, 531, 10.1128/IAI.65.2.531-536.1997

Herold, 2004, Shiga toxin-encoding bacteriophages – genomes in motion, Int. J. Med. Microbiol., 294, 115, 10.1016/j.ijmm.2004.06.023

Janka, 2002, Identification and distribution of the enterohemorrhagic Escherichia coli factor for adherence (efa1) gene in sorbitol-fermenting Escherichia coli O157: H, Int. J. Med. Microbiol., 292, 207, 10.1078/1438-4221-00206

Janke, 2001, A subtractive hybridisation analysis of genomic differences between the uropathogenic E. coli strain 536 and the E. coli K-12 strain MG1655, FEMS Microbiol. Lett., 199, 61, 10.1111/j.1574-6968.2001.tb10651.x

Jin, 2002, Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157, Nucleic Acids Res., 30, 4432, 10.1093/nar/gkf566

Johnson, 2002, Extraintestinal pathogenic Escherichia coli: “the other bad E coli”, J. Lab. Clin. Med., 139, 155, 10.1067/mlc.2002.121550

Johnson, 2001, Phylogenetic distribution of extraintestinal virulence-associated traits in Escherichia coli, J. Infect. Dis., 183, 78, 10.1086/317656

Johnson, 2001, Clonal relationships and extended virulence genotypes among Escherichia coli isolates from women with a first or recurrent episode of cystitis, J. Infect. Dis., 183, 1508, 10.1086/320198

Johnson, 2001, Ongoing horizontal and vertical transmission of virulence genes and papA alleles among Escherichia coli blood isolates from patients with diverse-source bacteremia, Infect. Immun., 69, 5363, 10.1128/IAI.69.9.5363-5374.2001

Jores, 2004, Impact of the locus of enterocyte effacement pathogenicity island on the evolution of pathogenic Escherichia coli, Int. J. Med. Microbiol., 294, 103, 10.1016/j.ijmm.2004.06.024

Lalioui, 2001, afa-8 Gene cluster is carried by a pathogenicity island inserted into the tRNA(Phe) of human and bovine pathogenic Escherichia coli isolates, Infect. Immun., 69, 937, 10.1128/IAI.69.2.937-948.2001

Lan, 2001, Molecular evolution of large virulence plasmid in Shigella clones and enteroinvasive Escherichia coli, Infect. Immun., 69, 6303, 10.1128/IAI.69.10.6303-6309.2001

La Ragione, 2002, Virulence factors of Escherichia coli serotypes associated with avian colisepticaemia, Res. Vet. Sci., 73, 27, 10.1016/S0034-5288(02)00075-9

Lawrence, 1998, Molecular archaeology of the Escherichia coli genome, Proc. Natl. Acad. Sci. USA, 95, 9413, 10.1073/pnas.95.16.9413

Liu, 1995, Rearrangements in the genome of the bacterium Salmonella typhi, Proc. Natl. Acad. Sci. USA, 92, 1018, 10.1073/pnas.92.4.1018

Liu, 1996, Highly plastic chromosomal organization in Salmonella typhi, Proc. Natl. Acad. Sci. USA, 93, 10303, 10.1073/pnas.93.19.10303

Mainil, 1998, Virulence plasmids of enterotoxigenic Escherichia coli isolates from piglets, Vet. Microbiol., 62, 291, 10.1016/S0378-1135(98)00225-9

Mainil, 2000, Identification of the F17 fimbrial subunit- and adhesin-encoding (f17A and f17G) gene variants in necrotoxigenic Escherichia coli from cattle, pigs and humans, Vet. Microbiol., 73, 327, 10.1016/S0378-1135(00)00179-6

Martinez, 1994, The organization of intercistronic regions of the aerobactin operon of pColV-K30 may account for the differential expression of the iucABCD iutA genes, J. Mol. Biol., 238, 288, 10.1006/jmbi.1994.1290

Mazaitis, 1981, Structure of a naturally occurring plasmid with genes for enterotoxin production and drug resistance, J. Bacteriol., 145, 97, 10.1128/JB.145.1.97-105.1981

Milkman, 1990, Molecular evolution of the Escherichia coli chromosome. III. Clonal frames, Genetics, 126, 505, 10.1093/genetics/126.3.505

Milkman, 1993, Molecular evolution of the Escherichia coli chromosome. IV. Sequence comparisons, Genetics, 133, 455, 10.1093/genetics/133.3.455

Milkman, 1988, Molecular evolution of the Escherichia coli chromosome. II. Clonal segments, Genetics, 120, 359, 10.1093/genetics/120.2.359

Miyazaki, 2002, Identification of a type III secretion system in uropathogenic Escherichia coli, FEMS Microbiol. Lett., 212, 221, 10.1111/j.1574-6968.2002.tb11270.x

Mokady, 2005, Extensive gene diversity in septicemic Escherichia coli strains, J. Clin. Microbiol., 43, 66, 10.1128/JCM.43.1.66-73.2005

Nataro, 1998, Diarrheagenic Escherichia coli, Clin. Microbiol. Rev., 11, 142, 10.1128/CMR.11.1.142

Nataro, 1995, Identification and cloning of a novel plasmid-encoded enterotoxin of enteroinvasive Escherichia coli and Shigella strains, Infect. Immun., 63, 4721, 10.1128/IAI.63.12.4721-4728.1995

Neidhardt, 1996

Ochman, 2000, Evolutionary dynamics of full genome content in Escherichia coli, EMBO J., 19, 6637, 10.1093/emboj/19.24.6637

Ochman, 2000, Lateral gene transfer and the nature of bacterial innovation, Nature, 405, 299, 10.1038/35012500

Ohnishi, 2001, Diversification of Escherichia coli genomes: are bacteriophages the major contributors?, Trends Microbiol., 9, 481, 10.1016/S0966-842X(01)02173-4

Ohnishi, 2002, Genomic diversity of enterohemorrhagic Escherichia coli O157 revealed by whole genome PCR scanning, Proc. Natl. Acad. Sci. USA, 99, 17043, 10.1073/pnas.262441699

Ørskov, 1992, Escherichia coli serotyping and disease in man and animals, Can. J. Microbiol., 38, 699, 10.1139/m92-115

Otto, 1998, Characterization of a hemoglobin protease secreted by the pathogenic Escherichia coli strain EB1, J. Exp. Med., 188, 1091, 10.1084/jem.188.6.1091

Perna, 2001, Genome sequence of enterohaemorrhagic Escherichia coli O157:H7, Nature, 409, 529, 10.1038/35054089

Redford, 2002, Extraintestinal Escherichia coli as a model system for the study of pathogenicity islands, Curr. Top. Microbiol. Immunol., 264, 15

Reid, 2000, Parallel evolution of virulence in pathogenic Escherichia coli, Nature, 406, 64, 10.1038/35017546

Rodriguez-Siek, 2005, Comparison of Escherichia coli isolates implicated in human urinary tract infection and avian colibacillosis, Microbiology, 151, 2097, 10.1099/mic.0.27499-0

Rumer, 2003, Dissemination of pheU- and pheV-located genomic islands among enteropathogenic (EPEC) and enterohemorrhagic (EHEC) E. coli and their possible role in the horizontal transfer of the locus of enterocyte effacement (LEE), Int. J. Med. Microbiol., 292, 463, 10.1078/1438-4221-00229

Rutherford, 2000, Artemis: sequence visualization and annotation, Bioinformatics, 16, 944, 10.1093/bioinformatics/16.10.944

Schouler, 2004, Genomic subtraction for the identification of putative new virulence factors of an avian pathogenic Escherichia coli strain of O2 serogroup, Microbiology, 150, 2973, 10.1099/mic.0.27261-0

Schubert, 1998, Prevalence of the “high-pathogenicity island” of Yersinia species among Escherichia coli strains that are pathogenic to humans, Infect. Immun., 66, 480, 10.1128/IAI.66.2.480-485.1998

Schubert, 2004, A novel integrative and conjugative element (ICE) of Escherichia coli: the putative progenitor of the Yersinia high-pathogenicity island, Mol. Microbiol., 51, 837, 10.1046/j.1365-2958.2003.03870.x

Sorsa, 2003, Characterization of an iroBCDEN gene cluster on a transmissible plasmid of uropathogenic Escherichia coli: evidence for horizontal transfer of a chromosomal virulence factor, Infect. Immun., 71, 3285, 10.1128/IAI.71.6.3285-3293.2003

Sorsa, 2004, Identification of novel virulence-associated loci in uropathogenic Escherichia coli by suppression subtractive hybridization, FEMS Microbiol. Lett., 230, 203, 10.1016/S0378-1097(03)00893-0

Stocki, 2002, Identification of genomic differences between Escherichia coli strains pathogenic for poultry and E. coli K-12 MG1655 using suppression subtractive hybridization analysis, Microb. Pathog., 33, 289, 10.1006/mpat.2002.0536

Stoltzfus, 1988, Molecular evolution of the Escherichia coli chromosome. I. Analysis of structure and natural variation in a previously uncharacterized region between trp and tonB, Genetics, 120, 345, 10.1093/genetics/120.2.345

Sun, 2005, Genomic peculiarity of coding sequences and metabolic potential of probiotic Escherichia coli strain Nissle 1917 inferred from raw genome data, J. Biotechnol., 117, 147, 10.1016/j.jbiotec.2005.01.008

Tatsuno, 2001, toxB gene on pO157 of enterohemorrhagic Escherichia coli O157:H7 is required for full epithelial cell adherence phenotype, Infect. Immun., 69, 6660, 10.1128/IAI.69.11.6660-6669.2001

Tobe, 1999, Complete DNA sequence and structural analysis of the enteropathogenic Escherichia coli adherence factor plasmid, Infect. Immun., 67, 5455, 10.1128/IAI.67.10.5455-5462.1999

Valvano, 1984, Aerobactin iron transport genes commonly encoded by certain ColV plasmids occur in the chromosome of a human invasive strain of Escherichia coli K1, Infect. Immun., 46, 159, 10.1128/IAI.46.1.159-167.1984

Venkatesan, 2001, Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri, Infect. Immun., 69, 3271, 10.1128/IAI.69.5.3271-3285.2001

Vial, 1988, Characterization of enteroadherent-aggregative Escherichia coli, a putative agent of diarrheal disease, J. Infect. Dis., 158, 70, 10.1093/infdis/158.1.70

Wang, 2001, Sequence analysis of four Shigella boydii O-antigen loci: implication for Escherichia coli and Shigella relationships, Infect. Immun., 69, 6923, 10.1128/IAI.69.11.6923-6930.2001

Waters, 1991, Colicin V virulence plasmids, Microbiol. Rev., 55, 437, 10.1128/MMBR.55.3.437-450.1991

Wei, 2003, Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T, Infect. Immun., 71, 2775, 10.1128/IAI.71.5.2775-2786.2003

Welch, 2002, Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli, Proc. Natl. Acad. Sci. USA, 99, 17020, 10.1073/pnas.252529799

Wold, 1992, Resident colonic Escherichia coli strains frequently display uropathogenic characteristics, J. Infect. Dis., 165, 46, 10.1093/infdis/165.1.46