Comparative sequence analysis identified multiple replication systems and virulence determinants to be frequently encoded on large plasmids of Escherichia coli

Kaper, 2004, Pathogenic Escherichia coli, Nat. Rev. Microbiol., 2, 123, 10.1038/nrmicro818 Johnson, 2009, Pathogenomics of the virulence plasmids of Escherichia coli, Microbiol. Mol. Biol. Rev., 73, 750, 10.1128/MMBR.00015-09 Francia, 2004, A classification scheme for mobilization regions of bacterial plasmids, FEMS Microbiol. Rev., 28, 79, 10.1016/j.femsre.2003.09.001 Smillie, 2010, Mobility of plasmids, Microbiol. Mol. Biol. Rev., 74, 434, 10.1128/MMBR.00020-10 Cohen, 1973, Construction of biologically functional bacterial plasmids in vitro, Proc. Natl. Acad. Sci. U. S. A., 70, 3240, 10.1073/pnas.70.11.3240 Birnboim, 1979, A rapid alkaline extraction procedure for screening recombinant plasmid DNA, Nucleic Acids Res., 7, 1513, 10.1093/nar/7.6.1513 Schmidt, 1995, Molecular analysis of the plasmid-encoded hemolysin of Escherichia coli O157:H7 strain EDL 933, Infect. Immun., 63, 1055, 10.1128/IAI.63.3.1055-1061.1995 Trevors, 1986, Plasmid curing in bacteria, FEMS Microbiol. Lett., 32, 149, 10.1111/j.1574-6968.1986.tb01189.x Normark, 2002, Evolution and spread of antibiotic resistance, J. Intern. Med., 252, 91, 10.1046/j.1365-2796.2002.01026.x Wang, 2006, Food commensal microbes as a potentially important avenue in transmitting antibiotic resistance genes, FEMS Microbiol. Rev., 254, 226, 10.1111/j.1574-6968.2005.00030.x Couturier, 1988, Identification and classification of bacterial plasmids, Microbiol. Rev., 52, 375, 10.1128/MR.52.3.375-395.1988 Villa, 2010, Replicon sequence typing of IncF plasmids carrying virulence and resistance determinants, J. Antimicrob. Chemother., 65, 2518, 10.1093/jac/dkq347 Jerke, 2008, Comparative analysis of eight Arthrobacter plasmids, Plasmid, 59, 73, 10.1016/j.plasmid.2007.12.003 Kuenne, 2010, Comparative analysis of plasmids in the genus Listeria, PLoS One, 5, 10.1371/journal.pone.0012511 Johnson, 2011, Comparative genomics and phylogeny of the IncI1 plasmids: a common plasmid type among porcine enterotoxigenic Escherichia coli, Plasmid, 66, 144, 10.1016/j.plasmid.2011.07.003 Makino K1, 1998, Complete nucleotide sequences of 93-kb and 3.3-kb plasmids of an enterohemorrhagic Escherichia coli O157:H7 derived from Sakai outbreak, DNA Res., 5, 1, 10.1093/dnares/5.1.1 Burland, 1998, The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157:H7, Nucleic Acids Res., 26, 4196, 10.1093/nar/26.18.4196 Adamczuk, 2015, Diversity and global distribution of IncL/M plasmids enabling horizontal dissemination of beta-lactam resistance genes among the Enterobacteriaceae, BioMed Res. Int., 414681 Lim, 2010, A brief overview of Escherichia coli O157:H7 and its plasmid O157, J. Microbiol. Biotechnol., 20, 5, 10.4014/jmb.0908.08007 Lowe, 1997, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res., 25, 955, 10.1093/nar/25.5.0955 Lagesen, 2007, RNAmmer: consistent and rapid annotation of ribosomal RNA genes, Nucleic Acids Res., 35, 3100, 10.1093/nar/gkm160 Thompson, 1994, Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res., 22, 4673, 10.1093/nar/22.22.4673 Wang, 2000, The Escherichia coli O111 and Salmonella enterica O35 gene clusters: gene clusters encoding the same colitose-containing O antigen are highly conserved, J. Bacteriol., 182, 5256, 10.1128/JB.182.18.5256-5261.2000 Wilson, 2002, Mechanisms of bacterial pathogenicity, Postgrad. Med., 78, 216, 10.1136/pmj.78.918.216 Gerlach, 2007, Protein secretion systems and adhesins: the molecular armory of Gram-negative pathogens, Int. J Med. Microbiol., 297, 401, 10.1016/j.ijmm.2007.03.017 Kulkarni, 2009, Roles of putative type II secretion and type IV pilus systems in the virulence of uropathogenic Escherichia coli, PLoS One, 4, 10.1371/journal.pone.0004752 Lawley, 2003, F factor conjugation is a true type IV secretion system, FEMS Microbiol. Lett., 224, 1, 10.1016/S0378-1097(03)00430-0 Blank, 2000, Molecular variation among type IV pilin (bfpA) genes from diverse enteropathogenic Escherichia coli strains, Infect. Immun., 68, 7028, 10.1128/IAI.68.12.7028-7038.2000 Hyland, 2008, The bundlin pilin protein of enteropathogenic Escherichia coli is an N-acetyllactosamine-specific lectin, Cell Microbiol., 10, 177 Croxen, 2013, Recent advances in understanding enteric pathogenic Escherichia coli, Clin. Microbiol. Rev., 26, 822, 10.1128/CMR.00022-13 Bugarel, 2011, Virulence gene profiling of enterohemorrhagic (EHEC) and enteropathogenic (EPEC) Escherichia coli strains: a basis for molecular risk assessment of typical and atypical EPEC strains, BMC Microbiol., 11, 142, 10.1186/1471-2180-11-142 Sheikh, 2002, A novel dispersin protein in enteroaggregative Escherichia coli, J. Clin. Investig., 110, 1329, 10.1172/JCI16172 Schmidt, 1997, A gene cluster closely related to type II secretion pathway operons of gram-negative bacteria is located on the large plasmid of enterohemorrhagic Escherichia coli O157 strains, FEMS Microbiol. Lett., 148, 265, 10.1111/j.1574-6968.1997.tb10299.x Eisenreich, 2013, Metabolic host responses to infection by intracellular bacterial pathogens, Front. Cell. Infect. Microbiol., 3, 24, 10.3389/fcimb.2013.00024 Braun, 2001, Iron uptake mechanisms and their regulation in pathogenic bacteria, Int. J Med. Microbiol., 291, 67, 10.1078/1438-4221-00103 Heinemann, 2008, The biochemistry of heme biosynthesis, Arch. Biochem. Biophys., 474, 238, 10.1016/j.abb.2008.02.015 Kuhnert, 2000, Target genes for virulence assessment of Escherichia coli isolates from water, food and the environment, FEMS Microbiol. Rev., 24, 107, 10.1111/j.1574-6976.2000.tb00535.x Rasko, 2008, The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates, J. Bacteriol., 190, 6881, 10.1128/JB.00619-08 Ho, 2015, The complete sequence and comparative analysis of a multidrug-resistance and virulence multireplicon IncFII plasmid pEC302/04 from an extraintestinal pathogenic Escherichia coli EC302/04 indicate extensive diversity of IncFII plasmids, Front. Microbiol., 6, 1547 Moscoso, 1997, Initiation of replication of plasmid pMV158: mechanisms of DNA strand-transfer reactions mediated by the initiator RepB protein, J. Mol. Biol., 268, 840, 10.1006/jmbi.1997.1012