Comparative genomics and phylogeny of the IncI1 plasmids: A common plasmid type among porcine enterotoxigenic Escherichia coli

Plasmid

Volumn 66, Issue 3, 2011, Pages 144-151

  Johnson, Timothy J ^a   Shepard, Sara M ^a   Rivet, Bernadette ^a   Danzeisen, Jessica L ^a   Carattoli, Alessandra ^b  

^a UNIVERSITY OF MINNESOTA   (United States)

^b ISTITUTO SUPERIORE DI SANITÀ   (Italy)

Author keywords

Escherichia coli; Genomics; IncI1; Plasmid; Porcine

Indexed keywords

EXTENDED SPECTRUM BETA LACTAMASE; GENOMIC DNA;

ANTIBIOTIC RESISTANCE; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIUM ISOLATE; BETA LACTAMASE CMY 2 GENE; BETA LACTAMASE TEM GENE; COMPARATIVE STUDY; CONTROLLED STUDY; DNA BASE COMPOSITION; ENTEROTOXIGENIC ESCHERICHIA COLI; GENE; GENE LOCUS; GENETIC CONSERVATION; HORIZONTAL GENE TRANSFER; INCL1 PLASMID; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENETIC TREE; PHYLOGENOMICS; PLASMID; SALMONELLA ENTERICA; SEQUENCE ALIGNMENT;

ANIMALS; DRUG RESISTANCE, BACTERIAL; ENTEROTOXIGENIC ESCHERICHIA COLI; GENE ORDER; GENOMICS; PHYLOGENY; PLASMIDS; SWINE;

ENTEROBACTERIACEAE; ESCHERICHIA COLI; SALMONELLA ENTERICA; SUIDAE; SUS;

EID: 81055156189     PISSN: 0147619X     EISSN: 10959890     Source Type: Journal    
DOI: 10.1016/j.plasmid.2011.07.003     Document Type: Article

References (50)

1. Altschul S.F., et al. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
2. Brzuszkiewicz, E., et al., 2011. Genome sequence analysis of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Hemorrhagic Escherichia coli (EAHEC). Arch. Microbiol. (Epub ahead of print).
3. Bortolaia V., et al. High diversity of extended-spectrum beta-lactamases in Escherichia coli isolates from Italian broiler flocks. Antimicrob. Agents Chemother. 2010, 54:1623-1626.
4. Bradley D.E. Transfer systems of K88 and K99 plasmids. Plasmid 1985, 13:118-128.
5. Call D.R., et al. blaCMY-2-positive IncA/C plasmids from Escherichia coli and Salmonella enterica are a distinct component of a larger lineage of plasmids. Antimicrob. Agents Chemother. 2010, 54:590-596.
6. Cascales E., et al. Colicin biology. Microbiol. Mol. Biol. Rev. 2007, 71:158-229.
7. Cloeckaert A., et al. Dissemination of an extended-spectrum-beta-lactamase blaTEM-52 gene-carrying IncI1 plasmid in various Salmonella enterica serovars isolated from poultry and humans in Belgium and France between 2001 and 2005. Antimicrob. Agents Chemother. 2007, 51:1872-1875.
8. Cloeckaert A., et al. IncI1 plasmid carrying extended-spectrum-beta-lactamase gene blaCTX-M-1 in Salmonella enterica isolates from poultry and humans in France, 2003 to 2008. Antimicrob. Agents Chemother. 2010, 54:4484-4486.
9. Crossman L.C., et al. A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407. J. Bacteriol. 2010, 192:5822-5831.
10. Darling A.C., et al. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004, 14:1394-1403.
11. Delver E.P., et al. Nucleotide sequence of the gene (ard) encoding the antirestriction protein of plasmid ColIb-P9. J. Bacteriol. 1991, 173:5887-5892.
12. Dierikx C., et al. Increased detection of extended spectrum beta-lactamase producing Salmonella enterica and Escherichia coli isolates from poultry. Vet. Microbiol. 2010, 145:273-278.
13. Diestra K., et al. Characterization of plasmids encoding blaESBL and surrounding genes in Spanish clinical isolates of Escherichia coli and Klebsiella pneumoniae. J. Antimicrob. Chemother. 2009, 63:60-66.
14. Dudley E.G., et al. An IncI1 plasmid contributes to the adherence of the atypical enteroaggregative Escherichia coli strain C1096 to cultured cells and abiotic surfaces. Infect. Immun. 2006, 74:2102-2114.
15. Folster J.P., et al. Identification and characterization of CTX-M-producing Shigella isolates in the United States. Antimicrob. Agents Chemother. 2010, 54:2269-2270.
16. Fricke W.F., et al. Comparative genomics of the IncA/C multidrug resistance plasmid family. J. Bacteriol. 2009, 191:4750-4757.
17. Froehlich B., et al. The pCoo plasmid of enterotoxigenic Escherichia coli is a mosaic cointegrate. J. Bacteriol. 2005, 187:6509-6516.
18. Garcia-Fernandez A., et al. Multilocus sequence typing of IncI1 plasmids carrying extended-spectrum beta-lactamases in Escherichia coli and Salmonella of human and animal origin. J. Antimicrob. Chemother. 2008, 61:1229-1233.
19. Gyohda A., Komano T. Purification and characterization of the R64 shufflon-specific recombinase. J. Bacteriol. 2000, 182:2787-2792.
20. Howland C.J., et al. The ssb gene of plasmid ColIb-P9. J. Bacteriol. 1989, 171:2466-2473.
21. Hradecka H., et al. Characterization of Salmonella enterica serovar Typhimurium conjugative plasmids transferring resistance to antibiotics and their interaction with the virulence plasmid. J. Antimicrob. Chemother. 2008, 62:938-941.
22. Ishiwa A., Komano T. Thin pilus PilV adhesins of plasmid R64 recognize specific structures of the lipopolysaccharide molecules of recipient cells. J. Bacteriol. 2003, 185:5192-5199.
23. Ishiwa A., Komano T. PilV adhesins of plasmid R64 thin pili specifically bind to the lipopolysaccharides of recipient cells. J. Mol. Biol. 2004, 343:615-625.
24. Johnson J.R., Stell A.L. Extended virulence genotypes of Escherichia coli strains from patients with urosepsis in relation to phylogeny and host compromise. J. Infect. Dis. 2000, 181:261-272.
25. Johnson T.J., et al. Complete DNA sequence, comparative genomics, and prevalence of an IncHI2 plasmid occurring among extraintestinal pathogenic Escherichia coli isolates. Antimicrob. Agents Chemother. 2006, 50:3929-3933.
26. Kim S.R., Komano T. The plasmid R64 thin pilus identified as a type IV pilus. J. Bacteriol. 1997, 179:3594-3603.
27. Komano T., et al. Physical and genetic analyses of IncI2 plasmid R721: evidence for the presence of shufflon. Plasmid 1990, 23:248-251.
28. Komano T., et al. Transfer region of IncI1 plasmid R64 and role of shufflon in R64 transfer. J. Bacteriol. 1990, 172:2230-2235.
29. Komano T., et al. Distribution of shufflon among IncI plasmids. J. Bacteriol. 1987, 169:5317-5319.
30. Komano T., et al. The transfer region of IncI1 plasmid R64: similarities between R64 tra and legionella icm/dot genes. Mol. Microbiol. 2000, 35:1348-1359.
31. Leverstein-van Hall M.A., et al. Dutch patients, retail chicken meat and poultry share the same ESBL genes, plasmids and strains. Clin. Microbiol. Infect. 2011, 17:873-880.
32. Literak I., et al. Antibiotic-resistant Escherichia coli bacteria, including strains with genes encoding the extended-spectrum beta-lactamase and QnrS, in waterbirds on the Baltic Sea Coast of Poland. Appl. Environ. Microbiol. 2010, 76:8126-8134.
33. Liu S.Y., et al. Characterisation of plasmids encoding CTX-M-3 extended-spectrum beta-lactamase from Enterobacteriaceae isolated at a university hospital in Taiwan. Int. J. Antimicrob. Agents 2007, 29:440-445.
34. Mainil J.G., et al. Virulence plasmids of enterotoxigenic Escherichia coli isolates from piglets. Vet. Microbiol. 1998, 62:291-301.
35. Marcade G., et al. Replicon typing of plasmids in Escherichia coli producing extended-spectrum beta-lactamases. J. Antimicrob. Chemother. 2009, 63:67-71.
36. Moissenet D., et al. Meningitis caused by Escherichia coli producing TEM-52 extended-spectrum beta-lactamase within an extensive outbreak in a neonatal ward: epidemiological investigation and characterization of the strain. J. Clin. Microbiol. 2010, 48:2459-2463.
37. Overbeek R., et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005, 33:5691-5702.
38. Rangnekar V.M., et al. Antimicrobial resistance and incompatibility groups of R plasmids in Salmonella typhimurium isolated from human sources in Bombay from 1978 to 1980. Antimicrob. Agents Chemother. 1983, 23:54-58.
39. Rasko D.A., et al. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J. Bacteriol. 2008, 190:6881-6893.
40. Rees C.E., et al. Organization and regulation of the conjugation genes of IncI1 plasmid ColIb-P9. Plasmid 1987, 18:223-236.
41. Rodriguez-Siek K.E., et al. Characterizing the APEC pathotype. Vet. Res. 2005, 36:241-256.
42. Sampei G., et al. Complete genome sequence of the incompatibility group I1 plasmid R64. Plasmid 2010, 64:92-103.
43. Sedgwick S.G., et al. Mutagenic DNA repair genes on plasmids from the 'pre-antibiotic era'. Mol. Gen. Genet. 1989, 218:323-329.
44. Smet A., et al. Complete nucleotide sequence of CTX-M-15-plasmids from clinical Escherichia coli isolates: insertional events of transposons and insertion sequences. PLoS ONE 2010, 5:e11202.
45. Tamura K., et al. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
46. Tato M., et al. Complex clonal and plasmid epidemiology in the first outbreak of Enterobacteriaceae infection involving VIM-1 metallo-beta-lactamase in Spain: toward endemicity?. Clin. Infect. Dis. 2007, 45:1171-1178.
47. Welch T.J., et al. Multiple antimicrobial resistance in plague: an emerging public health risk. PLoS ONE 2007, 2:e309.
48. Woodford N., et al. Complete nucleotide sequences of plasmids pEK204, pEK499, and pEK516, encoding CTX-M enzymes in three major Escherichia coli lineages from the United Kingdom, all belonging to the international O25:H4-ST131 clone. Antimicrob. Agents Chemother. 2009, 53:4472-4482.
49. Wu S., et al. Prevalence and characterization of plasmids carrying sulfonamide resistance genes among Escherichia coli from pigs, pig carcasses and human. Acta Vet. Scand. 2010, 52:47.
50. Yoshida T., et al. Twelve pil genes are required for biogenesis of the R64 thin pilus. J. Bacteriol. 1999, 181:2038-2043.