Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug-resistant Enterobacteriaceae

Plasmid

Volumn 68, Issue 1, 2012, Pages 43-50

  Johnson, Timothy J ^a   Bielak, Eliza M ^b   Fortini, Daniela ^c   Hansen, Lars Hestbjerg ^b   Hasman, Henrik ^b   Debroy, Chitrita ^d   Nolan, Lisa K ^e   Carattoli, Alessandra ^c  

^a UNIVERSITY OF MINNESOTA   (United States)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^c ISTITUTO SUPERIORE DI SANITÀ   (Italy)

^d PENNSYLVANIA STATE UNIVERSITY   (United States)

^e IOWA STATE UNIVERSITY   (United States)

Author keywords

Genomics; IncX; Plasmid; Replicon typing; Resistance

Indexed keywords

AMINO ACID SEQUENCE; ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENOME; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; ENTEROBACTERIACEAE; GENE SEQUENCE; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASMID; REPLICON; SEQUENCE HOMOLOGY;

BACTERIAL TYPING TECHNIQUES; DRUG RESISTANCE, BACTERIAL; ENTEROBACTERIACEAE; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLASMIDS; POLYMERASE CHAIN REACTION; REPLICON;

BACTERIA (MICROORGANISMS); ENTEROBACTERIACEAE;

EID: 84861749911     PISSN: 0147619X     EISSN: 10959890     Source Type: Journal    
DOI: 10.1016/j.plasmid.2012.03.001     Document Type: Article

References (46)

1. Allen B.L., et al. Nucleotide sequence and functions of mrk determinants necessary for expression of type 3 fimbriae in Klebsiella pneumoniae. J. Bacteriol. 1991, 173:916-920.
2. Altschul S.F., et al. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
3. Bielak E., et al. Investigation of diversity of plasmids carrying the blaTEM-52 gene. J. Antimicrob. Chemother. 2011, 66:2465-2474.
4. Bradley D.E. Determination of pili by conjugative bacterial drug resistance plasmids of incompatibility groups B, C, H, J, K, M, V, and X. J. Bacteriol. 1980, 141:828-837.
5. Brown D.J., et al. Phage type conversion in Salmonella enterica serotype Enteritidis caused by the introduction of a resistance plasmid of incompatibility group X (IncX). Epidemiol. Infect. 1999, 122:19-22.
6. Carattoli A., et al. Identification of plasmids by PCR-based replicon typing. J. Microbiol. Meth. 2005, 63:219-228.
7. Cattoir V., Nordmann P. Plasmid-mediated quinolone resistance in gram-negative bacterial species: an update. Curr. Med. Chem. 2009, 16:1028-1046.
8. Chah K.F., et al. Antimicrobial resistance, integrons and plasmid replicon typing in multiresistant clinical Escherichia coli strains from Enugu State. Nigeria. J. Basic Microbiol. 2010, 50(Suppl 1):S18-S24.
9. Chu C., et al. Evolution of genes on the Salmonella Virulence plasmid phylogeny revealed from sequencing of the virulence plasmids of S. enterica serotype Dublin and comparative analysis. Genomics 2008, 92:339-343.
10. Coetzee J.N., et al. Bacteriophage X-2: a filamentous phage lysing IncX-plasmid-harbouring bacterial strains. J. Gen. Microbiol. 1988, 134:2535-2541.
11. Couturier M., et al. Identification and classification of bacterial plasmids. Microbiol. Rev. 1988, 52:375-395.
12. Cuzon G., et al. Worldwide diversity of Klebsiella pneumoniae that produce beta-lactamase blaKPC-2 gene. Emerg. Infect. Dis. 2010, 16:1349-1356.
13. Darling A.C., et al. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome. Res. 2004, 14:1394-1403.
14. Di Martino P., et al. Klebsiella pneumoniae type 3 pili facilitate adherence and biofilm formation on abiotic surfaces. Res. Microbiol. 2003, 154:9-16.
15. Dolejska M., et al. Plasmids carrying blaCTX-M-1 and qnr genes in Escherichia coli isolates from an equine clinic and a horseback riding centre. J. Antimicrob. Chemother. 2011, 66:757-764.
16. Dong X., et al. PlasMapper: a web server for drawing and auto-annotating plasmid maps. Nucleic Acids Res. 2004, 32:W660-W664.
17. Fortini D., et al. Plasmid-mediated quinolone resistance and beta-lactamases in Escherichia coli from healthy animals from Nigeria. J. Antimicrob. Chemother. 2011, 66:1269-1272.
18. Gonzalez-Pastor J.E., et al. Structure and organization of plasmid genes required to produce the translation inhibitor microcin C7. J. Bacteriol. 1995, 177:7131-7140.
19. 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.
20. Johnson T.J., et al. Pyrosequencing of the Vir plasmid of necrotoxigenic Escherichia coli. Vet. Microbiol. 2009, 144:100-109.
21. Johnson T.J., et al. Examination of the source and extended virulence genotypes of Escherichia coli contaminating retail poultry meat. Foodborne Pathog. Dis. 2009, 6:657-667.
22. Johnson T.J., Shepard S.M., Rivet B., Danzeisen J.L., Carattoli A. Comparative genomics and phylogeny of the IncI1 plasmids, a common plasmid type among porcine enterotoxigenic Escherichia coli. Plasmid 2011, 66:144-151.
23. Johnson T.J., et al. Comparison of extraintestinal pathogenic Escherichia coli strains from human and avian sources reveals a mixed subset representing potential zoonotic pathogens. Appl. Environ. Microbiol. 2008, 74:7043-7050.
24. Jones C., Stanley J. Salmonella plasmids of the pre-antibiotic era. J. Gen. Microbiol. 1992, 138:189-197.
25. Jones C.S., et al. Molecular comparison of the IncX plasmids allows division into IncX1 and IncX2 subgroups. J. Gen. Microbiol. 1993, 139:735-741.
26. 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.
27. Mak J.K., et al. Antibiotic resistance determinants in nosocomial strains of multidrug-resistant Acinetobacter baumannii. J. Antimicrob. Chemother. 2009, 63:47-54.
28. Marcade G., et al. Replicon typing of plasmids in Escherichia coli producing extended-spectrum beta-lactamases. J. Antimicrob. Chemother. 2009, 63:67-71.
29. Norman A., et al. Nucleotide sequence of pOLA52: a conjugative IncX1 plasmid from Escherichia coli which enables biofilm formation and multidrug efflux. Plasmid 2008, 60:59-74.
30. Nunez B., et al. Genes involved in conjugative DNA processing of plasmid R6K. Mol. Microbiol. 1997, 24:1157-1168.
31. Olsen J.E., et al. Differences in the carriage and the ability to utilize the serotype associated virulence plasmid in strains of Salmonella enterica serotype Typhimurium investigated by use of a self-transferable virulence plasmid, pOG669. Microb Pathog. 2004, 36:337-347.
32. Ong C.L., et al. Conjugative plasmid transfer and adhesion dynamics in an Escherichia coli biofilm. Appl. Environ. Microbiol. 2009, 75:6783-6791.
33. Ong C.L., et al. Identification of type 3 fimbriae in uropathogenic Escherichia coli reveals a role in biofilm formation. J. Bacteriol. 2008, 190:1054-1063.
34. 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.
35. Partridge S.R., et al. Complete sequence of pJIE143, a pir-type plasmid carrying ISEcp1-blaCTX-M-15 from an Escherichia coli ST131 isolate. Antimicrob. Agents Chemother. 2011, 55:5933-5935.
36. Prager R., et al. DNA fingerprinting of conjugative plasmids incompatible with R6K (IncX). J. Basic Microbiol. 1988, 28:385-388.
37. Shepard S.M., et al. Genome sequences and phylogenetic analysis of K88- and F18-positive porcine enterotoxigenic Escherichia coli. J. Bacteriol. 2012, 194:395-405.
38. Smajs D., et al. Complete sequence of low-copy-number plasmid MccC7-H22 of probiotic Escherichia coli H22 and the prevalence of mcc genes among human E. coli. Plasmid 2008, 59:1-10.
39. Sorensen A.H., et al. Conjugative plasmid conferring resistance to olaquindox. Antimicrob. Agents Chemother. 2003, 47:798-799.
40. Stalker D.M., Helinski D.R. DNA segments of the IncX plasmid R485 determining replication and incompatibility with plasmid R6K. Plasmid 1985, 14:245-254.
41. Stanley J., et al. The insertion sequence IS200 fingerprints chromosomal genotypes and epidemiological relationships in Salmonella Heidelberg. J. Gen. Microbiol. 1992, 138:2329-2336.
42. Struve C., et al. Identification of a conserved chromosomal region encoding Klebsiella pneumoniae type 1 and type 3 fimbriae and assessment of the role of fimbriae in pathogenicity. Infect. Immun. 2009, 77:5016-5024.
43. Tamura K., et al. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
44. Tamura K., et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28:2731-2739.
45. Tardif G., Grant R.B. Transfer of plasmids from Escherichia coli to Pseudomonas aeruginosa: characterization of a Pseudomonas aeruginosa mutant with enhanced recipient ability for enterobacterial plasmids. Antimicrob. Agents Chemother. 1983, 24:201-208.
46. Tettelin H., et al. Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project. Genomics 1999, 62:500-507.