Assessing genetic diversity in plasmids from Escherichia coli and Salmonella enterica using a mixed-plasmid microarray

Journal of Applied Microbiology

Volumn 100, Issue 1, 2006, Pages 15-28

  Call, D R ^a   Kang, M S ^a   Daniels, J ^a   Besser, T E ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

blaCMY 2; Comparative genomics; DNA fingerprint; Mosaic; Transposase

Indexed keywords

BIOMOLECULES; CLONING; CLUSTER ANALYSIS; DNA; GENES; MICROARRAYS; PROBES; SALMONELLA;

BLACMY-2; COMPARATIVE GENOMICS; DNA FINGERPRINTS; E. COLI; GENETICS DIVERSITIES; HYBRIDISATION; MOSAIC; PLASMID DNA; SALMONELLA ENTERICA; TRANSPOSASE;

ESCHERICHIA COLI;

AMPICILLIN; CEFTAZIDIME; CHLORAMPHENICOL; CIPROFLOXACIN; COTRIMOXAZOLE; GENTAMICIN; KANAMYCIN; NITROFURANTOIN; PLASMID DNA; STREPTOMYCIN; TETRACYCLINE; TRISULFAPYRIMIDINE;

PLASMID;

ANTIBIOTIC RESISTANCE; ARTICLE; CLUSTER ANALYSIS; COMPARATIVE STUDY; CORRELATION ANALYSIS; DIAGNOSTIC PROCEDURE; ENTEROHEMORRHAGIC ESCHERICHIA COLI; ESCHERICHIA COLI; GENE AMPLIFICATION; GENE REPLICATION; GENE SEQUENCE; GENETIC VARIABILITY; HYBRIDIZATION; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; SALMONELLA ENTERICA; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS;

ESCHERICHIA COLI; SALMONELLA ENTERICA;

EID: 33645115674     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/j.1365-2672.2005.02775.x     Document Type: Article

References (40)

1. Bauernfeind A. Stemplinger I. Jungwirth R. Giamarellou H. 1996 Characterization of the plasmidic beta-lactamase CMY-2, which is responsible for cephamycin resistance Antimicrob Agent Chemother 40 221 224
2. Berge A.C. Adaska J.M. Sischo W.M. 2004 Use of antibiotic susceptibility patterns and pulsed-field gel electrophoresis to compare historic and contemporary isolates of multi-drug-resistant Salmonella enterica subsp. enterica serovar Newport Appl Environ Microbiol 70 318 323
3. Bilge S.S. Vary J.C.J. Dowell S.F. Tarr P.I. 1996 Role of the Escherichia coli O157:H7 O side chain in adherence and analysis of the rfb locus Infect Immun 64 4795 4801
4. Böltner D. MacMahon C. Pembroke J.T. Strike P. Osborn A.M. 2002 R391: a conjugative integrating mosaic comprised of phage, plasmid, and transposon elements J Bacteriol 184 5158 5169
5. Borucki M.K. Krug M.J. Muraoka W.T. Call D.R. 2003 Discrimination among Listeria monocytogenes isolates using a mixed genome DNA microarray Vet Microbiol 92 351 362
6. Boyd E.F. Hill C.W. Rich S.M. Hartl D.L. 1996 Mosaic structure of plasmids from natural populations of Escherichia coli Genetics 143 1091 1100
7. Browning L.M. Wray C. Platt D.J. 1995 Diversity and molecular variation among plasmids in Salmonella enterica serotype Dublin based on restriction enzyme fragmentation pattern analysis Epidemiol Infect 114 237 248
8. Bushman F. 2002 Lateral DNA Transfer: Mechanisms and Consequences Cold Spring Harbor, New York, USA CSHL Press
9. Call D.R. Bakko M.K. Krug M.J. Roberts M.C. 2003a Identifying antimicrobial resistance genes using DNA microarrays Antimicrob Agents Chemother 47 3290 3295
10. Call D.R. Borucki M.K. Besser T.E. 2003b Mixed-genome microarrays reveal multiple serotype and lineage-specific differences among strains of Listeria monocytogenes J Clin Microbiol 41 632 639
11. Carattoli A. Bertini A. Villa L. Falbo V. Hopkins K.L. Threlfall E.J. 2005 Identification of plasmids by PCR-based replicon typing J Microbiol Meth 2005 May 31; [Epub ahead of print]
12. CDC 2002 Outbreak of multidrug-resistant Salmonella Newport-United States, January-April 2002 Morb Mortal Wkly Rep 51 545 548
13. Charpentier E. Gerbaud G. Courvalin P. 1999 Conjugative mobilization of the rolling-circle plasmid pIP823 from Listeria monocytogenes BM4293 among gram-positive and gram-negative bacteria J Bacteriol 181 3368 3374
14. Chiu C.H. Lin T.Y. Ou J.T. 1999 Prevalence of the virulence plasmids of nontyphoid Salmonella in the serovars isolated from humans and their association with bacteremia Microbiol Immunol 43 899 903
15. Chu C. Chiu C.H. Wu W.Y. Chu C.H. Liu T.P. Ou J.T. 2001 Large drug resistance virulence plasmids of clinical isolates of Salmonella enterica serovar Choleraesuis Antimicrob Agents Chemother 45 2299 2303
16. Chu C. Hong S.F. Tsai C. Lin W.S. Liu T.P. Ou J.T. 1999 Comparative physical and genetic maps of the virulence plasmids of Salmonella enterica serovars typhimurium, enteritidis, choleraesuis, and dublin Infect Immun 67 2611 2614
17. Eberhard W.G. 1989 Why do bacterial plasmids carry some genes and not others Plasmid 21 167 174
18. CMY-2 from multiple Salmonella plasmid backbones Antimicrob Agents Chemother 48 2845 2852
19. Gish W. States D.J. 1993 Identification of protein coding regions by database similarity search Nature Genet 3 266 272
20. González V. Bustos P. Ramírez-Romero M.A. Medrano-Soto A. Salgado H. Hernández-González I. Hernández-Celis J.C. Quintero V. et al. 2003 The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments Genome Biol 4 R36
21. Kado C. Lui S. 1981 Rapid procedure for detection and isolation of large and small plasmids J Bacteriol 145 1365 1373
22. Khachatryan A.R. Hancock D.D. Besser T.E. Call D.R. 2004 The role of calf-adapted Escherichia coli in maintenance of antimicrobial resistance in dairy calves Appl Environ Microbiol 70 752 757
23. Maeda K. Nojiri H. Shintani M. Yoshida T. Habe H. Omori T. 2003 Complete nucleotide sequence of carbazole/dioxin-degrading plasmid pCAR1 in Pseudomonas resinovorans strain CA10 indicates its mosaicity and the presence of large catabolic transposon Tn4676 J Mol Biol 326 21 33
24. McClelland M. Sanderson K.E. Spieth J. Clifton S.W. Latreille P. Courney L. Porwollik S. Ali J. et al. 2001 Complete genome sequence of Salmonella enterica serovar Typhimurium LT2 Nature 413 852 856
25. NCCLS 2003 Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria that Grow Aerobically Approved Standard M7-A6 National Committee for Clinical Laboratory Standards Wayne, PA
26. Nelson K.E. Fouts D.E. Mongodin E.F. Ravel J. DeBoy R.T. Kolonay J.F. Rasko D.A. Angiuoli S.V. et al. 2004 Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species Nucleic Acids Res 32 2386 2395
27. Osborn A.M. Boltner D. 2002 When phage, plasmids, and transposons collide: genomic islands, and conjugative- and mobilizable-transposons as a mosaic continuum Plasmid 48 202 212
28. Osborn M. Bron S. Firth N. Holsappel S. Huddleston A. Kiewiet R. Meijer W. Seegers J. et al. 2000 The evolution of bacterial plasmids In The Horizontal Gene Pool ed Thomas C. pp 301 361 Amsterdam, the Netherlands Harwood Academic Publishers
29. Rodriguez P.J.M. Buisan M. Ibanez M. Rotger R. 1997 Genetic map of the virulence plasmid of Salmonella enteritidis and nucleotide sequence of its replicons Gene 188 53 61
30. Salyers A.A. Amábile-Cuevas C.F. 1997 Why are antibiotic resistance genes so resistant to elimination? Antimicrob Agent Chemother 41 2321 2325
31. Sambrook J. Fritsch E.F. Maniatis T. 1989 Molecular Cloning Cold Spring Harbor, NY Cold Spring Harbor Laboratory Press
32. Shoemaker N.B. Vlamakis H. Hayes K. Salyers A.A. 2001 Evidence for extensive resistance gene transfer among Bacteroides spp. and among Bacterioides and other genera in the human colon Appl Environ Microbiol 67 561 568
33. Smalla K. Osborn M. Wellington E.M.H. 2000 Isolation and characterization of plasmids from bacteria In The Horizontal Gene Pool ed Thomas C.M. pp 207 248 Amsterdam, the Netherlands Harwood Academic Publishers
34. Tauch A. Krieft S. Kalinowski J. Puhler A. 2000 The 51,409-bp R-plasmid pTP10 from the multiresistant clinical isolate Corynebacterium striatum M82B is composed of DNA segments initially identified in soil bacteria and in plant, animal, and human pathogens Mol Gen Genet 263 1 11
35. Tauch A. Schneiker S. Selbitschka W. Puhler A. van Overbeek L.S. Smalla K. Thomas C.M. Bailey M.J. et al. 2002 The complete nucleotide sequence and environmental distribution of the cryptic, conjugative, broad-host-range plasmid pIPO2 isolated from bacteria of the wheat rhizosphere Microbiol 148 1637 1653
36. Thomas C.M. ed. 2000 The Horizontal Gene Pool. Bacterial Plasmids and Gene Spread Amsterdam, the Netherlands Harwood Academic Publishers
37. van Elsas J.D. Fry J. Hirsch P. Molin S. 2000 Ecology of plasmid transfer and spread In The Horizontal Gene Pool ed Thomas C. pp 175 206
38. Wu L. Thompson D.K. Li G. Hurt R.A. Tiedge J.M. Zhou J. 2001 Development and evaluation of functional gene arrays for detection of selected genes in the environment Appl Environ Microbiol 67 5780 5790
39. Zhao S. Qaiyumi S. Friedman S. Singh R. Foley S.L. White D.G. McDermott P.F. Donkar T. et al. 2003 Characterization of Salmonella enterica serotype newport isolated from humans and food animals J Clin Microbiol 41 5366 5371
40. Zhao S. White D.G. McDermott P.F. Friedman S. English L. Ayers S. Meng J. Maurer J.J. et al. 2001 Identification and expression of cephamycinase bla(CMY) genes in Escherichia coli and Salmonella isolates from food animals and ground meat Antimicrob Agent Chemother 45 3647 3650