The plasmidome of a Salmonella enterica serovar Derby isolated from pork meat

Plasmid

Volumn 69, Issue 3, 2013, Pages 202-210

  Bleicher, Anne ^a   Schöfl, Gerhard ^a   Rodicio, Maria del Rosario ^b   Saluz, Hans Peter ^a,c  

^a HANS KNÖLL INSTITUTE   (Germany)

^b DEPARTAMENTO DE BIOQUÍMICA Y BIOLOGÍA MOLECULAR   (Spain)

^c FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

Antibiotic resistance; Conjugative plasmid; Copy number determination; IncI1 plasmid phylogeny; Salmonella Derby

Indexed keywords

NALIDIXIC ACID; PLASMID DNA;

AADA1 GENE; ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIUM CONJUGATION; CONTROLLED STUDY; DHFRA1 GENE; ESCHERICHIA COLI; GENE DOSAGE; MULTIDRUG RESISTANCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASMID; PORK; QACE DELTA1 GENE; REAL TIME POLYMERASE CHAIN REACTION; REPLICON; SALMONELLA ENTERICA; SEQUENCE HOMOLOGY; STRAB GENE; SUL1 GENE; SUL2 GENE;

ANIMALS; BASE SEQUENCE; CHROMOSOMES, BACTERIAL; CONJUGATION, GENETIC; DNA REPLICATION; DNA, BACTERIAL; DRUG RESISTANCE, MULTIPLE, BACTERIAL; FOOD MICROBIOLOGY; GENES, BACTERIAL; MEAT; MOLECULAR SEQUENCE ANNOTATION; NALIDIXIC ACID; PHYLOGENY; PLASMIDS; SALMONELLA ENTERICA; SWINE; SYNTENY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; SALMONELLA ENTERICA; SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR DERBY;

EID: 84877126916     PISSN: 0147619X     EISSN: 10959890     Source Type: Journal    
DOI: 10.1016/j.plasmid.2013.01.001     Document Type: Article

References (49)

1. European Food Safety Authority (EFSA) Report of the Task Force on Zoonoses data collection on the analysis of the baseline survey on the prevalence of Salmonella in slaughter pigs, in the EU, 2006-2007. EFSA J. 2008, 135:1-111.
2. The Community Summary Report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in the European Union in 2008. EFSA J. 2010, 8:1-410.
3. Analysis of the baseline survey of Salmonella in holdings with breeding pigs, in the EU, 2008; Part B: Analysis of factors potentially associated with Salmonella pen positivity. EFSA J. 2011, 9(7232):1-159.
4. The European Union Summary Report on Trends and Sources of Zoonoses, zoonotic agents and food-borne outbreaks in 2009. EFSA J. 2011 2011, 9(3209):1-378.
5. Akahane K., Sakai D., Furuya N., Komano T. Analysis of the pilU gene for the prepilin peptidase involved in the biogenesis of type IV pili encoded by plasmid R64. Mol. Genet. Genomics 2005, 273:350-359.
6. Avasthi T.S., Kumar N., Baddam R., Hussain A., Nandanwar N., Jadhav S., Ahmed N. Genome of multidrug-resistant uropathogenic Escherichia coli strain NA114 from India. J. Bacteriol. 2011, 193:4272-4273.
7. Bennett P.M. Plasmid encoded antibiotic resistance acquisition and transfer of antibiotic resistance genes in bacteria. Brit. J. Pharmacol. 2008, 153(S1):S347-S357.
8. Beutlich J., Rodríguez I., Schroeter A., Käsbohrer A., Helmuth R., Guerra B. A predominant multidrug-resistant Salmonella enterica serovar Saintpaul clonal line in German turkey and related food products. Appl. Environ. Microb. 2010, 76:3657-3667.
9. Bouet J.-Y., Nordström K., Lane D. Plasmid partition and incompatibility - the focus shifts. Mol. Microbiol. 2007, 65:1405-1414.
10. Carattoli A. Importance of integrons in the diffusion of resistance. Vet. Res. 2001, 32:243-259.
11. Carattoli A. Plasmid-mediated antimicrobial resistance in Salmonella enterica. Curr. Issues Mol. Biol. 2003, 5:113-122.
12. Carattoli A., Bertini A., Villa L., Falbo V., Hopkins K.L., Threlfall E.J. Identification of plasmids by PCR-based replicon typing. J. Microbiol. Met. 2005, 63:219-228.
13. Cascales E., Christie P.J. The versatile bacterial type IV secretion systems. Nat. Rev. Microbiol. 2003, 1:137-149.
14. Chen, H., 2012. VennDiagram. Generate high-resolution Venn and Euler plots. Retrieved from: >http://cran.r-project.org/package=VennDiagram<
15. TEM-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 2007, 51:1872-1875.
16. del Solar G., Alonso J.C., Espinosa M. Broad-host-range plasmid replication- an open question. Mol. Microbiol. 1996, 21:661-666.
17. del Solar G., Giraldo R., Ruiz-Echevarría M.J., Espinosa M., Díaz-Orejas R. Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. R. 1998, 62:434-464.
18. Delcher A.L., Harmon D., Kasif S., White O., Salzberg S.L. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999, 27:4636-4641.
19. Francia M.V., Varsaki A., Garcillán-Barcia M.P., Latorre A., Drainas C., de la Cruz F. A classification scheme for mobilization regions of bacterial plasmids. FEMS Microbiol. Rev. 2004, 28:79-100.
20. Fricke W.F., McDermott P.F., Mammel M.K., Zhao S., Johnson T.J., Rasko D.A., Fedorka-Cray P.J., Pedroso A., Whichard J.M., LeClerc J.E., White D.G., Cebula T.A., Ravel J. Antimicrobial resistance-conferring plasmids with similarity to virulence plasmids from avian pathogenic Escherichia coli strains in Salmonella enterica serovar Kentucky isolates from poultry. Appl. Environ. Microb. 2009, 75:5963-5971.
21. Fu J., Li D., Xia S., Song H., Dong Z., Chen F., Sun X., Tang Z. Absolute quantification of plasmid DNA by real-time PCR with genomic DNA as external standard and its application to a biodistribution study of an HIV DNA vaccine. Anal. Sci. 2009, 25:675-680.
22. García-Fernández A., Chiaretto G., Bertini A., Villa L., Fortini D., Ricci A., Carattoli A. Multilocus sequence typing of IncI1 plasmids carrying extended-spectrum beta-lactamases in Escherichia coli and Salmonella of human and animal origin. J. Antimicrob. Chemoth. 2008, 61:1229-1233.
23. Guy L., Roat Kultima J., Andersson S.G.E. GenoPlotR: comparative gene and genome visualization. R. Bioinform. 2010, 26:2334-2335.
24. Hauser E., Hebner F., Tietze E., Helmuth R., Junker E., Prager R., Schroeter A., Rabsch W., Fruth A., Malorny B. Diversity of Salmonella enterica serovar Derby isolated from pig, pork and humans in Germany. Int. J. Food Microbiol. 2011, 151:141-149.
25. 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.
26. Katoh K., Kuma K., Toh H., Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005, 33:511-518.
27. Kent W.J. BLAT - the BLAST-like alignment tool. Genome Res. 2002, 12:656-664.
28. Kim S.-R., Komano T. The plasmid R64 thin pilus identified as a type IV pilus. J. Bacteriol. 1997, 179:3594-3603.
29. Komano T., Funayama N., Kim S.-R., Nisioka T. Transfer region of IncI1 plasmid R64 and role of shufflon in R64 transfer. J. Bacteriol. 1990, 172:2230-2235.
30. Leplae R., Geeraerts D., Hallez R., Guglielmini J., Drèze P., Van Melderen L. Diversity of bacterial type II toxin-antitoxin systems: a comprehensive search and functional analysis of novel families. Nucleic Acids Res. 2011, 39:5513-5525.
31. Lucarelli C., Dionisi A.M., Torpdahl M., Villa L., Graziani C., Hopkins K., Threlfall J., Caprioli A., Luzzi I. Evidence for a second genomic island conferring multidrug resistance in a clonal group of strains of Salmonella enterica serovar Typhimurium and its monophasic variant circulating in Italy, Denmark, and the United Kingdom. J. Clin. Microbiol. 2010, 48:2103-2109.
32. Mahillon J., Chandler M. Insertion sequences. Microbiol. Mol. Biol. R. 1998, 62:725-774.
33. Mazel D. Integrons: agents of bacterial evolution. Nat. Rev. Microbiol. 2006, 4:608-620.
34. Moura A., Soares M., Pereira C., Leitão N., Henriques I., Correia A. INTEGRALL: a database and search engine for integrons, integrases and gene cassettes. Bioinformatics 2009, 25:1096-1098.
35. Novick R.P. Plasmid incompatibility. Microbiol. Rev. 1987, 51:381-395.
36. Oshima K., Toh H., Ogura Y., Sasamoto H., Morita H., Park S.-H., Ooka T., Iyoda S., Taylor T.D., Hayashi T., Itoh K., Hattori M. Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult. DNA Res. 2008, 15:375-386.
37. Poirel L., Carrër A., Pitout J.D., Nordmann P. Integron mobilization unit as a source of mobility of antibiotic resistance genes. Antimicrob. Agents Ch. 2009, 53:2492-2498.
38. R Core Team, 2012. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. Retrieved from >http://www.r-project.org/<.
39. Rondon M.R., Raffel S.J., Goodman R.M., Handelsman J. Toward functional genomics in bacteria: analysis of gene expression in Escherichia coli from a bacterial artificial chromosome library of Bacillus cereus. P. Natl. Acad. Sci. USA 1999, 96:6451-6455.
40. Rozen S., Skaletsky H. Primer3 on the WWW for general users and for biologist programmers in bioinformatics. Meth. Mol. Biol. 2000, 132:365-386.
41. Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M.A., Barrell B. Artemis sequence visualization and annotation. Bioinformatics (Oxford, England) 2000, 16:944-945.
42. Sambrook J., Fritsch E.F., Maniatis T. Molecular Cloning A Laboratory Manual 1989, Cold Spring Harbor laboratory press, New York, Cold Spring Harbor.
43. Sampei G.-I., Furuya N., Tachibana K., Saitou Y., Suzuki T., Mizobuchi K., Komano T. Complete genome sequence of the incompatibility group I1 plasmid R64. Plasmid 2010, 64:92-103.
44. San Millan A., Escudero J.A., Gutierrez B., Hidalgo L., Garcia N., Llagostera M., Dominguez L., Gonzalez-Zorn B. Multiresistance in Pasteurella multocida is mediated by coexistence of small plasmids. Antimicrob. Agents 2009, 53:3399-3404.
45. San Millan, A., Heilbron, K., MacLean, C., 2012. Positive epistasis between plasmids promote the maintenance of multidrug resistance in a bacterial pathogen. International Plasmid Biology Conference. Santander, Spain 12nd to 16th September 2012.
46. Schliep K.P. Phangorn: phylogenetic analysis. R. Bioinform. 2011, 27:592-593.
47. Veldman K., Cavaco L.M., Mevius D., Battisti A., Franco A., Botteldoorn N., Bruneau M., Perrin-Guyomard A., Cerny T., De Frutos Escobar C., Guerra B., Schroeter A., Gutierrez M., Hopkins K., Myllyniemi A.-L., Sunde M., Wasyl D., Aarestrup F.M. International collaborative study on the occurrence of plasmid-mediated quinolone resistance in Salmonella enterica and Escherichia coli isolated from animals, humans, food and the environment in 13 European countries. J. Antimicrob. Chemoth. 2011, 66:1278-1286.
48. Vignoli R., Cordeiro N.F., García V., Mota M.I., Betancor L., Power P., Chabalgoity J.A., Schelotto F., Gutkind G., Ayala J.A. New TEM-derived extended-spectrum-beta-lactamase and its genomic context in plasmids from Salmonella enterica serovar Derby isolates from Uruguay. Antimicrob. Agents 2006, 50:781-784.
49. Whelan J.A., Russell N.B., Whelan M.A. A method for the absolute quantification of cDNA using real-time PCR. J. Immunol. Meth. 2003, 278:261-269.