Comparative genomics of IncP-1ε plasmids from water environments reveals diverse and unique accessory genetic elements

Plasmid

Volumn 70, Issue 3, 2013, Pages 412-419

  Oliveira, Cláudia S ^a   Moura, Alexandra ^a   Henriques, Isabel ^a   Brown, Celeste J ^b   Rogers, Linda M ^b   Top, Eva M ^b   Correia, António ^a  

^a UNIVERSITY OF AVEIRO   (Portugal)

^b UNIVERSITY OF IDAHO   (United States)

Author keywords

Broad host range plasmid; Class 1 integron; IncP 1 ; Insertion sequence; Tn402

Indexed keywords

ANTIBIOTIC RESISTANCE; AQUATIC ENVIRONMENT; ARTICLE; BACTERIAL GENETICS; BACTERIUM ISOLATION; COMPARATIVE STUDY; ESTUARY; GENE DELETION; GENE INSERTION; GENE ISOLATION; GENE SEQUENCE; GENETIC IDENTIFICATION; GENETIC VARIABILITY; GENOMICS; GEOGRAPHIC DISTRIBUTION; INTEGRON; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENETIC TREE; PLASMID; PLASMID INCP 1 EPSILON; PLASMID MLUA1; PLASMID MLUA3; PLASMID MLUA4; REPLICON; SEQUENCE ANALYSIS; TRANSPOSON; UNINDEXED SEQUENCE;

EPSILONPROTEOBACTERIA;

BROAD-HOST-RANGE PLASMID; CLASS 1 INTEGRON; INCP-1Ε; INSERTION SEQUENCE; TN402;

ANTI-BACTERIAL AGENTS; DNA TRANSPOSABLE ELEMENTS; DRUG RESISTANCE, BACTERIAL; ESCHERICHIA COLI; ESTUARIES; GENETIC VARIATION; GENOMICS; MICROBIAL SENSITIVITY TESTS; OPEN READING FRAMES; PHYLOGENY; PLASMIDS; SEQUENCE ANALYSIS, DNA;

EID: 84887620046     PISSN: 0147619X     EISSN: 10959890     Source Type: Journal    
DOI: 10.1016/j.plasmid.2013.06.002     Document Type: Article

References (41)

1. Anjum R., Grohmann E., Malik A. Molecular characterization of conjugative plasmids in pesticide tolerant and multi-resistant bacterial isolates from contaminated alluvial soil. Chemosphere 2011, 84:175-181.
2. Aziz R.K., Bartels D., Best A.A., De Jongh M., Edwards R.A., Formsma K., Gerdes S., Glass E.M., Kubal M., Meyer F., Olsen G.J., Olsen R., Osterman A.L., Overbeek R.A., McNeil L.K., Paarmann D., Paczian T., Parrello B., Pusch G.D., Reich C., Stevens R., Vassieva O., Vonstein V., Wilke A., Zagnitko O. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 2008, 9:75-89.
3. Bahl M.I., Burmølle M., Meisner A., Hansen L.H., Sørensen S.H. All IncP-1 plasmid subgroups, including the novel e subgroup, are prevalent in the influent of a Danish wastewater treatment plant. Plasmid 2009, 62:34-139.
4. Bahl M.I., Hansen L.H., Goesmann A., Sorensen S.J. The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established alpha, beta and delta subgroups. Plasmid 2007, 58:31-43.
5. Brown H.J., Stokes H.W., Hall R.M. The integrons In0, In2, and In5 are defective transposon derivatives. J. Bacteriol. 1996, 178:4429-4437.
6. Brown M.R.W., Gilbert P.J. Sensitivity of biofilms to antimicrobial agents. Appl. Microbiol. 1993, 74(s22):87S-97S.
7. Carattoli A., Bertini A., Villa L., Falbo V., Hopkins K.L., Threlfall E.J. Identification of plasmids by PCR-based replicon typing. J. Microbiol. Methods 2005, 63(3):219-228.
8. Chapman J.S. Disinfectant resistance mechanisms, cross-resistance, and co-resistance. Int. Biodeterior. Biodegrad. 2003, 51(4):271-276.
9. Cunliffe M., Engel A., Frka S., Gašparovic B., Guitart C., Murrell J.C., Salter M., Stolle C., Upstill-Goddard R., Wurl O. Sea surface microlayers: A unified physicochemical and biological perspective of the air-ocean interface. Prog. Oceanogr. 2013, 109:104-116.
10. del Castillo Janga, H.B., Hikimaa J., Junga T.S., Moriib H., Hironoc I., Kondoc H., Kurosakac C., Aokia T. Comparative analysis and distribution of pP9014, a novel drug resistance IncP-1 plasmid from Photobacterium damselae subsp. Piscicida. Int. J. Antimicrob. Ag. 2013, 42:10-18.
11. Dronen A.K., Torsvik V., Top E. Comparison of the plasmid types obtained by two distantly related recipients in biparental exogenous plasmid isolations from soil. FEMS Microbiol. Lett. 1999, 176:105-110.
12. Eikmeyer F., Hadiati A., Szczepanowski R., Wibberg D., Schneiker-Bekel S., Rogers L.M., Brown C.J., Top E.M., Pühler A., Schlüter A. The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution. Plasmid 2012, 68(1):13-24.
13. Garcillán-Barcia M.P., Francia M.V., de la Cruz F. The diversityof conjugative relaxases and its application in plasmid classification. FEMS Microbiol. Rev. 2009, 33:657-687.
14. Gillings M.R., Holley M.P., Stokes H.M. Evidence for dynamic exchange of qac gene cassettes between class 1 integrons and other integrons in freshwater biofilms. FEMS Microbiol. Lett. 2009, 296(2):282-288.
15. Grant J.R., Stothard P. The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res. 2008, 36:181-184.
16. Gotz A., Pukall R., Smit E., Tietze E., Prager R., Tschape H., Van Elsas J.D., Smalla K. Detection and characterization of broad-host-range plasmids in environmental bacteria by PCR. Appl. Environ. Microbiol. 1996, 62(7):2621-2628.
17. Haines A.S., Akhtar P., Stephens E.R., Jones K., Thomas C.M., Perkins C.D., Williams J.R., Day M.J., Fry J.C. Plasmids from freshwater environments capable of IncQ retrotransfer are diverse and include pQKH54, a new IncP-1 subgroup archetype. Microbiology 2006, 152:2689-2701.
18. Heuer H., Binh C.T.T., Jechalke S., Kopmann C., Zimmerling U., Krögerrecklenfort E., Ledger T., González B., Top E., Smalla K. IncP-1 ε plasmids are important vectors of antibiotic resistance genes in agricultural systems: diversification driven by class 1 integron gene cassettes. Front. Microbiol. 2012, 3. article 2.
19. Heuer H., Smalla K. Plasmids foster diversification and adaptation of bacterial populations in soil. FEMS Microbiol. Rev. 2012, 36(6):1083-1104.
20. Jové T., Da Re S., Denis F., Mazel D., Ploy M.C. Inverse correlation between promoter strength and excision activity in class 1 integrons. PLoS Genetics 2010, 6:e1000793.
21. Lopes J.F., Dias J.M., Cardoso A.C., Silva C.I. The water quality of the Ria de Aveiro lagoon, Portugal: from the observations to the implementation of a numerical model. Mar. Environ. Res. 2005, 60(5):594-628.
22. Michael G.B., Kadlec K., Sweeney M.T., Brzuszkiewicz E., Liesegang H., Daniel R., Murray R.W., Watts J.L., Schwarz S. ICEPmu1, an integrative conjugative element (ICE) of Pasteurella multocida: structure and transfer. J. Antimicrob. Chemother. 2012, 67:91-100.
23. 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.
24. Norberg P., Bergström M., Jethava V., Dubhashi D., Hermansson M. The IncP-1 plasmid backbone adapts to different host bacterial species and evolves through homologous recombination. Nat. Commun. 2011, 2:268.
25. Norman A., Hansen L.H., Sørensen SJ. Conjugative plasmids: vessels of the communal gene pool. Phil. Trans. R. Soc. B 2009, 364:2275-2289.
26. Oliveira C.S., Lázaro B., Azevedo J.S.N., Henriques I., Almeida A., Correia A. New molecular variants of epsilon and beta IncP-1 plasmids are present in estuarine waters. Plasmid 2012, 67:252-258.
27. Pachulec E., van der Does C. Conjugative plasmids of Neisseria gonorrhoeae. PLoS One 2010, 5:e9962.
28. Performance standards for antimicrobial susceptibility testing. Twentieth informational supplement. CLSI document M100-S20, Clinical and Laboratory Institute, Wayne, 2010.
29. Popowska M., Krawczyk-Balska A. Broad-host-range IncP-1 plasmids and their resistance potential. Front. Microbiol. 2013, 4:1-8.
30. Rosche T.M., Siddique A., Larsen M.H., Figurski D.H. Incompatibility protein IncC and global regulator KorB interact in active partition of promiscuous plasmid RK2. J. Bacteriol. 2000, 182:6014-6026.
31. Schluter A., Szczepanowski R., Puhler A., Top E.M. Genomics of IncP-1antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool. FEMS Microbiol. Rev. 2007, 31:449-477.
32. Sen D., Brown C.J., Top E.M., Sullivan J. Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees. Mol. Biol. Evol. 2013, 30:154-166.
33. Sen D., Van der Auwera G.A., Rogers L.M., Thomas C.M., Brown C.J., Top E.M. Broad-host-range plasmids from agricultural soils have Incp-1 backbones with diverse accessory genes. Appl. Environ. Microbiol. 2011, 77:7975-7983.
34. Siguier P., Perochon J., Lestrade L., Mahillon J., Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 2006, 34:D32-D36.
35. Smith K., Hunter I.S. Efficacy of common hospital blocides with biofilms of multi-drug resistant clinical isolates. J. Med. Microbiol. 2008, 57:966-973.
36. Sullivan M.J., Petty N.K., Beatson S.A. Easyfig: a genome comparison visualizer. Bioinformatics 2011, 27:1009-1010.
37. Sun H.F., Takata A., Hata N., Kasahara I., Taguchi S. Transportation and fate of cationic surfactant in river water. J. Environ. Monitor. 2003, 5:891-895.
38. Thomas C. Paradigms of plasmid organization. Mol. Microbiol. 2000, 37(3):485-491.
39. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
40. Top E.M., Springaely D. The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Curr. Opin. Microbiol. 2003, 14:262-269.
41. Vedler E., Vahter M., Heinaru A. The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation. J. Bacteriol. 2004, 186:7161-7174.