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Linking the resistome and plasmidome to the microbiome.

Stalder T, Press MO, Sullivan S, Liachko I, Top EM.

ISME J. 2019 May 30. doi: 10.1038/s41396-019-0446-4. [Epub ahead of print]


The Transferable Resistome of Produce.

Blau K, Bettermann A, Jechalke S, Fornefeld E, Vanrobaeys Y, Stalder T, Top EM, Smalla K.

MBio. 2018 Nov 6;9(6). pii: e01300-18. doi: 10.1128/mBio.01300-18.


Targeted metagenomics demonstrates the ecological role of IS1071 in bacterial community adaptation to pesticide degradation.

Dunon V, Bers K, Lavigne R, Top EM, Springael D.

Environ Microbiol. 2018 Nov;20(11):4091-4111. doi: 10.1111/1462-2920.14404. Epub 2018 Oct 5.


Characterization of Four Multidrug Resistance Plasmids Captured from the Sediments of an Urban Coastal Wetland.

Botts RT, Apffel BA, Walters CJ, Davidson KE, Echols RS, Geiger MR, Guzman VL, Haase VS, Montana MA, La Chat CA, Mielke JA, Mullen KL, Virtue CC, Brown CJ, Top EM, Cummings DE.

Front Microbiol. 2017 Oct 10;8:1922. doi: 10.3389/fmicb.2017.01922. eCollection 2017.


Compensatory mutations improve general permissiveness to antibiotic resistance plasmids.

Loftie-Eaton W, Bashford K, Quinn H, Dong K, Millstein J, Hunter S, Thomason MK, Merrikh H, Ponciano JM, Top EM.

Nat Ecol Evol. 2017 Sep;1(9):1354-1363. doi: 10.1038/s41559-017-0243-2. Epub 2017 Aug 7.


Emerging patterns of plasmid-host coevolution that stabilize antibiotic resistance.

Stalder T, Rogers LM, Renfrow C, Yano H, Smith Z, Top EM.

Sci Rep. 2017 Jul 7;7(1):4853. doi: 10.1038/s41598-017-04662-0.


Persistence of antibiotic resistance plasmids in bacterial biofilms.

Ridenhour BJ, Metzger GA, France M, Gliniewicz K, Millstein J, Forney LJ, Top EM.

Evol Appl. 2017 May 8;10(6):640-647. doi: 10.1111/eva.12480. eCollection 2017 Jul.


Annotation of plasmid genes.

Thomas CM, Thomson NR, Cerdeño-Tárraga AM, Brown CJ, Top EM, Frost LS.

Plasmid. 2017 May;91:61-67. doi: 10.1016/j.plasmid.2017.03.006. Epub 2017 Mar 30. Review.



Rood JI, Thomas CM, Top EM.

Plasmid. 2017 May;91:1. doi: 10.1016/j.plasmid.2017.01.002. Epub 2017 Jan 18. No abstract available.


Evolved plasmid-host interactions reduce plasmid interference cost.

Yano H, Wegrzyn K, Loftie-Eaton W, Johnson J, Deckert GE, Rogers LM, Konieczny I, Top EM.

Mol Microbiol. 2016 Sep;101(5):743-56. doi: 10.1111/mmi.13407. Epub 2016 Jun 15.


Responses of Soil Bacterial Communities to Nitrogen Deposition and Precipitation Increment Are Closely Linked with Aboveground Community Variation.

Li H, Xu Z, Yang S, Li X, Top EM, Wang R, Zhang Y, Cai J, Yao F, Han X, Jiang Y.

Microb Ecol. 2016 May;71(4):974-89. doi: 10.1007/s00248-016-0730-z. Epub 2016 Feb 2.


High Diversity of CTX-M Extended-Spectrum β-Lactamases in Municipal Wastewater and Urban Wetlands.

Borgogna TR, Borgogna JL, Mielke JA, Brown CJ, Top EM, Botts RT, Cummings DE.

Microb Drug Resist. 2016 Jun;22(4):312-20. doi: 10.1089/mdr.2015.0197. Epub 2015 Dec 15.


Evolutionary Paths That Expand Plasmid Host-Range: Implications for Spread of Antibiotic Resistance.

Loftie-Eaton W, Yano H, Burleigh S, Simmons RS, Hughes JM, Rogers LM, Hunter SS, Settles ML, Forney LJ, Ponciano JM, Top EM.

Mol Biol Evol. 2016 Apr;33(4):885-97. doi: 10.1093/molbev/msv339. Epub 2015 Dec 14.


Diversification of broad host range plasmids correlates with the presence of antibiotic resistance genes.

Li X, Wang Y, Brown CJ, Yao F, Jiang Y, Top EM, Li H.

FEMS Microbiol Ecol. 2016 Jan;92(1). pii: fiv151. doi: 10.1093/femsec/fiv151. Epub 2015 Dec 2.


Plasmid Detection, Characterization, and Ecology.

Smalla K, Jechalke S, Top EM.

Microbiol Spectr. 2015 Feb;3(1):PLAS-0038-2014. doi: 10.1128/microbiolspec.PLAS-0038-2014. Review.


Draft Genome Sequence of Pseudomonas sp. nov. H2.

Loftie-Eaton W, Suzuki H, Bashford K, Heuer H, Stragier P, De Vos P, Settles ML, Top EM.

Genome Announc. 2015 Apr 2;3(2). pii: e00241-15. doi: 10.1128/genomeA.00241-15.


The broad-host-range plasmid pSFA231 isolated from petroleum-contaminated sediment represents a new member of the PromA plasmid family.

Li X, Top EM, Wang Y, Brown CJ, Yao F, Yang S, Jiang Y, Li H.

Front Microbiol. 2015 Jan 12;5:777. doi: 10.3389/fmicb.2014.00777. eCollection 2014.


Flow cytometry and real-time quantitative PCR as tools for assessing plasmid persistence.

Loftie-Eaton W, Tucker A, Norton A, Top EM.

Appl Environ Microbiol. 2014 Sep;80(17):5439-46. doi: 10.1128/AEM.00793-14. Epub 2014 Jun 27.


Draft Genome Sequence of Pseudomonas moraviensis R28-S.

Hunter SS, Yano H, Loftie-Eaton W, Hughes J, De Gelder L, Stragier P, De Vos P, Settles ML, Top EM.

Genome Announc. 2014 Feb 20;2(1). pii: e00035-14. doi: 10.1128/genomeA.00035-14.


Diverse broad-host-range plasmids from freshwater carry few accessory genes.

Brown CJ, Sen D, Yano H, Bauer ML, Rogers LM, Van der Auwera GA, Top EM.

Appl Environ Microbiol. 2013 Dec;79(24):7684-95. doi: 10.1128/AEM.02252-13. Epub 2013 Oct 4.


Host range diversification within the IncP-1 plasmid group.

Yano H, Rogers LM, Knox MG, Heuer H, Smalla K, Brown CJ, Top EM.

Microbiology. 2013 Nov;159(Pt 11):2303-15. doi: 10.1099/mic.0.068387-0. Epub 2013 Sep 3.


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

Oliveira CS, Moura A, Henriques I, Brown CJ, Rogers LM, Top EM, Correia A.

Plasmid. 2013 Nov;70(3):412-9. doi: 10.1016/j.plasmid.2013.06.002. Epub 2013 Jul 2.


Invasion of E. coli biofilms by antibiotic resistance plasmids.

Król JE, Wojtowicz AJ, Rogers LM, Heuer H, Smalla K, Krone SM, Top EM.

Plasmid. 2013 Jul;70(1):110-9. doi: 10.1016/j.plasmid.2013.03.003. Epub 2013 Apr 2.


Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees.

Sen D, Brown CJ, Top EM, Sullivan J.

Mol Biol Evol. 2013 Jan;30(1):154-66. doi: 10.1093/molbev/mss210. Epub 2012 Aug 30.


Cointegrate-resolution of toluene-catabolic transposon Tn4651: determination of crossover site and the segment required for full resolution activity.

Yano H, Genka H, Ohtsubo Y, Nagata Y, Top EM, Tsuda M.

Plasmid. 2013 Jan;69(1):24-35. doi: 10.1016/j.plasmid.2012.07.004. Epub 2012 Aug 1.


Strain-specific transfer of antibiotic resistance from an environmental plasmid to foodborne pathogens.

Van Meervenne E, Van Coillie E, Kerckhof FM, Devlieghere F, Herman L, De Gelder LS, Top EM, Boon N.

J Biomed Biotechnol. 2012;2012:834598. doi: 10.1155/2012/834598. Epub 2012 Jun 27.


The role of clonal interference in the evolutionary dynamics of plasmid-host adaptation.

Hughes JM, Lohman BK, Deckert GE, Nichols EP, Settles M, Abdo Z, Top EM.

MBio. 2012 Jul 3;3(4):e00077-12. doi: 10.1128/mBio.00077-12. Print 2012.


IncP-1β plasmids of Comamonas sp. and Delftia sp. strains isolated from a wastewater treatment plant mediate resistance to and decolorization of the triphenylmethane dye crystal violet.

Stolze Y, Eikmeyer F, Wibberg D, Brandis G, Karsten C, Krahn I, Schneiker-Bekel S, Viehöver P, Barsch A, Keck M, Top EM, Niehaus K, Schlüter A.

Microbiology. 2012 Aug;158(Pt 8):2060-72. doi: 10.1099/mic.0.059220-0. Epub 2012 May 31.


The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution.

Eikmeyer F, Hadiati A, Szczepanowski R, Wibberg D, Schneiker-Bekel S, Rogers LM, Brown CJ, Top EM, Pühler A, Schlüter A.

Plasmid. 2012 Jul;68(1):13-24. doi: 10.1016/j.plasmid.2012.01.011. Epub 2012 Feb 2.


Roles of long and short replication initiation proteins in the fate of IncP-1 plasmids.

Yano H, Deckert GE, Rogers LM, Top EM.

J Bacteriol. 2012 Mar;194(6):1533-43. doi: 10.1128/JB.06395-11. Epub 2012 Jan 6.


Role of IncP-1β plasmids pWDL7::rfp and pNB8c in chloroaniline catabolism as determined by genomic and functional analyses.

Król JE, Penrod JT, McCaslin H, Rogers LM, Yano H, Stancik AD, Dejonghe W, Brown CJ, Parales RE, Wuertz S, Top EM.

Appl Environ Microbiol. 2012 Feb;78(3):828-38. doi: 10.1128/AEM.07480-11. Epub 2011 Nov 18.


On the meaning and estimation of plasmid transfer rates for surface-associated and well-mixed bacterial populations.

Zhong X, Droesch J, Fox R, Top EM, Krone SM.

J Theor Biol. 2012 Feb 7;294:144-52. doi: 10.1016/j.jtbi.2011.10.034. Epub 2011 Nov 9.


Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes.

Sen D, Van der Auwera GA, Rogers LM, Thomas CM, Brown CJ, Top EM.

Appl Environ Microbiol. 2011 Nov;77(22):7975-83. doi: 10.1128/AEM.05439-11. Epub 2011 Sep 23.


Increased transfer of a multidrug resistance plasmid in Escherichia coli biofilms at the air-liquid interface.

Król JE, Nguyen HD, Rogers LM, Beyenal H, Krone SM, Top EM.

Appl Environ Microbiol. 2011 Aug;77(15):5079-88. doi: 10.1128/AEM.00090-11. Epub 2011 Jun 3.


[Degradative mobile genetic elements (MGEs) and their potential use in MGE-mediated biodegradation].

Li H, Zhou LS, Wang YF, Top EM, Zhang Y, Xu H.

Ying Yong Sheng Tai Xue Bao. 2011 Feb;22(2):526-36. Review. Chinese.


Selection pressure required for long-term persistence of blaCMY-2-positive IncA/C plasmids.

Subbiah M, Top EM, Shah DH, Call DR.

Appl Environ Microbiol. 2011 Jul;77(13):4486-93. doi: 10.1128/AEM.02788-10. Epub 2011 May 20.


Special issue of Current Opinion in Microbiology, focused on 'Ecology and Industrial Microbiology'.

Top EM, Wilson DB.

Curr Opin Microbiol. 2011 Jun;14(3):227-8. doi: 10.1016/j.mib.2011.04.008. Epub 2011 May 11. No abstract available.


Sequencing and comparative analysis of IncP-1α antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions.

Szczepanowski R, Eikmeyer F, Harfmann J, Blom J, Rogers LM, Top EM, Schlüter A.

J Biotechnol. 2011 Aug 20;155(1):95-103. doi: 10.1016/j.jbiotec.2010.11.018. Epub 2010 Nov 27.


Predicting plasmid promiscuity based on genomic signature.

Suzuki H, Yano H, Brown CJ, Top EM.

J Bacteriol. 2010 Nov;192(22):6045-55. doi: 10.1128/JB.00277-10. Epub 2010 Sep 17.


Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein.

Sota M, Yano H, Hughes JM, Daughdrill GW, Abdo Z, Forney LJ, Top EM.

ISME J. 2010 Dec;4(12):1568-80. doi: 10.1038/ismej.2010.72. Epub 2010 Jun 3.


Dual reporter system for in situ detection of plasmid transfer under aerobic and anaerobic conditions.

Król JE, Rogers LM, Krone SM, Top EM.

Appl Environ Microbiol. 2010 Jul;76(13):4553-6. doi: 10.1128/AEM.00226-10. Epub 2010 May 7.


Comparative genomics of pAKD4, the prototype IncP-1delta plasmid with a complete backbone.

Sen D, Yano H, Suzuki H, Król JE, Rogers L, Brown CJ, Top EM.

Plasmid. 2010 Mar;63(2):98-107. doi: 10.1016/j.plasmid.2009.11.005. Epub 2009 Dec 16.


Accounting for mating pair formation in plasmid population dynamics.

Zhong X, Krol JE, Top EM, Krone SM.

J Theor Biol. 2010 Feb 21;262(4):711-9. doi: 10.1016/j.jtbi.2009.10.013. Epub 2009 Oct 14.


Plasmids captured in C. metallidurans CH34: defining the PromA family of broad-host-range plasmids.

Van der Auwera GA, Król JE, Suzuki H, Foster B, Van Houdt R, Brown CJ, Mergeay M, Top EM.

Antonie Van Leeuwenhoek. 2009 Aug;96(2):193-204. doi: 10.1007/s10482-009-9316-9. Epub 2009 Mar 4.


Spreading antibiotic resistance through spread manure: characteristics of a novel plasmid type with low %G+C content.

Heuer H, Kopmann C, Binh CT, Top EM, Smalla K.

Environ Microbiol. 2009 Apr;11(4):937-49. doi: 10.1111/j.1462-2920.2008.01819.x. Epub 2008 Dec 3.


Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes.

Suzuki H, Sota M, Brown CJ, Top EM.

Nucleic Acids Res. 2008 Dec;36(22):e147. doi: 10.1093/nar/gkn753. Epub 2008 Oct 25.


Comparison of correspondence analysis methods for synonymous codon usage in bacteria.

Suzuki H, Brown CJ, Forney LJ, Top EM.

DNA Res. 2008 Dec;15(6):357-65. doi: 10.1093/dnares/dsn028. Epub 2008 Oct 21.


Spatial structure and nutrients promote invasion of IncP-1 plasmids in bacterial populations.

Fox RE, Zhong X, Krone SM, Top EM.

ISME J. 2008 Oct;2(10):1024-39. doi: 10.1038/ismej.2008.53. Epub 2008 Jun 5.


Adaptive plasmid evolution results in host-range expansion of a broad-host-range plasmid.

De Gelder L, Williams JJ, Ponciano JM, Sota M, Top EM.

Genetics. 2008 Apr;178(4):2179-90. doi: 10.1534/genetics.107.084475.


Modelling the spatial dynamics of plasmid transfer and persistence.

Krone SM, Lu R, Fox R, Suzuki H, Top EM.

Microbiology. 2007 Aug;153(Pt 8):2803-16.

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