Eva Top publications list.


Some of Dr. Top's publications are available for download from her section at Scientific Commons. Dr. Top's publications are also available on Google Scholar, and PubMed

Selection of publications in peer-reviewed journals (from over 70 total)


Hughes, J.M., B.K. Lohman, G.E. Deckert, E.P. Nichols, M. Settles, Z. Abdo, and E.M. Top. 2012. The role of clonal interference in the evolutionary dynamics of plasmid-host adaptation. mBio, In press.

Stolze, Y., F. Eikmeyer, D. Wibberg, G. Brandis, C. Karsten, I. Krahn, S. Schneiker-Bekel, P. Viehöver, A. Barsch, M. Keck, E.Top, K. Niehaus, A.Pühler, and A. Schlüter. 2012. IncP-1beta 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.
Microbiology. In press.

Van Meervenne, E., E. Van Coillie, F. Devlieghere, L. Herman, L.S.P. De Gelder, E.M. Top, and N. Boon. Strain specific transfer of antibiotic resistance from an environmental plasmid to foodborne pathogens. J. Biomed. Biotechnol. In press.

Yano, H., G. E. Deckert, L. M. Rogers, and E.M Top. 2012. The role of long and short replication initiation protein in the fate of IncP-1 plasmids. J. Bacteriol. 194: 1533–1543. http://www.ncbi.nlm.nih.gov/pubmed/22228734

Eikmeyer, F.G., R. Szczepanowski, D.Wibberg, A. Hadiati, S. Schneiker-Bekel, L. M. Rogers, C.J. Brown, E.M. Top, A. Pühler, A. Schlüter. 2012. The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution. Plasmid 68: 13-24

Heuer, H., C.T.T. Binh, S. Jechalke, C. Kopmann, U. Zimmerling, E. Krögerrecklenfort, T. Ledger, B. Gonzalez, E. M. Top, K. Smalla. 2012. IncP-1ε plasmids are important vectors of antibiotic resistance genes in agricultural systems: diversification driven by class 1 integron gene cassettes. Frontiers in Microbiology 3: Article 2. http://www.ncbi.nlm.nih.gov/pubmed/22279444

Król, J.E., J.T. Penrod, H. McCaslin, L.M. Rogers, H. Yano, W. Dejonghe, C.J. Brown, R.E. Parales, S. Wuertz, E.M. Top. 2012. Genomic and functional analysis of the IncP-1β plasmids pNB8c and pWDL7::rfp explains their role in 3-chloroaniline catabolism. Appl. Environ. Microbiol. 78: 828-838. http://www.ncbi.nlm.nih.gov/pubmed/22101050

Zhong, X., J. Droesch, R. Fox, E. M. Top, and S M. Krone. 2012. On the meaning and estimation of plasmid transfer rates for surface-associated and well-mixed bacterial populations. J. Theor. Biol. 294: 144–152. http://www.ncbi.nlm.nih.gov/pubmed/22085738


Sen, D., G. Van Der Auwera, L. Rogers, C.M. Thomas, C.J. Brown, and E.M. Top. 2011. Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes. Appl. Environ. Microbiol. 77: 7975-7983.

Król, J.E., H. D. Nguyen, L. M. Rogers, H. Beyenal, S. M. Krone, E. M. Top. 2011. Increased plasmid transfer in E. coli K12 biofilms at the liquid-air interface [pdf]. Appl. Environ. Microbiol. 77: 5079-5088.

Subbiah, M., D. Shah, E. M. Top, and D. Call. 2011. The long-term persistence of blaCMY-2 positive, IncA/C plasmids requires selection pressure [pdf]. Appl. Environ. Microbiol. 77: 4486-4493.

Szczepanowski R, F. Eikmeyer, J. Harfmann, J. Blom, L.M. Rogers, E.M. Top, and A. Schlüter. 2011. Sequencing and comparative analysis of IncP-1α antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions. J. Biotechnol. 155:95-103


Suzuki, H., H. Yano, C.J. Brown and E.M. Top. 2010. Predicting plasmid promiscuity based on genomic signature. J. Bacteriol. 192: 6045-6055. (doi:10.1128/JB.00277-10)

Sota, M., Yano, H., Hughes, J., G.W. Daughdrill, Z. Abdo, L.J. Forney, and E.M. Top. 2010. Shifts in host range of a promiscuous plasmid through parallel evolution of its replication initiation protein. The ISME J. 4: 1568-15801. (doi:10.1038/ismej.2010.72).

Król, J.E, L.M. Rogers, S.M. Krone, and E. M. Top. A dual reporter system for in situ detection of plasmid transfer in aerobic and anaerobic conditions. Appl.Environ. Microbiol.76: 4553 - 4556 (doi:10.1128/AEM.00226-10)
AEM: Accepts published online ahead of print [pdf]

Sen, D., H. Yano, H. Suzuki, J.E. Król, L. Rogers, C.J. Brown, and E.M. Top. Comparative genomics of pAKD4, the prototype IncP-1δ plasmid with a complete backbone. Plasmid, 63: 98-107. (PMC2819548). 20018208[PMID].

Zhong, X., J. Krol, E. M. Top and S.M. Krone. Accounting for mating pair formation in plasmid population dynamics. J. Theor. Biol. 262: 711 – 719. (doi:10.1016/j.jtbi.2009.10.013)


Van der Auwera, G.A., J.E. Król, H. Suzuki, B. Foster, R. Van Houdt, C.J. Brown, M. Mergeay, and E. M. Top. Plasmids captured in C. metallidurans: defining the PromA family of broad-host-range plasmids. Antonie van Leeuwenhoek 96:193-204. doi: 10.1007/s10482-009-9316-9 (PMID: 19259779)

Heuer , H., C. Kopmann, C.T.T. Binh, E. M. Top, and K. Smalla. Spreading antibiotic resistance through spread manure: characteristics of a novel plasmid type with low %G+C content. Environ. Microbiol. 11: 937-949 (PMID: 19055690)


Fox, R., X. Zhong, S.M. Krone, and E.M. Top. Spatial structure and nutrients promote invasion of IncP-1 plasmids in bacterial populations. ISME J 2: 1024-1039.

De Gelder, L., J. J. Williams, J. Ponciano, M. Sota, and E.M. Top. 2008. Adaptive plasmid evolution results in host range expansion of a broad-host-range plasmid. Genetics 178: 2179-2190.

Sota, M, and E.M. Top. 2008. Host-specific factors determine the persistence of IncP-1 plasmids. World J. Microbiol. Biotechnol. 24: 1951-1954. (doi: 10.1007/s11274-008-9653-2)

Suzuki, H., C.J. Brown, L. J. Forney, and E.M. Top. Comparison of correspondence analysis methods for synonymous codon usage in bacteria. DNA Research. 15: 357-365. (doi: 10.1093/dnares/dsn028) (PMC2608848).

Suzuki, H., M. Sota, C.J. Brown, and E. M. Top. Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes. Nucl. Acids Res. 36: e147. (doi: 10.1093/nar/gkn753) (PMC2602791).


Krone, S.M., R. Lu, R. Fox, H. Suzuki, and E.M. Top. 2007. Modeling the spatial dynamics of plasmid transfer and persistence. Microbiology 153: 2803-2816.

Schlüter, A., R. Szczepanowski, A. Pühler, and E.M. Top. 2007. Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool. [pdf] FEMS Microbiol. Rev. 31: 449-477.

Sota, M., M. Tsuda, H. Yano, H. Suzuki, L.J. Forney, and E.M. Top. 2007. Region-specific insertion of transposons in combination with selection for high plasmid transferability and stability accounts for the structural similarity of IncP-1 plasmids. [pdf] J. Bacteriol. 189: 3091-3098.

Ponciano, J., L. De Gelder, E.M. Top and P. Joyce. 2007. The population biology of bacterial plasmids: a Hidden-Markov model approach. Genetics 176: 957-968

De Gelder, L., J. M. Ponciano, P. Joyce, and E.M. Top. 2007. Stability of a promiscuous plasmid in different hosts: No guarantee for a long-term relationship. [pdf] Microbiology 153: 452-463.

Heuer, H., R. Fox, and E.M. Top. 2007. Frequent conjugative transfer accelerates adaptation of a broad-host-range plasmid to an unfavourable Pseudomonas putida host. FEMS Microbiol. Ecol. 59: 738-748.


Kamachi, K., M. Sota, Y. Tamai, N. Nagata, T. Konda, T. Inoue, E.M. Top, and Y. Arakawa. 2006. Plasmid pBP136 from Bordetella pertussis represents an ancestral form of IncP-1b plasmids without accessory mobile elements. Microbiology 152:3477-3484.

Sota, M., H. Yano, A. Ono, R. Miyazaki, H. Ishii, H. Genka, E.M. Top, and M. Tsuda. 2006. Genomic and functional analysis of the IncP-9 naphthalene-catabolic plasmid NAH7 and its transposon Tn4655 suggests catabolic gene spread by a tyrosine recombinase. J. Bacteriol. 188: 4057-4067.

Hendrickx, B., W. Dejonghe, F. Fabert, W. Boënne, L. Bastiaens, W. Verstraete, E.M. Top, and D. Springael. 2006. PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites. FEMS Microbiol. Ecol. 55: 262-273.


De Gelder, L., F. P.J. Vandecasteele, C. J. Brown, L. J. Forney, and E.M. Top. 2005. Plasmid Donor Affects Host Range of Promiscuous IncP-1β Plasmid pB10 in an Activated-Sludge Microbial Community. [pdf] Appl. Environ. Microbiol. 71:5309-5317.

Joyce, P., Z. Abdo, J. Ponciano, L. De Gelder, L.J. Forney, and E.M. Top. 2005. Modeling the impact of periodic bottlenecks, unidirectional mutation, and observational error in experimental evolution. J. Math. Biol. 50: 645-662.

Schlüter, A., H. Heuer, R. Szczepanowski, S.M. Poler, S. Schneiker, A. Pühler, and E.M. Top. 2005. Plasmid pB8 is closely related to the prototype IncP-1b plasmid R751 but transfers poorly to E. coli and carries a new transposon encoding a small multidrug resistance (SMR) efflux protein. Plasmid 54:135-148.

Hendrickx, B., W. Dejonghe, W. Boënne, M. Brennerova, M. Cernik, T. Lederer, M. Bucheli-Witschel, L. Bastiaens, W. Verstraete, E.M. Top, L. Diels, and D. Springael. 2005. Dynamics of an oligotrophic bacterial aquifer community during contact with a groundwater plume contaminated with benzene, toluene, ethylbenzene, and xylenes: an in situ mesocosm study. Appl. Environ. Microbiol. 71: 3815-3825.

Leys, N., A. Ryngaert, L. Bastiaens, E.M. Top, W. Verstraete, and D. Springael. 2005. Culture independent detection of Sphingomonas sp. EPA 505 related strains in soils contaminated with polycyclic aromatic hydrocarbons (PAHs). Microbial Ecology 49: 443-450.


De Gelder, L., J. Ponciano, Z. Abdo, P. Joyce, L.J. Forney, and E.M. Top. 2004. Combining mathematical models and statistical methods to understand and predict the dynamics of antibiotic sensitive mutants in a population of resistant bacteria during experimental evolution. [pdf] Genetics 168: 1131-1144.

Heuer, H., R. Szczepanowski, S. Schneiker, A. Pühler, E.M. Top, and A. Schlüter.2004. The complete sequences of plasmids pB2 and pB3 provide evidence for a recent ancestor of the IncP-1β group without any accessory genes. Microbiology. 150:3591-3599.

Leys, N.M.E.J., A. Ryngaert, L. Bastiaens, W. Verstraete, E.M. Top, and D. Springael. 2004. Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons. Appl. Environ. Microbiol. 70: 1944-1955.

Seghers, D., L. Wittebolle, E.M. Top, W. Verstraete, and S.D. Siciliano. 2004. Impact of agricultural practices on the Zea mays L. endophytic community. Appl. Environ. Microbiol. 70:1475-1482.

Springael, D. and E.M. Top. 2004. Horizontal gene transfer and microbial adaptation to xenobiotics: new types of mobile genetic elements and lessons from ecological studies. Trends in Microbiology 12: 53-58.


Boon, N., E.M. Top, W. Verstraete, and S.D. Siciliano. 2003. Bioaugmentation as a tool to protect the structure and function of an activated sludge microbial community against a 3-chloroaniline shock load. [pdf] Appl. Environ. Microbiol. 69:1511-1520.

Dejonghe, W., E. Berteloot, J. Goris, N. Boon, K. Crul, S. Maertens, M. Höfte, P. De Vos, W. Verstraete, and E.M. Top. 2003. Synergistic degradation of linuron by a bacterial consortium and isolation of a single linuron degrading Variovorax sp. strain. [pdf] Appl. Environ. Microbiol. 69: 1532-1541.

Gstalder, M-E., M. Faelen, N. Mine, E.M. Top, M. Mergeay, and M. Couturier. 2003. Replication functions of new broad host range plasmids isolated from polluted soils. Research in Microbiology 154: 499-509.

Schlüter A., H. Heuer, R. Szczepanowski, L. J. Forney, C. M. Thomas, A. Pühler & E.M. Top. 2003. The 64,508 bp IncP-1β antibiotic multiresistance plasmid pB10 isolated from a wastewater treatment plant provides evidence for recombination between members of different branches of the IncP-1β group. [pdf] Microbiology 149: 3139-3153.

Seghers, D., K. Verthé, D. Reheul, R. Bulcke, S.D. Siciliano, W. Verstraete, and E.M. Top. 2003. Effect of long-term herbicide applications on the bacterial community structure and function in an agricultural soil. FEMS Microbiology Ecology 46: 139-146.

Seghers, D., E.M. Top, D. Reheul, R. Bulcke, P. Boeckx, W. Verstraete, and S. D. Siciliano. 2003. Long-term effects of mineral versus organic fertilizers on activity and structure of the methanotrophic community in agricultural soils. Environ. Microbiol. 5: 867-877.

Top, E.M., and D. Springael. 2003. The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Current Opinion in Biotechnology 14: 262-269.


Top, E.M., Springael, D., and N. Boon. 2002. Erratum to Catabolic mobile genetic elements and their potential use in bioaugmentation of polluted soils and waters. [pdf] FEMS Microbiology Ecology 42 (2002) 199-208.

Dejonghe, W., J. Goris, A. Dierickx, V. De Dobbeleer, K. Crul, P. De Vos, W. Verstraete, and E.M. Top. 2002. Diversity of 3-chloroaniline and 3,4-dichloroaniline degrading bacteria isolated from three different soils and involvement of their plasmids in chloroaniline degradation. FEMS Microbiol. Ecol. 42: 315-325.

Boon, N., L. De Gelder, H. Lievens, S. D. Siciliano, E.M. Top, and W. Verstraete. 2002. Bioaugmenting bioreactors for the continuous removal of 3-chloroaniline by a slow release approach. Environ. Sci. Technol. 36:4698-4704.

Goris, J., W. Dejonghe, E. Falsen, E. De Clerck, B. Geeraerts, B., A. Willems, E.M. Top, P. Vandamme, and P. De Vos. 2002. Diversity of transconjugants that acquired plasmid pJP4 or pEMT1 after inoculation of a donor strain in the A- and B-horizon of an agricultural soil and description of Burkholderia hospita sp. nov. and Burkholderia terricola sp. nov. Syst. Appl. Microbiol. 25: 340-352.

Boon, N., W. De Windt, W. Verstraete, and E.M. Top. 2002. Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants. FEMS Microbiol. Ecol. 39, 101-112.


Boon, N., J. Goris, P. De Vos, W. Verstraete, and E.M. Top. 2001. Genetic diversity among 3-chloroaniline- and aniline-degrading strains of the Comamonadaceae. [pdf] Appl. Environ. Microbiol. 67: 1107-1115.


El-Fantroussi, S., W. Verstraete, and E.M. Top. 2000. Enrichment and molecular characterization of a bacterial culture that degrades methoxy-methyl urea herbicides and their aniline derivatives. Appl. Environ. Microbiol. 66: 5110-5150. Author's correction

Dejonghe, W., J. Goris, S. El Fantroussi, M. Höfte, P. De Vos, W. Verstraete, and E.M. Top. 2000. Effect of dissemination of 2,4-dichlorophenoxyacetic acid (2,4-D) degradation plasmids on 2,4-D degradation and on bacterial community structure in two different soil horizons. [pdf] Appl. Environ. Microbiol. 66:3297-3304.

Boon, N., J. Goris, P. De Vos, W. Verstraete, and E.M. Top. 2000. Bioaugmentation of activated sludge by an indigenous 3-chloroaniline degrading Comamonas testosteroni strain I2gfp. [pdf] Appl. Environ. Microbiol. 66: 2906-2913.


El Fantroussi, S., L. Verschuere, W. Verstraete, and E.M. Top. 1999. Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles. Appl. Environ. Microbiol. 65: 982-988.

Drønen, A.K., V. Torsvik, and E.M. Top. 1999. Comparison of the plasmid types obtained by two distantly related recipients in biparental exogenous plasmid isolations from soil.[pdf] FEMS Microbiol. Letters 176: 105-110.

Szpirer, C., E.M. Top, M. Couturier and M. Mergeay. 1999. Retrotransfer or gene capture: a feature of conjugative plasmids, with ecological and evolutionary significance. [pdf] Microbiology 145: 3321-3329.


Hill, K.E., and E.M. Top. 1998. Gene transfer in soil systems using microcosms. [pdf] FEMS Microbiol. Ecol. 25: 319-329.

Drønen, A.K., V. Torsvik, J. Goksøyr, and E.M. Top. 1998. Effect of mercury addition on plasmid incidence and gene mobilising capacity in bulk soil. [pdf] FEMS Microbiol. Ecol. 27: 381-394.


Top, E.M., O. Maltseva, and L.J. Forney. 1996. Capture of a catabolic plasmid that encodes only 2,4-dichlorophenoxyacetic acid:a-ketoglutaric acid dioxygenase (TfdA) by genetic complementation. [pdf] Appl. Environ. Microbiol. 62:1470-1476.


Top, E.M., W.E. Holben, and L.J. Forney. 1995. Characterization of diverse 2,4-dichlorophenoxyacetic acid- degradative plasmids isolated from soil by complementation.[pdf] Appl. Environ. Microbiol. 61: 1691-1698.


Top, E.M., I. De Smet, W. Verstraete, R. Dijkmans, and M. Mergeay. 1994. Exogenous isolation of mobilizing plasmids from polluted soils and sludges. [pdf] Appl. Environ. Microbiol. 60:831-839.


Top, E.M., P. Vanrolleghem, M. Mergeay, and W. Verstraete. 1992. Determination of the mechanism of retrotransfer by mechanistic mathematical modeling. [pdf] J. Bacteriol. 174:5953-5960.


Top, E.M., M. Mergeay, D. Springael, and W. Verstraete. 1990. Gene escape model: transfer of heavy metal resistance genes from Escherichia coli to Alcaligenes eutrophus on agar plates and in soil samples. [pdf] Appl. Environ. Microbiol. 56:2471-2479.

Selection of publications in books:

Sota, M. and E.M. Top 2008. Horizontal gene transfer mediated by plasmids. In Georg Lipps (ed.). Plasmids: Current Research and Future Trends. Horizon Scientific Press, p. 111-181.

Top, E.M. 2002. Transfer of catabolic plasmids in soil and activated sludge: a feasible bioaugmentation strategy? In: M. Hofman and J. Anné (eds), Focus on Biotechnology, volume 3A, Biotechnology for the environment: Strategy and Fundamentals (S.N. Agathos and W. Reineke, eds). Kluwer Academic Publishers, The Netherlands, p. 105-130.

Top, E.M., Y. Moënne-Loccoz, T. Pembroke, C.M. Thomas. 2000. Phenotypic traits conferred by plasmids. In: C.M. Thomas (Ed.), The horizontal gene pool: bacterial plasmids and gene spread. Harwood Academic Publishers, p. 249-285.