TY - BOOK PY - 2014 DA - 2014// TI - Antimicrobial resistance: global report on surveillance PB - World Health Organization CY - Geneva, Switzerland ID - ref1 ER - TY - JOUR AU - Venter, H. AU - Mowla, R. AU - Ohene-Agyei, T. AU - Ma, S. PY - 2015 DA - 2015// TI - RND-type drug e ffl ux pumps from Gram-negative bacteria: molecular mechanism and inhibition JO - Front Microbiol VL - 6 UR - https://doi.org/10.3389/fmicb.2015.00377 DO - 10.3389/fmicb.2015.00377 ID - Venter2015 ER - TY - JOUR AU - Li, X. Z. AU - Plesiat, P. AU - Nikaido, H. PY - 2015 DA - 2015// TI - The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria JO - Clin Microbiol Rev VL - 28 UR - https://doi.org/10.1128/CMR.00117-14 DO - 10.1128/CMR.00117-14 ID - Li2015 ER - TY - JOUR AU - Muller, B. AU - Borrell, S. AU - Rose, G. AU - Gagneux, S. PY - 2013 DA - 2013// TI - The heterogeneous evolution of multidrug-resistant mycobacterium tuberculosis JO - Trends in genetics : TIG VL - 29 UR - https://doi.org/10.1016/j.tig.2012.11.005 DO - 10.1016/j.tig.2012.11.005 ID - Muller2013 ER - TY - JOUR AU - Martinez, J. L. AU - Sanchez, M. B. AU - Martinez-Solano, L. AU - Hernandez, A. AU - Garmendia, L. AU - Fajardo, A. AU - Alvarez-Ortega, C. PY - 2009 DA - 2009// TI - Functional role of bacterial multidrug efflux pumps in microbial natural ecosystems JO - FEMS Microbiol Rev VL - 33 UR - https://doi.org/10.1111/j.1574-6976.2008.00157.x DO - 10.1111/j.1574-6976.2008.00157.x ID - Martinez2009 ER - TY - JOUR AU - Serres, M. H. AU - Kerr, A. R. AU - McCormack, T. J. AU - Riley, M. PY - 2009 DA - 2009// TI - Evolution by leaps: gene duplication in bacteria JO - Biol Direct VL - 4 UR - https://doi.org/10.1186/1745-6150-4-46 DO - 10.1186/1745-6150-4-46 ID - Serres2009 ER - TY - JOUR AU - Saier, M. H. AU - Paulsen, I. T. AU - Sliwinski, M. K. AU - Pao, S. S. AU - Skurray, R. A. AU - Nikaido, H. PY - 1998 DA - 1998// TI - Evolutionary origins of multidrug and drug-specific efflux pumps in bacteria JO - FASEB J VL - 12 ID - Saier1998 ER - TY - JOUR AU - Kondrashov, F. A. AU - Kondrashov, A. S. PY - 2006 DA - 2006// TI - Role of selection in fixation of gene duplications JO - J Theor Biol VL - 239 UR - https://doi.org/10.1016/j.jtbi.2005.08.033 DO - 10.1016/j.jtbi.2005.08.033 ID - Kondrashov2006 ER - TY - JOUR AU - Craven, S. H. AU - Neidle, E. L. PY - 2007 DA - 2007// TI - Double trouble: medical implications of genetic duplication and amplification in bacteria JO - Future Microbiol VL - 2 UR - https://doi.org/10.2217/17460913.2.3.309 DO - 10.2217/17460913.2.3.309 ID - Craven2007 ER - TY - JOUR AU - Sandegren, L. AU - Andersson, D. I. PY - 2009 DA - 2009// TI - Bacterial gene amplification: implications for the evolution of antibiotic resistance JO - Nat Rev Microbiol VL - 7 UR - https://doi.org/10.1038/nrmicro2174 DO - 10.1038/nrmicro2174 ID - Sandegren2009 ER - TY - JOUR AU - Kondrashov, F. A. PY - 2012 DA - 2012// TI - Gene duplication as a mechanism of genomic adaptation to a changing environment JO - Proc Biol Sci VL - 279 UR - https://doi.org/10.1098/rspb.2012.1108 DO - 10.1098/rspb.2012.1108 ID - Kondrashov2012 ER - TY - JOUR AU - Lynch, M. AU - Force, A. PY - 2000 DA - 2000// TI - The probability of duplicate gene preservation by subfunctionalization JO - Genetics VL - 154 ID - Lynch2000 ER - TY - JOUR AU - Force, A. AU - Cresko, W. A. AU - Pickett, F. B. AU - Proulx, S. R. AU - Amemiya, C. AU - Lynch, M. PY - 2005 DA - 2005// TI - The origin of subfunctions and modular gene regulation JO - Genetics VL - 170 UR - https://doi.org/10.1534/genetics.104.027607 DO - 10.1534/genetics.104.027607 ID - Force2005 ER - TY - JOUR AU - Alvarez-Ortega, C. AU - Olivares, J. AU - Martinez, J. L. PY - 2013 DA - 2013// TI - RND multidrug efflux pumps: what are they good for? JO - Front Microbiol VL - 4 UR - https://doi.org/10.3389/fmicb.2013.00007 DO - 10.3389/fmicb.2013.00007 ID - Alvarez-Ortega2013 ER - TY - JOUR AU - Martinez, J. L. PY - 2008 DA - 2008// TI - Antibiotics and antibiotic resistance genes in natural environments JO - Science VL - 321 UR - https://doi.org/10.1126/science.1159483 DO - 10.1126/science.1159483 ID - Martinez2008 ER - TY - JOUR AU - Saier, M. H. AU - Paulsen, I. T. PY - 2001 DA - 2001// TI - Phylogeny of multidrug transporters JO - Semin Cell Dev Biol VL - 12 UR - https://doi.org/10.1006/scdb.2000.0246 DO - 10.1006/scdb.2000.0246 ID - Saier2001 ER - TY - JOUR AU - Poole, K. AU - Krebes, K. AU - McNally, C. AU - Neshat, S. PY - 1993 DA - 1993// TI - Multiple antibiotic resistance in Pseudomonas aeruginosa: evidence for involvement of an efflux operon JO - J Bacteriol VL - 175 UR - https://doi.org/10.1128/jb.175.22.7363-7372.1993 DO - 10.1128/jb.175.22.7363-7372.1993 ID - Poole1993 ER - TY - JOUR AU - Podnecky, N. L. AU - Rhodes, K. A. AU - Schweizer, H. P. PY - 2015 DA - 2015// TI - E ffl ux pump-mediated drug resistance in Burkholderia JO - Front Microbiol VL - 6 UR - https://doi.org/10.3389/fmicb.2015.00305 DO - 10.3389/fmicb.2015.00305 ID - Podnecky2015 ER - TY - STD TI - De Smet B, Mayo M, Peeters C, Zlosnik JE, Spilker T, Hird TJ, LiPuma JJ, Kidd TJ, Kaestli M, Ginther JL et al: Burkholderia stagnalis sp. nov. and Burkholderia territorii sp. nov., two novel Burkholderia cepacia complex species from environmental and human sources. Int J Syst Evol Microbiol 2015, 65(7):2265-2271. ID - ref19 ER - TY - JOUR AU - Perrin, E. AU - Fondi, M. AU - Papaleo, M. C. AU - Maida, I. AU - Buroni, S. AU - Pasca, M. R. AU - Riccardi, G. AU - Fani, R. PY - 2010 DA - 2010// TI - Exploring the HME and HAE1 efflux systems in the genus Burkholderia JO - BMC Evol Biol VL - 10 UR - https://doi.org/10.1186/1471-2148-10-164 DO - 10.1186/1471-2148-10-164 ID - Perrin2010 ER - TY - JOUR AU - Perrin, E. AU - Fondi, M. AU - Papaleo, M. C. AU - Maida, I. AU - Emiliani, G. AU - Buroni, S. AU - Pasca, M. R. AU - Riccardi, G. AU - Fani, R. PY - 2013 DA - 2013// TI - A census of RND superfamily proteins in the Burkholderia genus JO - Future Microbiol VL - 8 UR - https://doi.org/10.2217/fmb.13.50 DO - 10.2217/fmb.13.50 ID - Perrin2013 ER - TY - JOUR AU - Holden, M. T. AU - Seth-Smith, H. M. AU - Crossman, L. C. AU - Sebaihia, M. AU - Bentley, S. D. AU - Cerdeno-Tarraga, A. M. AU - Thomson, N. R. AU - Bason, N. AU - Quail, M. A. AU - Sharp, S. PY - 2009 DA - 2009// TI - The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients JO - J Bacteriol VL - 191 UR - https://doi.org/10.1128/JB.01230-08 DO - 10.1128/JB.01230-08 ID - Holden2009 ER - TY - JOUR AU - Buroni, S. AU - Pasca, M. R. AU - Flannagan, R. S. AU - Bazzini, S. AU - Milano, A. AU - Bertani, I. AU - Venturi, V. AU - Valvano, M. A. AU - Riccardi, G. PY - 2009 DA - 2009// TI - Assessment of three resistance-nodulation-cell division drug efflux transporters of Burkholderia cenocepacia in intrinsic antibiotic resistance JO - BMC Microbiol VL - 9 UR - https://doi.org/10.1186/1471-2180-9-200 DO - 10.1186/1471-2180-9-200 ID - Buroni2009 ER - TY - JOUR AU - Bazzini, S. AU - Udine, C. AU - Sass, A. AU - Pasca, M. R. AU - Longo, F. AU - Emiliani, G. AU - Fondi, M. AU - Perrin, E. AU - Decorosi, F. AU - Viti, C. PY - 2011 DA - 2011// TI - Deciphering the role of RND efflux transporters in Burkholderia cenocepacia JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0018902 DO - 10.1371/journal.pone.0018902 ID - Bazzini2011 ER - TY - STD TI - Buroni S, Matthijs N, Spadaro F, Van Acker H, Scoffone VC, Pasca MR, Riccardi G, Coenye T: Differential roles of RND efflux pumps in antimicrobial drug resistance of sessile and planktonic Burkholderia cenocepacia cells. Antimicrob Agents Chemother 2014, 58(12):7424-7429. ID - ref25 ER - TY - STD TI - Coenye T, Van Acker H, Peeters E, Sass A, Buroni S, Riccardi G, Mahenthiralingam E: Molecular mechanisms of chlorhexidine tolerance in Burkholderia cenocepacia biofilms. Antimicrob Agents Chemother 2011, 55(5):1912-1919. ID - ref26 ER - TY - STD TI - Scoffone VC, Spadaro F, Udine C, Makarov V, Fondi M, Fani R, De Rossi E, Riccardi G, Buroni S: Mechanism of resistance to an antitubercular 2-thiopyridine derivative that is also active against Burkholderia cenocepacia. Antimicrob Agents Chemother 2014, 58(4):2415-2417. ID - ref27 ER - TY - JOUR AU - Gamberi, T. AU - Rocchiccioli, S. AU - Papaleo, M. C. AU - Magherini, F. AU - Citti, L. AU - Buroni, S. AU - Bazzini, S. AU - Udine, C. AU - Perrin, E. AU - Modesti, A. PY - 2013 DA - 2013// TI - RND-4 efflux transporter gene deletion in Burkholderia cenocepacia J2315: a proteomic analysis JO - J Proteome Sci Comput Biol 2013 VL - 2 UR - https://doi.org/10.7243/2050-2273-2-1 DO - 10.7243/2050-2273-2-1 ID - Gamberi2013 ER - TY - STD TI - Guglierame P, Pasca MR, De Rossi E, Buroni S, Arrigo P, Manina G, Riccardi G: Efflux pump genes of the resistance-nodulation-division family in Burkholderia cenocepacia genome. BMC Microbiol 2006, 6:66. ID - ref29 ER - TY - JOUR AU - Cardona, S. T. AU - Valvano, M. A. PY - 2005 DA - 2005// TI - An expression vector containing a rhamnose-inducible promoter provides tightly regulated gene expression in Burkholderia cenocepacia JO - Plasmid VL - 54 UR - https://doi.org/10.1016/j.plasmid.2005.03.004 DO - 10.1016/j.plasmid.2005.03.004 ID - Cardona2005 ER - TY - JOUR AU - Agnoli, K. AU - Schwager, S. AU - Uehlinger, S. AU - Vergunst, A. AU - Viteri, D. F. AU - Nguyen, D. T. AU - Sokol, P. A. AU - Carlier, A. AU - Eberl, L. PY - 2012 DA - 2012// TI - Exposing the third chromosome of Burkholderia cepacia complex strains as a virulence plasmid JO - Mol Microbiol VL - 83 UR - https://doi.org/10.1111/j.1365-2958.2011.07937.x DO - 10.1111/j.1365-2958.2011.07937.x ID - Agnoli2012 ER - TY - JOUR AU - Agnoli, K. AU - Frauenknecht, C. AU - Freitag, R. AU - Schwager, S. AU - Jenul, C. AU - Vergunst, A. AU - Carlier, A. AU - Eberl, L. PY - 2014 DA - 2014// TI - The third replicon of members of the Burkholderia cepacia complex, plasmid pC3, plays a role in stress tolerance JO - Appl Environ Microbiol VL - 80 UR - https://doi.org/10.1128/AEM.03330-13 DO - 10.1128/AEM.03330-13 ID - Agnoli2014 ER - TY - JOUR AU - Stoebel, D. M. AU - Hokamp, K. AU - Last, M. S. AU - Dorman, C. J. PY - 2009 DA - 2009// TI - Compensatory evolution of gene regulation in response to stress by Escherichia Coli lacking RpoS JO - PLoS Genet VL - 5 UR - https://doi.org/10.1371/journal.pgen.1000671 DO - 10.1371/journal.pgen.1000671 ID - Stoebel2009 ER - TY - JOUR AU - Choi, K. H. AU - Kumar, A. AU - Schweizer, H. P. PY - 2006 DA - 2006// TI - A 10-min method for preparation of highly electrocompetent Pseudomonas Aeruginosa cells: application for DNA fragment transfer between chromosomes and plasmid transformation JO - J Microbiol Methods VL - 64 UR - https://doi.org/10.1016/j.mimet.2005.06.001 DO - 10.1016/j.mimet.2005.06.001 ID - Choi2006 ER - TY - BOOK AU - Sambrook, J. AU - Fritsch, E. F. AU - Maniatis, T. PY - 1989 DA - 1989// TI - Molecular cloning : a laboratory manual PB - Cold Spring Harbor Laboratory CY - Cold Spring Harbor, N.Y ID - Sambrook1989 ER - TY - JOUR AU - Miller, V. L. AU - Mekalanos, J. J. PY - 1988 DA - 1988// TI - A novel suicide vector and its use in construction of insertion mutations: osmoregulation of outer membrane proteins and virulence determinants in Vibrio cholerae requires toxR JO - J Bacteriol VL - 170 UR - https://doi.org/10.1128/jb.170.6.2575-2583.1988 DO - 10.1128/jb.170.6.2575-2583.1988 ID - Miller1988 ER - TY - JOUR AU - Figurski, D. H. AU - Helinski, D. R. PY - 1979 DA - 1979// TI - Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans JO - Proc Natl Acad Sci U S A VL - 76 UR - https://doi.org/10.1073/pnas.76.4.1648 DO - 10.1073/pnas.76.4.1648 ID - Figurski1979 ER - TY - JOUR AU - Craig, F. F. AU - Coote, J. G. AU - Parton, R. AU - Freer, J. H. AU - Gilmour, N. J. PY - 1989 DA - 1989// TI - A plasmid which can be transferred between Escherichia Coli and Pasteurella haemolytica by electroporation and conjugation JO - J Gen Microbiol VL - 135 ID - Craig1989 ER - TY - JOUR AU - Ulrich, R. L. AU - Deshazer, D. AU - Kenny, T. A. AU - Ulrich, M. P. AU - Moravusova, A. AU - Opperman, T. AU - Bavari, S. AU - Bowlin, T. L. AU - Moir, D. T. AU - Panchal, R. G. PY - 2013 DA - 2013// TI - Characterization of the Burkholderia thailandensis SOS response by using whole-transcriptome shotgun sequencing JO - Appl Environ Microbiol VL - 79 UR - https://doi.org/10.1128/AEM.00538-13 DO - 10.1128/AEM.00538-13 ID - Ulrich2013 ER - TY - STD TI - Mocali S, Galeffi C, Perrin E, Florio A, Migliore M, Canganella F, Bianconi G, Di Mattia E, Dell'Abate MT, Fani R et al: Alteration of bacterial communities and organic matter in microbial fuel cells (MFCs) supplied with soil and organic fertilizer. Appl Microbiol Biotechnol 2013, 97(3):1299-1315. ID - ref40 ER - TY - JOUR AU - Mori, E. AU - Lio, P. AU - Daly, S. AU - Damiani, G. AU - Perito, B. AU - Fani, R. PY - 1999 DA - 1999// TI - Molecular nature of RAPD markers from Haemophilus influenzae rd genome JO - Res Microbiol VL - 150 UR - https://doi.org/10.1016/S0923-2508(99)80026-6 DO - 10.1016/S0923-2508(99)80026-6 ID - Mori1999 ER - TY - STD TI - Di Cello F, Bevivino A, Chiarini L, Fani R, Paffetti D, Tabacchioni S, Dalmastri C: Biodiversity of a Burkholderia cepacia population isolated from the maize rhizosphere at different plant growth stages. Appl Environ Microbiol 1997, 63(11):4485-4493. ID - ref42 ER - TY - JOUR AU - Perrin, E. AU - Fondi, M. AU - Maida, I. AU - Mengoni, A. AU - Chiellini, C. AU - Mocali, S. AU - Cocchi, P. AU - Campana, S. AU - Taccetti, G. AU - Vaneechoutte, M. PY - 2015 DA - 2015// TI - Genomes analysis and bacteria identification: the use of overlapping genes as molecular markers JO - J Microbiol Methods VL - 117 UR - https://doi.org/10.1016/j.mimet.2015.07.025 DO - 10.1016/j.mimet.2015.07.025 ID - Perrin2015 ER - TY - JOUR AU - Seemann, T. PY - 2014 DA - 2014// TI - Prokka: rapid prokaryotic genome annotation JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu153 DO - 10.1093/bioinformatics/btu153 ID - Seemann2014 ER - TY - JOUR AU - Cox, M. P. AU - Peterson, D. A. AU - Biggs, P. J. PY - 2010 DA - 2010// TI - SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data JO - BMC bioinformatics VL - 11 UR - https://doi.org/10.1186/1471-2105-11-485 DO - 10.1186/1471-2105-11-485 ID - Cox2010 ER - TY - JOUR AU - Koboldt, D. C. AU - Zhang, Q. AU - Larson, D. E. AU - Shen, D. AU - McLellan, M. D. AU - Lin, L. AU - Miller, C. A. AU - Mardis, E. R. AU - Ding, L. AU - Wilson, R. K. PY - 2012 DA - 2012// TI - VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.129684.111 DO - 10.1101/gr.129684.111 ID - Koboldt2012 ER - TY - JOUR AU - Walker, B. J. AU - Abeel, T. AU - Shea, T. AU - Priest, M. AU - Abouelliel, A. AU - Sakthikumar, S. AU - Cuomo, C. A. AU - Zeng, Q. AU - Wortman, J. AU - Young, S. K. PY - 2014 DA - 2014// TI - Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0112963 DO - 10.1371/journal.pone.0112963 ID - Walker2014 ER - TY - JOUR AU - Li, H. AU - Handsaker, B. AU - Wysoker, A. AU - Fennell, T. AU - Ruan, J. AU - Homer, N. AU - Marth, G. AU - Abecasis, G. AU - Durbin, R. PY - 2009 DA - 2009// TI - The sequence alignment/map format and SAMtools JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Li2009 ER -