Domain Committee "essem"
Publications by DARE participants
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Publications by DARE participants: New Negreanu, Y., Pasternak, Z. Jurkevitch, E. and Cytryn, E. (2012) Impact of treated wastewater irrigation on antibiotic resistance in agricultural soils. Environ. Sci.Technol. 6: 4800-4808. Gatica, J., and Cytryn, E. (2013) Impact of treated wastewater irrigation on antibiotic resistance in the soil microbiome. Environ. Sci. Pollut. 46:4800-48088. Cytryn, E. (2013) The soil resistome: The anthropogenic, the native, and the unknown. Soil Biol. & Biochem. 63:18–23. Kaplan, E., Offek, M., Jurkevitch, E. and Cytryn, E. (2013) Characterization of fluoroquinolone resistance and qnr diversity in Enterobacteriaceae from municipal biosolids. Front. Antimicrob. Resist. Chemother. doi: 10.3389/fmicb.2013.00144. R. Byberg, J. Cobb , L. Diez Martin, R.W. Thompson, T. A. Camesano, O. Zahraa, M. N. Pons (2013) Comparison of photocatalytic degradation of dyes in relation to their structure. Environ Sci Pollut Res. 20:3570–3581. Michael, I., Hapeshi, E., Michael, C., Varela, R., Kyriakou, S., Manaia, C. M., Fatta Kassinos. 2012. Solar photo-Fenton process on the abatement of antibiotics at a pilot scale: Degradation kinetics, ecotoxicity and phytotoxicity assessment and removal of antibiotic resistant enterococci. Water Research, 46, 5621-5634. Rizzo, L., Manaia, C.M., Merlin, C., Schwartz, T., Dagot, D., Ploy, M. C., Michael, I., Fatta-Kassinos, D. 2013. Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: A review. Science of the Total Environment 447: 345–360. Michael, I., Rizzo, L., McArdell, C.S., Manaia, C.M., Merlin, C., Schwartz, T., Dagot, D., Fatta-Kassinos, D. 2013 Urban wastewater treatment plants as hotspots for the release of antibiotics in the environment: A review. Water Research 47: 9 5 7-9 9 5. Varela, A.V. , Ferro, G., Vredenburg, J., Yanık, M., Vieira, L., Rizzo, L., Lameiras, C., Manaia, C.M. Vancomycin resistant enterococci: from the hospital effluent to the urban wastewater treatment plant. Science of the Total Environment, 450–451: 155–161. Cantas L., Shah SQA, Cavaco LM., Manaia C.M., Walsh F., Popowska M., Garelick H., Bürgmann H and Sørum H. A brief multi-disciplinary review on antimicrobial resistance in medicine and its linkage to the global environmental microbiota. Frontiers in Antimicrobials, Resistance and Chemotherapy. Voolaid, Veiko; Tenson, Tanel; Kisand, Veljo (2013). Aeromonas and Pseudomonas spp. carriers of ampC FOX gene in the aquatic environment. Applied and Environmental Microbiology, 79(3), 1055 - 1057. Voolaid, Veiko; Jõers, Arvi; Kisand, Veljo; Tenson, Tanel (2012). Co-occurrence of resistance to different antibiotics among aquatic bacteria. BMC Microbiology, 12, 225. Li, Wen; Atkinson, Gemma C; Thakor, Nehal S; Allas, Ülar; Lu, Chuao-Chao; Chan, Kwok-Yan; Tenson, Tanel; Schulten, Klaus; Wilson, Kevin S; Hauryliuk, Vasili; Frank, Joachim (2013). Mechanism of Tetracycline Resistance by Ribosomal Protection Protein Tet(O). Nature Communications, accpeted L. Cantas, S.Q.A. Shah, L.M. Cavaco, C. Manaia, F. Walsh, M. Popowska, H. Garelick, H. Bürgmann, H. SørumA. (2013). brief multi-disciplinary review on antimicrobial resistance in medicine and its linkage to the global environmental microbiota Frontiers in microbiology., 4:96. Popowska M., Krawczyk-Balska AQ. (2013). Broad-host-range IncP-1 plasmids and their resistance potential. Frontiers in microbiology, 4:44. Krawczyk-Balska A., Popowska M., Markiewicz Z. (2012). Re-evaluation of the significance of penicillin binding protein 3 in the susceptibility of Listeria monocytogenes to β-lactam antibiotics. BMC Microbiology, 12:57 Challenging the concept of bacteria subsisting on antibiotics. F. Walsh, S.G. Amyes, B. Duffy. International Journal of Antimicrobial Agents. 2013 Mar 18. Investigating antibiotic resistance in non-clinical environments. F. Walsh. Frontiers in Microbiology 2013 Feb 4(19). Seiler, C., and Berendonk, T.U. (2012). Heavy metal driven co-selection of antibiotic resistance in soil and water bodies impacted by agriculture and aquaculture. Frontiers in Microbiology 3, 399-399. Bruchmann, J. / Kirchen, S. / Schwartz, T. (2013). Sub-inhibitory concentrations of antibiotics and wastewater influencing biofilm formation and gene expression of multi-resistant Pseudomonas aeruginosa wastewater isolates. Environmental Science and Pollution Research 20, 3539-49 Increased levels of multiresistant bacteria and resistance genes after wastewater treatment and their dissemination into lake geneva, Switzerland. Czekalski N, Berthold T, Caucci S, Egli A, Bürgmann H. Frontiers in Microbiology Corona, F., Martínez, J. L. Phenotypic resistance to antibiotics (2013). Antibiotics 2: 237-255 Olivares, J. Bernardini, A., García-León, G., Corona, F., Sánchez. M. B., Martínez, J. L. The intrinsic resistome of bacterial pathogens (2013). Frontiers in Microbiology : 103 Rosado-Coelho, J., Carrico, J. A., Knight, D., Martinez, J. L., Morrisey, I., Oggioni, M. R., Freitas, A. T. (2013) The use of machine learning methodologies to analyse antibiotic and biocide susceptibility in Staphylococcus aureus PLoS One 8(2): e55582 Fernández L, Alvarez-Ortega C, Wiegand I, Olivares J, Kocíncová D, Lam JS, Martínez JL, Hancock RE. (2013) Characterization of the polymyxin B resistome of Pseudomonas aeruginosa. Antimicrobial Agents and Chemotherapy 57:110-119 Alvarez-Ortega, C., Olivares J., Martínez, J. L. (2013) RND multidrug efflux pumps: what they are good for? Frontiers in Microbiology 4:7 José L. Martínez. Bacterial pathogens: from natural ecosystems to human hosts (2013). Environmental Microbiology. 15: 325-333 Oggioni MR, Ciusa ML, Furi L, Baldassarri L, Orefici G, Cirasola D, Martinez JL, Morrissey I, Borghi E. (2012) Lack of Evidence for Reduced Fitness of Clinical Staphylococcus aureus Isolates with Reduced Susceptibility to Triclosan. Antimicrobial Agents and Chemotherapy 56: 6068-6069 García-León, G., Sánchez, M. B., Martínez, J. L. (2012) The inactivation of intrinsic antibiotic resistance determinants widens the mutant selection window of Stenotrophomonas maltophilia Antimicrobial Agents and Chemotherapy 56: 6397-6399 Maria Laura Ciusaa, Leonardo Furia, Daniel Knight, Francesca Decorosi, Marco Fondi, Carla Raggi, Joana Rosado Coelho, Luis Aragones, Laura Moce, Pilar Visa, Ana Teresa Freitas, Lucilla Baldassarri, Renato Fani, Carlo Viti, Graziella Orefici, Jose Luis Martinez, the BIOHYPO Consortium, Ian Morrissey, Marco Rinaldo Oggioni (2012) A novel resistance mechanism to triclosan that suggests horizontal gene transfer and demonstrates a potential selective pressure for reduced biocide susceptibility in clinical strains of Staphylococcus aureus. International Journal of Antimicrobial Agents. 40: 210-220. Olivares, J., Alvarez-Ortega, C., Linares, J. F., Rojo, F., Köhler, T., Martínez, J. L. (2012) Overproduction of the multidrug efflux pump MexEF-OprN does not impair Pseudomonas aeruginosa fitness in competition tests, but produces specific changes in bacterial regulatory networks. Environmental Microbiology 14: 1968-1981 Garmendia, L., Hernandez, A., Sanchez, M.B:, Martinez, J.L. (2012) Metagenomics and antibiotics. Clin Microbiol Infect 18 Suppl 4: 27-31 Lira, F., Hernandez, A., Belda, E., Sanchez, M.B., Moya, A., Silva, F. J, Martinez, J. L. (2012) Whole genome sequence of Stenotrophomonas maltophilia D457R, a clinical isolate and a model strain. J. Bacteriol 194: 3563-3564 Sánchez. M. B., Martínez, J. L. (2012) Differential epigenetic compatibility of qnr antibiotic resistance determinants with the chromosome of Escherichia coli. PLoS One 7: e35149. Olivares, J., Martínez, J. L. (2012) Environmental pollution by antibiotic resistance genes. pp. 151-172. In Antibiotic Resistance in the Environment. Ed. Patricia Keen and Mark Montforts. Wiley Blackwell Publishers Martínez, J. L. (2012) The antibiotic resistome: challenge and opportunity for therapeutic intervention. Future Medicinal Chemistry 4: 347-359. Martínez, J. L. (2012) Natural antibiotic resistance and contamination by antibiotic resistance determinants: the two ages in the evolution of resistance to antimicrobials. Frontiers in Microbiology 3: 1. A brief multi-disciplinary review on antimicrobial resistance in medicine and its linkage to the global environmental microbiota (2013) Cantas L., Shah S.Q.A., Cavaco L.M., Manaia C., Walsh F., Popowska M., Garelick H., Bürgmann H., and Sørum H. Frontiers in Microbiology - Antimicrobials, Resistance and Chemotherapy, 4(96), doi: 10.3389/fmicb.2013.00096 Increased levels of multiresistant bacteria and resistance genes after waste water treatment and their dissemination into Lake Geneva, Switzerland (2012). Czekalski, N., Berthold, T., Caucci, S., Egli, A., and Bürgmann, H. Frontiers in Microbiology - Antimicrobials, Resistance and Chemotherapy, 3, 00106, doi: 10.3389/fmicb.2012.00106 Efficiency of real-time qPCR depends on template: a simple absolute quantification method correcting for qPCR efficiency variations in microbial community samples (2012) Brankatschk, R., Bodenhausen, N., Zeyer, J., and Bürgmann, H. Applied and Environmental Microbiology, 78(12), 4481-4489, doi: 10.1128/AEM.07878-11
Pereira A., Santos A., Tacão M., Alves A., Henriques I., Correia A. (2013) Genetic diversity and antimicrobial resistance of Escherichia coli from Tagus estuary (Portugal). Science of the Total Environment. 461, 65-71. Oliveira C.S., Lázaro B., Azevedo J.N., Henriques I., Almeida A., Correia A. (2012) New Molecular Variants of Epsilon and Beta IncP-1 Plasmids are Present in Estuarine Waters. Plasmid. 67, 252-258. Moura A., Pereira C., Henriques I., Correia A. (2012) Novel gene cassettes and integrons in bacteria isolated from an urban wastewater treatment plant. Research in Microbiology. 163, 2, 92–100. Henriques I., Araújo S., Azevedo J.S.N., Alves M.S., Chouchani C., Pereira A., Correia A. (2012) Prevalence and diversity of carbapenem-resistant bacteria in untreated drinking water in Portugal. Microbial Drug Resistance. 18, 531-537. Tacão M., Correia A., Henriques I. (2012) Resistance to broad-spectrum antibiotics in aquatic systems: anthropogenic activities modulate the dissemination of blaCTX-M-like genes. Applied and Environmental Microbiology. 78, 4134-4140. Rizzo L., Fiorentino A., Anselmo A. (2012). Effect of solar radiation on multidrug resistant E. coli strains and antibiotic mixture photodegradation in wastewater polluted stream. Science of the Total Environment 427-428, 263-268. Mattheus, W., Botteldoorn, N., Heylen, K., Pochet, B., Dierick, K. Surveillance and trend analysis of antimicrobial resistance in Campylobacter jejuni and Campylobacter coli isolated from Belgian meat products 2004-2009. Foodborne Pathogens and Disease 2012, 9(5):465-72. Adriaenssens, E., Mattheus, W., Cornelissen, A., Shaburova, O., Krylov, V., Kropinski, A., Lavigne, R. Complete genome sequence of the giant Pseudomonas phage Lu11. Journal of Virology 2012, 86(11):6369-70. Cornelissen, A., Hardies, SC., Shaburova, OV., Krylov, VN., Mattheus, W., Kropinski, AM., Lavigne, R. Complete genome sequence of the giant virus OBP and comparative genome analysis of the diverse phi-KZ-related phages. Journal of Virology. 2012;86(3): 1844-1852. Vandersteegen, K., Mattheus, W., Ceyssens, PJ., Bilocq, F., De Vos, D., Pirnay, JP., Noben, JP., Merabishvili, M., Lipinska, U., Hermans, K., Lavigne, R. Microbiological and molecular assessment of bacteriophage ISP for the control of Staphylococcus aureus. PLoS One. 2011;6(9): e24418. Bush K, Courvalin P, Dantas G, Davies J, Eisenstein B, Huovinen P ym. Tackling antibiotic resistance. Nature Rev Microbiol 2011; doi:10.1038/nrmicro2693. Alam C, Bittoun E, Bhagwat D, Valkonen S, Saari A, Jaakkola U, Eerola E, Huovinen P, Hänninen A: Effects of a germ-free environment on gut immune regulation and diabetes progression in non-obese diabetic (NOD) mice. Diabetologia 2011;54:1398-1406. Virta L, Auvinen A, Helenius H, Huovinen P, Kolho K-L. Repeated exposure to antibiotics is associated with the development of pediatric Crohn's disease - a Finnish nationwide register-based, case-control study. Am J Epidemiol 2012; 175:775-84. The culturable intestinal microbiota of triploid and diploid juvenile Atlantic salmon (Salmo salar) - a comparison of composition and drug resistance. Cantas L, Fraser TW, Fjelldal PG, Mayer I, Sørum H. BMC Vet Res. 2011 Nov 17;7:71. Culturable gut microbiota diversity in zebrafish. Cantas L, Sørby JR, Aleström P, Sørum H. Zebrafish. 2012 Mar;9(1):26-37. Impact of antibiotic treatments on the expression of the R plasmid tra genes and on the host innate immune activity during pRAS1 bearing Aeromonas hydrophila infection in zebrafish (Danio rerio). Cantas L, Midtlyng PJ, Sørum H. BMC Microbiol. 2012 Mar 19;12:37. Chattopadhyay, M., Grossart, H.-P. (2011) Antibiotic and heavy metal resistance of bacterial isolates obtained from some lakes in northern Germany. NSHM Journal of Pharmacy and Healthcare Management, Vol. 02: 74-75.
Peil, L.; Starosta, A.; Virumäe, K.; Atkinson, G.C.; Tenson, T.; Remme, J.; Wilson, D.N. (2012). Lysine 34 of translation elongation factor EF-P is hydroxylated by YfcM. Nature Chemical Biology, x - x. [in press] Atkinson, Gemma; Kuzmenko, Anton; Kamenski, Piotr; Vysokikh, Mikhail; Lakunina, Valentina; Tankov, Stoyan; Smirnova, Ekaterina; Soosaar, Aksel; Tenson, Tanel; Hauryliuk, Vasili (2012). Evolutionary and genetic analyses of mitochondrial translation initiation factors identify the missing mitochondrial IF3 in S. cerevisiae. Nucleic Acids Research, x - x. [in press] Kuzmenko, A.; Tankov, S.; English, B.; Tarassov, I.; Tenson, T.; Kamenski, P.; Elf, J.; Hauryliuk, V. (2011). Single molecule tracking fluorescence microscopy in mitochondria reveals highly dynamic but confined movement of Tom40. Scientific Reports, x - x. [in press] Luidalepp H, Jõers A, Kaldalu N, Tenson T. (2011). Age of inoculum strongly influences persister frequency and can mask effects of mutations implicated in altered persistence. Journal of Bacteriology, 193(14), 3598 - 3605. Margus, T.; Remm, M.; Tenson, T. (2011). A Computational Study of Elongation Factor G (EFG) Duplicated Genes: Diverged Nature Underlying the Innovation on the Same Structural Template. PLoS ONE, 6, e22789 Atkinson, Gemma C.; Tenson, Tanel; Hauryliuk, Vasili (2011). The RelA/SpoT Homolog (RSH) Superfamily: Distribution and Functional Evolution of ppGpp Synthetases and Hydrolases across the Tree of Life. PLoS ONE, 6, e23479 Piir, K.; Paier, A.; Liiv, A.; Tenson, T.; Maiväli, Ü. (2011). Ribosome degradation in growing bacteria. EMBO Reports, 12(5), 458 - 462. Siibak, T.; Peil, L.; Dönhofer, A.; Tats, A.; Remm, M.; Wilson, D.; Tenson, T.; Remme, J. (2011). Antibiotic-induced ribosomal assembly defects result from changes in the synthesis of ribosomal proteins. Molecular Microbiology, 80(1), 54 - 67. Atkinson, G.C; Hauryliuk, V.; Tenson, T. (2011). An ancient family of SelB elongation factor-like proteins with a broad but disjunct distribution across archaea. BMC Evolutionary Biology, 22(11), Article nr 22 Tammert, Helen; Lignell, Risto; Kisand, Veljo; Olli, Kalle (2012). Labile carbon supplement induces growth of filamentous bacteria in the Baltic Sea. Aquatic Biology, 15, 121 – 134. Rocker, D.; Kisand, V.; Scholz-Böttcher, B.; Kneib, T.; Lemke, A.; Rullkötter, J.; Simon, M. (2011). Differential decomposition of humic acids by marine and estuarine bacterial communities at varying salinities. Biogeochemistry, 1 - 16. Online First Tšertova, N.; Kisand, A.; Tammert, H.; Kisand, V. (2011). Low seasonal variability in community composition of sediment bacteria in large and shallow lake. Environmental Microbiology Reports, 3(2), 270 - 277. Antibiotic resistant bacteria proliferate in agricultural soils. ASM Press Release 2012 Mar. Influence of Soil Use on Prevalence of Tetracycline, Streptomycin, and Erythromycin Resistance and Associated Resistance Genes. M. Popowska, M. Rzeczycka, A. Miernik, A. Krawczyk-Balska, F. Walsh, B. Duffy. Antimicrobial Agents and Chemotherapy 2012 Mar 56(3):1434-1443.
F. Walsh, T.R. Rogers. Journal of Medical Microbiology 2012 Jan 61(1):142-147.
Walsh, F., Ingenfeld, A., Zampicolli, M., Hilber-Bodmer, M., Frey, J.E., Duffy, B., Journal of Microbiological Methods 2011 Aug 86(2):150-5.
Duffy, B., Walsh, F., Pelludat, C., Holliger, Ouvelet J, Widmer, F. Acta Hort ISHS 2011 896:483-488. Schwartz, T. (2012) Strategies to assess and minimize the biological risk of antibiotic resistance in the environment. In: Keen, P., Montforts, M. (eds): Antimicrobial Resistance in the Environment. John Wiley & Sons, p. 251-264. Artigaz-Alejo J., Fund K., Kirchen S., Morin S., Obst U., Romani A., Sabater S., Schwartz T. (2012) Patterns of biofilm formation in two streams from different bioclimatic regions: analysis of microbial community structure and metabolism. Hydrobiologica DOI 10.1007/s10750-012-1111-3. Diler E, Obst U., Schmitz K., Schwartz T. (2011) A lysozyme and magnetic bead based separation method of intact bacteria. Analytical & Bioanalytical Chemistry 401, 253-265. Kraft S., Obst U., Schwartz T. (2011) Immunological detection of UV induced cyclobutane pyrimidine dimers and (6-4) photoproducts in DNA from reference bacteria and natural aquatic population. J. Microbiol. Methods 84, 435-441 Rieder A., Ladnorg T., Wöll C., Obst U., Fischer R., Schwartz, T. (2011) Does surface wettability influence bacterial adhesion? Biofouling 27(10), 1073-1085. Adamek M., Overhage J., Bathe S., Winter J., Fischer R., Schwartz T. (2011) Genotyping of environmental and clinical Stenotrophomonas maltophilia Isolates and their Pathogenic Potential. PLoS One 6(11), e27615. Diaz V., Font J., Schwartz T., Romani A. (2011) Biofilm formation at warming temperature: acceleration of microbial colonization and microbial interactive effects. Biofouling 27, 59-71 Gerce, B.; Schwartz, T.; Syldatk, C.;Hausmann, R. (2011) Differences between Bacterial Communities Associated with the Surface or Tissue of Mediterranean Sponge Species. Microbial Ecology 61 (2011), 4, 769-782. old
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