A high-throughput approach to the culture-based estimation of plasmid transfer rates

Andrup, 1999, A comparison of the kinetics of plasmid transfer in the conjugation systems encoded by the F plasmid from Escherichia coli and plasmid pCF10 from Enterococcus faecalis, Microbiology, 145, 2001, 10.1099/13500872-145-8-2001 Bahl, 2009, All IncP-1 plasmid subgroups, including the novel ε subgroup, are prevalent in the influent of a Danish wastewater treatment plant, Plasmid, 62, 134, 10.1016/j.plasmid.2009.05.004 Bennett, 2008, Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in bacteria, Br. J. Pharmacol., 153, 347, 10.1038/sj.bjp.0707607 Cabezón, 2015, Towards an integrated model of bacterial conjugation, FEMS Microbiol. Rev., 39, 81 Christensen, 1996, Bacterial plasmid conjugation on semi-solid surfaces monitored with the green fluorescent protein (gfp) from Aequorea victoria as a marker, Gene, 173, 59, 10.1016/0378-1119(95)00707-5 Dahlberg, 1998, In situ detection of high levels of horizontal plasmid transfer in marine bacterial communities, Appl. Environ. Microbiol., 64, 2670, 10.1128/AEM.64.7.2670-2675.1998 Davies, 1994, Inactivation of antibiotics and the dissemination of resistance genes, Science, 264, 375, 10.1126/science.8153624 Enne, 2004, Enhancement of host fitness by the sul2-coding plasmid p9123 in the absence of selective pressure, J. Antimicrob. Chemother., 53, 958, 10.1093/jac/dkh217 Fernandez-Astorga, 1992, Biotic and abiotic factors affecting plasmid transfer in Escherichia coli strains, Appl. Environ. Microbiol., 58, 392, 10.1128/AEM.58.1.392-398.1992 Fox, 2008, Spatial structure and nutrients promote invasion of IncP-1 plasmids in bacterial populations, ISME, 2, 1024, 10.1038/ismej.2008.53 Gordon, 1992, Rate of plasmid transfer among Escherichia coli strains isolated from natural populations, J. General Microbiol., 138, 17, 10.1099/00221287-138-1-17 Heß, 2018, Antibiotic resistant bacteria and resistance genes in the bottom sediment of a small stream and the potential impact of remobilization, FEMS Microbiol. Ecol., 94, fiy128, 10.1093/femsec/fiy128 Heß, 2018 Johnsen, 2007, Effects of stress and other environmental factors on horizontal plasmid transfer assessed by direct quantification of discrete transfer events, FEMS Microbiol. Ecol., 59, 718, 10.1111/j.1574-6941.2006.00230.x Kneis, 2017, An R-package to boost fitness and life expectancy of environmental models, Environ. Modeling Software, 96, 123, 10.1016/j.envsoft.2017.06.036 Levin, 1979, The kinetics of conjugative plasmid transmission: Fit of a simple mass action model, Plasmid, 2, 247, 10.1016/0147-619X(79)90043-X Lorenzo-Diaz, 2009, Large-scale filter mating assay for intra- and inter-specific conjugal transfer of the promiscuous plasmid pmv158 in gram-positive bacteria, Plasmid, 61, 65, 10.1016/j.plasmid.2008.09.005 Normander, 1998, Effect of bacterial distribution and activity on conjugal gene transfer on the phylloplane of the bush bean (Phaseolus vulgaris), Appl. Environ. Microbiol., 64, 1902, 10.1128/AEM.64.5.1902-1909.1998 Ochman, 2000, Lateral gene transfer and the nature of bacterial evolution, Nature, 405, 299, 10.1038/35012500 Pinedo, 2005, Conjugal TOL transfer from Pseudomonas putida to Pseudomonas aeruginosa: effects of restriction proficiency, toxicant exposure, cell density ratios, and conjugation detection method on observed transfer efficiencies, Appl Environ Microbiol, 71, 51, 10.1128/AEM.71.1.51-57.2005 Pinilla-Redondo, 2018, Monitoring plasmid-mediated horizontal gene transfer in microbiomes: recent advances and future perspectives, Plasmid, 10.1016/j.plasmid.2018.08.002 R Core Team, 2018 Rysz, 2013, Tetracycline resistance gene maintenance under varying bacterial growth rate, substrate and oxygen availability and tetracycline concentration, Environ. Sci. Technol., 47, 6995, 10.1021/es3035329 San Millan, 2014, Positive epistasis between co-infecting plasmids promotes plasmid survival in bacterial populations, ISME J., 8, 601, 10.1038/ismej.2013.182 Simonsen, 1990, Estimating the rate of plasmid transfer: an end-point method, J. Gen. Microbiol., 136, 2319, 10.1099/00221287-136-11-2319 Soetaert, 2010, Solving differential equations in R: Package deSolve, J. Stat. Softw., 33, 1, 10.18637/jss.v033.i09 Sørensen, 2005, Studying plasmid horizontal transfer in situ: A critical review, Nat. Rev. Microbiol., 3, 700, 10.1038/nrmicro1232 Toomey, 2009, Assessment of antimicrobial resistance transfer between lactic acid bacteria and potential foodborne pathogens using in vitro methods and mating in a food matrix, Foodborne Pathog. Dis., 6, 925, 10.1089/fpd.2009.0278 Vogwill, 2014, The genetic basis of the fitness costs of antimicrobial resistance: a meta-analysis approach, Evolut. Appl., 8, 284, 10.1111/eva.12202 Wan, 2011, Measuring the rate of conjugal plasmid transfer in a bacterial population using quantitative PCR, Biophys. J., 101, 237, 10.1016/j.bpj.2011.04.054 Wellington, 2013, The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria, Lancet Infect. Dis., 13, 155, 10.1016/S1473-3099(12)70317-1 World Health Organization, 2014 Wu, 2018, Fitness advantage of mcr-1-bearing IncI2 and IncX4 plasmids in vitro, Front. Microbiol., 9 Yates, 2006, Enhancement of bacterial competitive fitness by apramycin resistance plasmids from non-pathogenic Escherichia coli, Biol. Lett., 2, 463, 10.1098/rsbl.2006.0478 Zhong, 2010, Accounting for mating pair formation in plasmid population dynamics, J. Theor. Biol., 262, 711, 10.1016/j.jtbi.2009.10.013 Zhong, 2012, On the meaning and estimation of plasmid transfer rates for surface-associated and well-mixed bacterial populations, J Theor Biol, 294, 144, 10.1016/j.jtbi.2011.10.034