Levy SB, Marshall B. Antibacterial resistance worldwide: causes, challenges and responses. Nat Med. 2004;10:S122.
Google Scholar
Davies J, Davies D. Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev. 2010;74:417–33.
Google Scholar
Blair JM, Webber MA, Baylay AJ, Ogbolu DO, Piddock LJ. Molecular mechanisms of antibiotic resistance. Nat Rev Microbiol. 2015;13:42.
Google Scholar
Meredith HR, Srimani JK, Lee AJ, Lopatkin AJ, You L. Collective antibiotic tolerance: mechanisms, dynamics, and intervention. Nat Chem Biol. 2015;11:182.
Google Scholar
Vega NM, Gore J. Collective antibiotic resistance: mechanisms and implications. Curr Opin Microbiol. 2014;21:28–34. http://www.sciencedirect.com/science/article/pii/S1369527414001234, antimicrobials.
Google Scholar
Flemming HC, Wingender J, Szewzyk U, Steinberg P, Rice SA, Kjelleberg S. Biofilms: an emergent form of bacterial life. Nat Rev Microbiol. 2016;14:563.
Google Scholar
Liu J, Prindle A, Humphries J, Gabalda-Sagarra M, Asally M, Lee DyD, et al. Metabolic codependence gives rise to collective oscillations within biofilms. Nature. 2015;523:550.
Google Scholar
Liu J, Martinez-Corral R, Prindle A, Dong-yeon DL, Larkin J, Gabalda- Sagarra M, et al. Coupling between distant biofilms and emergence of nutrient time-sharing. Science. 2017;356:638–42.
Google Scholar
Donlan RM. Biofilms and device-associated infections. Emerg Infect Dis. 2001;7:277.
Google Scholar
Costerton JW, Stewart PS, Greenberg EP. Bacterial biofilms: a common cause of persistent infections. Science. 1999;284:1318–22.
Google Scholar
Hauert C, Doebeli M. Spatial structure often inhibits the evolution of cooperation in the snowdrift game. Nature. 2004;428:643–6.
Google Scholar
Hallatschek O, Hersen P, Ramanathan S, Nelson DR. Genetic drift at expanding frontiers promotes gene segregation. Proc Natl Acad Sci USA. 2007;104:19926–30.
Google Scholar
Korolev KS, Avlund M, Hallatschek O, Nelson DR. Genetic demixing and evolution in linear stepping stone models. Rev Mod Phys. 2010;82:1691.
Google Scholar
Müller MJ, Neugeboren BI, Nelson DR, Murray AW. Genetic drift opposes mutualism during spatial population expansion. Proc Natl Acad Sci USA. 2014;111:1037–42.
Google Scholar
Momeni B, Brileya KA, Fields MW, Shou W. Strong inter-population co- operation leads to partner intermixing in microbial communities. eLife. 2013;2:e00230.
Google Scholar
Momeni B, Waite AJ, Shou W. Spatial self-organization favors heterotypic cooperation over cheating. eLife. 2013;2:e00960.
Google Scholar
Lavrentovich MO, Nelson DR. Asymmetric mutualism in two- and three-dimensional range expansions. Phys Rev Lett. 2014;112:138102.
Google Scholar
Gandhi SR, Yurtsev EA, Korolev KS, Gore J. Range expansions transition from pulled to pushed waves as growth becomes more cooperative in an experimental microbial population. Proc Natl Acad Sci USA. 2016;113:6922–7.
Kayser J, Schreck CF, Gralka M, Fusco D, Hallatschek O. Collective motion conceals fitness differences in crowded cellular populations. Nat Ecol Evol. 2019;3:125–34.
Google Scholar
Gandhi SR, Korolev KS, Gore J. Cooperation mitigates diversity loss in a spatially expanding microbial population. Proc Natl Acad Sci USA. 2019;116:23582–7.
Google Scholar
Datta MS, Korolev KS, Cvijovic I, Dudley C, Gore J. Range expansion promotes cooperation in an experimental microbial metapopulation. Proc Natl Acad Sci USA. 2013;110:7354–9.
Google Scholar
Kimmel GJ, Gerlee P, Brown JS, Altrock PM. Neighborhood size-effects shape growing population dynamics in evolutionary public goods games. Commun Biol. 2019;2:1–10.
Google Scholar
Kimmel GJ, Gerlee P, Altrock PM. Time scales and wave formation in non-linear spatial public goods games. PLoS Comput Biol. 2019;15:e1007361.
Google Scholar
Gerlee P, Altrock PM. Persistence of cooperation in diffusive public goods games. Phys Rev E. 2019;99:062412.
Google Scholar
Celik Ozgen V, Kong W, Blanchard AE, Liu F, Lu T. Spatial interference scale as a determinant of microbial range expansion. Sci. Adv. 2018;4:eaau0695.
Steenackers HP, Parijs I, Foster KR, Vanderleyden J. Experimental evolu- tion in biofilm populations. FEMS Microbiol Rev. 2016;40:373–97.
Google Scholar
Kepler TB, Perelson AS. Drug concentration heterogeneity facili- tates the evolution of drug resistance. Proc Natl Acad Sci USA. 1998;95:11514–9.
Google Scholar
Hermsen R, Deris JB, Hwa T. On the rapidity of antibiotic resistance evolution facilitated by a concentration gradient. Proc Natl Acad Sci USA. 2012;109:10775–80.
Google Scholar
Zhang Q, Lambert G, Liao D, Kim H, Robin K, Tung CK, et al. Acceleration of emergence of bacterial antibiotic resistance in connected microenvironments. Science. 2011;333:1764–7.
Google Scholar
Greulich P, Waclaw B, Allen RJ. Mutational pathway determines whether drug gradients accelerate evolution of drug-resistant cells. Phys Rev Lett. 2012;109:088101.
Google Scholar
Fu F, Nowak MA, Bonhoeffer S. Spatial heterogeneity in drug concen- trations can facilitate the emergence of resistance to cancer therapy. PLoS Comput Biol. 2015;11:e1004142.
Google Scholar
Moreno-Gamez S, Hill AL, Rosenbloom DI, Petrov DA, Nowak MA, Pen- nings PS. Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multidrug resistance. Proc Natl Acad Sci USA. 2015;112:E2874–E2883.
Google Scholar
Baym M, Lieberman TD, Kelsic ED, Chait R, Gross R, Yelin I, et al. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 2016;353:1147–51.
Google Scholar
De Jong MG, Wood KB. Tuning spatial profiles of selection pressure to modulate the evolution of drug resistance. Phys Rev Lett. 2018;120:238102.
Google Scholar
Lenski RE, Hattingh SE. Coexistence of two competitors on one re- source and one inhibitor: a chemostat model based on bacteria and antibiotics. J Theor Biol. 1986;122:83–93.
Google Scholar
Dugatkin LA, Perlin M, Lucas JS, Atlas R. Group-beneficial traits, frequency-dependent selection and genotypic diversity: an antibiotic resistance paradigm. Proc R Soc B. 2005;272:79–83.
Google Scholar
Clark DR, Alton TM, Bajorek A, Holden P, Dugatkin LA, Atlas RM, et al. Evolution of altruists and cheaters in near-isogenic populations of Escherichia coli. Front Biosci. 2009;14:4815.
Google Scholar
Perlin MH, Clark DR, McKenzie C, Patel H, Jackson N, Kormanik C, et al. Protection of Salmonella by ampicillin-resistant Escherichia coli in the presence of otherwise lethal drug concentrations. Proc R Soc B 2009;276:3759–68.
Google Scholar
Yurtsev EA, Chao HX, Datta MS, Artemova T, Gore J. Bacterial cheating drives the population dynamics of cooperative antibiotic resistance plasmids. Mol Syst Biol. 2013. https://doi.org/10.1038/msb.2013.39.
Koster DA, Mayo A, Bren A, Alon U. Surface growth of a motile bac- terial population resembles growth in a chemostat. J Mol Biol. 2012;424:180–91.
Google Scholar
Sorg RA, Lin L, van Doorn GS, Sorg M, Olson J, Nizet V. et al. Collective resistance in microbial communities by intracellular antibiotic deactivation. PLoS Biol. 2016;14:e2000631 https://doi.org/10.1371/journal.pbio.2000631.
Google Scholar
Hallinen KM, Karslake J, Wood KB. Delayed antibiotic exposure induces population collapse in enterococcal communities with drug-resistant subpopulations. eLife. 2020;9:e52813.
Google Scholar
Bagge N, Hentzer M, Andersen JB, Ciofu O, Givskov M, Høiby N. Dynamics and spatial distribution of β-lactamase expression in Pseudomonas aeruginosa biofilms. Antimicrob Agents Chemother. 2004;48:1168–74.
Google Scholar
Allen B, Gore J, Nowak MA. Spatial dilemmas of diffusible public goods. eLife. 2013;2:e01169.
Google Scholar
Medaney F, Dimitriu T, Ellis RJ, Raymond B. Live to cheat another day: bacterial dormancy facilitates the social exploitation of β-lactamases. ISME J. 2016;10:778.
Google Scholar
Frost I, Smith WP, Mitri S, San Millan A, Davit Y, Osborne JM, et al. Cooperation, competition and antibiotic resistance in bacterial colonies. ISME J. 2018;12:1582–93.
Google Scholar
Estrela SBS. Community interactions and spatial structure shape selection on antibiotic resistant lineages. PLoS Comput Biol. 2018;14:e1006179.
Google Scholar
Amanatidou E, Matthews AC, Kuhlicke U, Neu TR, McEvoy JP, Raymond B. Biofilms facilitate cheating and social exploitation of β-lactam resistance in Escherichia coli. npj Biofilms Microbiomes. 2019;5:1–10.
Google Scholar
Santos-Lopez A, Marshall CW, Scribner MR, Snyder DJ, Cooper VS. Evolutionary pathways to antibiotic resistance are dependent upon environmental structure and bacterial lifestyle. eLife. 2019;8:e47612.
Google Scholar
Seligman SJ, Hewitt WL. Kinetics of the action of ampicillin on Escherichia coli. J Bacteriol. 1963;85:1160–4.
Google Scholar
Klementiev AD, Jin Z, Whiteley M. Micron scale spatial measurement of the O2 gradient surrounding a bacterial biofilm in real time. mBio. 2020;11:e02536-20.
van Tatenhove-Pel RJ, Rijavec T, Lapanje A, van Swam I, Zwering E, Hernandez-Valdes JA, et al. Microbial competition reduces metabolic interaction distances to the low µm-range. ISME J. 2021;15:688–70.
Kumar RK, Meiller-Legrand T, Alcinesio A, Gonzalez D, Mavridou DA, Meacock OJ, et al. Droplet printing reveals the importance of micron-scale structure for bacterial ecology. Nat Commun. 2021;12:857.
Gilmore MS, Clewell DB, Ike Y, Shankar N, editors. Enterococci: From Commensals to Leading Causes of Drug Resistant Infection [Internet]. Boston: Massachusetts Eye and Ear Infirmary; 2014.
Huycke MM, Sahm DF, Gilmore MS. Multiple-drug resistant enterococci: the nature of the problem and an agenda for the future. Emerg Infect Dis. 1998;4:239.
Google Scholar
Mohamed JA, Huang DB. Biofilm formation by enterococci. J Med Microbiol. 2007;56:1581–8.
Google Scholar
Ch’ng JH, Chong KK, Lam LN, Wong JJ, Kline KA. Biofilm-associated infection by enterococci. Nat Rev Microbiol. 2018;1:82–94.
Murray BE, Mederski-Samaroj B. Transferable β-lactamase. A new mechanism for in vitro penicillin resistance in Streptococcus faecalis. J Clin Investig. 1983;72:1168–71. https://doi.org/10.1172/JCI111042.
Google Scholar
Rice L, Eliopoulos G, Wennersten C, Goldmann D, Jacoby G, Moellering R. Chromosomally mediated β-lactamase production and gentamicin resistance in Enterococcus faecalis. Antimicrob Agents Chemother. 1991;35:272–6.
Google Scholar
Murray BE. Beta-lactmase-producing enterococci. Antimicrob Agents Chemother. 1992;36:2355–9.
Google Scholar
Miller WR, Munita JM, Arias CA. Mechanisms of antibiotic resistance in enterococci. Expert Rev Antiinfect Ther. 2014;12:1221–36.
Google Scholar
Dunny GM, Lee LN, LeBlanc DJ. Improved electroporation and cloning vector system for gram-positive bacteria. Appl Environ Microbiol. 1991;57:1194–201.
Google Scholar
Aymanns S, Mauerer S, van Zandbergen G, Wolz C, Spellerberg B. High-level fluorescence labeling of gram-positive pathogens. PLoS ONE. 2011;6:e19822.
Google Scholar
Zscheck KK, Murray BE. Nucleotide sequence of the β-lactamase gene from Enterococcus faecalis HH22 and its similarity to staphylococcal β-lactamase genes. Antimicrob Agents Chemother. 1991;35:1736–40.
Google Scholar
Hallinen KM, Guardiola-Flores KA, Wood KB. Fluorescent reporter plas- mids for single-cell and bulk-level composition assays in E. faecalis. PLoS ONE. 2020;15:e0232539.
Google Scholar
AU Levin-Reisman I, AU Fridman O, AU Balaban NQ. Scan- Lag: high- throughput quantification of colony growth and lag time. JoVE 2014;51456.
Schindelin J, Arganda-Carreras I, Frise EEA. Fiji: an open-source plat- form for biological-image analysis. Nat Methods. 2012;9:676–82.
Google Scholar
Eden M. A two-dimensional growth process. Dyn Fractal Surf. 1961;4:223–39.
Smith WP, Davit Y, Osborne JM, Kim W, Foster KR, Pitt-Francis JM. Cell morphology drives spatial patterning in microbial communities. Proc Natl Acad Sci USA. 2017;114:E280–E286.
Google Scholar
Gralka M, Stiewe F, Farrell F, Möbius W, Waclaw B, Hallatschek O. Allele surfing promotes microbial adaptation from standing variation. Ecol Lett. 2016;19:889–98.
Google Scholar
Paulose J, Hallatschek O. The impact of long-range dispersal on gene surfing. Proc Natl Acad Sci USA. 2020;117:7584–93.
Google Scholar
Kaznatcheev A, Peacock J, Basanta D, Marusyk A, Scott JG. Fibroblasts and alectinib switch the evolutionary games played by non-small cell lung cancer. Nat Ecol Evol. 2019;3:450–6.
Google Scholar
Levin B. Frequency-dependent selection in bacterial populations. Philos Trans R Soc Lond B Biol Sci. 1988;319:459–72.
Google Scholar
Kaznatcheev A. Two conceptions of evolutionary games: reductive vs effective. bioRxiv. 2017; 231993; https://doi.org/10.1101/231993.
van Gestel J, Weissing FJ, Kuipers OP, Kovács ÁT. Density of founder cells affects spatial pattern formation and cooperation in Bacillus subtilis biofilms. ISME J. 2014;8:2069–79.
Google Scholar
Bamford CH, Tipper C, Compton R. Diffusion-limited reactions, vol. 25. Elsevier; 1985.
Berg HC, Purcell EM. Physics of chemoreception. Biophys J. 1977;20:193–219.
Google Scholar
Christensen H, Martin MT, Waley SG. Beta-lactamases as fully effcient enzymes. Determination of all the rate constants in the acyl-enzyme mechanism. Biochem J. 1990;266:853.
Google Scholar
Hardy LW, Kirsch JF. Diffusion-limited component of reactions catalyzed by Bacillus cereus. Beta-lactamase I. Biochemistry. 1984;23:1275–82.
Google Scholar
Dubus A, Ledent P, Lamotte-Brasseur J, Frère JM. The roles of residues Tyr150, Glu272, and His314 in class C β-lactamases. Proteins. 1996;25:473–85.
Google Scholar
Voladri R, Tummuru M, Kernodle DS. Structure-function relationships among wild-type variants of Staphylococcus aureus β-lactamase: importance of amino acids 128 and 216. J Bacteriol. 1996;178:7248–53.
Google Scholar
Livermore DM. β-Lactamases: quantity and resistance. Clin Microbiol Infect. 1997;3:4S10–4S19.
Google Scholar
Nikaido H, Normark S. Sensitivity of Escherichia coli to various, β-lactams is determined by the interplay of outer membrane permeability and degradation by periplasmic β-lactamases: a quantitative predictive treatment. Mol Microbiol. 1987;1:29–36.
Google Scholar
Stewart PS. Diffusion in biofilms. J Bacteriol. 2003;185:1485–91.
Google Scholar
Mah TFC, O’Toole GA. Mechanisms of biofilm resistance to antimicrobial agents. Trends Microbiol. 2001;9:34–39.
Google Scholar
Lee HH, Molla MN, Cantor CR, Collins JJ. Bacterial charity work leads to population-wide resistance. Nature. 2010;467:82–85. https://doi.org/10.1038/nature09354.
Google Scholar
Meredith HR, Andreani V, Ma HR, Lopatkin AJ, Lee AJ, Anderson DJ, et al. Applying ecological resistance and resilience to dissect bacterial antibiotic responses. Sci Adv. 2018;4:eaau1873.
Google Scholar
Udekwu KI, Parrish N, Ankomah P, Baquero F, Levin BR. Functional relationship between bacterial cell density and the effcacy of antibiotics. J Antimicrob Chemother. 2009;63:745–57. https://doi.org/10.1093/jac/dkn554.
Google Scholar
Tan C, Smith RP, Srimani JK, Riccione KA, Prasada S, Kuehn M, et al. The inoculum effect and band-pass bacterial response to periodic antibiotic treatment. Mol Syst Biol. 2012;8:617.
Karslake J, Maltas J, Brumm P, Wood KB. Population density modulates drug inhibition and gives rise to potential bistability of treatment outcomes for bacterial infections. PLoS Comput Biol. 2016;12:e1005098.
Google Scholar
Nadell CD, Foster XJ. Emergence of spatial structure in cell groups and the evolution of cooperation. PLoS Comput Biol. 2010;6:e1000716
Google Scholar
Nadell CD, Drescher K, Foster KR. Spatial structure, cooperation and competition in biofilms. Nat Rev Microbiol. 2016;14:589.
Google Scholar
Yuste S, Acedo L, Lindenberg K. Reaction front in an A+BC reaction-subdiffusion process. Phys Rev E. 2004;69:036126.
Google Scholar
Grebenkov DS. Diffusion toward non-overlapping partially reactive spherical traps: fresh insights onto classic problems. J Chem Phys. 2020;152:244108.
Google Scholar
Adamowicz EM, Flynn J, Hunter RC, Harcombe WR. Cross-feeding modulates antibiotic tolerance in bacterial communities. ISME J. 2018;12:2723–35.
Google Scholar
Tanouchi Y, Pai A, Buchler NE, You L. Programming stress-induced altruistic death in engineered bacteria. Mol Syst Biol. 2012;8:626.
Xie H, Jiao Y, Fan Q, Hai M, Yang J, Hu Z, et al. Modeling three-dimensional invasive solid tumor growth in het- erogeneous microenvironment under chemotherapy. PLoS ONE. 2018;13:e0206292.
Google Scholar
Bowness R, Chaplain MA, Powathil GG, Gillespie SH. Modelling the effects of bacterial cell state and spatial location on tuberculosis treatment: insights from a hybrid multiscale cellular automaton model. J Theor Biol. 2018;446:87–100.
Google Scholar
Dai X, Xiang S, Li J, Gao Q, Yang K. Development of a colorimetric assay for rapid quantitative measurement of clavulanic acid in microbial samples. Sci China Life Sci. 2012;55:158–63.
Google Scholar
Kobayashi S, Arai S, Hayashi S, Sakaguchi T. Simple assay of β- lactamase with agar medium containing a chromogenic cephalosporin, pyridinium-2-azo-p-dimethylaniline chromophore (PADAC). Antimicrob Agents Chemother. 1988;32:1040–5.
Google Scholar
Source: Ecology - nature.com
