Article

Cooperation, competition and antibiotic resistance in bacterial colonies

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Abstract

Bacteria commonly live in dense and genetically diverse communities associated with surfaces. In these communities, competition for resources and space is intense, and yet we understand little of how this affects the spread of antibiotic-resistant strains. Here, we study interactions between antibiotic-resistant and susceptible strains using in vitro competition experiments in the opportunistic pathogen Pseudomonas aeruginosa and in silico simulations. Selection for intracellular resistance to streptomycin is very strong in colonies, such that resistance is favoured at very low antibiotic doses. In contrast, selection for extracellular resistance to carbenicillin is weak in colonies, and high doses of antibiotic are required to select for resistance. Manipulating the density and spatial structure of colonies reveals that this difference is partly explained by the fact that the local degradation of carbenicillin by β-lactamase-secreting cells protects neighbouring sensitive cells from carbenicillin. In addition, we discover a second unexpected effect: the inducible elongation of cells in response to carbenicillin allows sensitive cells to better compete for the rapidly growing colony edge. These combined effects mean that antibiotic treatment can select against antibiotic-resistant strains, raising the possibility of treatment regimes that suppress sensitive strains while limiting the rise of antibiotic resistance. We argue that the detailed study of bacterial interactions will be fundamental to understanding and overcoming antibiotic resistance.

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References

  1. 1.

    Howard DH, Scott RD, Packard R, Jones D. The global impact of drug resistance. Clin Infect Dis. 2003;36:S4–10.

  2. 2.

    Stewart PS, Costerton JW. Antibiotic resistance of bacteria in biofilms. Lancet. 2001;358:135–8.

  3. 3.

    Hughes D, Andersson DI. Evolutionary consequences of drug resistance: shared principles across diverse targets and organisms. Nat Rev Genet. 2015;16:459–71.

  4. 4.

    MacLean RC, Hall AR, Perron GG, Buckling A. The population genetics of antibiotic resistance: integrating molecular mechanisms and treatment contexts. Nat Rev Genet. 2010;11:405–14.

  5. 5.

    zur Wiesch PA, Kouyos R, Engelstädter J, Regoes RR, Bonhoeffer S. Population biological principles of drug-resistance evolution in infectious diseases. Lancet Infect Dis. 2011;11:236–47.

  6. 6.

    Hall-Stoodley L, Costerton JW, Stoodley P. Bacterial biofilms: from the natural environment to infectious diseases. Nat Rev Microbiol. 2004;2:95–108.

  7. 7.

    Nadell CD, Xavier JB, Foster KR. The sociobiology of biofilms. FEMS Microbiol Rev. 2009;33:206–24.

  8. 8.

    Stacy A, McNally L, Darch SE, Brown SP, Whiteley M. The biogeography of polymicrobial infection. Nat Rev Microbiol. 2016;14:93–105.

  9. 9.

    Vlamakis H, Kolter R. Biofilms. Cold Spring Harb Perspect Biol. 2010;2:a000398.

  10. 10.

    Ceri H, Olson ME, Stremick C, Read RR, Morck D, Buret A. The calgary biofilm device: New technology for rapid determination of antibiotic susceptibilities of bacterial biofilms. J Clin Microbiol. 1999;37:1771–76.

  11. 11.

    Parsek MR, Singh PK. Bacterial biofilms: an emerging link to disease pathogenesis. Annu Rev Microbiol. 2003;57:677–701.

  12. 12.

    Costerton JW, Lewandowski Z, Caldwell D, Korber D. Microbial biofilms. Annu Rev Microbiol. 1995;49:711–45.

  13. 13.

    Koch G, Yepes A, Forstner KU, Wermser C, Stengel ST, Modamio J, et al. Evolution of resistance to a last-resort antibiotic in Staphylococcus aureus via bacterial competition. Cell. 2014;158:1060–71.

  14. 14.

    Kim W, Racimo F, Schluter J, Levy SB, Foster KR. Importance of positioning for microbial evolution. PNAS. 2014;111:E1639–47.

  15. 15.

    Schluter J, Nadell CD, Bassler BL, Foster KR. Adhesion as a weapon in microbial competition. ISME J. 2015;9:139–49.

  16. 16.

    Griffin AS, West SA, Buckling A. Cooperation and competition in pathogenic bacteria. Nature. 2004; 430: 1024–27.

  17. 17.

    Sorg RA, Lin L, Sander Van Doorn G, Sorg M, Olson J, Nizet V, et al. Collective resistance in microbial communities by intracellular antibiotic deactivation. PLoS Biol. 2016;14:1–19.

  18. 18.

    Rakoff-Nahoum S, Foster KR, Comstock LE. The evolution of cooperation within the gut microbiota. Nature. 2016;533:255–9.

  19. 19.

    West SA, Griffin AS, Gardner A. Social semantics: altruism, cooperation, mutualism, strong reciprocity and group selection. J Evol Biol. 2007;20:415–32.

  20. 20.

    West SA, Griffin AS, Gardner A, Diggle SP. Social evolution theory for microorganisms. Nat Rev Microbiol. 2006;4:597–607.

  21. 21.

    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;9:683.

  22. 22.

    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 Biol Sci. 2005;272:79–83.

  23. 23.

    Iredell J, Brown J, Tagg K. Antibiotic resistance in Enterobacteriaceae: mechanisms and clinical implications. BMJ. 2016;352:6420.

  24. 24.

    Ciofu O, Beveridge TJ, Kadurugamuwa J, Walther-rasmussen J, Høiby N. Chromosomal beta-lactamase is packaged into membrane vesicles and secreted from Pseudomonas aeruginosa. J Antimicrob Biol. 2000;45:9–13.

  25. 25.

    Haines AS, Jones K, Cheung M, Thomas CM. The IncP-6 plasmid Rms149 consists of a small mobilizable backbone with multiple large insertions. J Bacteriol. 2005;187:4728–38.

  26. 26.

    Lenski RE, Rose MR, Simpson SC, Tadler SC. Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. Am Nat. 1991;138:1315–41.

  27. 27.

    Gullberg E, Albrecht LM, Karlsson C, Sandegren L, Andersson DI. Selection of a multidrug resistance plasmid by sublethal levels of antibiotics and heavy metals. MBio. 2014;5:19–23.

  28. 28.

    Bottery MJ, Wood AJ, Brockhurst MA. Selective conditions for a multidrug resistance plasmid depend on the sociality of antibiotic resistance. Antimicrob Agents Chemother. 2016;60:2524–7.

  29. 29.

    Vogwill T, MacLean RC. The genetic basis of the fitness costs of antimicrobial resistance: a meta-analysis approach. Evol Appl. 2015;8:284–95.

  30. 30.

    Yurtsev EA, Conwill A, Gore J. Oscillatory dynamics in a bacterial cross-protection mutualism. Proc Natl Acad Sci USA. 2016;113:6236–41

  31. 31.

    Mitri S, Clarke E, Foster KR. Resource limitation drives spatial organization in microbial groups. ISME J. 2015;10:1471–82.

  32. 32.

    Mitri S, Xavier JB, Foster KR. Social evolution in multispecies biofilms. Proc Natl Acad Sci. 2011;108:10839–46.

  33. 33.

    Nadell C, Drescher K, Foster KR. Spatial structure, cooperation, and competition in biofilms. Nat Rev Microbiol. 2016; 14: 589-600.

  34. 34.

    Nadell CD, Foster KR, Xavier JB. Emergence of spatial structure in cell groups and the evolution of cooperation. PLoS Comput Biol. 2010;6:e1000716.

  35. 35.

    Van Dyken JD, Müller MJI, Mack KML, Desai MM. Spatial population expansion promotes the evolution of cooperation in an experimental Prisoner’s Dilemma. Curr Biol. 2013;23:919–23.

  36. 36.

    Nicoloff H, Andersson DI. Indirect resistance to several classes of antibiotics in cocultures with resistant bacteria expressing antibiotic-modifying or -degrading enzymes. J Antimicrob Chemother. 2016;71:100–10.

  37. 37.

    Blázquez J, Gómez-Gómez JM, Oliver A, Juan C, Kapur V, Martín S. PBP3 inhibition elicits adaptive responses in Pseudomonas aeruginosa. Mol Microbiol. 2006;62:84–99.

  38. 38.

    Miller C, Thomsen LE, Gaggero C, Mosseri R, Ingmer H, Cohen SN. SOS response induction by beta-lactams and bacterial defense against antibiotic lethality. Science (80-). 2004;305:1629–31.

  39. 39.

    Kohanski Ma, Dwyer DJ, Collins JJ. How antibiotics kill bacteria: from targets to networks. Nat Rev Microbiol. 2010;8:423–35.

  40. 40.

    Oliveira NM, Niehus R, Foster KR. Evolutionary limits to cooperation in microbial communities. Proc Natl Acad Sci. 2014;111:17941–6.

  41. 41.

    Xavier JB, Foster KR. Cooperation and conflict in microbial biofilms. Proc Natl Acad Sci. 2007;104:876–81.

  42. 42.

    van Gestel J, Weissing FJ, Kuipers OP, Kovács AT. Density of founder cells affects spatial pattern formation and cooperation in Bacillus subtilis biofilms. ISME J. 2014;10:2069–79.

  43. 43.

    Korolev KS, Xavier JB, Nelson DR, Foster KR. A quantitative test of population genetics using spatiogenetic patterns in bacterial colonies. Am Nat. 2011;178:538–52.

  44. 44.

    Mitri S, Clarke E, Foster KR. Resource limitation drives spatial organization in microbial groups. ISME J. 2016;10:1471–82.

  45. 45.

    van Ditmarsch D, Boyle KE, Sakhtah H, Oyler JE, Nadell CD, Déziel É, et al. Convergent evolution of hyperswarming leads to impaired biofilm formation in pathogenic bacteria. Cell Rep. 2013;4:697–708.

  46. 46.

    Smith WPJ, Davit Y, Osborne JM, Kim W, Foster KR, Pitt-Francisa JM. Cell morphology drives spatial patterning in microbial communities. PNAS. 2016;114:E280–86

  47. 47.

    van Gestel J, Vlamakis H, Kolter R. From cell differentiation to cell collectives: Bacillus subtilis uses division of labor to migrate. PLOS Biol. 2015;13:e1002141.

  48. 48.

    Mitri S, Foster KR. The genotypic view of social interactions in microbial communities. Annu Rev Genet. 2013;47:247–73.

  49. 49.

    Hallatschek O, Nelson DR. Life at the front of an expanding population. Evolution. 2010;64:193–206.

  50. 50.

    Kouyos RD, Metcalf CJE, Birger R, Klein EY, Abel zur Wiesch P, Ankomah P, et al. The path of least resistance: aggressive or moderate treatment? Proc Biol Sci. 2014;281:20140566.

  51. 51.

    Read AF, Day T, Huijben S. The evolution of drug resistance and the curious orthodoxy of aggressive chemotherapy. Proc Natl Acad Sci. 2011;108:10871–7.

  52. 52.

    Drusano GL. Antimicrobial pharmacodynamics: critical interactions of ‘bug and drug’. Nat Rev Microbiol. 2004;2:289–300.

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Acknowledgements

We thank Christopher Thomas for kindly providing plasmids. IF and WPJS received funding from the Systems Biology Doctoral Training Centre, funded by the EPSRC (grant number EP/G03706X/1). SM was supported by a Marie Curie Intra-European Fellowship and an Ambizione grant from the Swiss National Science Foundation. ASM is supported by a Miguel Servet fellowship from the Instituto de Salud Carlos III (MS15/00012) co-financed by the European Social Fund and The European Development Regional Fund “A way to achieve Europe” (ERDF). KRF was supported by European Research Council Grant 242670 and a grant from the Calleva Research Centre for Evolution and Human Science (Magdalen College, Oxford). RCM was funded by the Royal Society, European Research Council grant 281591, and Wellcome Trust Grant 106918/Z/15/Z.

Author information

Affiliations

  1. Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK

    • Isabel Frost
    • , R. Craig MacLean
    •  & Kevin R. Foster
  2. Center for Disease Dynamics, Economics & Policy, New Delhi, 110020, India

    • Isabel Frost
  3. Department of Computer Science, University of Oxford, Oxford, OX1 3QD, UK

    • William P. J. Smith
    •  & Joe M. Pitt-Francis
  4. Département de Microbiologie Fondamentale (DMF), Université de Lausanne, Lausanne, 1015, Switzerland

    • Sara Mitri
  5. Department of Microbiology, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, 28034, Spain

    • Alvaro San Millan
  6. Institut de Mécanique des Fluides de Toulouse (IMFT)—Université de Toulouse, CNRS-INPT-UPS, Toulouse, France

    • Yohan Davit
  7. School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia

    • James M. Osborne

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Conflict of interest

The authors declare that they have no conflict of interest.

Corresponding authors

Correspondence to R. Craig MacLean or Kevin R. Foster.

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