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Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance

PLoS Comput Biol. 2015 Sep 11;11(9):e1004493. doi: 10.1371/journal.pcbi.1004493. eCollection 2015 Sep.

Abstract

The increasing rate of antibiotic resistance and slowing discovery of novel antibiotic treatments presents a growing threat to public health. Here, we consider a simple model of evolution in asexually reproducing populations which considers adaptation as a biased random walk on a fitness landscape. This model associates the global properties of the fitness landscape with the algebraic properties of a Markov chain transition matrix and allows us to derive general results on the non-commutativity and irreversibility of natural selection as well as antibiotic cycling strategies. Using this formalism, we analyze 15 empirical fitness landscapes of E. coli under selection by different β-lactam antibiotics and demonstrate that the emergence of resistance to a given antibiotic can be either hindered or promoted by different sequences of drug application. Specifically, we demonstrate that the majority, approximately 70%, of sequential drug treatments with 2-4 drugs promote resistance to the final antibiotic. Further, we derive optimal drug application sequences with which we can probabilistically 'steer' the population through genotype space to avoid the emergence of resistance. This suggests a new strategy in the war against antibiotic-resistant organisms: drug sequencing to shepherd evolution through genotype space to states from which resistance cannot emerge and by which to maximize the chance of successful therapy.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Anti-Bacterial Agents / pharmacology*
  • Computational Biology
  • Drug Resistance, Bacterial / drug effects*
  • Drug Resistance, Bacterial / genetics
  • Escherichia coli / drug effects
  • Escherichia coli / genetics
  • Escherichia coli Infections / microbiology
  • Evolution, Molecular
  • Genetic Fitness / drug effects*
  • Genetic Fitness / genetics
  • Humans
  • Models, Biological*
  • Selection, Genetic / drug effects*
  • Selection, Genetic / genetics

Substances

  • Anti-Bacterial Agents