Box 1: Antibiotic resistance and tolerance
The rise and spread of antibiotic resistance presents a unique challenge to both science and medicine. Today, the crisis is epitomized by the spread of multidrug-resistant 'ESKAPE' organisms (Enterococcus spp., Staphylococcus aureus, Klebsiella spp., Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.)83. Indeed, in the case of some Gram-negative bacteria, such as A. baumannii, there are strains that are resistant to all currently available antibiotics84.
Antibiotics shut down or subvert essential cellular functions, and resistance mechanisms appear to exploit every possible strategy of preventing a drug from hitting its target. The major types of clinically relevant resistance mechanisms have been studied for a long time and are generally well understood (reviewed in Refs 3, 4) and are shown in the figure. These include destruction of the antibiotic (for example, by β-lactamases); target modification (for example, mutation in the 30S ribosomal protein RpsL confers resistance to streptomycin); as well as restricted penetration and/or efflux of the drug (for example, efflux of linezolid by the AcrAB–TolC multidrug pump)85, 86.
The same cannot be said about tolerance. The main culprit responsible for the tolerance of pathogens to antibiotics is a specialized survivor — a persister87, 88. Persisters are not mutants; they are phenotypic variants of actively dividing cells produced stochastically in the population, and their relative abundance rises — reaching 1% — at the late-exponential phase of growth89. Persisters are non-growing90 dormant91, 92 cells, which explains their tolerance to bactericidal antibiotics that depend on the presence of active targets for killing the cell93. All of the pathogens examined so far form persisters88, but the mechanisms underlying the formation of persisters is still largely unknown. Studies have shown, however, that in the model organism Escherichia coli, toxin–antitoxin modules are the principal mechanism of persister formation92, 93, 94, 95, and that pathways of persister formation are highly redundant96. Owing to this redundancy, a realistic target for drug discovery has yet to be identified.
The significance of persisters and drug tolerance in the clinical manifestation of disease was recently demonstrated when it was shown that elevated levels of persisters are selected for in the course of antimicrobial therapy in infections caused by Candida albicans97 and Pseudomonas aeruginosa98. Persisters also have an important role in the development of conventional antibiotic-resistant mutants. Persisters are killed only slowly, if at all, and resume growth when antibiotic concentrations fall. The result is a relapsing infection with a large effective population size that favours the development of resistance99. The importance of persisters in the recalcitrance of infectious diseases raises the bar for drug discovery; there is an urgent need to develop therapies that effectively kill both actively dividing and dormant pathogens. The figure is reproduced, with permission, from Ref. 100 © (2002) Macmillan Publishers Ltd. All rights reserved.
Department of Biology and Antimicrobial Discovery Center, Northeastern University, Boston, Massachusetts 02115, USA.
- Kim Lewis
Competing interests statement
The author is a member of the scientific advisory board of NovoBiotic Pharmaceuticals, Arietis Corporation and Seres Health.
Kim Lewis is a professor of biology and Director of the Antimicrobial Discovery Center at Northeastern University in Boston, Massachusetts, USA, and a fellow of the American Society of Microbiology. His interests are in antimicrobial drug resistance, tolerance and discovery. His findings include the discovery of synergistically acting antimicrobials in medicinal plants, a general method to grow previously uncultured bacteria (which make up >99% of the biodiversity on the planet) and the discovery of the culprit of recalcitrant biofilm infections — drug-tolerant persisters.
Metabolically quiescent cells that neither grow nor die when exposed to bactericidal concentrations of antibiotics.
- High-throughput screening
(HTS). An automated instrumental process for detecting the binding or activity of hundreds of thousands of compounds to an isolated receptor target or whole cells, thereby identifying worthwhile leads for development.
- Rational drug design
A strategy by which drug molecules are developed based on the analysis of the three-dimensional structure of a protein interacting with a ligand.
- Lipinski's 'rule of five' guidelines
Guidelines (from Lipinski's analysis of the World Drug Index) identifying several key properties that should be considered for small molecules that are intended for oral delivery. These properties are: molecular mass <500 Da, number of hydrogen-bond donors <5; number of hydrogen-bond acceptors <10; and calculated octanol–water partition coefficient (an indication of the ability of a molecules to cross biological membranes) <5.
- MDR efflux
Multidrug-resistant (MDR) efflux; an active transport system for the removal of several structurally non-related antibiotics from cells. The major facilitator (MF) family of MDRs are drug or proton antiporters present in all bacteria that are primarily responsible for efflux of hydrophobic cations and have some role in protecting bacteria from disinfectants, but not from systemically used antibiotics. The resistance nodulation cell division (RND) MDRs of Gram-negative bacteria are very broad- spectrum and will extrude most amphipathic compounds. These MDRs span the entire cell envelope and extrude compounds across the outer membrane — the main penetration barrier for antibiotics.
The entire collection of microorganisms (bacteria, archaea and fungi, as well as protozoa and viruses) that are resident on or in the host.
Loci consisting of two or more genes that are transcribed as a unit and expressed in a coordinated manner.
The rapid identification of known compounds to avoid the duplication of efforts (also called counterscreening).
- Transcription profiling
Large-scale studies of the expression of genes at the mRNA level, typically with microarray technology.
- Polymyxin B nonapeptide
A small cationic peptide that disrupts the outer membrane of Gram-negative bacteria by binding to lipopolysaccharide.
- Quorum sensing
A system by which bacteria communicate. Signalling molecules — chemicals that are similar to pheromones that are produced by an individual bacterium — can affect the behaviour of surrounding bacteria.
A cell–cell or surface-adherent assemblage of microorganisms that are encased in an extracellular matrix of self-produced polymers and exhibit distinctive phenotypes.