The role of bacterial metabolism in antimicrobial resistance

Abstract

The relationship between bacterial metabolism and antibiotic treatment is complex. On the one hand, antibiotics leverage cell metabolism to function. On the other hand, increasing research has highlighted that the metabolic state of the cell also impacts all aspects of antibiotic biology, from drug efficacy to the evolution of antimicrobial resistance (AMR). Given that AMR is a growing threat to the current global antibiotic arsenal and ability to treat infectious diseases, understanding these relationships is key to improving both public and human health. However, quantifying the contribution of metabolism to antibiotic activity and subsequent bacterial evolution has often proven challenging. In this Review, we discuss the complex and often bidirectional relationships between metabolism and the various facets of antibiotic treatment and response. We first summarize how antibiotics leverage metabolism for their function. We then focus on the converse of this relationship by specifically delineating the unique contribution of metabolism to three distinct but related arms of antibiotic biology: antibiotic efficacy, AMR evolution and AMR mechanisms. Finally, we note the relevance of metabolism in clinical contexts and explore the future of metabolic-based strategies for personalized antimicrobial therapies. A deeper understanding of these connections is crucial for the broader scientific community to address the growing crisis of AMR and develop future effective therapeutics.

Fig. 1 |. Interactions between antibiotics and metabolism.

The bacterial metabolic state, host context and the drug mechanism of action collectively impact the bacterial response to antibiotics. In turn, antibiotics can directly alter the metabolic state of a bacterium, further shaping this interaction. This bidirectional relationship can be understood through four main aspects: antibiotic efficacy, antimicrobial resistance (AMR) mechanisms, AMR evolution and metabolic dysregulation. Modulation of antibiotic efficacy may manifest in bacteria that adopt distinct metabolic growth physiologies or phenotypically metabolically dormant states (for example, biofilms). Antibiotics may also demonstrate different efficacies depending on the metabolic environment of the pathogen or host. AMR mechanisms impact metabolism via primary (for example, metabolic bypass), secondary (for example, altered nutrient preferences with target mutations), or indirect (for example, altered metabolism gene expression levels) routes. Metabolic dysregulation may occur by altering ATP levels, the tricarboxylic acid cycle (TCA) or other metabolic cell processes (for example, cell wall biosynthesis). AMR evolution may be observed via altered selection dynamics, processes of horizontal gene transfer (HGT), or de novo mutations.

Fig. 2 |. Bactericidal and bacteriostatic antibiotics leverage metabolism for their function.

Bactericidal antibiotics (upper cell panel) induce cell death through various mechanisms that, following initial target inhibition (not shown), primarily stimulate cell metabolism, including upregulating stress response networks and electron chain and tricarboxylic acid cycle (TCA) cycle activity. Bacteriostatic antibiotics (lower cell panel) inhibit cell growth. Classically, following initial target inhibition (not shown), growth inhibition occurs via the downregulation of key cell processes, including the glycolysis pathway and the TCA cycle. Macromolecular biosynthesis and protein translation processes may also be limited, resulting in a build-up of energy within the cell and ultimately cell stasis.

Fig. 3 |. The unique impact of metabolism on antibiotic resistance, tolerance and lethality in Mycobacterium tuberculosis.

A, Bactericidal antibiotics can induce the SOS response pathway. Antibiotics activate the RecA protein. Activated RecA represses LexA, which allows multiple genes in the SOS pathway to be expressed, including error-prone polymerases. This can result in mutations, including those to the antibiotic target, which confer resistance. B, Antibiotics can alter tricarboxylic acid cycle (TCA) cycle activity. During antibiotic treatment, isocitrate lyase (ICL) activates the glyoxylate shunt, reducing activity through the reductive steps of the TCA. This coincides with an overall reduction in metabolism and the expression of genes (for example, katG, furA, trxB1) involved in detoxifying reactive oxygen species (ROS). Together, this confers tolerance. C, Antibiotic-specific mechanisms that promote M. tuberculosis resistance and tolerance. Treatment of M. tuberculosis with the antibiotic bedaquiline activates two transcription factors, Rv0324 and Rv0880, increasing the expression of genes involved in virulence, detoxification, adaptation and cell wall processes, resulting in tolerance (part Ca). Treatment of M. tuberculosis with the antibiotic isoniazid may either promote metabolic rewiring, induce tolerance or successfully kill susceptible cells (part Cb). Isoniazid treatment, combined with intracellular KatG and NAD⁺, inhibits the enzyme isonicotinoyl–NAD (InhA), which is required for mycolic acid biosynthesis. Inhibition of InhA prevents cell wall synthesis in M. tuberculosis, resulting in cell death. D, Targeting multiple metabolic pathways can increase antibiotic lethality. Bedaquiline represses the activity of ATP synthase and the TCA cycle by increasing activity through the glyoxylate shunt. This forces M. tuberculosis to use glycolysis and substrate-level phosphorylation for ATP production. However, inhibiting substrate-level phosphorylation can increase bedaquiline lethality. E, Supplementing antibiotics with thiols, including cysteine, potentiates antibiotic lethality. When M. tuberculosis is treated with cysteine, it enters the cell and is converted to cystine, generating reactive oxygen species. Thus, when cysteine is provided in conjunction with an antibiotic, the increased ROS potentiate antibiotic lethality.

Fig. 4 |. Unique properties of biofilms confer antibiotic tolerance via altered metabolism.

A, Biochemical characteristics of biofilms relevant to antibiotic treatment. Biofilms are communities of bacteria affixed to a surface surrounded by a layer of extrapolymeric substances (EPS). EPS is primarily comprised of extracellular DNA (eDNA), pili and polysaccharides. Although interstitial voids carrying nutrients and oxygen into the inner layers of the biofilm can form, overall nutrient and oxygen transport is limited by EPS (part Aa). Bacteria closer to the surface of the biofilm experience more nutrients and oxygen, whereas those towards the base have limited access to both, and consequently, exhibit increased tolerance to antibiotics (part Ab). B, Antibiotic effects on biofilm communities. The presence of metabolically dormant persister cells is increased in biofilms following antibiotic treatment (part Ba; purple); these cells are more tolerant to antibiotics. The frequency and efficiency of conjugation is increased between biofilm members, allowing for genes that confer resistance to quickly increase in abundance (part Bb). Quorum sensing is enhanced in biofilms (part Bc). This can result in a rewiring of metabolic pathways, including glucose import, the pentose phosphate pathway and nucleotide synthesis. These changes may increase antibiotic tolerance. Increasing metabolism in biofilms using a metabolite can increase antibiotic lethality (part Bd).

Fig. 5 |. Metabolism promotes antimicrobial resistance evolution via its effect on conjugation.

a, Manipulating the metabolic state of a cell modulates conjugation efficiency. Conjugation is a mechanism of horizontal gene transfer by which bacteria transfer their circular components of DNA (that is, plasmids) from one cell to another through direct contact. Conjugation efficiencies (that is, the kinetic rate of plasmid transfer) can be promoted by activating metabolism (for example, increasing carbon consumption). Increased conjugation efficiency increases plasmid spread. High conjugation efficiency may also be sustained by quorum sensing, which regulates cell metabolism to encourage bacteria to adopt a cooperative state. Often, this cooperative state is characterized by factors that increase bacterial virulence. b, Transient acquisition costs depend on the metabolic efficiency of the cell. Immediately after conjugation, newly acquired plasmids impose a short-term disruption to the cell by activating the SOS response and dysregulating plasmid regulatory networks. This intracellular perturbation results in a growth defect on the brand-new plasmid-carrying host strain, referred to as an acquisition cost. Manipulation of the metabolic state of the cell via changing the nutrient composition (beaker) can modulate acquisition costs. c, The long-term implications of metabolism on the competitiveness of conjugative plasmids. Compared with a plasmid-free host (right cell), hosts carrying a plasmid (left cell) may also experience a long-term growth defect or burden (that is, plasmid fitness cost), especially in the absence of antibiotic selection. The fitness cost impacts diverse pathways implicated in metabolism.

Fig. 6 |. Classic and metabolic mechanisms of antimicrobial resistance.

A bacterial cell exhibiting antimicrobial resistance (AMR) will have a chromosome and, in some cases, one or more circular plasmids that encode for antibiotic resistance genes and/or mutations. The most common canonical mechanisms of antimicrobial resistance (red) include target modification, enzymatic inactivation and reduced antibiotic intake. These may also have indirect metabolic effects (for example, porins that alter nutrient uptake). Direct mechanisms (blue) by which metabolism promotes AMR include differential metabolic gene expression, activation of alternative metabolic pathways and insertion of metabolic genes. Other cellular characteristics which may also potentially impact AMR through indirect metabolic effects include the presence of biofilms and porins. Biofilms may structurally protect the cell from antibiotic treatment and often demonstrate unique and heterogenic metabolic states. Porins may also modulate both antibiotic resistance levels and cell metabolism. Minimizing cell membrane porin expression reduces both nutrient and antibiotic uptake.