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Tolerance and resistance of microbial biofilms

Abstract

Chronic infections caused by microbial biofilms represent an important clinical challenge. The recalcitrance of microbial biofilms to antimicrobials and to the immune system is a major cause of persistence and clinical recurrence of these infections. In this Review, we present the extent of the clinical problem, and the mechanisms underlying the tolerance of biofilms to antibiotics and to host responses. We also explore the role of biofilms in the development of antimicrobial resistance mechanisms.

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Fig. 1: Tolerance of microbial biofilms to host immune responses.
Fig. 2: The mechanisms of antimicrobial tolerance of a biofilm.
Fig. 3: The development of antimicrobial resistance in planktonic and biofilm-growing bacterial populations.

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Acknowledgements

C.M. is supported by Novo Nordisk Foundation (Borregaard Clinical Scientist Fellowship in translational research; grant no. NNF17OC0025074).

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Supplementary information

Glossary

Tolerance

A tolerant population is characterized by a slow rate of killing due to slow growth and low metabolic activity of the bacterial cells, requiring a longer time to kill 99% of the bacterial population than a susceptible population despite the similar values of the minimum inhibitory concentration of antibiotics against both populations.

Resistance

A resistant population is characterized by the lack of killing by antibiotic concentrations above the minimum inhibitory concentration of antibiotics against the susceptible bacterial population.

Aggregates

An assemblage of bacterial cells that can develop into structured biofilms through embedding in a polymeric matrix.

Lipopolysaccharides

Surface molecules, part of the outer membrane of the bacteria with a Gram-negative cell wall.

Respiratory burst

Production of superoxide upon the activation of polymorphonuclear leukocytes with rapid consumption of oxygen.

Degranulation

The liberation of the granular content of antimicrobial agents during the activation of polymorphonuclear leukocytes.

Pf bacteriophages

Temperate filamentous phages that can initiate a chronic infection cycle, during which virions are continuously extruded from the bacterial surface without cell lysis. They can be activated under various conditions such as antibiotic treatment or biofilm growth.

Rhamnolipids

Virulence factors with biosurfactant activity produced by Pseudomonas aeruginosa.

Persister cells

Non-dividing cells that can resume growth and cause relapse of the infection when antibiotic treatment is terminated.

Bacteriophage

Often referred to as simply phages. Naturally occurring viruses that infect bacteria. Lytic phages replicate inside their hosts and release new bacteriophages able to infect more bacteria. Temperate phages incorporate their genetic material into the bacterial chromosome and can be activated under special conditions (for example, treatment with antibiotics).

Small colony variants

(SCVs). Phenotypic variants that are slow-growing and tolerant to immune cells and antimicrobials. They strongly adhere to surfaces and can auto-aggregate.

Stringent response

A universal stress response that is induced by starvation and results in decreased cell growth to promote cell survival.

SOS response

A stress response that counteracts various types of DNA damage.

RpoS response

RpoS is a global stress response regulator induced under various stress conditions dependent on the RpoS alternative sigma factor and a central regulator of many stationary-phase inducible genes. This response enables cells to become more resistant not only to the stress that they first encounter but also to other stress-inducing treatments.

Membrane vesicles

Small (20–400 nm in diameter) lipid bilayer-enclosed particles released from Gram-negative bacteria. They contain both cytoplasmic and periplasmic components. Membrane vesicles from Gram-positive bacteria have also been described.

Nitrosative stress

Stress response to reactive nitrogen species such as nitric oxide (NO) and its derivatives (nitrous acid (HNO2), peroxinitrite (ONOO), alkylperoxynitrate (ROONO).

CRISPR–Cas

An immunity mechanism in archaea and bacteria that confers resistance to foreign genetic elements, such as phages and plasmids, and represents an acquired form of immunity.

Fitness cost

The consequence of mutation-induced resistance on the bacterial growth rate.

Clinical resistance breakpoint

Concentrations of antimicrobial that are used to distinguish strains with a high likelihood of treatment success and those in which treatment is more likely to fail.

Antimicrobial resistance genes

(ARGs). Examples of ARGs transmitted by horizontal gene transfer. Conjugation: plasmid-encoded extended spectrum β-lactamases (ESBLs), carbapenemases, plasmid-encoded quinolone resistance genes (qnr), usually on multi-drug resistance plasmids, between different Gram-negative species such as Escherichia coli and Klebsiella pneumoniae, vancomycin-resistance genes between Enterococcus faecalis and Staphylococcus aureus. Transduction: tetracycline and penicillin resistance between S. aureus strains. Natural transformation: resistance to metronidazole in Helicobacter pylori.

Integrases

Enzymes required for the site-specific recombination of integrons. Integrons are genetic elements that facilitate the acquisition and reassembly of gene cassettes encoding products with a variety of functions, including drug resistance.

Pharmacokinetics and pharmacodynamics

Parameters that describe the time-dependent concentration of the antibiotic in the host (pharmacokinetics) and its effect at the infection site (pharmacodynamics).

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Ciofu, O., Moser, C., Jensen, P.Ø. et al. Tolerance and resistance of microbial biofilms. Nat Rev Microbiol (2022). https://doi.org/10.1038/s41579-022-00682-4

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