Intermittent antibiotic treatment of bacterial biofilms favors the rapid evolution of resistance

In vitro models for studying implant-associated biofilms - A review from the perspective of bioengineering 3D microenvironments

Biofilm research has grown exponentially over the last decades, arguably due to their contribution to hospital acquired infections when they form on foreign body surfaces such as catheters and implants. Yet, translation of the knowledge acquired in the laboratory to the clinic has been slow and/or often it is not attempted by research teams to walk the talk of what is defined as 'bench to bedside'. We therefore reviewed the biofilm literature to better understand this gap. Our search revealed substantial development with respect to adapting surfaces and media used in models to mimic the clinical settings, however many of the in vitro models were too simplistic, often discounting the composition and properties of the host microenvironment and overlooking the biofilm-implant-host interactions. Failure to capture the physiological growth conditions of biofilms in vivo results in major differences between lab-grown- and clinically-relevant biofilms, particularly with respect to phenotypic profiles, virulence, and antimicrobial resistance, and they essentially impede bench-to-bedside translatability. In this review, we describe the complexity of the biological processes at the biofilm-implant-host interfaces, discuss the prerequisite for the development and characterization of biofilm models that better mimic the clinical scenario, and propose an interdisciplinary outlook of how to bioengineer biofilms in vitro by converging tissue engineering concepts and tools.

Protective effects of antibiotic resistant bacteria on susceptibles in biofilm: Influential factors, mechanism, and modeling

In environmental biofilms, antibiotic-resistant bacteria facilitate the persistence of susceptible counterparts under antibiotic stresses, contributing to increased community-level resistance. However, there is a lack of quantitative understanding of this protective effect and its influential factors, hindering accurate risk assessment of biofilm resistance in diverse environment. This study isolated an opportunistic Escherichia coli pathogen from soil, and engineered it with plasmids conferring antibiotic resistance. Protective effects of the ampicillin resistant strain (AmpR) on their susceptible counterparts (AmpS) were observed in ampicillin-stress colony biofilms. The concentration of ampicillin delineated protective effects into 3 zones: continuous protection (<1 MIC of AmpS), initial AmpS/R dependent (1-8 MIC of AmpS), and ineffective (>8 MIC of AmpS). Intriguingly, Zone 2 exhibited a surprising "less is more" phenomenon tuned by the initial AmpS/R ratio, where biofilm with an initially lower AmpR (1:50 vs 50:1) harbored 30-90 % more AmpR after 24 h growth under antibiotic stress. Compared to AmpS, AmpR displayed superiority in adhesion, antibiotic degradation, motility, and quorum sensing, allowing them to preferentially colonize biofilm edge and areas with higher ampicillin. An agent-based model incorporating protective effects successfully simulated tempo-spatial dynamics of AmpR and AmpS influenced by antibiotic stress and initial AmpS/R. This study provides a holistic view on the pervasive but poorly understood protective effects in biofilm, enabling development of better risk assessment and precisely targeted control strategies of biofilm resistance in diverse environment.

Supramolecular Switch for the Regulation of Antibacterial Efficacy of Near-Infrared Photosensitizer

The global antibiotic resistance crisis has drawn attention to the development of treatment methods less prone to inducing drug resistance, such as antimicrobial photodynamic therapy (aPDT). However, there is an increasing demand for new photosensitizers capable of efficiently absorbing in the near-infrared (NIR) region, enabling antibacterial treatment in deeper sites. Additionally, advanced strategies need to be developed to avert drug resistance stemming from prolonged exposure. Herein, we have designed a conjugated oligoelectrolyte, namely TTQAd, with a donor-acceptor-donor (D-A-D) backbone, enabling the generation of reactive oxygen species (ROS) under NIR light irradiation, and cationic adamantaneammonium groups on the side chains, enabling the host-guest interaction with curcubit[7]uril (CB7). Due to the amphiphilic nature of TTQAd, it could spontaneously form nanoassemblies in aqueous solution. Upon CB7 treatment, the positive charge of the cationic adamantaneammonium group was largely shielded by CB7, leading to a further aggregation of the nanoassemblies and a reduced antibacterial efficacy of TTQAd. Subsequent treatment with competitor guests enables the release of TTQAd and restores its antibacterial effect. The reversible supramolecular switch for regulating the antibacterial effect offers the potential for the controlled release of active photosensitizers, thereby showing promise in preventing the emergence of drug-resistant bacteria.

Layer-by-layer designer nanoarchitectonics for physical and chemical communications in functional materials

Nanoarchitectonics, as a post-nanotechnology concept, constructs functional materials and structures using nanounits of atoms, molecules, and nanomaterials as materials. With the concept of nanoarchitectonics, asymmetric structures, and hierarchical organization, rather than mere assembly and organization of structures, can be produced, where rational physical and chemical communications will lead to the development of more advanced functional materials. Layer-by-layer assembly can be a powerful tool for this purpose, as exemplified in this feature paper. This feature article explores the possibility of constructing advanced functional systems based on recent examples of layer-by-layer assembly. We will illustrate both the development of more basic methods and more advanced nanoarchitectonics systems aiming towards practical applications. Specifically, the following sections will provide examples of (i) advancement in basics and methods, (ii) physico-chemical aspects and applications, (iii) bio-chemical aspects and applications, and (iv) bio-medical applications. It can be concluded that materials nanoarchitectonics based on layer-by-layer assembly is a useful method for assembling asymmetric structures and hierarchical organization, and is a powerful technique for developing functions through physical and chemical communication.

In vivo evolution of antimicrobial resistance in a biofilm model of Pseudomonas aeruginosa lung infection

The evolution of antimicrobial resistance (AMR) in biofilms has been repeatedly studied by experimental evolution in vitro, but rarely in vivo. The complex microenvironment at the infection site imposes selective pressures on the bacterial biofilms, potentially influencing the development of AMR. We report here the development of AMR in an in vivo mouse model of Pseudomonas aeruginosa biofilm lung infection. The P. aeruginosa embedded in seaweed alginate beads underwent four successive lung infection passages with or without ciprofloxacin (CIP) exposure. The development of CIP resistance was assessed at each passage by population analysis of the bacterial populations recovered from the lungs of CIP-treated and control mice, with subsequent whole-genome sequencing of selected isolates. As inflammation plays a crucial role in shaping the microenvironment at the infection site, its impact was explored through the measurement of cytokine levels in the lung homogenate. A rapid development of AMR was observed starting from the second passage in the CIP-treated mice. Genetic analysis revealed mutations in nfxB, efflux pumps (mexZ), and two-component systems (parS) contribution to CIP resistance. The control group isolates exhibited mutations in the dipA gene, likely associated with biofilm dispersion. In the initial two passages, the CIP-treated group exhibited an elevated inflammatory response compared to the control group. This increase may potentially contribute to the release of mutagenic reactive oxygen species and the development of AMR. In conclusion, this study illustrates the complex relationship between infection, antibiotic treatment, and immune response.

Aminoglycoside uptake, stress, and potentiation in Gram-negative bacteria: new therapies with old molecules

SUMMARYAminoglycosides (AGs) are long-known molecules successfully used against Gram-negative pathogens. While their use declined with the discovery of new antibiotics, they are now classified as critically important molecules because of their effectiveness against multidrug-resistant bacteria. While they can efficiently cross the Gram-negative envelope, the mechanism of AG entry is still incompletely understood, although this comprehension is essential for the development of new therapies in the face of the alarming increase in antibiotic resistance. Increasing antibiotic uptake in bacteria is one strategy to enhance effective treatments. This review aims, first, to consolidate old and recent knowledge about AG uptake; second, to explore the connection between AG-dependent bacterial stress and drug uptake; and finally, to present new strategies of potentiation of AG uptake for more efficient antibiotic therapies. In particular, we emphasize on the connection between sugar transport and AG potentiation.

Polyhexamethylene biguanide promotes adaptive cross-resistance to gentamicin in Escherichia coli biofilms

Antimicrobial resistance is a critical public health issue that requires a thorough understanding of the factors that influence the selection and spread of antibiotic-resistant bacteria. Biocides, which are widely used in cleaning and disinfection procedures in a variety of settings, may contribute to this resistance by inducing similar defense mechanisms in bacteria against both biocides and antibiotics. However, the strategies used by bacteria to adapt and develop cross-resistance remain poorly understood, particularly within biofilms -a widespread bacterial habitat that significantly influences bacterial tolerance and adaptive strategies. Using a combination of adaptive laboratory evolution experiments, genomic and RT-qPCR analyses, and biofilm structural characterization using confocal microscopy, we investigated in this study how Escherichia coli biofilms adapted after 28 days of exposure to three biocidal active substances and the effects on cross-resistance to antibiotics. Interestingly, polyhexamethylene biguanide (PHMB) exposure led to an increase of gentamicin resistance (GenR) phenotypes in biofilms formed by most of the seven E. coli strains tested. Nevertheless, most variants that emerged under biocidal conditions did not retain the GenR phenotype after removal of antimicrobial stress, suggesting a transient adaptation (adaptive resistance). The whole genome sequencing of variants with stable GenR phenotypes revealed recurrent mutations in genes associated with cellular respiration, including cytochrome oxidase (cydA, cyoC) and ATP synthase (atpG). RT-qPCR analysis revealed an induction of gene expression associated with biofilm matrix production (especially curli synthesis), stress responses, active and passive transport and cell respiration during PHMB exposure, providing insight into potential physiological responses associated with adaptive crossresistance. In addition, confocal laser scanning microscopy (CLSM) observations demonstrated a global effect of PHMB on biofilm architectures and compositions formed by most E. coli strains, with the appearance of dense cellular clusters after a 24h-exposure. In conclusion, our results showed that the PHMB exposure stimulated the emergence of an adaptive cross-resistance to gentamicin in biofilms, likely induced through the activation of physiological responses and biofilm structural modulations altering gradients and microenvironmental conditions in the biological edifice.

The Role of Stakeholders' Understandings in Emerging Antimicrobial Resistance: A One Health Approach

The increasing misuse of antibiotics in human and veterinary medicine and in agroecosystems and the consequent selective pressure of resistant strains lead to multidrug resistance (AMR), an expanding global phenomenon. Indeed, this phenomenon represents a major public health target with significant clinical implications related to increased morbidity and mortality and prolonged hospital stays. The current presence of microorganisms multi-resistant to antibiotics isolated in patients is a problem because of the additional burden of disease it places on the most fragile patients and the difficulty of finding effective therapies. In recent decades, international organizations like the World Health Organization (WHO) and the European Centre for Disease Prevention and Control (ECDC) have played significant roles in addressing the issue of AMR. The ECDC estimates that in the European Union alone, antibiotic resistance causes 33,000 deaths and approximately 880,000 cases of disability each year. The epidemiological impact of AMR inevitably also has direct economic consequences related not only to the loss of life but also to a reduction in the number of days worked, increased use of healthcare resources for diagnostic procedures and the use of second-line antibiotics when available. In 2015, the WHO, recognising AMR as a complex problem that can only be addressed by coordinated multi-sectoral interventions, promoted the One Health approach that considers human, animal, and environmental health in an integrated manner. In this review, the authors try to address why a collaboration of all stakeholders involved in AMR growth and management is necessary in order to achieve optimal health for people, animals, plants, and the environment, highlighting that AMR is a growing threat to human and animal health, food safety and security, economic prosperity, and ecosystems worldwide.

Regulation Transcriptional of Antibiotic Resistance Genes (ARGs) in Bacteria Isolated from WWTP

The incidence of antibiotics and transcriptional regulation of ARGs in isolated bacteria from wastewater needs to be explored. By HPLC, in samples of untreated wastewater, ampicillin (49.74 ± 5.70 µg/mL), chloramphenicol (0.60 ± 0.03 µg/mL), tylosin (72.95 ± 2.03 µg/mL), and oxytetracycline (0.22 ± 0.01 µg/mL) was determined. Through metagenomic analysis identified 58 bacterial species belonging to 9 phyla and at least 14 species have shown resistance to a variety of antibiotics. Twenty-two bacterial isolates were proved to be resistant to fifteen antibiotics of new generation and used in medical research to combat infectious diseases. Fourteen strains were shown to harbor plasmids in size ranges of 2-5 Kb, 6-10 Kb and plasmids with size greater than 10 Kb. By quantitative PCR it was possible to identify genes sul, qnr, cat1, aadA1, and sat-1 gene were shown to be present in gDNA samples from treated and untreated samples of wastewater and by relative expression analysis, differential expression of cat1, ermB, act, and tetA genes was demonstrated in strains that showed identity with Escherichia coli, Bacteroides fragilis, and Salmonella thyphi, and that were stressed with different concentrations of antibiotics. The presence of ARGs in untreated water samples, as well as in bacterial isolates, was indicative that in these habitats there are microorganisms that can resist β-lactams, aminoglycosides, tetracyclines, sulfonamides, and quinolones.

Evolution of antimicrobial resistance in E. coli biofilm treated with high doses of ciprofloxacin

The evolution of antimicrobial resistance (AMR) has mainly been studied in planktonic bacteria exposed to sub-inhibitory antimicrobial (AM) concentrations. However, in a number of infections that are treated with AMs the bacteria are located in biofilms where they tolerate high doses of AM. In the present study, we continuously exposed biofilm residing E. coli at body temperature to high ciprofloxacin (CIP) concentrations increasing from 4 to 130 times the minimal inhibitory concentration (MIC), i.e., from 0.06 to 2.0 mg/L. After 1 week, the biofilms were full of CIP resistant bacteria. The evolutionary trajectory observed was the same as described in the literature for planktonic bacteria, i.e., starting with a single mutation in the target gene gyrA followed by mutations in parC, gyrB, and parE, as well as in genes for regulation of multidrug efflux pump systems and outer membrane porins. Strains with higher numbers of these mutations also displayed higher MIC values. Furthermore, the evolution of CIP resistance was more rapid, and resulted in strains with higher MIC values, when the bacteria were biofilm residing than when they were in a planktonic suspension. These results may indicate that extensive clinical AM treatment of biofilm-residing bacteria may not only fail to eradicate the infection but also pose an increased risk of AMR development.

Light-Based Anti-Biofilm and Antibacterial Strategies

Biofilm formation and antimicrobial resistance pose significant challenges not only in clinical settings (i.e., implant-associated infections, endocarditis, and urinary tract infections) but also in industrial settings and in the environment, where the spreading of antibiotic-resistant bacteria is on the rise. Indeed, developing effective strategies to prevent biofilm formation and treat infections will be one of the major global challenges in the next few years. As traditional pharmacological treatments are becoming inadequate to curb this problem, a constant commitment to the exploration of novel therapeutic strategies is necessary. Light-triggered therapies have emerged as promising alternatives to traditional approaches due to their non-invasive nature, precise spatial and temporal control, and potential multifunctional properties. Here, we provide a comprehensive overview of the different biofilm formation stages and the molecular mechanism of biofilm disruption, with a major focus on the quorum sensing machinery. Moreover, we highlight the principal guidelines for the development of light-responsive materials and photosensitive compounds. The synergistic effects of combining light-triggered therapies with conventional treatments are also discussed. Through elegant molecular and material design solutions, remarkable results have been achieved in the fight against biofilm formation and antibacterial resistance. However, further research and development in this field are essential to optimize therapeutic strategies and translate them into clinical and industrial applications, ultimately addressing the global challenges posed by biofilm and antimicrobial resistance.