Chemical and biological strategies to disrupt biofilms: A new era in infectious disease management and antimicrobial resistance control

Abstract

Biofilm-associated infections are a major medical problem that is responsible for nearly 80% of human microbial infections. These bacterial communities are protected by a strong extracellular matrix that limits antibiotic penetration and supports persister cells and quorum-sensing–driven resistance. Biofilm development occurs in several stages and ultimately forms complex structures that block antimicrobial action. To overcome this, chemical strategies include quorum-sensing inhibitors, matrix-degrading agents, antimicrobial peptides, and photodynamic therapy. Biological approaches use bacteriophages, enzymes such as DNase, and probiotics that disrupt biofilms through competitive mechanisms. Combination therapies—such as antibiotic-phage or enzyme-antibiotic treatments—show improved effectiveness. Advanced delivery systems involving nanoparticles, liposomes, and hydrogels enhance drug penetration in biofilms, particularly in wound care. New technologies, including AI-guided drug discovery and CRISPR targeting, are advancing future anti-biofilm treatments.

Full Article

Chemical and Biological Strategies to Disrupt Biofilms: A New Era in Infectious Disease Management and Antimicrobial Resistance Control

Samy Selim  *

Biofilm-associated infections are a major medical problem that is responsible for nearly 80% of human microbial infections. These bacterial communities are protected by a strong extracellular matrix that limits antibiotic penetration and supports persister cells and quorum-sensing–driven resistance. Biofilm development occurs in several stages and ultimately forms complex structures that block antimicrobial action. To overcome this, chemical strategies include quorum-sensing inhibitors, matrix-degrading agents, antimicrobial peptides, and photodynamic therapy. Biological approaches use bacteriophages, enzymes such as DNase, and probiotics that disrupt biofilms through competitive mechanisms. Combination therapies—such as antibiotic-phage or enzyme-antibiotic treatments—show improved effectiveness. Advanced delivery systems involving nanoparticles, liposomes, and hydrogels enhance drug penetration in biofilms, particularly in wound care. New technologies, including AI-guided drug discovery and CRISPR targeting, are advancing future anti-biofilm treatments.

DOI: 10.15376/biores.21.1.Selim

Keywords: Biofilms; Antimicrobial resistance; Quorum sensing; Bacteriophages; Drug delivery; Infectious diseases; Combination therapy; Nanotechnology

Contact information: Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Saudi Arabia; *Corresponding authors: sabdulsalam@ju.edu.sa

INTRODUCTION

The discovery that bacteria form complex, structured communities has fundamentally reshaped our understanding of microbial life (Costerton et al. 1999). What van Leeuwenhoek first described as “animalcules” on teeth is now recognized as biofilms. These can be regarded as organized microbial cities encased in extracellular polymeric substances (Flemming and Wingender 2010). Their clinical relevance grew during the late 20^th century as chronic and device-associated infections became more common (Donlan 2002). Persistent infections that resisted standard antibiotic therapy were increasingly linked to biofilms, marking a major shift in infectious disease thinking (Donlan and Costerton 2002; Stewart and Costerton 2001). Standard susceptibility tests failed to predict outcomes because planktonic bacteria tested in vitro did not reflect the high tolerance of biofilm-associated cells (Anderl et al. 2000).

Bacterial cellulose is a key structural element of many biofilms, providing mechanical strength, hydration, and cohesion. Produced by the cellulose synthase complex (BcsA/B) and regulated by c-di-GMP and CsgD, this β-1,4-glucan polymer forms strong hydrogels with properties distinct from plant cellulose. Together with other matrix components such as curli fibres, it contributes to the stability and elasticity of biofilm communities.

Biofilms contribute to an estimated 80% of microbial infections worldwide and impose massive healthcare and economic burdens (Høiby et al. 2011). They are difficult to treat because of matrix-mediated diffusion barriers (Walters et al. 2003), metabolically inactive subpopulations (Stewart and Franklin 2008), quorum-sensing–driven collective responses (Waters and Bassler 2005), and active efflux systems (Ciofu and Tolker-Nielsen 2019). Their dense structure promotes horizontal gene transfer and accelerates antimicrobial resistance (Høiby et al. 2010; Molin and Tolker-Nielsen 2003). Biofilm bacteria often require antibiotic doses hundreds of times higher than planktonic cells, making traditional MIC-based therapy inadequate (Stewart 2002; Nickel et al. 1985).

Over the past two decades, research has expanded into strategies that prevent, disrupt, or weaken biofilms (Roy et al. 2018). These include chemical approaches such as quorum-sensing inhibitors (Rasmussen and Givskov 2006), matrix-degrading enzymes (Kaplan 2010), and biofilm-targeted antimicrobials. Biological strategies employ bacteriophages (Abedon et al. 2011), probiotics (Abdel-Aziz et al. 2016), and other naturally occurring antagonists, while physical methods use ultrasound or electric fields. Increasingly, combination therapies target multiple biofilm mechanisms simultaneously (Koo et al. 2017). Advanced delivery systems including nanoparticles, hydrogels, and other controlled-release platforms further enhance drug penetration and therapeutic persistence within biofilms (Fig. 1).

Early clinical applications show promise in wound management (Percival et al. 2012), device-associated infection prevention (Zimmerli et al. 2004), and respiratory therapies (Hurley et al. 2012). Nonetheless, challenges remain regarding regulatory approval, scaling, and integration into clinical practice. This review will examine recent advances in chemical and biological anti-biofilm strategies (Table 1), their mechanisms of action, relevance to persistent infections and AMR, and the translational barriers that must be addressed for successful clinical adoption.

Fig. 1. Biofilm formation stages: Sequential progression from initial bacterial attachment through irreversible attachment, early biofilm development, and biofilm maturation, culminating in bacterial dispersal

Table 1. Comparison of Chemical and Biological Strategies for Biofilm Disruption

UNDERSTANDING BIOFILM BIOLOGY: FROM SIMPLE AGGREGATES TO COMPLEX COMMUNITIES

The modern study of bacterial biofilms began in the 1970s and 1980s, when researchers realized that bacteria on surfaces formed highly organized communities rather than simple aggregates (Costerton et al. 1999). What van Leeuwenhoek first observed on teeth has since been recognized as one of the most sophisticated forms of microbial organization (Flemming et al. 2016). Biofilm development is closely regulated and begins with reversible attachment, during which bacteria evaluate surface properties such as chemistry and roughness (Stoodley et al. 2002; Hall-Stoodley et al. 2004). Once cells commit to adhesion, they produce adhesins and begin forming the extracellular polymeric substances (EPS) that constitute the biofilm matrix (Donlan and Costerton 2002; Flemming and Wingender 2010). This matrix—composed of polysaccharides, proteins, nucleic acids, and lipids—provides structural stability, protection, nutrient retention, and a scaffold for communication (Ghafoor et al. 2011; Jennings et al. 2015; Whitchurch et al. 2002).

As biofilms mature, they develop striking spatial organization, forming three-dimensional structures with channels that distribute nutrients and remove waste (Tolker-Nielsen 2015). Gradients of oxygen, pH, and nutrients create diverse microenvironments that support physiologically distinct populations (Stewart and Franklin 2008). Quorum-sensing coordinates community-wide behaviors throughout this process, regulating attachment, matrix production, and dispersal (Waters and Bassler 2005; LaSarre and Federle 2013; McDougald et al. 2012). Dispersal involves enzymatic degradation of the matrix, releasing bacteria capable of colonizing new sites, often with increased virulence and antibiotic tolerance (Kaplan et al. 2003).

Biofilm communities display metabolic heterogeneity that contributes to their resilience (Fux et al. 2005). Surface cells may be actively growing, while interior cells adopt slow or alternative metabolic states adapted to low-oxygen environments (Yoon et al. 2002). These slow-growing “persister” cells survive antibiotic exposure and can repopulate the biofilm after treatment (Lewis 2007). Genome-wide studies show that biofilm-associated bacteria express hundreds of genes differently than planktonic cells, influencing metabolism, stress responses, and virulence (Parsek and Singh 2003). Mechanical forces such as fluid shear also shape biofilm structure and behavior.

Biofilms interact with host immunity in complex ways. The EPS matrix protects bacteria from phagocytes and complement, and slow growth reduces immune recognition (Xavier and Foster 2007). Some biofilms induce chronic inflammation that damages host tissues and supports microbial survival. Biofilms are also major contributors to antimicrobial resistance: their dense structure promotes horizontal gene transfer, enhances mutation rates, and selects for highly tolerant phenotypes (Van Acker et al. 2014; Molin and Tolker-Nielsen 2003). These features allow biofilms to act as reservoirs of resistance genes even after treatment appears successful.

CHEMICAL WARFARE AGAINST BIOFILMS: INNOVATIVE MOLECULAR STRATEGIES

The development of chemical strategies for biofilm disruption (Fig. 2) has advanced far beyond traditional antimicrobial treatments.

Fig. 2. Biofilm disruption strategies: Comprehensive illustration of chemical and biological approaches for biofilm treatment including quorum-sensing inhibitors, matrix-degrading enzymes, antimicrobial peptides, bacteriophages, nanoparticle drug delivery, and photodynamic therapy

Researchers now recognize that successful biofilm control requires targeting the unique features that give these communities their resilience (Rasmussen and Givskov 2006). This shift has driven innovation ranging from small-molecule inhibitors to specialized delivery systems.

Quorum-sensing inhibition is one of the most sophisticated approaches (Brackman and Coenye 2015). Rather than killing bacteria directly, QS inhibitors target the signaling processes that are essential for coordinated biofilm behavior. Natural QSIs from plants, marine organisms, and bacteria first demonstrated the potential of this strategy (Givskov et al. 1996). Furanones from marine algae provided early lead compounds by disrupting AHL signaling (Hentzer et al. 2003), although toxicity and instability limited their direct clinical use (Kalia 2013). Medicinal chemistry efforts have since produced synthetic analogs with markedly improved potency and safety.

Antimicrobial peptides (AMPs) form another important class of anti-biofilm agents (Batoni et al. 2016). As components of innate immunity, many AMPs display enhanced activity against biofilms compared to planktonic bacteria. Their multi-target mechanisms—ranging from membrane disruption to interference with matrix components or quorum sensing—reduce the likelihood of resistance (Jorge et al. 2012).

Matrix-degrading enzymes offer a more direct approach, breaking down the structural components that maintain biofilm integrity (Kaplan 2010). DNase is especially effective because extracellular DNA is a key matrix component (Whitchurch et al. 2002). DNase treatment can significantly reduce biomass and improve antimicrobial penetration (Tetz et al. 2009).

Chemical strategies also include compounds designed specifically for biofilm environments. These often target metabolic processes unique to oxygen-limited biofilm interiors (Hurdle et al. 2011). Nitric oxide and NO-releasing molecules show strong potential because they penetrate biofilms and act through multiple mechanisms, including direct killing and matrix disruption (Barraud et al. 2006). Their natural production by immune cells supports good biocompatibility.

Photodynamic therapy adds spatially controlled killing through light-activated generation of reactive oxygen species (Hamblin and Hasan 2004). Electrochemical approaches, including the “bioelectric effect,” also enhance antimicrobial efficacy by generating reactive species or altering conditions in ways that are unfavorable to biofilm survival (Costerton et al. 1994).

BIOLOGICAL SOLUTIONS: HARNESSING NATURE’S ANTI-BIOFILM ARSENAL

The search for effective biofilm treatments has increasingly shifted toward biological solutions, recognizing that nature has spent millions of years developing mechanisms to counter microbial communities (Abedon et al. 2011). Among these natural tools, bacteriophages are particularly promising (Chan et al. 2013). Phages have co-evolved with bacteria for billions of years and possess highly specific mechanisms for locating and destroying their hosts. Their ability to penetrate biofilm matrices, replicate at the site of infection, and adapt alongside their targets makes them well suited for biofilm therapy. Although phage therapy declined after the rise of antibiotics, its resurgence reflects growing concerns about antimicrobial resistance and the effectiveness of phages against biofilm infections (Sulakvelidze et al. 2001).

Phages also produce enzymes such as depolymerases, which degrade polysaccharide components of biofilm matrices and enhance bacterial access (Hughes et al. 1998). Enzymatic disruption more broadly represents another promising biological approach (Kaplan 2010). Because biofilm matrices contain multiple polymers, enzyme cocktails are often needed. DNase is especially effective because extracellular DNA forms a key structural component of many biofilms (Whitchurch et al. 2002). DNase treatment reduces biomass and improves antimicrobial penetration (Tetz et al. 2009).

Probiotics and beneficial bacteria offer an additional strategy (Abdel-Aziz et al. 2016). These organisms naturally produce compounds that inhibit or disrupt biofilms and can outcompete pathogens for nutrients and adhesion sites. Their anti-biofilm effects may involve antimicrobial production, enzymatic matrix degradation, or competitive exclusion (Valdez et al. 2005). Bacteriocins—antimicrobial peptides produced by bacteria—represent another potent biological tool (Cotter et al. 2005). Their ability to penetrate matrices and kill target bacteria makes them strong candidates for biofilm control.

THE POWER OF COMBINATION: SYNERGISTIC APPROACHES TO BIOFILM DISRUPTION

The complexity of biofilm resistance mechanisms (Fig. 3) has made it clear that single-agent treatments rarely achieve reliable biofilm eradication (Koo et al. 2017). This understanding has driven the development of combination strategies that target multiple aspects of biofilm physiology to achieve synergistic effects—an approach long proven effective in fields such as cancer and HIV therapy (Borisy et al. 2003).

Fig. 3. Biofilm resistance mechanisms. Cross-sectional view of a mature biofilm showing multiple resistance mechanisms including matrix barrier preventing antibiotic penetration, metabolic gradients, efflux pumps, and horizontal gene transfer

Applying similar principles to biofilms represents a natural progression in treatment design. Pairing quorum-sensing inhibitors (QSIs) with conventional antimicrobials is one promising strategy (Rasmussen and Givskov 2006). QSIs disrupt the communication systems that coordinate biofilm defenses, thereby increasing bacterial susceptibility to antibiotics. Studies show that combining QSIs with antibiotics can enable biofilm removal at much lower antimicrobial concentrations than monotherapies.

Matrix-disrupting agents combined with antimicrobials form another effective approach (Kaplan 2010). Enzymes or chemicals that degrade the biofilm matrix improve antibiotic penetration and expose previously protected bacteria. Such approaches can be especially valuable for device-associated infections where matrices are thick and highly impermeable.

Physical-chemical combinations also show strong potential. Ultrasound can mechanically disturb biofilm structure, while electrical currents enhance antimicrobial activity through the bioelectric effect (Stewart et al. 2001). When paired with antimicrobials, these interventions outperform either modality alone.

Phage-antibiotic combinations represent a particularly innovative strategy (Comeau et al. 2007). Phages can penetrate and disrupt biofilms, while antibiotics eliminate surviving bacteria and help prevent resistance to phages. Together, these agents often demonstrate clear synergistic effects, especially against multidrug-resistant pathogens.

DRUG DELIVERY SYSTEMS: GETTING TREATMENTS WHERE THEY NEED TO GO

The development of effective delivery systems has become a crucial aspect of successful biofilm therapy (Forier et al. 2014). Even highly potent anti-biofilm agents cannot work if they fail to reach their targets within the dense, hydrated biofilm matrix. This barrier has driven the creation of innovative delivery technologies. Nanoparticle-based systems show strong potential because they can penetrate biofilm structures more effectively than free drugs, provide sustained release, and be engineered to target specific biofilm components (Huh and Kwon 2011). Their small size enables movement through complex biofilm architecture, while surface modifications improve interaction with matrix elements.

Liposomal delivery systems offer another valuable strategy (Drulis-Kawa and Dorotkiewicz-Jach 2010). These lipid vesicles can encapsulate diverse drugs, protect them from degradation, and enhance controlled release at the infection site. Some formulations are tailored to bind to biofilm matrices, improving penetration and retention. Hydrogel-based systems provide distinct advantages, especially in wound care (Zhao et al. 2017). Hydrogels can be loaded with anti-biofilm agents and applied directly to infected tissues, offering sustained release while maintaining a moist environment that supports healing.

FROM LABORATORY TO CLINIC: REAL-WORLD APPLICATIONS

The translation of biofilm research from laboratory to clinic has been challenging but increasingly successful (Percival et al. 2012). Several anti-biofilm strategies have now been implemented in clinical practice, providing valuable insights into the practical challenges and opportunities for biofilm management. Chronic wound care represents one of the most successful areas for clinical application of anti-biofilm strategies (Wolcott et al. 2010). The recognition that chronic wounds often harbor biofilm infections has led to the development of specialized wound care products that incorporate anti-biofilm agents (Table 2). These products have shown improved healing rates compared to conventional wound care approaches.

Table 2. Clinical Applications and Outcomes of Anti-Biofilm Strategies

Device-associated infection prevention has been another area of significant clinical progress (Zimmerli et al. 2004). Anti-biofilm coatings for medical devices, including catheters, implants, and prosthetic devices, have shown promise in reducing infection rates. Such coatings often incorporate multiple anti-biofilm mechanisms, including antimicrobial agents, anti-adhesive surfaces, and biofilm-disrupting compounds. Respiratory therapy for cystic fibrosis patients has benefited from anti-biofilm approaches (Hurley et al. 2012). Inhaled DNase therapy has become a standard treatment for cystic fibrosis, helping to reduce the viscosity of respiratory secretions and improve lung function. This represents one of the first successful clinical applications (Table 3) of enzymatic biofilm disruption.

Table 3. Emerging Technologies and Future Directions

NEW FRONTIERS: EMERGING TECHNOLOGIES AND INNOVATIONS

The future of biofilm research and therapy is being shaped by several emerging technologies that promise to revolutionize our approach to biofilm management (Roy et al. 2018). These technologies span multiple disciplines, from artificial intelligence (AI) to nanotechnology to precision medicine. The AI and machine learning approaches are beginning to transform biofilm research (Rajput et al. 2021). These technologies can help identify optimal combination therapies, predict treatment outcomes, and design new anti-biofilm compounds. AI-driven drug discovery platforms are already being used to identify novel biofilm targets and design compounds with enhanced anti-biofilm activity.

Clustered regularly interspaced short palindromic repeats (CRISPR) and other gene editing technologies offer unprecedented opportunities for biofilm management (Bikard et al. 2014). These tools can be used to disrupt essential biofilm genes, enhance the susceptibility of biofilm bacteria to antimicrobials, or engineer beneficial bacteria with enhanced anti-biofilm properties. Precision medicine approaches are beginning to be applied to biofilm infections (Bjarnsholt et al. 2018). By characterizing the specific bacterial species and resistance mechanisms present in individual biofilm infections, it may be possible to tailor treatments to the specific characteristics of each infection. Advanced imaging technologies are providing new insights into biofilm structure and behavior (Neu et al. 2010). These technologies can monitor biofilm development in real-time, assess treatment efficacy, and guide therapeutic decision-making (Fig. 4).

Fig. 4. Future directions and emerging technologies in biofilm research: Innovative approaches including AI-guided drug discovery, smart nanoparticles, CRISPR gene editing, precision medicine, advanced imaging technologies, and combination therapies

CONCLUSIONS AND FUTURE PROSPECTS

Our growing understanding of biofilms has opened the door to a new era in treating biofilm-associated infections. Advances in biofilm biology, disruption strategies, and drug delivery technologies show clear potential to transform conditions once considered highly treatment-resistant. Future success will require continued innovation, improved diagnostics, and clinical frameworks that support complex, multi-agent therapies. Strong interdisciplinary collaboration and coordinated global action is essential given the widespread impact of biofilm related infections. A major challenge ahead is translating promising laboratory findings into real clinical solutions, which will require investment and regulatory support. Emerging technologies such as artificial intelligence, nanotechnology, and precision medicine will play a central role in shaping next-generation treatments. Although significant hurdles remain, current progress provides strong reason for cautious optimism about the future of biofilm management.

Funding

This study was funded by the Deanship of Graduate Studies and Scientific Research at Jouf University under grant No. (DGSSR-2025-01-01109).

Data Availability

All datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.

Conflicts of Interest

The authors declare that they have no conflicts of interest.

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Article submitted: July 31, 2025; Peer review completed: December 13, 2025; Revised version received and accepted: December 21, 2025; Published: December 31, 2025.

DOI: 10.15376/biores.21.1.Selim