Biofilm as an endodontic infection

Summary: This article explores the fundamental aspects of a topic highly relevant to modern endodontists — the biofilm in the root canal. A detailed study of this issue highlights the complexity of microbiological and immunological processes occurring within the root canal system. Understanding these processes reinforces the importance of thorough mechanical and antiseptic root canal preparation for dental practitioners.

Keywords: biofilm, root canal treatment, root canal microbiology.

A key aspect of an endodontist’s daily work is, in my opinion, a clear understanding of the underlying biological processes. For many years, topics like microbiology and immunology seemed distant from clinical practice. However, the accumulated knowledge today pushes us to reconsider our clinical decisions. One of the most studied and debated topics today is biofilm.

A biofilm is a conglomerate of microbial colonies embedded in an extracellular matrix and attached to a surface. The microcolonies occupy about 15% of the biofilm's total mass.

The extracellular matrix, consisting of exopolysaccharides secreted by microbes, plays vital roles in the biofilm's function and accounts for 85% of the biofilm mass. Despite its name, a biofilm is not a homogeneous substance — it is spatially and temporally heterogeneous, with water channels running through it that deliver nutrients and remove waste products.

The extracellular matrix acts as a powerful biological glue that firmly anchors the biofilm to surfaces. In dentistry, this means tooth enamel in early caries and root surfaces in periodontal pathology. In endodontics, the biofilm adheres to the dentin walls of the root canal. Furthermore, the extracellular matrix can also serve as a nutrient source for bacteria. In fact, biofilms in endodontics were described as early as 1987 by Nair R., who identified them as microbial conglomerates embedded in an amorphous extracellular matrix [1]. However, the term "biofilm" was not yet in use, and the significance of this finding was overlooked.

Today, it is widely accepted that over 80% of infections in the human body occur in the form of biofilm-associated infections. Therefore, Nair R.’s suggestion to treat chronic apical periodontitis as an infectious disease caused by intra-canal biofilms is entirely logical [2].

So what makes this structure so important? Within a biofilm, unique microbial interactions occur: close contact between microorganisms significantly increases genetic exchange, accelerating the development of resistant strains far more than in planktonic (free-floating) forms. Microbial colonies also communicate through pheromone-like signaling molecules that alter behavior, growth rates, and phenotypic traits [3]. Finally, complex food chains form within the biofilm, where the waste of some organisms sustains others.

The extracellular matrix protects microbes from external influences — including our antimicrobial interventions. Most microbiological studies have focused on planktonic bacteria, which explains the discrepancy between in vitro and in vivo results. A striking example is the observation that microbes in biofilms can be up to 1,000 times more resistant to amoxicillin than their planktonic counterparts [4].

Understanding these biofilm interactions helps us answer a long-standing microbiological question: Are all the microbes found in infected canals responsible for apical periodontitis, or are some merely bystanders? Knowing what we now know about biofilms, we understand that even seemingly harmless microbes can play essential roles in extracellular matrix formation and food chains [5].

These insights paint a complex picture of the challenges posed by infections in both general medicine and dentistry. Mechanical removal of the biofilm from surfaces is the most logical approach. In restorative dentistry, this often means debriding affected surfaces. Periodontists have long emphasized the importance of calculus removal and root planing as the foundation of any periodontal treatment. In endodontics, we naturally focus on shaping the canal as the main step in biofilm removal. However, studies from the last few decades are sobering: even with aggressive canal preparation using rotary nickel-titanium instruments, 25–35% of canal surfaces remain untouched [6]. It is crucial to remember that the main goal of instrumentation is shaping — actual cleaning largely depends on irrigation and intra-canal antisepsis.

With the introduction of the term "biofilm," many researchers began seeking antidotes. Two main directions emerged: the development of new technologies and reevaluation of traditional agents in the context of biofilm. One of the most promising methods is photodynamic therapy (PDT or PAD). Originally developed in oncology, this technique uses non-toxic dyes called photosensitizers that bind to malignant or precancerous cells and are activated by low-energy laser light, producing reactive oxygen species and free radicals that destroy the cells [7].

In endodontics, methylene blue or toluidine blue is typically used as the photosensitizer, which binds to the outer surfaces of microbes. A low-energy laser (CO₂) with a wavelength of 665 nm is then applied. This leads to bacterial destruction. While the method is 100% effective on planktonic bacteria, biofilms prevent the dye from reaching deeper layers. Therefore, many researchers [8] conclude that this method can serve as a strong adjunct but not as a standalone solution [9].

Other approaches, such as electrochemically activated water [10] or ozone systems [11], have unfortunately failed to prove effective against biofilms. Researchers reexamining traditional irrigants in the context of biofilms unanimously agree that sodium hypochlorite (NaOCl) is the most effective [12, 13]. Its crucial property is the ability to dissolve the organic matrix — in this case, the extracellular matrix of the biofilm — allowing it to penetrate deeper into the biofilm. Modern high-quality endodontic care is impossible without NaOCl irrigation. Naturally, methods that enhance NaOCl's effectiveness — such as passive ultrasonic irrigation — are of great interest to researchers.

Based on scientific evidence that calcium hydroxide (Ca(OH)₂) can dissolve organic tissues [14], it also makes sense to use it in cases involving complex anatomy and chronic infections.

In the future, the most exciting direction may be the development of biological infection control methods, based on decoding microbial communication and managing biofilms through signal molecules or targeted disruption of key bacteria vital to biofilm structure and function.

In summary, we must continue to study biofilms in depth, keeping up with discoveries not only in dental research but also in general microbiology and medicine. When evaluating studies that claim antibacterial efficacy of various agents, we must always check whether the tests were conducted on biofilms or only on planktonic microbes.