The development of a small-scale biofilm model suitable for studying the effects of antibiotics on biofilms of gram-negative bacteria

Microbial fuel cell compared to a chemostat

Microbial Fuel Cells (MFCs) represent a green and sustainable energy conversion system that integrate bacterial biofilms within an electrochemical two-electrode set-up to produce electricity from organic waste. In this review, we focus on a novel exploratory model, regarding "thin" biofilms forming on highly perfusable (non-diffusible) anodes in small-scale, continuous flow MFCs due to the unique properties of the electroactive biofilm. We discuss how this type of MFC can behave as a chemostat in fulfilling common properties including steady state growth and multiple steady states within the limit of biological physicochemical conditions imposed by the external environment. With continuous steady state growth, there is also continuous metabolic rate and continuous electrical power production, which like the chemostat can be controlled. The model suggests that in addition to controlling growth rate and power output by changing the external resistive load, it will be possible instead to change the flow rate/dilution rate.

Microbial fuel cells and their electrified biofilms

Bioelectrochemical systems (BES) represent a wide range of different biofilm-based bioreactors that includes microbial fuel cells (MFCs), microbial electrolysis cells (MECs) and microbial desalination cells (MDCs). The first described bioelectrical bioreactor is the Microbial Fuel Cell and with the exception of MDCs, it is the only type of BES that actually produces harvestable amounts of electricity, rather than requiring an electrical input to function. For these reasons, this review article, with previously unpublished supporting data, focusses primarily on MFCs. Of relevance is the architecture of these bioreactors, the type of membrane they employ (if any) for separating the chambers along with the size, as well as the geometry and material composition of the electrodes which support biofilms. Finally, the structure, properties and growth rate of the microbial biofilms colonising anodic electrodes, are of critical importance for rendering these devices, functional living 'engines' for a wide range of applications.

Discovery, development and exploitation of steady-state biofilms

Early in vitro biofilm models go back even beyond the invention of the word 'biofilm'. In the dental field, biofilms were simply known as dental plaque and many of the first in vitro models were termed 'artificial mouth microcosm plaques'. The purpose of this review is to highlight important elements of research from over the years regarding in vitro biofilm models, including data from our own laboratories. This helps us to interpret the models and point the way to the future development of biofilm testing. Many hypotheses regarding biofilm phenomena, particularly ecology, metabolism and physiology of volatile sulphur compounds (VSCs) and volatile organic compound (VOC) production could potentially be supported or disproved. In this way, the methods we use for screening biologically active agents including inhibitors, biocides and antimicrobial compounds in general can be improved. Hopefully, any lessons learnt in the past may be of value for the future. In this review, we focus around the need for growth rate controlled long-term biofilms; being continuously monitored using recent technical advances in bioluminescence, selective real-time electrodes, pH electrodes and continuous on-line analysis of the gas phase (both qualitatively and quantitatively). These features allow for accurate determination of growth rate and/or metabolic rate as well as pave the way towards automated assays and fine control of metabolism; impossible to achieve according to conventional biofilm theory. We also attempt to address the questions; can biofilm systems be improved to maintain long term 'real' or 'true' steady states over weeks or months, or are we limited to quasi-steady state systems for a limited period of time.

Hybrid combinations containing natural products and antimicrobial drugs that interfere with bacterial and fungal biofilms

BACKGROUND

Biofilms contribute to the pathogenesis of many chronic and difficult-to eradicate infections whose treatment is complicated due to the intrinsic resistance to conventional antibiotics. As a consequence, there is an urgent need for strategies that can be used for the prevention and treatment of biofilm-associated infections. The combination therapy comprising an antimicrobial drug with a low molecular weight (MW) natural product and an antimicrobial drug (antifungal or antibacterial) appeared as a good alternative to eradicate biofilms.

PURPOSE

The aims of this review were to perform a literature search on the different natural products that have showed the ability of potentiating the antibiofilm capacity of antimicrobial drugs, to analyze which are the antimicrobial drugs most used in combination, and to have a look on the microbial species most used to prepare biofilms.

RESULTS

Seventeen papers, nine on combinations against antifungal biofilms and eight against antibacterial biofilms were collected. Within the text, the following topics have been developed: breaf history of the discovery of biofilms; stages in the development of a biofilm; the most used methodologies to assess antibiofilm-activity; the natural products with capacity of eradicating biofilms when acting alone; the combinations of low MW natural products with antibiotics or antifungal drugs as a strategy for eradicating microbial biofilms and a list of the low MW natural products that potentiate the inhibition capacity of antifungal and antibacterial drugs against biofilms.

CONCLUSIONS AND PERSPECTIVES

Regarding combinations against antifungal biofilms, eight over the nine collected works were carried out with in vitro studies while only one was performed with in vivo assays by using Caenorhabditis elegans nematode. All studies use biofilms of the Candida genus. A 67% of the potentiators were monoterpenes and sesquiterpenes and six over the nine works used FCZ as the antifungal drug. The activity of AmpB and Caspo was enhanced in one and two works respectively. Regarding combinations against bacterial biofilms, in vitro studies were performed in all works by using several different methods of higher variety than the used against fungal biofilms. Biofilms of both the gram (+) and gram (-) bacteria were prepared, although biofilm of Staphylococcus spp. were the most used in the collected works. Among the discovered potentiators of antibacterial drugs, 75% were terpenes, including mono, di- and triterpenes, and, among the atibacterial drugs, several structurally diverse types were used in the combinations: aminoglycosides, β-lactams, glucopeptides and fluoroquinolones. The potentiating capacity of natural products, mainly terpenes, on the antibiofilm effect of antimicrobial drugs opens a wide range of possibilities for the combination antimicrobial therapy. More in vivo studies on combinations of natural products with antimicrobial drugs acting against biofilms are highly required to cope the difficult to treat biofilm-associated infections.

Review: Antimicrobial efficacy validation using in vitro and in vivo testing methods

Pre-clinical antimicrobial validation testing for single and combination products, and parameters that should be considered when testing the antimicrobial performance of a medical device, are discussed. Guidance is provided on key elements required for in vitro and in vivo antimicrobial validation, including validation of microbial growth, microbial recovery, neutralization, and antimicrobial activity. An important consideration, both in terms of practicality and economics, is designing in vitro studies that bridge to in vivo testing: A representative in vitro model is used to generate data on many clinically relevant microorganisms, and then one microorganism is selected for use in in vivo testing. If the in vivo results correlate to the in vitro results, it can reasonably be extrapolated that the same would be true for the remaining microorganisms tested in vitro. Thus, the selection of relevant in vitro models for testing is critical for successful antimicrobial validation testing.

Colonization of Abiotic Surfaces

E. coli is a relevant model organism for the study of the molecular mechanisms underlying surface colonization. This process requires two essential steps: adhesion to a surface, followed by cell-cell adhesion counteracting the shear forces of the environment, with both steps contributing to the formation of a biofilm. This review provides an overview of the current knowledge of the genetic analyses aiming at identifying factors involved in both of these two highly related biological processes, with a particular emphasis on studies performed in Escherichia coli K-12. Bacterial adhesion to abiotic surfaces is likely to be highly dependent on the physicochemical and electrostatic interactions between the bacterial envelope and the substrate, which is itself often conditioned by the fluids to which it is exposed. Genetic analyses have revealed the diversity of genetic factors in E. coli that participate in colonization and biofilm formation on abiotic surfaces. The study of surface colonization and biofilm formation represents a rapidly expanding field of investigation. The use of E. coli K-12 to investigate the genetic basis of bacterial interactions with surfaces has led to the identification of a large repertoire of adhesins whose expression is subject to a complex interplay between regulatory networks. Understanding how E. coli K-12 behaves in complex biofilm communities will certainly contribute to an understanding of how natural commensal and pathogenic E. coli isolates develop.

Macrolides decrease the minimal inhibitory concentration of anti-pseudomonal agents against Pseudomonas aeruginosa from cystic fibrosis patients in biofilm

BACKGROUND

Biofilm production is an important mechanism for bacterial survival and its association with antimicrobial resistance represents a challenge for the patient treatment. In this study we evaluated the in vitro action of macrolides in combination with anti-pseudomonal agents on biofilm-grown Pseudomonas aeruginosa recovered from cystic fibrosis (CF) patients.

RESULTS

A total of 64 isolates were analysed. The biofilm inhibitory concentration (BIC) results were consistently higher than those obtained by the conventional method, minimal inhibitory concentration, (MIC) for most anti-pseudomonal agents tested (ceftazidime: P = 0.001, tobramycin: P = 0.001, imipenem: P < 0.001, meropenem: P = 0.005). When macrolides were associated with the anti-pseudomonal agents, the BIC values were reduced significantly for ceftazidime (P < 0.001) and tobramycin (P < 0.001), regardless the concentration of macrolides. Strong inhibitory quotient was observed when azithromycin at 8 mg/L was associated with all anti-pseudomonal agents tested in biofilm conditions.

CONCLUSIONS

P. aeruginosa from CF patients within biofilms are highly resistant to antibiotics but macrolides proved to augment the in vitro activity of anti-pseudomonal agents.

Chapter 4: In vitro biofilm models: an overview

Observing naturally occurring biofilms in situ or ex situ has revealed the wide distribution of sessile microbial communities. The ubiquity, variety and complexity of biofilms is now widely accepted by microbiologists. While they are associated with many beneficial functions such as nutrient cycling, bioremediation and colonization resistance, adverse effects including recalcitrance, their involvement in industrial fouling, contamination and infection have made biofilms a priority research topic. We know that most biofilms, other than within certain infections and laboratory flasks, are composed of multiple species and that there is arguably no unifying biofilm architecture. Biofilms do however share certain properties including the presence of gradients of nutrients, gasses and metabolic products, relatively increased cell density, deposition of extracellular polymeric substances and marked recalcitrance towards antimicrobial treatments. Much of our understanding of biofilm physiology and micro-ecology originates from experiments using in vitro biofilm models. Broadly speaking, such models may be used to replicate environmental conditions within the laboratory or to focus on selected variables such a growth rate or fluid flow, etc. This chapter provides an overview of some commonly used biofilm models including microtitre plate systems, flow cells, the constant depth film fermenter, annular reactors and the perfused biofilm fermenter. While perfused biofilm fermenters, in particular, enable growth rate to be controlled within thin, relatively homogenous, quasi steady-state biofilms through modulation of flow rate nutrient availability, other models provide representative modelling of in situ conditions where steady states may be uncommon.

In vitro models for oral malodor

A model is a representation of some real phenomena and contains aspects or elements of the real system to be modeled. The model reflects (or duplicates) the type of behavior (or mechanisms) seen in the real system. The main characteristic of any model is the mapping of elements or parameters found in the system being studied (e.g. tongue dorsum biofilm in situ) on to the model being devised (e.g. laboratory perfusion biofilm). Such parameters include correct physico-chemical (abiotic) conditions as well as biotic conditions that occur in both model and reality. The main purpose of a model is to provide information that better explains the processes observed or thought to occur in the real system. Such models can be abstract (mental, conceptual, theoretical, mathematical or computational) or 'physical', e.g. in the form of a real disaggregated in vitro system or laboratory model. A wide range of different model systems have been used in oral biofilm research. These will be briefly reviewed with special emphasis on those models that have contributed most to knowledge in breath odor research. The different model systems used in breath odor research are compared. Finally, the requirements for developing an overall 'bad breath model' from considering the processes as a whole (real oral cavity, substrates in saliva, biotransformation by tongue microflora, odor gases in the breath) and extending this to the detection of malodor by the human nose will be outlined and discussed.

In vitrobiofilm model for studying tongue flora and malodour

AIMS

To develop a perfusion biofilm system to model tongue biofilm microflora and their physiological response to sulfur-containing substrates (S-substrates) in terms of volatile sulfide compound (VSC) production.

METHODS AND RESULTS

Tongue-scrape inocula were used to establish in vitro perfusion biofilms which were examined in terms of ecological composition using culture-dependent and independent (PCR-DGGE) approaches. VSC-specific activity of cells was measured by a cell suspension assay, using a portable industrial sulfide monitor which was also used to monitor VSC production from biofilms in situ. Quasi steady states were achieved by 48 h and continued to 96 h. The mean (+/-SEM) growth rate for 72-h biofilms (n=4) was micro=0.014 h(-1) (+/-0.005 h(-1)). Comparison of biofilms, perfusate and original inoculum showed their ecological composition to be similar (Pearson coefficient>0.64). Perfusate and biofilm cells derived from the same condition (co-sampled) were equivalent with regard to VSC-specific activities which were up-regulated in the presence of S-substrates.

CONCLUSIONS

The model maintained a stable tongue microcosm suitable for studying VSC production; biofilm growth in the presence of S-substrates up-regulated VSC activity.

SIGNIFICANCE AND IMPACT OF THE STUDY

The method is apt for studying ecological and physiological aspects of oral biofilms and could be useful for screening inhibitory agents.

Effect of shear stress on growth, adhesion and biofilm formation of Pseudomonas aeruginosa with antibiotic-induced morphological changes

The aim of this study was to investigate the effect of shear stress and antibiotic-induced morphological changes on the growth, adhesion and biofilm formation ability of Pseudomonas aeruginosa. A modified microtitre plate assay was used to quantify adhesion, biofilm formation and planktonic culture density of P. aeruginosa ATCC 27853 under the effect of 0.5x minimal inhibitory concentrations (MICs) of piperacillin/tazobactam, imipenem and meropenem. Hydrodynamic conditions were achieved by orbital shaking at 250 rpm with the presence of a glass bead in each microtitre well. These conditions decreased adhesion and biofilm formation abilities, increased planktonic culture density over 1h and decreased planktonic culture density over 16 h for bacteria with antibiotic-induced morphological changes in comparison with static conditions. Our results demonstrate the importance of using a high-throughput dynamic model to assess the adhesion and biofilm formation behaviour of P. aeruginosa with antibiotic-induced morphological changes and suggest the possible use of sub-MIC antibiotics in clinical applications to prevent infections acquired by haematogenous spread. This dynamic model provides a better simulation of in vivo conditions of adhesion and biofilm formation of P. aeruginosa with altered morphologies induced by beta-lactam antibiotics.

Phenotypic antibiotic tolerance of Staphylococcus aureus in implant-related infections: relationship with in vitro colonization of artificial surfaces

Antibiotic therapy of deep-seated staphylococcal infections, especially when they are associated with foreign implants, such as orthopedic prostheses and permanently inserted catheters, is a difficult challenge. Semi-synthetic penicillins, glycopeptides and quinolones are found effective when given prophylactically in clinical and experimental trials of implant-related infections, but are frequently poorly effective after implant-related infections are established. Thus, removal of the medical devices is often required to obtain cure. The failure of antibiotic therapy to cure staphylococcal foreign body infections may arise from a broad-spectrum phenotypic tolerance to different classes of antimicrobial agents, whose molecular basis and physiological mechanisms are poorly understood.

Metabolic activity of Staphylococcus epidermidis is high during initial and low during late experimental foreign-body infection

Foreign-body infection (FBI) is notoriously resistant to eradication by antibiotic treatment. It is hypothesized that reduced bacterial metabolic activity contributes to this resistance. We examined the metabolic activity of Staphylococcus epidermidis in 204 samples recovered during in vitro foreign-body colonization and in 424 samples recovered during in vivo FBI in a rat model. Metabolic activity was measured by determining the amount of 16S rRNA per genome by quantitative PCR. The initial foreign-body-associated growth proved to be a metabolically active process, both in vitro and in vivo. The initial 16S rRNA content was similar to that observed during in vitro exponential-growth phase. However, during late in vivo FBI, a 114-fold (P << 0.0001) decrease in the 16S rRNA content was observed, indicating that there was markedly decreased metabolic activity. This decreased metabolic activity during late FBI can explain at least in part why such infections are so difficult to eradicate with conventional antibiotic treatment.

Bacterial adhesion: seen any good biofilms lately?

The process of surface adhesion and biofilm development is a survival strategy employed by virtually all bacteria and refined over millions of years. This process is designed to anchor microorganisms in a nutritionally advantageous environment and to permit their escape to greener pastures when essential growth factors have been exhausted. Bacterial attachment to a surface can be divided into several distinct phases, including primary and reversible adhesion, secondary and irreversible adhesion, and biofilm formation. Each of these phases is ultimately controlled by the expression of one or more gene products. Ultrastructurally, the mature bacterial biofilm resembles an underwater coral reef containing pyramidal or mushroom-shaped microcolonies of organisms embedded within an extracellular glycocalyx, with channels and cavities to allow the exchange of nutrients and waste. The biofilm protects its inhabitants from predators, dehydration, biocides, and other environmental extremes while regulating population growth and diversity through primitive cell signals. From a physiological standpoint, surface-bound bacteria behave quite differently from their planktonic counterparts. Recognizing that bacteria naturally occur as surface-bound and often polymicrobic communities, the practice of performing antimicrobial susceptibility tests using pure cultures and in a planktonic growth mode should be questioned. That this model does not reflect conditions found in nature might help explain the difficulties encountered in the management and treatment of biomedical implant infections.

Standardized method for in vitro antifungal susceptibility testing of Candida albicans biofilms

Candida albicans is implicated in many biomaterial-related infections. Typically, these infections are associated with biofilm formation. Cells in biofilms display phenotypic traits that are dramatically different from those of their free-floating planktonic counterparts and are notoriously resistant to antimicrobial agents. Consequently, biofilm-related infections are inherently difficult to treat and to fully eradicate with normal treatment regimens. Here, we report a rapid and highly reproducible microtiter-based colorimetric assay for the susceptibility testing of fungal biofilms, based on the measurement of metabolic activities of the sessile cells by using a formazan salt reduction assay. The assay was used for in vitro antifungal susceptibility testing of several C. albicans strains grown as biofilms against amphotericin B and fluconazole and the increased resistance of C. albicans biofilms against these antifungal agents was demonstrated. Because of its simplicity, compatibility with a widely available 96-well microplate platform, high throughput, and automation potential, we believe this assay represents a promising tool for the standardization of in vitro antifungal susceptibility testing of fungal biofilms.

An evaluation of the potential of the multiple antibiotic resistance operon (mar) and the multidrug efflux pump acrAB to moderate resistance towards ciprofloxacin in Escherichia coli biofilms

The chromosomal multiple antibiotic resistance operon, mar, is widely represented amongst Gram-negative bacteria and has been implicated in resistance towards oxidative stress agents, organic solvents and a large number of structurally unrelated antimicrobial agents. The major mechanism associated with such increased resistance is an upregulation of the efflux pump acrAB. Growth as a biofilm is often associated with similar generalized reductions in susceptibility to inimical agents. Escherichia coli K12 (AG100), an isogenic mutant of AG100 constitutive for mar expression (AG102) and an isolate deleted of the mar locus (MCH164) were grown as biofilms in cellulose-fibre depth filters and perfused with a simple salts, minimal medium (CDM) over 120 h. Biofilms were exposed to various concentrations of ciprofloxacin (0.004, 0.015 and 0.1 mg/L) for 42 h. The numbers of viable cells within the perfusate and within the biofilm were estimated throughout. Whereas no differences were seen between the wild-type and mar-deleted isolates, that constitutive for mar displayed reduced susceptibility to ciprofloxacin at concentrations of 0.004 mg/L (MIC for AG100 was 0.0052 mg/L). Similar antibiotic perfusion experiments were conducted using isolates in which the efflux pump acrAB was either deleted (AG100-A) or constitutively expressed (AG100-B). Exposure of AG100-A biofilms to ciprofloxacin at 0.004 and 0.1 mg/L showed similar susceptibilities to those seen in the wild-type (AG100) and mar-deleted (MCH164) isolates and suggested that acrAB was not induced within the attached population. On the other hand, constitutive expression of acrAB (AG100-B) protected biofilms against the lower concentration of ciprofloxacin used (0.004 mg/L). This protection was again lost at concentrations of 0.1 mg/L. Overall, these results show that ciprofloxacin resistance in biofilms is not mediated by the upregulation of the mar or acrAB operons.