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Candida albicans SNO1 and SNZ1 expressed in stationary-phase planktonic yeast cells and base of biofilm.

The Candida albicans homologues of the most studied Saccharomyces cerevisiae stationary-phase genes, SNO1 and SNZ1, were used to test the hypothesis that, within a biofilm, some cells reach stationary phase within continuously fed, as well as static, C. albicans biofilms grown on dental acrylic. The authors first studied the expression patterns of these two genes in planktonic growth conditions. Using real-time RT-PCR (RT-RTPCR), increased peak expression of both SNZ1 and SNO1 was observed at 5 and 6 days, respectively, in C. albicans grown in suspension culture. SNZ1-yellow fluorescent protein (YFP) and SNO1-YFP were constructed to study expression at the cellular level and protein localization in C. albicans. Snz1p-YFP and Sno1p-YFP localized to the cytoplasm with maximum expression (>90 %) at 5 and 6 days, respectively, in planktonic conditions. When yeast growth was reinitiated, loss of fluorescence began immediately. Germ tubes and hyphae were non-fluorescent. Pseudohyphae began appearing at 9 days in planktonic yeast culture and expressed each protein by 11 days; however, the cells budding from pseudohyphae were not fluorescent. Biofilm was formed in vitro under either static or continuously fed conditions. Increased expression of the two genes was shown by RT-RTPCR, beginning by day 3 and increasing through to day 15 (continuously fed biofilm). Only the bottommost layer of acrylic-adhered cells in the biofilm showed 25 and 40 % fluorescence at 6 and 15 days, respectively. These observations suggest that only a few cells in C. albicans biofilms express genes associated with the planktonic stationary phase and that these are found at the bottom of the biofilm adhered to the surface.

Biofilms↗

Contribution of the SirA regulon to biofilm formation in Salmonella enterica serovar Typhimurium.

Orthologues of the Salmonella enterica serovar Typhimurium (S. typhimurium) BarA/SirA two-component system are important for biofilm formation and virulence in many gamma-Proteobacteria. In S. typhimurium, SirA activates the csrB and csrC carbon storage regulatory RNAs and the virulence gene regulators hilA and hilC. The regulatory RNAs antagonize the activity of the CsrA protein, allowing translation of those same virulence genes, and inhibiting the translation of flagellar genes. In this report, it was determined that SirA and the Csr system also control the fim operon that encodes type 1 fimbriae. sirA orthologues in other bacterial species, and the fim operon of S. typhimurium, are known to play a role in biofilm formation; therefore, all members of the S. typhimurium sirA regulon were tested for in vitro biofilm production. A sirA mutant, a csrB csrC double mutant, and a fimI mutant, were all defective in biofilm formation. Conversely, inactivation of flhDC increased biofilm formation. Therefore, SirA activates csrB, csrC and the fim operon to promote biofilm formation. In turn, csrB and csrC promote the translation of the fim operon, while at the same time inhibiting the translation of flagella, which are inhibitory to biofilm formation.

Bacterial Proteins↗

Inactivation of Escherichia coli O157:H7 in biofilm on stainless steel by treatment with an alkaline cleaner and a bacteriophage.

AIMS: To determine the effectiveness of an alkaline cleaner used in food-processing plants and a lytic bacteriophage specific for Escherichia coli O157:H7 in killing wild type and rpoS-deficient cells of the pathogen in a biofilm. METHODS AND RESULTS: Wild type and rpoS-deficient cells were attached to stainless steel coupons (c. 7-8 log CFU per coupon) on which biofilms were developed during incubation at 22 degrees C for 96 h in M9 minimal salts media (MSM) with one transfer to fresh medium. Coupons were treated with 100 and 25% working concentrations of a commercial alkaline cleaner (pH 11.9, with 100 microg ml(-1) free chlorine) used in the food industry, chlorine solutions (50 and 100 microg ml(-1) free chlorine), or sterile deionized water (control) at 4 degrees C for 1 and 3 min. Treatment with 100% alkaline cleaners reduced populations by 5-6 log CFU per coupon, a significant (P < or = 0.05) reduction compared with treatment with water. Initial populations (2.6 log CFU per coupon) of attached cells of both strains were reduced by 1.2 log CFU per coupon when treated with bacteriophage KH1 (7.7 log PFU ml(-1)) for up to 4 days at 4 degrees C. Biofilms containing low populations (2.7-2.8 log CFU per coupon) of wild type and rpoS-deficient cells that had developed for 24 h at 22 degrees C were not decreased by more than 1 log CFU per coupon when treated with KH1 (7.5 log PFU ml(-1)) at 4 degrees C. CONCLUSIONS: Higher numbers of cells of E. coli O157:H7 in biofilms are killed by treatment with an alkaline cleaner than with hypochlorite alone, possibly through a synergistic mechanism of alkaline pH and hypochlorite. Populations of cells attached on coupons were reduced by treating with bacteriophage but cells enmeshed in biofilms were protected. SIGNIFICANCE AND IMPACT OF THE STUDY: The alkaline pH, in combination with hypochlorite, in a commercial cleaner is responsible for killing E. coli O157:H7 in biofilms. Treatment with bacteriophage KH1 reduces populations of cells attached to coupon surfaces but not cells in biofilms.

Alkalies↗

Fatty acid analysis and spoilage potential of biofilms from two breweries.

AIM: The microbial composition of biofilms from different locations of beer bottling plants were compared based on fatty acid profiles and correlated with the product-spoiling potential of these biofilms. METHODS AND RESULTS: The whole cell fatty acid profiles of 78 biofilms from bottling plants of two breweries were analysed. About half of the lipid profiles were dominated by oleic and linoleic acid, which refer to a high proportion of yeasts. In addition, more than half of all samples contained dimethylacetals indicating the presence of strictly anaerobic bacteria. Typical fatty acids for potentially beer-spoiling genera were detected in three biofilms. The majority of the biofilms contained no beer-spoiling organisms, as shown by inoculation experiments in beer. CONCLUSIONS: Biofilms from different locations of bottling plants were different with respect to their microbial composition. Potentially product-spoiling populations could be detected in a small number of samples. SIGNIFICANCE AND IMPACT OF THE STUDY: Biofilms on industrial plants can be characterized by a fast and cultivation-independent method with respect to overall microbial composition and presence of potentially product-spoiling micro-organisms.

Bacteria↗

Influence of starvation, surface attachment and biofilm growth on the biocide susceptibility of the biodeteriogenic yeast Aureobasidium pullulans.

AIM: To investigate the effect of starvation, surface attachment and growth in a biofilm on the susceptibility of Aureobasidium pullulans to the biocides 2-n-octyl-4-isothiazolin-3-one (OIT) and sodium hypochlorite (NaOCl). METHODS AND RESULTS: Fluorescence loss from a green fluorescent protein (GFP)-transformed strain was used to monitor real-time loss in viability as previously described in situ in 96-well plates. Exponential phase, yeast-like (YL) cells were settled in the bottom of the wells as a low-density monolayer (LDM) and were susceptible to all biocide concentrations (25-100 mug ml(-1)). The exponential phase YL cells were either starved for 48 h in suspension or starved for 48 h as LDMs in the wells. Starvation in both cases led to a small reduction in susceptibility to the biocides. In contrast, 48-h biofilms grown in malt extract broth showed an apparent lack of susceptibility to 25 and 50 mug ml(-1) OIT and to 25-100 mug ml(-1) NaOCl. However, when the OIT concentration was increased to compensate for the higher cell density in the biofilm, the biofilms were found to be equally susceptible to the LDM. CONCLUSIONS: Starvation of A. pullulans YL cells either in suspension or as attached LDM resulted in a decrease in susceptibility to low concentrations of both OIT and NaOCl while the apparent reduced susceptibility of mature biofilms was due to the increase in biofilm cell density rather than true biofilm resistance per se. SIGNIFICANCE AND IMPACT OF THE STUDY: Monitoring fluorescence loss from the GFP-transformed strain of A. pullulans can be used as a fast and reliable method for monitoring cell death in real time as a response to biocide and antimicrobial challenge.

Biodegradation, Environmental↗

Role of the GGDEF protein family in Salmonella cellulose biosynthesis and biofilm formation.

Salmonella enterica serovar Typhimurium is capable of producing cellulose as the main exopolysaccharide compound of the biofilm matrix. It has been shown for Gluconacetobacter xylinum that cellulose biosynthesis is allosterically regulated by bis-(3',5') cyclic diguanylic acid, whose synthesis/degradation depends on diguanylate cyclase/phosphodiesterase enzymatic activities. A protein domain, named GGDEF, is present in all diguanylate cyclase/phosphodiesterase enzymes that have been studied to date. In this study, we analysed the molecular mechanisms responsible for the failure of Salmonella typhimurium strain SL1344 to form biofilms under different environmental conditions. Using a complementation assay, we were able to identify two genes, which can restore the biofilm defect of SL1344 when expressed from the plasmid pBR328. Based on the observation that one of the genes, STM1987, contains a GGDEF domain, and the other, mlrA, indirectly controls the expression of another GGDEF protein, AdrA, we proceeded on a mutational analysis of the additional GG[DE]EF motif containing proteins of S. typhimurium. Our results demonstrated that MlrA, and thus AdrA, is required for cellulose production and biofilm formation in LB complex medium whereas STM1987 (GGDEF domain containing protein A, gcpA) is critical for biofilm formation in the nutrient-deficient medium, ATM. Insertional inactivation of the other six members of the GGDEF family (gcpB-G) showed that only deletion of yciR (gcpE) affected cellulose production and biofilm formation. However, when provided on plasmid pBR328, most of the members of the GGDEF family showed a strong dominant phenotype able to bypass the need for AdrA and GcpA respectively. Altogether, these results indicate that most GGDEF proteins of S. typhimurium are functionally related, probably by controlling the levels of the same final product (cyclic di-GMP), which include among its regulatory targets the cellulose production and biofilm formation of S. typhimurium.

Amino Acid Motifs↗

The Yak1p kinase controls expression of adhesins and biofilm formation in Candida glabrata in a Sir4p-dependent pathway.

Biofilm is the predominant type of microbial development in natural environments, and potentially represents a major form of resistance or source of recurrence during host infection. Although a large number of studies have focussed on the genetics of bacterial biofilm formation, very little is known about the genes involved in this type of growth in fungi. A genetic screen for Candida glabrata Biofilm mutants was performed using a 96-well plate model of biofilm formation. Study of the isolated mutant strains allowed the identification of four genes involved in biofilm formation (RIF1, SIR4, EPA6 and YAK1). Epa6p is a newly identified adhesin required for biofilm formation in this pathogenic yeast. EPA6 and its close paralogue EPA7 are located in subtelomeric regions and their transcription is regulated by Sir4p and Rif1p, two proteins involved in subtelomeric silencing. Biofilm growth conditions induce the transcription of EPA6 and EPA7: this is dependent on the presence of an intact subtelomeric silencing machinery and is independent of the Mpk1p signalling pathway. Finally, the kinase Yak1p is required for expression of both adhesin genes and acts through a subtelomeric silencing machinery-dependent pathway.

Biofilms↗

A characterization of DNA release in Pseudomonas aeruginosa cultures and biofilms.

Pseudomonas aeruginosa produces extracellular DNA which functions as a cell-to-cell interconnecting matrix component in biofilms. Comparison of extracellular DNA and chromosomal DNA by the use of polymerase chain reaction and Southern analysis suggested that the extracellular DNA is similar to whole-genome DNA. Evidence that the extracellular DNA in P. aeruginosa biofilms and cultures is generated via lysis of a subpopulation of the bacteria was obtained through experiments where extracellular beta-galactosidase released from lacZ-containing P. aeruginosa strains was assessed. Experiments with the wild type and lasIrhlI, pqsA, pqsL and fliMpilA mutants indicated that the extracellular DNA is generated via a mechanism which is dependent on acyl homoserine lactone and Pseudomonas quinolone signalling, as well as on flagella and type IV pili. Microscopic investigation of flow chamber-grown wild-type P. aeruginosa biofilms stained with different DNA stains suggested that the extracellular DNA is located primarily in the stalks of mushroom-shaped multicellular structures, with a high concentration especially in the outer part of the stalks forming a border between the stalk-forming bacteria and the cap-forming bacteria. Biofilms formed by lasIrhlI, pqsA and fliMpilA mutants contained less extracellular DNA than biofilms formed by the wild type, and the mutant biofilms were more susceptible to treatment with sodium dodecyl sulphate than the wild-type biofilm.

Biofilms↗

Yersinia pestis YrbH is a multifunctional protein required for both 3-deoxy-D-manno-oct-2-ulosonic acid biosynthesis and biofilm formation.

Bubonic plague is transmitted by fleas whose feeding is blocked by a Yersinia pestis biofilm in the digestive tract. Y. pestis also block feeding of Caenorhabditis elegans by forming a biofilm on the nematode head, making the nematode an experimentally tractable surrogate for fleas to study plague transmission. Arabinose 5-phosphate isomerase (API), encoded by Y. pestis yrbH, catalyses the conversion of ribulose 5-phosphate into arabinose 5-phosphate (A5P), the first committed step in the 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) biosynthesis pathway. Here we show that Y. pestis YrbH is a multifunctional protein required for both Kdo biosynthesis and biofilm formation on C. elegans. The YrbH protein contains four functional components: biofilm-related region 1 (B1), a sugar isomerase domain (SIS), biofilm-related region 2 (B2) and a cystathionine beta-synthase domain pair (CBS). B1, SIS and B2 are all required for API function, but any of the three is sufficient for a biofilm-related function. The CBS domain appears to negatively regulate the biofilm-related function.

Aldose-Ketose Isomerases↗

Susceptibility of biofilms of Streptococcus sanguis to chlorhexidine gluconate and cetylpyridinium chloride.

Biofilms of Streptococcus sanguis and planktonic cells of the organism were exposed to chlorhexidine gluconate and cetylpyridinium chloride, at concentrations used clinically, and survivors enumerated. S. sanguis exhibited a lower susceptibility to both antiseptics when it comprised a biofilm than when the organism was in the planktonic form. No viable bacteria were detectable after 5 min of exposure of planktonic cells to 0.2% (w/v) chlorhexidine gluconate or 0.05% (w/v) cetylpyridinium chloride, whereas viable bacterial survived in biofilms of S. sanguis even after exposure to these agents for 4 h. Older biofilms (7 days old) had similar susceptibilities to the antiseptics as younger biofilms (4 days old). Chlorhexidine achieved kills corresponding to approximately a 2 log10 reduction in the viable count of biofilms, containing approximately 10(7) colony-forming units after 5 min of incubation, whereas the corresponding kills achieved by cetylpyridinium chloride amounted to approximately a 1 log10 reduction. However, on a molar basis, cetylpyridinium chloride was the more effective of the two antiseptics. Minimum inhibitory concentration determinations showed chlorhexidine gluconate to be more effective against S. sanguis than cetylpyridinium chloride. The results of this study have revealed that the minimum inhibitory concentration is not a reliable predictor of the relative effectiveness of antimicrobial agents against S. sanguis biofilms.

Anti-Infective Agents, Local↗

The effects of tetracycline, minocycline, doxycycline and ofloxacin on Prevotella intermedia biofilm.

Prevotella intermedia, a black-pigmented, anaerobic, gram-negative bacterium, is associated with various type of periodontitis. Antibiotic treatments via a systemic or local route have been reported as being useful for treating periodontal disease. The purpose of this study was to examine the effects of four antibiotics, tetracycline (TET), minocycline (MINO), doxycycline (DOXY) and ofloxacin (OFLX) on P. intermedia biofilms at minimum inhibitory concentrations (MIC) from one-fold to 100-fold. MICs were determined for planktonic cells. Biofilm formation was determined with the crystal violet stain method and the bioactivities in the biofilms were determined with the adenosine triphosphate (ATP) -bioluminescent assay using a 96-well culture plate. At one-fold MIC, DOXY inhibited biofilm formation by P. intermedia ATCC 25611. Other antibiotics at one-fold MIC had no effects on the biofilm formation of tested bacterial strains. In P. intermedia ATCC 25611 biofilms, all the antibiotics tested showed inhibitory activities at five- to 100-fold MICs. In the biofilms of P. intermedia strains, except ATCC 25611, treated with three tetracycline antibiotics, the bioactivities were significantly increased, indicating the difficulties involved in designing antibiotic therapy for periodontal disease.

Adenosine Triphosphate↗

A framework for multidimensional modelling of activity and structure of multispecies biofilms.

Concepts from previous biofilm models were integrated to create a framework for the implementation of multidimensional (2D and 3D) multispecies biofilm models. The framework is here described at three levels: (i) mathematical representation of the processes involved in biofilm formation, (ii) numerical implementation into a computer program (freely available from our website http://www.biofilms.bt.tudelft.nl/frameworkMaterial) and (iii) using the program for the creation of biofilm models with multiple bacterial and solute species. An improved version of the individual-based modelling (IbM) that allows structured biomass was used. In this approach biomass composition may be discriminated into any number of particulate species, including extracellular polymeric substances (EPS) for which specific functionality was included. Detachment is also included, described as occurring at the biofilm surface with variable local rates derived from functions of state variables. The application of this modelling framework to a multispecies system with structured biomass is illustrated in a case study where the competition between an organism capable of accumulating polyhydroxybutyrate (PHB, an internal storage compound) and an EPS-producing organism in a two-species biofilm is analysed. Results illustrate that biofilms enriched in PHB-producing organisms may be obtained by supplying substrate intermittently in feast/famine cycles.

Bacteria↗

Candida biofilms on implanted biomaterials: a clinically significant problem.

In recent years there has been an increasing appreciation that microbial biofilms are ubiquitous, which has resulted in a number of studies on infectious diseases from a biofilm perspective. Biofilms are defined as structured microbial communities that are attached to a surface and encased in a matrix of exopolymeric material. A wide range of biomaterials used in clinical practice have been shown to support colonization and biofilm formation by Candida spp., and the increase in Candida infections in the last decades has almost paralleled the increase and widespread use of a broad range of medical implant devices, mainly in populations with impaired host defenses. Formation of Candida biofilms has important clinical repercussions because of their increased resistance to antifungal therapy and the ability of cells within biofilms to withstand host immune defenses. Further recognition and understanding of the role of Candida biofilms in human infection should help in the clinical management of these recalcitrant infections.

Biofilms↗

Protein expression by planktonic and biofilm cells of Streptococcus mutans.

Streptococcus mutans, a major causal agent of dental caries, functions in nature as a component of a biofilm on teeth (dental plaque) and yet very little information is available on the physiology of the organism in such surface-associated communities. As a consequence, we undertook to examine the synthesis of proteins by planktonic and biofilm cells growing in a biofilm chemostat at pH 7.5 at a dilution rate of 0.1 h(-1) (mean generation time=7 h). Cells were incubated with (14)C-labelled amino acids, the proteins extracted and separated by two-dimensional electrophoresis followed by autoradiography and computer-assisted image analysis. Of 694 proteins analysed, 57 proteins were enhanced 1.3-fold or greater in biofilm cells compared to planktonic cells with 13 only expressed in sessile cells. Diminished protein expression was observed with 78 proteins, nine of which were not expressed in biofilm cells. The identification of enhanced and diminished proteins by mass spectrometry and computer-assisted protein sequence analysis revealed that, in general, glycolytic enzymes involved in acid formation were repressed in biofilm cells, while biosynthetic processes were enhanced. The results show that biofilm cells possess novel proteins, of as yet unknown function, that are not present in planktonic cells.

Animals↗

The filamentation pathway controlled by the Efg1 regulator protein is required for normal biofilm formation and development in Candida albicans.

Candida albicans biofilms are structured microbial communities composed of a mixture of yeast cells and hyphal elements, suggesting a pivotal role for the dimorphic switch in the development of biofilms. We have used C. albicans mutants defective in genes involved in filamentation (Deltacph1, Deltaefg1, Deltahst7, and Deltacst20) and compared these mutants to wild-type strains to determine whether filamentation is an integral factor for biofilm formation. Scanning electron microscopy revealed that Deltacph1, Deltahst7 and Deltacst20 mutants were able to filament and form structured biofilms displaying three-dimensional architecture similar to those formed by wild-type strains. However, Deltaefg1 and Deltacph1/Deltaefg1 mutants were unable to filament and did not form biofilms, but rather sparse monolayers of loosely attached elongated, rod-like, cells. Antimicrobial susceptibility testing showed intrinsic resistance of all mutant strains to fluconazole and amphotericin B when attached to the surface of biomaterials. These results suggest that hyphal formation is pivotal for biofilm development in C. albicans. However, the sessile lifestyle associated with adherent cells confers antifungal resistance, regardless of coherent biofilm formation.

Amphotericin B↗

Alginate lyase enhances antibiotic killing of mucoid Pseudomonas aeruginosa in biofilms.

Once mucoid (alginate-producing) strains of Pseudomonas aeruginosa have become established in the respiratory tracts of cystic fibrosis patients they can rarely be eliminated by antibiotic treatment alone; we have investigated, in an in vitro biofilm system, the putative role of co-administration of alginate lyase with antibiotic. Biofilms were maintained in continuous flow culture in a medium resembling sputum from CF patients. Antibiotics and/or alginate lyase were added to some of the cultures. Biofilms of two mucoid CF strains of P. aeruginosa were, in most cases, not eradicated by a one-week course of treatment with 64 microg/ml of gentamicin; the same concentration of gentamicin, under the same conditions, led to the apparent elimination of all biofilms of non-mucoid derivatives of these strains. When alginate lyase and gentamicin were administered together the apparent elimination of mucoid bacteria from biofilms was achieved, whereas the mucoid bacteria in most control biofilms treated only with gentamicin persisted. Ceftazidime treatment of biofilms was more effective against those containing the non-mucoid strains than those with mucoid strains. These studies support the view that co-administration of antibiotics with alginate lyase, which degrades the exopolysaccharide produced by mucoid strains of P aeruginosa, might benefit CF patients by increasing the efficacy of antibiotic in the respiratory tract.

Anti-Bacterial Agents↗

Single species biofilm-forming ability of root canal isolates on gutta-percha points.

The participation of bacterial biofilms in the over-filled gutta-percha points associated with refractory periapical periodontitis has recently been reported. This study investigated the initial biofilm-forming ability of root canal isolates (Enterococcus faecalis, Streptococcus sanguis, Strep. intermedius, Strep. pyogenes, Staphylococcus aureus, Fusobacterium nucleatum, Propionibacterium acnes, Porphyromonas gingivalis and Prevotella intermedia) on gutta-percha points in vitro. Each bacterial strain was suspended in 100% cell culture medium or in culture medium containing 4.5, 45 or 90% (vol/vol) serum. The bacterial suspensions were then co-incubated anaerobically with gutta-percha points for 7 d. The gutta-percha points were processed for scanning electron microscopic observation and examined for biofilm presence and thickness. E. faecalis, Strep. sanguis, Strep. intermedius, Strep. pyogenes and Staph. aureus biofilms were generated on the surfaces of the specimens incubated in culture medium supplemented with 45 or 90% (vol/vol) serum. The E. faecalis and Strep. sanguis biofilms were significantly thicker than those of Strep. intermedius, Strep. pyogenes and Staph. aureus. No biofilms were detected on the specimens incubated with F. nucleatum, Prop. acnes, Porph. gingivalis and Prev. intermedia. These findings suggest that Gram-positive facultative anaerobes have the ability to colonize and form extracellular matrices on gutta-percha points, while serum plays a crucial role in biofilm formation.

Biofilms↗

In vitro biofilm formation on the surface of resin-based dentine adhesives.

Prevention of root caries on exposed root surfaces in the aging population is a significant challenge. Bonding resins can be applied to exposed root surfaces as sealants; however, minimal data exists regarding biofilm formation on the surface of these resins. We hypothesized that an antibacterial dentine-bonding resin containing methacryloxydodecyl-pyridiniumbromide (MDPB) may reduce biofilm formation. Biofilms were produced in pooled stimulated natural whole saliva, supplemented with 1% sucrose, on the surface of 5 dentine-bonding resins (Clearfil SE, OptiBond Solo, Protect Bond, Protect Bond Primer, and Xeno III) using untreated root surfaces as controls. Biofilms were stained using the Live:Dead Baclight bacterial viability stain, viewed with confocal microscopy, and analyzed using ImageJ image-analysis software. Resin surfaces encouraged attachment of live bacteria compared with root surfaces. All resins showed similar bacterial colonization in sections adjacent to the resin surface, but in the central and outer portions of biofilms, Xeno III and Protect Bond Primer showed a viable bacterial load similar to that of the root surface. Fluoride-releasing resins (OptiBond Solo/Protect Bond) did not show reduced biofilm formation. Thus, antibacterial agents within the resins have a minimal effect on biofilm formation, particularly when directly adjacent to the root surface.

Anti-Bacterial Agents↗