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Applied and Environmental Microbiology, December 2008, p. 7376-7382, Vol. 74, No. 23
0099-2240/08/$08.00+0 doi:10.1128/AEM.01310-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Microbial Adhesion Group, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
Received 12 June 2008/ Accepted 21 September 2008
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In order to get rid of toxic substances and waste products, bacteria have efficient efflux systems. Efflux refers to the pumping of a solute out of a cell. Efflux pump proteins occur as both single-component and multicomponent systems, and the latter are found exclusively in gram-negative bacteria (24). Whereas the single-component systems extrude their substrates into the periplasmic space, multicomponent systems, like the multiple drug resistance (MDR) pumps AcrAB-TolC (Escherichia coli) and MexAB-OprM (Pseudomonas aeruginosa), traverse both the inner and outer membranes and are therefore able to export their substrates directly from the cytoplasm to the surrounding medium (24). Since they are able to transport a wide range of antibiotics, MDR pumps play a crucial role in the increasing prevalence of multidrug-resistant bacteria (30, 36). The exact role of efflux pumps in biofilm growth and their importance in biofilm-mediated antibiotic resistance are, however, elusive, and studies of gram-negative bacteria have produced somewhat incongruous results. In E. coli, the putative multidrug resistance pump YhcQ was reported to be involved in antibiotic resistance of biofilms (26), and the AcrAB-TolC pump has been found to be upregulated under stress conditions, such as stationary-phase growth or, as in the natural habitat of this species, exposure to bile acids and other harmful agents (43). Interestingly, exposure to these agents renders E. coli resistant to lipophilic antibiotics, and it has been suggested that this finding is connected to the upregulation of AcrAB-TolC (43).
In P. aeruginosa, the MexAB-OprM and MexCD-OprJ efflux pumps have been shown to be involved in biofilm-specific mechanisms for resistance (17), particularly mechanisms for resistance to the macrolide azithromycin (17). In contrast, De Kievit et al. found that neither of these two pumps was upregulated in a developing biofilm (12). However, it was pointed out that the expression of these pumps may be influenced by factors like the growth rate and accumulation of metabolites. Zhang et al. recently reported on a novel efflux pump in P. aeruginosa, PA1874-1877, which shows a higher level of expression in a biofilm than during planktonic growth and which appears to be involved in biofilm-mediated antibiotic resistance (48). Most probably, biofilm-mediated resistance is achieved through multiple factors, such as slow growth due to deficient nutrition, reduced penetration due to production of protective extracellular polysaccharides, and efficient efflux, to mention a few (for reviews, see references 28 and 35). Additionally, Mah and coworkers found that the ndvB gene, coding for a glucosyltransferase, is a genetic determinant of antibiotic resistance in P. aeruginosa (29).
Efflux pump inhibitors (EPIs) are substances that block the activity of efflux pumps. EPIs have attracted a great deal of attention over the years due to their ability to block some types of antibiotic resistance in bacteria (for reviews, see references 30 and 36); the EPIs known to block MDR pumps are of particular interest, and three well-known EPIs of this type were assessed here (Table 1 and Fig. 1C). We studied the potency of EPIs as antibiofilm drugs, and we report below that EPIs can block biofilm formation in many bacteria. We also found that in some cases the inherent antibiotic resistance of biofilms can be blocked by EPIs.
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TABLE 1. MDR pumps inhibited by the EPIs used in this study
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FIG. 1. EPIs significantly reduce biofilm formation by E. coli UTI strain 83972, E. coli wild-type strain F18, and K. pneumoniae i222-86. The EPIs thioridazine (T) (50 µg/ml), PAβN (50 µg/ml), and NMP (100 µg/ml) or combinations of thioridazine and PAβN (50 µg/ml each) or of thioridazine and NMP (50 and 100 mg/ml, respectively) were added to static cultures at the time of inoculation, and the amount of biofilm after 24 h was determined by crystal violet staining. (A) Addition of either thioridazine or PAβN significantly reduced biofilm formation up to 80%, and addition of the combinations significantly reduced biofilm formation up to 99% compared with controls without EPIs (P < 0.001, as determined by a paired two-tailed t test for at least three independent experiments). However, NMP alone did not have a significant effect. (B) Biofilm formation by E. coli UTI strain 83972-yfp in the presence of the EPIs thioridazine and NMP (50 and 100 µg/ml, respectively) was monitored using scanning confocal laser microscopy at 16 and 24 h postinoculation. In the presence of the combination of EPIs biofilm formation was reduced 54% at 16 h and 83% at 24 h. Scale bars = 30 µm. (C) Molecular structures of the three EPIs that were used to study bacterial biofilm formation.
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tolC, 83972
yqgA, and 83972
aaeX were constructed using the
Red recombinase gene replacement system (11). Briefly, the npt gene from plasmid pKD4 was amplified using three sets of primers containing 40-nucleotide homology extensions of the target genes (i.e., tolC, yqgA, and aaeX). The PCR products were purified from agarose gels and transformed into strain 83972(pKD46), and kanamycin-resistant colonies were selected. The
Red helper plasmid pKD4 was cured by growth at 37°C, and the correct double-crossover and recombination events were confirmed by PCR. MICs of EPIs were determined by using LB (E. coli UTI strain 83972, E. coli wild-type strain F18, K. pneumoniae strain i222-86, and P. putida KT2442), FBA minimal medium (E. coli UTI strain 83972), or tryptic soy broth (S. aureus strain 8324) (32), and the concentrations used in the biofilm experiments were between one-half and one-quarter the MICs in liquid cultures for each strain to ensure that the concentrations were not toxic.
Biofilm formation in microtiter plates.
Cells were allowed to form biofilms overnight at 37°C in 24-well (Iwaki), 48-well (Iwaki), or 96-well (TPP) flat-bottom microplates, and biofilm formation was monitored by crystal violet staining, as described previously (14). In the experiment in which tetracycline and ethidium bromide (EtBr) were added, as well as for P. putida biofilm growth, the biofilm was dispersed, diluted, and plated on LB agar plates to determine the number of CFU/well.
Biofilm formation in flow cell chambers.
Flow cell experiments were performed at 37°C using FBA minimal medium, essentially as described previously (5, 14) except that there was an additional overnight wash of the flow cell system with sterile MilliQ water. Biofilm formation in the presence and in the absence of a combination of the EPIs thioridazine (50 µg/ml) and 1-(1-naphthylmethyl)-piperazine (NMP) (100 µg/ml) was monitored at 16 and 24 h postinoculation. The images acquired were processed for display using the IMARIS software (Bitplane), and the relative coverage of the substratum by the biofilm was estimated using the COMSTAT software (20). Each experiment in flow chambers was performed in triplicate channels and repeated twice.
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TABLE 2. Twenty efflux and transport genes upregulated during biofilm growth
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When three known inhibitors of bacterial efflux pumps were tested, in almost all cases they were able to reduce bacterial biofilm formation significantly (Fig. 1). Thus, addition of the inhibitor thioridazine, Phe-Arg β-naphthylamide (PAβN), or NMP significantly reduced formation of biofilms by several strains representative of the bacteria mentioned above (Fig. 1A and B). Furthermore, addition of thioridazine resulted in 84 to 89% and 63 to 91% reductions in the formation of biofilms by E. coli UTI strains VR50 and VR89 and by the uropathogenic Klebsiella sp. strains i225-86, i113-96, and i133-96, respectively (P < 0.001, as determined by a paired two-tailed t test for five independent experiments) (data not shown). To briefly assess whether the effect of EPIs on biofilm formation also applies to bacteria not belonging to the family Enterobacteriaceae, we included S. aureus strain 8324 and P. putida strain KT2442 in our study. Addition of 20 µg/ml thioridazine and PAβN resulted in 50 to 70% and 40 to 50% reductions, respectively, in the formation of biofilms by S. aureus 8324 and P. putida KT2442, while addition of 20 µg/ml NMP (Fig. 2) did not result in significant reductions in the formation of biofilms by these two strains.
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FIG. 2. Effects of the EPIs thioridazine, NMP, and PAβN on biofilm formation by S. aureus and P. putida. Thioridazine (T) (20 µg/ml), NMP (20 µg/ml), or PAβN (20 µg/ml) was added to static microtiter cultures of S. aureus 8324 and P. putida KTT2442 at the time of inoculation, and the amount of biofilm after 24 h was determined by crystal violet staining. Addition of thioridazine and addition of PAβN resulted in 50 to 70% and 40 to 50% reductions, respectively, in biofilm formation by S. aureus and P. putida compared with the biofilm formation in the absence of EPIs (*, P < 0.01, as determined by a paired two-tailed t test for five independent experiments).
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TABLE 3. Susceptibility of planktonic growth to the EPIs tested
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The urinary tract is a highly hydrodynamic environment. To better mimic the conditions in the urinary tract, we investigated the effect of EPIs on the biofilm-forming ability of E. coli UTI strain 83972 in the flow cell chamber system. To do this, a yellow fluorescent protein-producing version of E. coli 83972 (E. coli 83972-yfp) was used (15). There was an 83% reduction in the formation of biofilms by E. coli 83972-yfp at 24 h postinoculation in the presence of a combination of the EPIs thioridazine and NMP (Fig. 1B).
EPIs enhance the killing effect of antimicrobial agents on bacterial biofilms.
Biofilm-dwelling bacteria are known to be highly tolerant or resistant to antibiotics. Meanwhile, the detailed mechanisms underlying this important phenomenon are largely unknown. The expression of genes encoding efflux pumps was highly upregulated. Arguably, the cramped conditions of the biofilm growth mode confer severe waste management problems on the bacteria. Arguably, the enhanced pump activity not only rids the bacteria of "normal" waste but also pumps out many antibiotics. Therefore, the tolerance of bacterial biofilms to antibiotics, at least in some cases, may be a consequence of the enhanced efflux pump activity in biofilms. The least efficient of the three EPIs, NMP (Fig. 1A), was chosen in order to better visualize any significant effect that occurred in combination with an antimicrobial agent. The antibiotic tetracycline was used in combination with the selected EPI; NMP has been shown to have a significant effect on the susceptibility of clinical isolates of E. coli to tetracycline (21), and furthermore, it has also been shown that tetracycline rapidly reaches all the constituent cells of E. coli biofilms (45). Addition of tetracycline to overnight biofilms of E. coli UTI strains 83972 and VR50, E. coli F18, and K. pneumoniae i222-86 revealed that there was significantly higher sensitivity to tetracycline in the presence of the EPI NMP (Fig. 3A). While 33 to 51% of the biofilm-forming bacteria were killed by tetracycline after a 2 h of exposure, between 77 and 93% of the biofilm bacteria were killed by a combination of tetracycline and the EPI NMP, resulting in 5.2-, 4.2-, 2.6-, and 7.5-fold-increased killing effects on strains 83972, VR50, F18, and i222-86, respectively, while use of NMP alone did not result in any significant reduction in biofilm formation (Fig. 1A). To investigate whether the increased killing effect of tetracycline induced by NMP could be seen with another antimicrobial agent, EtBr was selected and tested with the two UTI strains. Significant effects of NMP on the MICs of EtBr have been observed for a large fraction of clinical isolates of E. coli; the MICs were reduced more than fourfold in 51 of 60 isolates (85%) by the presence of NMP, and this effect on EtBr MICs was observed when EtBr was used in combination with NMP but not when it was used with another EPI, PAβN (21). For our two clinical E. coli isolates, 83972 and VR50, there were 92 to 95% reductions in biofilm formation after 2 h of exposure to 200 µg/ml EtBr, and even though the effect of NMP on UTI strains 83972 and VR50 was limited (Fig. 1A) (no significant decrease in biofilm formation was observed), NMP increased the killing effect of EtBr 12.8- and 7.5-fold compared with the effect observed with EtBr alone (Fig. 3B). The presence of the EPI NMP in combination with 2 h of exposure to EtBr resulted in 264- and 93-fold reductions in the formation of biofilms by UTI strains 83972 and VR50, respectively.
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FIG. 3. Biofilm formation in the presence of antimicrobial agents in combination with the EPI NMP. (A) Biofilms of E. coli UTI strains 83972 and VR50, E. coli F18, and K. pneumoniae were significantly more sensitive to tetracycline in the presence of the EPI NMP. Tetracycline (100 µg/ml) was added to overnight biofilms that had been grown in media with and without NMP. After 2 h of exposure to tetracycline the biofilm density was determined by determining the number of CFU per microtiter well. In the presence of NMP (100 µg/ml) the killing effect of tetracycline was increased 2.6- to 7.5-fold (*, P < 0.01, as determined by a paired two-tailed t test for three independent experiments). (B) Biofilms of UTI strains 83972 and VR50 showed large increases in EtBr susceptibility in the presence of NMP. Overnight biofilms were exposed to EtBr (200 µg/ml) for 2 h after growth in media with and without NMP. The size of the viable biofilm was determined by determining the number of CFU per microtiter well. In the presence of NMP (100 µg/ml) the killing effect of EtBr was increased 13- and 7.5-fold for strains 83972 and VR50, respectively (*, P < 0.01, as determined by a paired two-tailed t test for five independent experiments).
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aaeX and
yqgA knockout mutants of E. coli UTI strain 83972 showed 33 and 26% reductions in biofilm formation. Furthermore, 83972
yqgA was more sensitive to the EPI thioridazine than the wild type; the reduction in biofilm formation in the presence of thioridazine was 36% greater for this strain than for strain 83972.
Multicomponent efflux pumps, like the AcrAB-TolC (E. coli) and MexAB-OprM (P. aeruginosa) systems, are dependent on outer membrane channel proteins (like TolC and OprM) to extrude their substrates directly into the external medium (34). A wide range of EPIs are known; some are highly system specific, whereas others can inhibit the action of several types of efflux pumps. The compositions of structurally diverse pumps also are different in different bacteria, and since the EPIs tested here might also act on pumps other than the AcrAB-TolC type, a strain not capable of producing TolC would be suspected to be more sensitive to EPIs than its nonmutated counterpart. Indeed, the MIC of thioridazine was four times lower for the knockout mutant E. coli UTI strain 83972
tolC than that for the nonmutated strain. When the organism was exposed to 10 µg/ml thioridazine, the biofilm formation by the
tolC mutant was reduced 88% compared with the biofilm formation in the absence of thioridazine (P < 0.01, as determined by a paired two-tailed t test for three independent experiments).
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Five main families of bacterial efflux pumps are known, and individual bacteria possess multiple efflux pumps belonging to these families. In light of this it is not surprising that one type of EPI was not able to fully suppress biofilm formation. However, when two complementary EPIs, potentially acting on different types of pumps, were used together, we observed close to 100% inhibition (Fig. 1A). The data resulting from biofilm inhibition with EPIs were also corroborated by using knockout mutants having genetic lesions in efflux pump-encoding genes. E. coli mutants with
aaeX and
yqgA knockout mutations exhibited significantly reduced biofilm formation compared to their parents. Also, such mutants were notably more sensitive to EPIs.
Our work has focused mainly on uropathogenic E. coli and Klebsiella strains. These organisms are significant pathogens, and UTI is one of the top bacterial diseases in humans, with more than 150 million cases per year globally (44). However, in order to get a rough idea of the extent of the phenomenon, two well-characterized biofilm-forming bacterial strains not belonging to the family Enterobacteriaceae were tested to determine the effect of EPI activity on biofilm formation. These strains were S. aureus strain 8324, a gram-positive organism, and P. putida strain KT2442, a gram-negative organism. In both cases biofilm formation could be significantly reduced by EPIs (Fig. 2). Although our results do not indicate that EPIs can abolish or reduce biofilm formation in all types of bacteria, they do suggest that EPI inhibition is not restricted to the family Enterobacteriaceae.
The intrinsic tolerance of biofilm-associated bacteria to external agents like detergents, biocides, and antibiotics makes biofilm-associated infections particularly recalcitrant to treatment. New types of antibiotics are, therefore, urgently needed; development of candidate drugs that target bacterial adhesion and biofilm formation should be of great importance for combating diseases (22). By virtue of their anti-efflux pump activities, it seems that EPIs have great potential as antibiofilm drugs. EPIs are generally simple, robust, and cheap chemicals. Also, in cases where they have been tested, EPIs are well tolerated by humans (30, 36). Indeed, EPIs could well constitute a long-needed new class of antibiotics. Furthermore, it is possible that EPIs could be used as enhancers of "classical" antibiotics when such antibiotics are used to treat biofilm-related diseases.
This work was supported by grants from the Danish Medical Research Council (grant 271-07-0291), Lundbeckfonden (R19-A2191), and FØSU (grant 2101-06-0009).
Published ahead of print on 3 October 2008. ![]()
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