# Patent

## Title
Bacterial glycosyltransferase polypeptides involved in antibiotic resistance

## Abstract

Disclosed are various genes encoding proteins that are shown to play a role, direct or indirect, in microbial resistance of an organism in a biofilm and homologs thereof. Also disclosed are methods of identifying a compound that modulates microbial resistance of an organism in a biofilm, and methods of identifying genes that encode proteins that play a role, direct or indirect, in biofilm resistance.

## Background
REFERENCE TO RELATED APPLICATIONS
This application claims priority from U.S. Provisional Application No. 60/323,241, filed Sep. 18, 2001, the entirety of which is incorporated by reference.


BACKGROUND OF THE INVENTION
Biofilms are complex communities of microorganisms, comprised either of a single or multiple species. Over the past few decades, there has been a growing realization that bacteria in most environments are not found in a unicellular, planktonic existence such as those typically studied in the laboratory, but exist predominantly in multi-cellular surface attached communities called biofilms. This realization has spurred much research into the physical and chemical properties of biofilms, their morphology, and the mechanism of their development.
The transition from the planktonic mode of existence to a biofilm is a regulated developmental process. This biofilm community has a number of distinct characteristics including the production of exopolysaccharides, the formation of chemical and pH gradients, a marked degree of structural heterogeneity, and the development of high level resistance to a variety of antimicrobial agents.
It has been shown that biofilm grown cells can become 10–1000× more resistant to the effects of antimicrobial agents than their planktonic counterparts. This characteristic of biofilms makes them extremely difficult to control in both medical and industrial settings. Traditional antibiotic therapies can eliminate planktonic bacteria, but organisms growing in a biofilm survive treatment and can eventually regrow once antibiotics are discontinued. The levels of antibiotic required to eliminate biofilm bacteria often cannot be achieved in the patient or are toxic. Therefore, biofilm-based infections can become chronic with the only recourse being removal of the contaminated surface.
The formation of biofilms can have serious negative consequences in medical, industrial, and natural settings, resulting in high costs both in human health and economic terms. Biofilm-associated infections extend hospital stays an average of about three days and it is estimated that up to 65% of nosocomial infections are biofilm-based with an associated treatment cost in excess of a billion dollars per year. In clinical settings, biofilms can form on a variety of surfaces. Biofilms formed on indwelling medical devices serve as a reservoir of bacteria that can be shed into the body, leading to a chronic systemic infection. Indeed, up to 82% of nosocomial bacteremias are the result of bacterial contamination of intravascular catheterizations. Examples of biofilms include oral microbes on teeth, chronic Pseudomonas aeruginosa infections in the lungs of cystic fibrosis patients and bacterial contaminants on medical devices such as pacemakers and catheters. Biofilms can form in almost any hydrated environment that has the proper nutrient conditions, and can develop on a wide variety of abiotic (both hydrophobic and hydrophilic) and biotic (e.g., eukaryotic cells) surfaces.
The formation of biofilms is an important aspect of normal development for many microbial species. The mechanisms responsible for the increased biofilm resistance, however, are not well understood. It has been suggested that the exopolysaccharide matrix that surrounds the cells in the biofilm prevent diffusion of antimicrobial agents through the biofilm, thus preventing access of the agent to the cells. While this may be the case for some antimicrobial agents, for many others it has been shown that antimicrobial agents can penetrate the biofilm matrix but are still unable to kill cells in the biofilm. It has also been suggested that cells within the biofilm grow slowly in response to nutrient deprivation and perhaps some form of stress. Therefore, antimicrobial agents that only act on actively dividing bacterial cells would be non-functional in this sort of environment. While a number of studies support the idea that slowed growth rate can explain some aspects of biofilm-related resistance, other studies have suggested that the full extent of resistance cannot be accounted for by this mechanism. Finally, while it has been suggested that quorum sensing is involved in resistance to antimicrobial agents, it is not clear what role, if any, this system plays in biofilm-related antimicrobial resistance. To date, none of the models put forward adequately explain the level of resistance to biocides attained by cells in a biofilm.
There is emerging evidence that the transition from planktonically growing bacteria to life in a biofilm requires a genetic program that responds to a variety of environmental cues. It is possible that the development of biofilm-related antibiotic resistance is also a regulated event, and taken together with the marked biochemical and physiological heterogeneity of biofilms, the induction of a biofilm-related resistance phenotype may occur within distinct regions of the biofilm. The subset of biocide-resistant cells in the biofilm is referred to as “persistors”. The term persistor refers to the fact that not all of the cells within the biofilm resist killing by antimicrobial agents resulting in the survival of a small population of very resistant cells after antibiotic treatment.
There exists a strong need to discover methods and compositions that will inhibit biofilm formation and overcome their resistance mechanisms.
SUMMARY OF THE INVENTION
The invention features method for identifying compounds that can alter, e.g., reduce the resistance of microbial cells growing in a biofilm to antimicrobial agents. Certain of the compounds may also be used reduce resistance to antimicrobial agents associated with other physiological states as well as resistance caused by genetic changes. The invention also features methods for identifying genes that play a role in biofilm resistance as well as certain such genes and the proteins they encode.
A compound or compounds that are identified by the invention as modulating biofilm resistance to an antimicrobial agent can be further analyzed in the context of a flow cell assay and a colony biofilm assay. Using the flow cell assay, a biofilm, allowed to form in the flow cell, can be monitored in the presence of an antimicrobial agent and a compound. The antimicrobial agent and the compound can be quickly removed and the effect of the treatment on biofilm viability can be determined using standard techniques.
A colony biofilm assay can also be utilized to test the effect of biofilm resistance to antimicrobial agents in the presence of compounds identified by the invention. Microorganisms are allowed to form a biofilm on a polycarbonate filter then transferred to solid media. The biofilm is exposed to an antimicrobial agent and a compound and tested for viability after a pre-determined amount of time. A biofilm treated with a compound identified by the invention will demonstrate reduced viability and/or increased sensitivity when exposed to the antimicrobial agent after or during exposure to the compound. These techniques are described in more detail below.
The invention features a method of identifying a candidate compound for altering the sensitivity of a microorganism to an antimicrobial agent, the method comprising: a) providing a sample comprising an efflux pump selected from the group consisting of: i) an efflux pump comprising a polypeptide comprising SEQ ID NO:4 (gene PA1874), ii) an efflux pump comprising a polypeptide comprising SEQ ID NO: 12 (gene PA4142), iii) an efflux pump comprising a polypeptide comprising SEQ ID NO:18 (gene PA2389),
b) contacting the sample with a test compound; and
c) measuring activity of the efflux pump, wherein a change in the activity of the efflux pump in the presence of the test compound relative to the activity of the efflux pump in a control sample in the absence of the test compound, indicates that the compound is a candidate compound for altering the sensitivity of a microorganism to an antimicrobial agent.
In various embodiments: the efflux pump comprising a polypeptide comprising SEQ ID NO:4 (gene PA1874), further comprises at least one of: a polypeptide comprising SEQ ID NO:6 (gene PA1875), a polypeptide comprising SEQ ID NO:8 (gene PA1876), and a polypeptide comprising SEQ ID NO:10 (gene PA1877); the efflux pump comprising a polypeptide comprising SEQ ID NO:12 (gene PA4142), further comprises at least one of: a polypeptide comprising SEQ ID NO:14 (gene PA4143), and a polypeptide comprising SEQ ID NO:16 (gene PA4144); and the efflux pump comprising a polypeptide comprising SEQ ID NO:18 (gene PA2389), further comprises at least one of: a polypeptide comprising SEQ ID NO:20 (gene PA2390), and a polypeptide comprising SEQ ID NO:22 (gene PA2391).
The invention also features: a method of identifying a candidate compound for altering the sensitivity of a microorganism to an antimicrobial agent, the method comprising: a)

    
    
        providing a sample comprising a polypeptide selected from the group consisting of: i) a polypeptide comprising SEQ ID NO:8 (gene PA1876), ii) an efflux pump comprising a polypeptide comprising SEQ ID NO: 14 (gene PA4143), iii) an efflux pump comprising a polypeptide comprising SEQ ID NO:20 (gene PA2390),
    
    


b) contacting the sample with a test compound; and
c) measuring the ATPase activity of the polypeptide, wherein a change in the ATPase activity of the polypeptide in the presence of the test compound relative to the activity of the polypeptide in a control sample in the absence of the test compound, indicates that the compound is a candidate compound for altering the sensitivity of a microorganism to an antimicrobial agent.
In various embodiments: the sample comprises cells expressing the polypeptide, the sample comprises cells harboring an expression vector encoding the polypeptide. The cells are grown in a biofilm, the cells are grown planktonically, the sample comprises vesicles containing the efflux pump or a membrane system containing the efflux pump; the method comprises measuring the activity of two or more efflux pumps selected from the group consisting of: i) an efflux pump comprising a polypeptide comprising SEQ ID NO:4 (gene PA1874), ii) an efflux pump comprising a polypeptide comprising SEQ ID NO: 12 (gene PA4142), and iii) an efflux pump comprising a polypeptide comprising SEQ ID NO:18 (gene PA2389).
The invention further features: a method of identifying a candidate compound for altering the sensitivity of a microorganism to an antimicrobial agent, the method comprising:
a) providing a sample comprising a glucosyltransferase polypeptide selected from the group consisting of: i) a polypeptide comprising SEQ ID NO:2 (gene PA1163), ii) a polypeptide comprising SEQ ID NO:27, iii) a polypeptide comprising SEQ ID NO:28, iv) a polypeptide comprising SEQ ID NO:29, and v) a polypeptide comprising SEQ ID NO:32,
b) contacting the sample with a test compound; and
c) measuring activity of the glucosyltransferase polypeptide, wherein a change in the activity of the glucosyltransferase polypeptide in the presence of the test compound relative to the activity of the glucosyltransferase polypeptide in a control sample in the absence of the test compound, indicates that the compound is a candidate compound for altering the sensitivity of a microorganism to an antimicrobial agent.
In various embodiments: the glucosyltransferase polypeptide is contacted with the test compound in the presence of an antimicrobial agent; the sample comprises cells expressing the glucosyltransferase polypeptide; sample comprises cells harboring an expression vector encoding the glucosyltransferase polypeptide; the cells are grown as a biofilm; the cells are grown planktonically; and activity is measured by measuring cyclic-b-(1,3)-glucan formation.
The invetion further features: a method of identifying a candidate compound for altering the sensitivity of a microoganism to an antimicrobial agent, the method comprising:
a) providing a sample comprising cells expressing a gene encoding a glucosyltransferase polypeptide selected from the group consisting of: i) a polypeptide comprising SEQ ID NO:2 (gene PA1163), ii) a polypeptide comprising SEQ ID NO:27, iii) a polypeptide comprising SEQ ID NO:28, iv) a polypeptide comprising SEQ ID NO:29, and v) a polypeptide comprising SEQ ID NO:32,
b) contacting the sample with a test compound; and
c) measuring the expression of a gene encoding a glucosyltransferase polypeptide in the cells, wherein a change in the expression of the gene encoding the glucosyltransferase polypeptide in the presence of the test compound relative to the expression of the gene encoding the glucosyltransferase polypeptide in a control sample in the absence of the test compound, indicates that the compound is a candidate compound for altering the sensitivity of a microorganism to an antimicrobial agent.
In various embodiments: the cells are contacted with the test compound in the presence of an antimicrobial agent; the expression of the gene is measured by measuring mRNA expression; expression of the gene is measured by measuring polypeptide expression; and the cells contacted with the test compound are growing as a biofilm.
The invention also features: A method of identifying a candidate compound for altering the sensitivity of a microorganism to an antimicrobial agent, the method comprising:
a) providing a sample of cells expressing an efflux pump selected from the group consisting of: i) an efflux pump comprising a polypeptide comprising SEQ ID NO: 4 (gene PA1874), ii) an efflux pump comprising a polypeptide comprising SEQ ID NO: 12 (gene PA4142), iii) an efflux pump comprising a polypeptide comprising SEQ ID NO: 18 (gene PA2389),
b) contacting the cells with a test compound; and
c) measuring expression of the efflux pump in the cells wherein a change in the expression of the efflux pump in the presence of the test compound relative to the expression of the efflux pump in a control sample in the absence of the test compound, indicates that the test compound is a candidate compound for altering the sensitivity of a microorganism to an antimicrobial agent.
In various embodiments: the efflux pump comprising a polypeptide comprising SEQ ID NO: 4 (gene PA1874), further comprises at least one of: a polypeptide comprising SEQ ID NO:6 (gene PA1875), a polypeptide comprising SEQ ID NO:8 (gene PA1876), and a polypeptide comprising SEQ ID NO:10 (gene PA1877); the efflux pump comprising a polypeptide comprising SEQ ID NO:12 (gene PA4142), further comprises at least one of: a polypeptide comprising SEQ ID NO:14 (gene PA4143), and a polypeptide comprising SEQ ID NO:16 (gene PA4144); the efflux pump comprising a polypeptide comprising SEQ ID NO:18 (gene PA2389), further comprises at least one of: a polypeptide comprising SEQ ID NO:20 (gene PA2390), and a polypeptide comprising SEQ ID NO:22 (gene PA2391); the cells are contacted with the test compound in the presence of an antimicrobial agent; expression is measured by measuring polypeptide expression; expression is measured by measuring mRNA expression; the cells are grown as a biofilm; and the cells are grown planktonically.
The invention also features: a purified polypeptide comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:4 (gene PA1874), SEQ ID NO:6 (gene PA1875), SEQ ID NO:8 (gene PA1876), SEQ ID NO:10 (gene PA1877), SEQ ID NO:12 (gene PA4142), SEQ ID NO:14 (gene PA4143), SEQ ID NO:16 (gene PA4144), SEQ ID NO:18 (gene PA2389), SEQ ID NO:20 (gene PA2390), SEQ ID NO:22 (gene PA2391) and a purified polypeptide comprising the amino acid sequence selected from the group consisting of: SEQ ID NO:2 (gene PA1163), SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29 and SEQ ID NO:31.
The invention includes a method of identifying a gene that functions in biofilm-related resistance to an antimicrobial agent, the method comprising:
(a) providing a library of clones of a selected microbial strain that have been subjected to mutagenesis;
(b) growing each of a plurality of clones from the library as a biofilm;
(c) identifying a clone having altered biofilm-related resistance to the antimicrobial agent relative the to biofilm-related resistance of the selected microbial stain;
(d) isolating from the identified clone a gene having a mutation.
In various embodiments: the antimicrobial agent is an antibiotic; the mutagenesis comprises random mutagenesis; the selected strain exhibits at least a two-fold change in resistance to the anti-microbial agent; the microorganism is a bacterial microorganism; the microorganism is a fungal microorganism; the mutagenesis comprises chemical mutagenesis.
The invention includes: a method of identifying a compound that increases the sensitivity of a microorganism to a selected antimicrobial agent, the method comprising:
(a) providing a sample comprising a microorganism in a biofilm;
(b) contacting the sample with a test compound and the selected antimicrobial agent; and
(c) measuring the sensitivity of the microorganism in the sample to the selected antimicrobial agent, wherein an increase in the sensitivity of the microorganism to the selected antimicrobial agent relative to the sensitivity of the microorganism in a biofilm to the selected antimicrobial agent in the absence of the test compound indicates that the test compound is a compound that increases the sensitivity of microorganism in a biofilm to the selected antimicrobial agent.
In various embodiments: the antimicrobial agent is selected from the group consisting of aminoglycosides, macrolides, tetracyclines, penicillins, β-lactam antibiotics (including cephalosporins, β-lactam/β-lactamase combinations), quinolones (including fluoroquinolones), glycopeptides, sulfonamides, sulfones, oxazolidinones, streptogramins; the microorganism is selected from the group consisting of Pseudomonas fluorescens, Pseudomonas aeruginosa, Pseudomonas acidovorans, Pseudomonas alcaligenes, Pseudomonas putida, Pseudomonas syringae, Pseudomonas aureofaciens, Pseudomonas fragi, Fusobacterium nucleatum, Treponema denticola, Porphyromonas gingivalis, Moraxella catarrhalis, Stenotrophomonas maltophilia, Burkholderia cepacia, Aeromonas hydrophilia, Escherichia coli, Citrobacter freundii, Salmonella typhimurium, Salmonella typhi, Salmonella paratyphi, Salmonella enteritidis, Shigella dysenteriae, Shigella flexneri, Shigella sonnei, Enterobacter cloacae, Enterobacter aerogenes, Klebsiella pneumoniae, Klebsiella oxytoca, Serratia marcescens, Francisella tularensis, Morganella morganii, Proteus mirabilis, Proteus vulgaris, Providencia alcalifaciens, Providencia rettgeri, Providencia stuartii, Acinetobacter calcoaceticus, Acinetobacter haemolyticus, Yersinia enterocolitica, Yersinia pestis, Yersinia pseudo tuberculosis, Yersinia intermedia, Bordetella pertussis, Bordetella parapertussis, Bordetella bronchiseptica, Haemophilus influenzae, Haemophilus parainfluenzae, Haemophilus haemolyticus, Haemophilus parahaemolyticus, Pasteurella multocida, Pasteurella haemolytica, Helicobacter pylori, Campylobacter fetus, Campylobacter jejuni, Campylobacter coli, Borrelia burgdorferi, Vibrio cholerae, Vibrio paramaemolyticus, Legionella pneumophila, Listeria monocytogenes, Neisseria gonorrhoeae, Neisseria meningitidis, Gardnerella vaginalis, Bacteroides spp., Clostridium difficile, Mycobacterium tuberculosis, Mycobacterium avium, Mycobacterium intracellulare, Mycrobacterium leprae, Corynebacterium diphtheriae, Corynebacterium ulcerans, Streptococcus spp., Enterococcus spp., Desulfvibrio spp., Actinomyces spp., Erwinia spp., Xanthomonas spp., Xylella spp., Clavibacter spp., Desulfomonas spp., Desulfovibrio spp., Desulfococcus spp., Desulfobacter spp., Desulfobulbus spp., Desulfosarcina spp., Deslfuromonas spp., Bacillus spp., Streptomyces spp., Clostridium spp., Rhodococcus spp., Thermatoga spp., Sphingomonas spp., Zymomonas spp., Micrococcus spp., Azotobacter spp., Norcardia spp., Brevibacterium spp., Alcaligenes spp., Microbispora spp., Micromonospora spp., Methylobacterium organophilum, Pseudomonas reptilivora, Pseudomonas carragienovora, Pseudomonas dentificans, Corynebacterium spp., Propionibacterium spp., Xanothomonas spp., Methylobacterium spp., Chromobacterium spp., Saccharopolyspora spp., Actinobacillus spp., Alteromonas spp., Aeronomonas spp., Agrobacterium tumefaciens, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus hominis, Staphylococcus haemolyticus, Staphylococcus warneri, Staphylococcus cohnii, Staphylococcus saprophyticus, Staphylococcus capitis, Staphylococcus lugdunensis, Staphlyococcus intermedius, Staphylococcus hyicus, Staphylococcus saccharolyticus and Rhizobium spp; the biofilm is associated with an abiotic surface; the biofilm is associated with a biotic surface; the biofilm is not associated with a surface; the microorganism has a mutation that reduces the expression or activity of a polypeptide selected from the group consisting of: SEQ ID NO:4 (gene PA1874), SEQ ID NO:6 (gene PA1875), SEQ ID NO:8 (gene PA1876), SEQ ID NO:10 (gene PA 1877), SEQ ID NO:12 (gene PA4142), SEQ ID NO:14 (gene PA4143), SEQ ID NO:16 (gene PA4144), SEQ ID NO:18 (gene PA2389), SEQ ID NO:20 (gene PA2390), SEQ ID NO:22 (gene PA2391); and the microorganism has a mutation that reduces the expression or activity of a polypeptide selected from the group consisting of: SEQ ID NO:2 (gene PA1163), SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29 and SEQ ID NO:31 (e.g., a deletion mutation or an insertion mutation).
The invention features a method of identifying a candidate compound for altering the sensitivity of a microoganism to an antimicrobial agent, the method comprising:
a) providing a sample comprising cells harboring a reporter gene comprising a nucleotide sequence encoding a detectable protein operably linked to an expression control sequence comprising a nucleotide sequence selected from the group consisting of: i) SEQ ID NO:23 (expression control for PA1874), ii) SEQ ID NO:24 (expression control for PA4242), iii) SEQ ID NO:25 (expression control for PA2389), and iv) SEQ ID NO:26 (expression control for PA1163),
b) measuring the expression of the reporter gene in the cells in the presence of a test compound, wherein a change in the expression of the reporter gene in the presence of the test compound relative to the expression of the reporter gene in a control sample in the absence of the test compound, indicates that the compound is a candidate compound for altering the sensitivity of a microorganism to an antimicrobial agent.
In certain embodiments expression of the reporter gene is measured by measuring the expression of the detectable protein.
The invention includes: a method of identifying a candidate compound for inhibiting the growth of a microorganism, the method comprising:
a) providing a sample comprising an efflux pump selected from the group consisting of: i) an efflux pump comprising a polypeptide comprising an amino acid sequence at least 70% identical to SEQ ID NO:4 (gene PA1874), ii) an efflux pump comprising a polypeptide comprising an amino acid sequence at least 70% identical to SEQ ID NO: 12 (gene PA4142), iii) an efflux pump comprising a polypeptide comprising SEQ ID NO:18 (gene PA2389),
b) contacting the sample with a test compound; and
c) measuring activity of the efflux pump, wherein a change in the activity of the efflux pump in the presence of the test compound relative to the activity of the efflux pump in a control sample in the absence of the test compound, indicates that the compound is a candidate compound for inhibiting the growth of a microorganism.
In certain embodiments: the efflux pump comprising a polypeptide comprising SEQ ID NO:4 (gene PA1874), further comprises at least one of: a polypeptide comprising SEQ ID NO:6 (gene PA1875), a polypeptide comprising SEQ ID NO:8 (gene PA1876), and a polypeptide comprising SEQ ID NO:10 (gene PA1877); the efflux pump comprising a polypeptide comprising SEQ ID NO:12 (gene PA4142), further comprises at least one of: a polypeptide comprising SEQ ID NO:14 (gene PA4143), and a polypeptide comprising SEQ ID NO:16 (gene PA4144).; the efflux pump comprising a polypeptide comprising SEQ ID NO:18 (gene PA2389), further comprises at least one of: a polypeptide comprising SEQ ID NO:20 (gene PA2390), and a polypeptide comprising SEQ ID NO:22 (gene PA2391); the sample comprises cells expressing the polypeptide; the cells are grown in a biofilm; and the cells are grown planktonially.
The invention features: a method of identifying a candidate compound that inhibits growth of a microorganism, the method comprising:
a) providing a sample comprising a glucosyltransferase polypeptide selected from the group consisting of: i) a polypeptide comprising SEQ ID NO:2 (gene PA1163), ii) a polypeptide comprising SEQ ID NO:27, iii) a polypeptide comprising SEQ ID NO:28, iv) a polypeptide comprising SEQ ID NO:29, and v) a polypeptide comprising SEQ ID NO:32,
b) contacting the sample with a test compound; and
c) measuring activity of the glucosyltransferase polypeptide, wherein a change in the activity of the glucosyltransferase polypeptide in the presence of the test compound relative to the activity of the glucosyltransferase polypeptide in a control sample in the absence of the test compound, indicates that the compound is a candidate compound inhibiting the growth of a microorganism.
“Naturally-occurring” as used herein, as applied to an object, refers to the fact that an object can be found in nature. For example, a polypeptide or polynucleotide sequence that is present in an organism (including viruses) that can be isolated from a source in nature is naturally-occurring.
By “compound,” “test compound,” or “candidate compound” we mean any substance or chemical. Encompassed within this definition are, for example, compound analogs, naturally occurring, synthetic and recombinant pharmaceuticals, hormones, or antimicrobials, antibiotics, nucleic acid molecules, polypeptides, and peptide nucleic acids.
By “test sample” we mean one or more of the components of a sample and a test compound.
By “control sample” we mean a test sample lacking a test compound. Therefore, the control sample has all of the characteristics of the test sample except for the presence of a test compound in the test sample.
By “cell component” we mean a protein, carbohydrate, lipid, nucleic acid molecule, ion, or any other constituent contained within or secreted by an organism.
By “biological activity” we mean a protein having structural, regulatory, or biochemical functions of a naturally occurring molecule.
By “efflux pump” we mean a protein assembly which exports substrate molecules, compounds, or antimicrobial agents from the cytoplasm or periplasm of a cell, in an energy dependent fashion. Thus an efflux pump will typically be located in the cytoplasmic membrane of the cell (spanning the cytoplasmic membrane). For example, in Gram-negative bacteria the pump may span the periplasmic space and there may also be portion of the efflux pump which spans the outer membrane.
“Expression cassette” refers to a recombinantly produced nucleic acid molecule which is capable of directing the expression of one or more proteins. The expression cassette must include a promoter capable of directing the expression of said protein(s), and a sequence encoding one or more proteins. Optionally, the expression cassette may include transcription termination, splice recognition, and polyadenylation addition sites. Desired promoters include the TK, CMV, MMTV, MoMLV, Ptac, Plac, Para, Pxyl, and PT7 promoters. In addition, the expression cassette may contain a selectable marker, for example, Neo, SV2 Neo, hygromycin, phleomycin, histidinol, DHFR, tetracycline, carbenecillin, gentamycin, kanamycin, and ampicillin; a chemiluminescent marker, for example, luciferase and green fluorescent protein; or an enzymatic marker, for example, chloramphenicol acetyltransferase.
“Reporter gene” means a gene that encodes a detectable protein, e.g., reporter enzyme, such as they are known in the art or are later developed, such as a reporter enzyme activity. A reporter gene may be a component of an expression cassette. “Reporter enzyme” means an enzyme that encode a reporter enzyme that has a detectable read-out, such as beta-lactamase, beta-galactosidase, or luciferase (for beta-lactamase, see WO 96/30540 to Tsien, published Oct. 3, 1996). Desirably, reporter enzymes localize in the cytosol of a cell, such as cytosolic beta-lactamase. Reporter enzymes can be detected using methods known in the art, such as the use of chromogenic or fluorogenic substrates for reporter enzymes as such substrates are known in the art. Such substrates are desirably membrane permeant. Chromogenic or fluorogenic readouts can be detected using, for example, optical methods such as absorbance or fluorescence. A reporter gene can be part of a reporter gene construct, such as a plasmid or viral vector, such as a retrovirus or adeno-associated virus. A reporter gene can also be extra-chromosomal or be integrated into the genome of a host cell. The expression of the reporter gene can be under the control of exogenous expression control sequences or expression control sequences within the genome of the host cell. Under the latter configuration, the reporter gene is desirably integrated into the genome of the host cell.
“Polypeptide” means any chain of amino acids, regardless of length or post-translational modification (e.g., glycosylation or phosphorylation). By the use of “precursor” we mean that a polypeptide can be encoded by a full length gene sequence or by any portion of the coding sequence so long as the enzymatic activity is retained.
“Substantially pure polypeptide” means a polypeptide which has been separated from components which naturally accompany it. Typically, the polypeptide is substantially pure when it is at least 60%, by weight, free from the proteins and naturally-occurring organic molecules with which it is naturally associated. It is desirable for the preparation to be at least 75%, more desirably at least 90%, and even more desirably 95%, and most desirably 99%, by weight the desired protein. A substantially pure polypeptide may be obtained, for example, by extraction from a natural source (e.g., a bacterial cell); by expression of a recombinant nucleic acid molecule encoding the polypeptide; or by chemically synthesizing the protein. Purification of polypeptides may be by techniques known in the art, for example, differential extraction, salt fractionation, chromatography on ion exchange resins, affinity chromatography, centrifugation, and the like. See, for example, Methods in Enzymology for a variety of methods for purifying proteins. Purity can be measured by any appropriate method, e.g., those described in column chromatography, polyacrylamide gel electrophoresis, or by HPLC analysis.
A protein is substantially free of naturally associated components when it is separated from those contaminants which accompany it in its natural state. Thus a protein which is chemically synthesized or produced in a cellular system different from the cell from which it naturally originates will be substantially free from its naturally associated components. Accordingly, substantially pure polypeptides include those derived from prokaryotic organisms, but synthesized in other prokaryotes or eukaryotes.
“Substantially pure DNA” means DNA that is free of the genes which, in the naturally occurring genome of the organism from which the DNA of the invention is derived, flank the gene. The term therefore includes, for example, a recombinant DNA which is incorporated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote; or which exists as a separate molecule (e.g., a cDNA or a genomic or cDNA fragment produced by PCR or restriction endonuclease digestion) independent of other sequences. It also includes a recombinant DNA which is part of a hybrid gene encoding additional polypeptide sequence.
By “antimicrobial agent” we mean an agent, e.g., a compound which reduces the rate of growth of an organism compared to the rate of growth of the organism in the absence of the composition. A reduction in the rate of growth of an organism may be by at least 5%, more desirably, by at least 10%, even more desirably, by at least 20%, 50%, or 75%, and most desirably, by 90% or more. The definition also extends to compositions which affect the viability, virulence, or pathogenicity of an organism. An antimicrobial agent can be natural (e.g., derived from bacteria), synthetic, or recombinant. An antimicrobial agent can be bacteriostatic, bactericidal or both. An antimicrobial agent is bacteriostatic if it inhibits cell division without affecting the viability of the inhibited cell. An antimicrobial agent is bactericidal if it causes cell death. Cell death is commonly detected by the absence of cell growth in liquid growth medium (e.g., absence of turbidity) or on a solid surface (e.g., absence of colony formation on agar). Those of skill in the art know that a composition which is bacteriostatic at a given concentration may be bactericidal at a higher concentration. Certain bacteriostatic compositions are not bactericidal at any concentration.
Encompassed within the definition of antimicrobial agents are compound analogs, naturally occurring, synthetic and recombinant pharmaceuticals, antibiotics, etc.
As used herein, the term “antimicrobial” refers to the ability of compounds to prevent, inhibit or destroy the growth or viability of microbes such as bacteria, fungi, protozoa, and viruses. The term may also refer to the ability of compounds to prevent, reduce, or inhibit the virulence, cytotoxicity, reactogenicity, or pathogenicity of microbes such as bacteria, fungi, protozoa, and viruses.
“MBC” means minimal bacteriocidal concentration defined as the lowest concentration of an antimicrobial compound that kills 99.9% of the original inoculum of a microganism, or more stringently as the lowest concentration of an antimicrobial compound that kills all of the mircroorganisms of the original inoculum.
“MIC” means minimal inhibitory concentration defined as the lowest concentration of an antimicrobial agent that results in inhibition of visible growth of a microorganism (i.e., colonies on a plate or turbidity in broth culture) under standard conditions known in the art.
The term “bacteria,” and “bacterial” refer to all prokaryotic organisms, including those within all of the phyla in the Kingdom Procaryotae. It is intended that the term encompass all microorganisms considered to be bacteria including Mycoplasma, Chlamydia, Actinomyces, Streptomyces, and Rickettsia. All forms of bacteria are included within this definition including cocci, bacilli, spirochetes, spheroplasts, protoplasts, etc. Also included within this term are prokaryotic organisms which are gram negative or gram positive. “Gram negative” and “gram positive” refer to staining patterns with the Gram-staining process which is well known in the art (Finegold and Martin, Diagnostic Microbiology, 6th Ed. (1982), C. V. Mosby St. Louis, pp 13–15). “Gram positive bacteria” are bacteria which retain the primary dye used in the Gram stain, causing the stained cells to appear dark blue to purple under the microscope. “Gram negative bacteria” do not retain the primary dye used in the Gram stain, but are stained by the counterstain. Thus, gram negative bacteria appear red. A bacterial organism can be one selected from the group consisting of, but not limited to, Pseudomonas fluorescens, Pseudomonas aeruginosa, Pseudomonas acidovorans, Pseudomonas alcaligenes, Pseudomonas putida, Pseudomonas syringae, Pseudomonas aureofaciens, Pseudomonas fragi, Fusobacterium nucleatum, Treponema denticola, Porphyromonas gingivalis, Moraxella catarrhalis, Stenotrophomonas maltophilia, Burkholderia cepacia, Aeromonas hydrophilia, Escherichia coli, Citrobacter freundii, Salmonella typhimurium, Salmonella typhi, Salmonella paratyphi, Salmonella enteritidis, Shigella dysenteriae, Shigella flexneri, Shigella sonnei, Enterobacter cloacae, Enterobacter aerogenes, Klebsiella pneumoniae, Klebsiella oxytoca, Serratia marcescens, Francisella tularensis, Morganella morganii, Proteus mirabilis, Proteus vulgaris, Providencia alcalifaciens, Providencia rettgeri, Providencia stuartii, Acinetobacter calcoaceticus, Acinetobacter haemolyticus, Yersinia enterocolitica, Yersinia pestis, Yersinia pseudo tuberculosis, Yersinia intermedia, Bordetella pertussis, Bordetella parapertussis, Bordetella bronchiseptica, Haemophilus influenzae, Haemophilus parainfluenzae, Haemophilus haemolyticus, Haemophilus parahaemolyticus, Pasteurella multocida, Pasteurella haemolytica, Helicobacter pylori, Campylobacter fetus, Campylobacter jejuni, Campylobacter coli, Borrelia burgdorferi, Vibrio cholerae, Vibrio paramaemolyticus, Legionella pneumophila, Listeria monocytogenes, Neisseria gonorrhoeae, Neisseria meningitidis, Gardnerella vaginalis, Bacteroides spp., Clostridium difficile, Mycobacterium tuberculosis, Mycobacterium avium, Mycobacterium intracellulare, Mycrobacterium leprae, Corynebacterium diphtheriae, Corynebacterium ulcerans, Streptococcus spp., Enterococcus spp., Desulfvibrio spp., Actinomyces spp., Erwinia spp., Xanthomonas spp., Xylella spp., Clavibacter spp., Desulfomonas spp., Desulfovibrio spp., Desulfococcus spp., Desulfobacter spp., Desulfobulbus spp., Desulfosarcina spp., Deslfuromonas spp., Bacillus spp., Streptomyces spp., Clostridium spp., Rhodococcus spp., Thermatoga spp., Sphingomonas spp., Zymomonas spp., Micrococcus spp., Azotobacter spp., Norcardia spp., Brevibacterium spp., Alcaligenes spp., Microbispora spp., Micromonospora spp., Methylobacterium organophilum, Pseudomonas reptilivora, Pseudomonas carragienovora, Pseudomonas dentificans, Corynebacterium spp., Propionibacterium spp., Xanothomonas spp., Methylobacterium spp., Chromobacterium spp., Saccharopolyspora spp., Actinobacillus spp., Alteromonas spp., Aeronomonas spp., Agrobacterium tumefaciens, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus hominis, Staphylococcus haemolyticus, Staphylococcus warneri, Staphylococcus cohnii, Staphylococcus saprophyticus, Staphylococcus capitis, Staphylococcus lugdunensis, Staphlyococcus intermedius, Staphylococcus hyicus, Staphylococcus saccharolyticus and Rhizobium spp.
“Fungi,” “Fungal,” “Fungus,” or “Fungal Organism” is intended to mean a eukaryotic cell having a nuclear membrane and cell wall. The subject fungi may grow as single cells (e.g., yeasts), chains (e.g., hyphae), aggregates, rafts and the like, and are not plant or mammalian cells. A fungal organism can be one selected from the group consisting of, but not limited to, Absidia spp., Actinomadura madurae, Actinomyces spp., Allescheria boydii, Altemaria spp., Anthopsis deltoidea, Aphanomyces spp., Apophysomyces eleqans, Armillaria spp., Arnium leoporinum, Aspergillus spp., Aureobasidium pullulans, Basidiobolus ranarum, Bipolaris spp., Blastomyces dermatitidis, Botrytis spp., Candida spp., Centrospora spp., Cephalosporium spp., Ceratocystis spp., Chaetoconidium spp., Chaetomium spp., Cladosporium spp., Coccidioides immitis, Colletotrichum spp, Conidiobolus spp., Corynebacterium tenuis, Cryptoporiopsis spp., Cylindrocladium spp., Cryptococcus spp., Cunninghamella bertholletiae, Curvularia spp., Dactylaria spp., Diplodia spp., Epidermophyton spp., Epidermophyton floccosum, Exserophilum spp., Exophiala spp., Fonsecaea spp., Fulvia spp., Fusarium spp., Geotrichum spp., Guignardia spp., Helminthosporium spp., Histoplasma spp., Lecythophora spp., Macrophomina spp., Madurella spp., Magnaporthe spp., Malassezia furfur, Microsporum spp., Monilinia spp., Mucor spp., Mycocentrospora acerina, Nectria spp., Nocardia spp., Oospora spp., Ophiobolus spp., Paecilomyces spp., Paracoccidioides brasiliensis, Penicillium spp., Phaeosclera dematioides, Phaeoannellomyces spp., Phialemonium obovatum, Phialophora spp., Phlyctaena spp., Phoma spp., Phomopsis spp., Phymatotrichum spp., Phytophthora spp., Pythium spp., Piedraia hortai, Pneumocystis carinii, Puccinia spp., Pythium insidiosum, Rhinocladiella aquaspersa, Rhizomucor pusillus, Rhizoctonia spp., Rhizopus spp., Saccharomyces spp., Saksenaea vasiformis, Sarcinomyces phaeomuriformis, Scerotium spp., Sclerotinia spp., Sphaerotheca spp., Sporothrix schenckii, Syncephalastrum racemosum, Taeniolella boppii, Taphrina spp., Thielaviopsis spp., Torulopsosis spp., Trichophyton spp., Trichosporon spp., Ulocladium chartarum, Ustilago spp., Venturia spp., Verticillium spp., Wangiella dermatitidis, Whetxelinia spp., Xylohypha spp., and their synonyms.
By “exponential” is meant the phase of microbial growth during which the microbial population is growing at a constant and maximum rate, dividing and doubling at regular intervals (i.e., log phase growth, actively growing cells).
By “glucosyltransferase activity” we mean the enzymatic activity which promotes the synthesis of complex oligosaccharides by catalyzing the addition or conformation of sugar residues, for example, the formation of cyclic-β-(1,3)-glucans.
By “glucan synthesis” we mean the formation of saccharide molecules, for example cyclic-β-(1,3)-glucan, through natural or recombinant means.
By “inhibitor” we mean a compound that is able to reduce the expression of a gene encoding a polypeptide and/or the expression of the polypeptide, or the biological activity of a polypeptide, e.g., a polypeptide that functions as an efflux pump or a glucosyltransferase, by at least 5%, more desirably, by at least 10%, even more desirably, by at least 25%, 50%, or 75%, and most desirably, by 90% or more.
By “binding” we mean a non-covalent or covalent interaction between components. By “component” we mean a protein, a nucleic acid molecule, a glucan, or a compound. The binding components interact with a binding constant (Kd) equal to less than 1 uM, more desirably less that 100 nM, and most desirably less than 10 nM.
“Transformed cell” means a cell into which (or into an ancestor of which) has been introduced, by means of recombinant DNA techniques, a DNA molecule encoding (as used herein) a polypeptide described herein (for example, an NvdB polypeptide).
“Operably linked” means that a gene and a regulatory sequence(s) are connected in such a way as to permit gene expression when the appropriate molecules (e.g., transcriptional activator proteins) are bound to the regulatory sequence(s).
“Transgene” means any piece of DNA which is inserted by artifice into a cell, and becomes part of the genome of the organism which develops from that cell. Such a transgene may include a gene which is partly or entirely heterologous (i.e., foreign) to the transgenic organism, or may represent a gene homologous to an endogenous gene of the organism.
The term “expression vector” as used herein refers to a recombinant DNA molecule containing a desired coding sequence and appropriate nucleic acid sequences necessary for the expression of the operably linked coding sequence in a particular host organism. Nucleic acid sequences necessary for expression in prokaryotes usually include a promoter, an operator (optional), and a ribosome binding site, often along with other sequences. Eukaryotic cells are known to utilize promoters, enhancers, and termination and polyadenylation signals.
“Promoter” means minimal sequence sufficient to direct transcription. Also included in the invention are those promoter elements which are sufficient to render promoter-dependent gene expression controllable for cell-type specific, tissue-specific or inducible by external signals or agents; such elements may be located in the 5′ or 3′ regions of the native gene.
“Positioned for expression” means that the DNA molecule is positioned adjacent to a DNA sequence which directs transcription and translation of the sequence (i.e., facilitates the production of, e.g., an NdvB polypeptide, a recombinant protein or a RNA molecule).
By “biofilm” is meant a population of microorganisms comprised of a single species or multiple species that form at an interface, e.g., on a biotic or abiotic surface exposed to liquid, and have increased resistance to antimicrobial agents relative to planktonic cells growing in the expotential phase. The population of cells may also have one or more of the following characteristics: a) produce or are enclosed by an extracellular matrix, b) adhere to a surface, c) form a complex architecture, d) have a gene and/or protein expression profile different from planktonic cells growing in the exponential phase under similar conditions.
By “biological activity” is meant an activity associated with a microbial organism, including the formation, development, and dissolution of biofilms.
By “culture system” is meant a fluid containing single-celled organisms living independently or as part of a multi-cellular community or colony. The major groups of microorganisms include archaea, bacteria, fungi, protozoa, and algae.
By “expose” is meant to allow contact between a substance, including a compound, culture supernatant, or extract thereof, and a microorganism or target organism.
By “environment” is meant the habitat or living conditions of a population of microorganisms, such as source microorganisms or target organisms.
By “extract” is meant a product obtained from treating supernatant from a culture system to at least one purification step of any kind. In a desired embodiment, the purification is designed to isolate or increase the concentration of a biofilm modulating compound or remove undesirable elements within the supernatant.
By “microorganism,” “microbial organism,” “microbe,” or “microbial” is meant a microscopic, single-celled organism that may either live independently or as part of a multi-cellular community or colony. The major groups of microorganisms include archaca, bacteria, fungi, protozoa, and algae.
By “resistant” is meant a increase greater than 5% in the MBC or MIC for at least one selected antimicrobial agent, or an decreased killing under a selected growth condition in the presence of at least one antimicrobial agent compared to a control microorganism grown under the same conditions. This term may refer to the ability of a microorganism to the ability of a microorganism to maintain viability, virulence or pathogenicity in the presence of at least one antimicrobial agent compared to a control mircroorganism grown under the same conditions.
By “sensitive” is meant a decrease greater than 5% in the MBC or MIC for at least one selected antimicrobial agent, or an increased killing under a selected growth condition in the presence of at least one antimicrobial agent compared to a control microorganism grown under the same conditions. This term may refer to the ability of a microorganism to the ability of a microorganism to maintain viability, virulence or pathogenicity in the presence of at least one antimicrobial agent compared to a control mircroorganism grown under the same conditions
By “modulating” is meant changing, by increase, decrease or otherwise. The change may be in amount, timing, or any other parameter. A decrease or increase in, for example, cell growth, viability, virulence, or pathogenicty, may be by at least 5%, more desirably at least 10%, even more desirably at least 25%, most desirably by 50% or more.
“Modulation” refers to the capacity to either enhance or inhibit a functional property of a biological activity or process (e.g., enzyme activity, receptor binding, cell growth, viability, virulence, or pathogenicty). Such enhancement or inhibition may be contingent on the occurrence of a specific event, such as activation of a signal transduction pathway, and/or may be manifest only in particular cell types.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a comparison of wild type (left panel) ad 45E7 (right panel) biofilm architecture. Flow cell grown strains are shown after 3 days of growth. Both strains exhibit the typical macrocolonies and channels characteristic of these biofilms formed by P. aeruginosa. These images are reconstructed from XZ slices through the biofilm  ̃35 μm in height) using the Volocity software package.
FIG. 2 presents the results of the flow cell assay for antibiotic resistance with 45E7. The left most panels (phase-contrast micrographs) show the architecture of the 24 hr old biofilm. The syto-9 panels indicate viable cells and the PI (propidium iodide) panels indicate dead cells.
FIG. 3 presents the results of the colony biofilm assay with 45E7. Colonies of the wild type (filled symbols) and the 45E7 mutant (open symbols) were transferred to solid medium without (triangles) or with 0.2 mg/ml Tb (squares). The viability of the wild-type drops  ̃100-fold over 48 hrs with Tb treatment, while the 45E7 mutant drops below detection (indicated by the asterisk). In the absence of antibiotic, there is no difference in viability between the two strains.
FIG. 4 demonstrates the difference between wild type and 45E7 fractiontation characteristics of periplasmic glucans. The elution profiles of periplasmic extracts of the wild type (squares) and 45E7 mutant (circle) on a G75 column are shown. Fractions 45–60 have anthrone positive material in periplasmic extracts from the wild type strain. This anthrone positive material is absent from the periplasmic extracts of the 45E7 mutant. Work in other organisms has shown that cyclic glucans typically elute in this size range. The Y-axis is a measure of absorbance at 620 nm.
FIG. 5 presents the results of the colony biofilm assay with 30B 1. The viable cell count for the wt (filled symbols) and 30B1 mutant (open symbols) either untreated (triangles) or treated with Tb (squares) are shown over 48 hrs. There is no difference in viable counts between these strains when grown in the absence of antibiotics. The wild type decreases 100-fold in the presence of Tb, while the viable count of the 30B1 mutant is below detection at 48 hrs (indicated by the asterisk).
FIGS. 6A–6E presents the nucleotide (SEQ ID NO:1) and amino acid (SEQ ID NO:2) sequence of NdvB (PA1163).
FIGS. 7A–7K presents the nucleotide (SEQ ID NO:3) and amino acid (SEQ ID NO:4) sequence of PA1874.
FIGS. 8A–8B presents the nucleotide (SEQ ID NO:5) and amino acid (SEQ ID NO:6) sequence of PA1875.
FIGS. 9A–9D presents the nucleotide (SEQ ID NO:7) and amino acid (SEQ ID NO:8) sequence of PA1876.
FIGS. 10A–10B presents the nucleotide (SEQ ID NO:9) and amino acid (SEQ ID NO:10) sequence of PA1877.
FIG. 11 presents the nucleotide (SEQ ID NO:11) and amino acid (SEQ ID NO:12) sequence of PA4142.
FIG. 12 presents the nucleotide (SEQ ID NO:13) and amino acid (SEQ ID NO:14) sequence of PA4143.
FIG. 13 presents the nucleotide (SEQ ID NO:15) and amino acid (SEQ ID NO:16) sequence of PA4144.
FIG. 14 presents the nucleotide (SEQ ID NO:17) and amino acid (SEQ ID NO:18) sequence of PA2389.
FIG. 15 presents the nucleotide (SEQ ID NO:19) and amino acid (SEQ ID NO:20) sequence of PA2390.
FIG. 16 presents the nucleotide (SEQ ID NO:21) and amino acid (SEQ ID NO:22) sequence of PA2391.
FIG. 17 presents the nucleotide sequence of a putative expression control sequence (SEQ ID NO:23) located upstream of PA1874.
FIG. 18 presents the nucleotide sequence of a putative expression control sequence (SEQ ID NO:24) located upstream of PA4142.
FIG. 19 presents the nucleotide sequence of a putative expression control sequence (SEQ ID NO:25) located upstream of PA2389.
FIG. 20 presents the nucleotide sequence of a putative expression control sequence (SEQ ID NO:26) located upstream of PA1163.
FIG. 21 presents the results the results of colony biofilm assay. The viable cell count for vector only (circles) or vector encoding PA4142-PA4144 (squares) was determined over 3 days in the presence (filled symbols) or absence (open symbols) of Tb.
FIG. 22 presents the amino acid sequence (SEQ ID NO:27) of B. japonicum ndvB (GenBank Accession No. AAC62210).
FIG. 23 presents the amino acid sequence (SEQ ID NO:28) of an Agrobacterium tumefaciens protein (GenBank Accession No. NP 357541).
FIGS. 24A–24C presents the nucleotide (SEQ ID NO:29) and amino acid SEQ ID NO:30) sequence of Pseudomonas putida KT2440.
FIGS. 25A–25C presents the nucleotide (SEQ ID NO:31) and amino acid (SEQ ID NO:32) sequence of a Pseudomonas syringae gene.



DETAILED DESCRIPTION OF THE INVENTION
We posit that biofilm resistance to antimicrobial agents is part of a regulated developmental process and thus would require an identifiable set of genetic determinants. Based upon this hypothesis, a screen was designed to identify genes which, when mutated, would affect the ability of biofilm cells to resist the effects of an antimicrobial agent, while having no substantial effect on the sensitivity of planktonic cells growing in the exponential phase cells to the same antimicrobial agent. This screen was based on a modification of the microtiter plate assay that yielded surface attachment mutants (sad) of Pseudomonas aeruginosa and P. fluorescens (O'Toole, G. A., and R. Kolter. Mol. Microbiol. 30(2):295–304, 1998; O'Toole, G. A., and R. Kolter, Mol. Microbiol. 28:449–461, 1998). In the present studies, bacteria were cultured on the same minimal M63 medium expect arginine (0.4%) was used as the sole source of carbon and energy, and cultures were incubated for 24 hours. Other screens and techniques for generating mutations in cell components that function in biofilm resistance to antimicrobial agents are well known in the art, for example, the use of transposon insertion and chemical mutagenesis.
The microtiter plate assay was modified to measure the increase in resistance developed by the wild type strain when growing in a biofilm. The wells of the microtiter dish are inoculated with bacteria and biofilms are allowed to form on the walls of the wells for 24 hrs in the absence of any shear force. After the biofilms had formed on the wells of the microtiter dish, the spent medium was replaced with the same media containing an antimicrobial agent. In this case, we used the aminoglycoside antibiotic tobramycin (Tb), an antibiotic that targets protein synthesis. Tb was selected because it is the primary antibiotic used to treat cystic fibrosis patients with chronic P. aeruginosa lung infections (Banerjee, D., and D. Stableforth, Drugs, 60(5):1053–64, 2000; Bonsignore, C. L., Pediatr Nurs. 24(3):258–9, 1998; Ratjen, F, Int J Antimicrob Agents 17(2):93–6, 2001). After exposing the biofilms to Tb for 24 hours, the antibiotic-containing medium is removed and replaced with fresh antibiotic-free medium. Any bacteria surviving in the biofilm outgrow and repopulate the planktonic phase of the wells. Viable cells were detected by plating on rich medium. Using this assay, we determined that the minimal bacteriocidal concentration (MBC) of Tb for the wt biofilm grown cells is 0.4 mg/ml. The MBC of planktonic cells was determined by adding the antibiotic to cells at the time they were inoculated into the microtiter dish, incubating the cells in the presence of antibiotic for 24 hrs, and assessing cell viability by plating on rich medium. Using this assay, the planktonic MBC was shown to be 0.008 mg/ml, a 50-fold decrease relative to the biofilm-grown bacteria.
Using the assay for biofilm-related antibiotic resistance described above, a library of random P. aeruginosa PA14 transposon insertion mutants was screened for the inability to develop characteristic increase in resistance of biofilm-grown cells. The concentration of Tb used in the screen was 0.2 mg/ml, a concentration 25-fold greater than the planktonic MBC, but still below the concentration that will kill biofilm grown cells. From a library of 4,320 transposon mutants, forty-three putative mutants defective in biofilm-related Tb resistance were identified.
The goal of the screen was to identify mutants with a biofilm-related defect in the development of antimicrobial agent resistance. Therefore, the 43 candidate mutants were subjected to a series of secondary tests to confirm the biofilm-related phenotype. Of the original 43 candidate mutants from the initial screen, two mutants grew as well as the wild type in liquid culture, formed a wild-type biofilm in the microtiter plates, and had a planktonic MBC indistinguishable from the parent strain. These mutants, designated 45E7 and 30 B1, were characterized further.
Characterization of the 45E7 Mutant.
In addition to the decrease in sensitivity to Tb, we determined the MBC of biofilm and planktonic cells growing in the expotential phase for gentamycin (Gm) and ciprofloxacin (Cip). Gm, like Tb, is an aminoglycoside protein synthesis inhibitor while Cip is a fluoroquinolone that targets DNA gyrase. Table 1 shows the results of these studies. For all antibiotics, there was no difference in the MBC of planktonic cells growing in the exponential phase between the wild type and 45E7 mutant. The MCB of biofilm grown 45E7 was lower for all three antibiotics when compared to the wt: Tb (16-fold), Gm (8-fold) and Cip (8-fold).







TABLE 1







Bioflim and planktonic (exponential phase) resistance


of the wild type and 45E7 mutant.












Tb
Gm
Cip














Strain
MBC-P
MBC-B
MBC-P
MBC-B
MBC-P
MBC-B





Wild-type
0.008
0.4 
0.04
0.5 
0.004
0.05 


45E7
0.008
0.025
0.04
0.06
0.004
0.006





Notes: MBC-P, MBC of planktonically grown cells; MBC-B, MBC of biofilm grown cells. All antibiotic concentrations are in mg/ml.






One of the characteristics of biofilm grown bacteria is their distinctive architecture. Currently, it is not clear what relationship, if any, exists between the architecture of the biofilm and resistance to antimicrobial agents. Early studies of biofilm grown cells suggested that inhibition of antibiotic diffusion through the biofilm could account for the increased resistance of these communities (Costerton et al., Microbial biofilms, p. 711–745. In L. N. Omston, A. Balows, and E. P. Greenberg (ed.), Annu. Rev. Microbiol., vol. 49. Annual Reviews, Inc., Palo Alto, Calif., 1995). Therefore, it was possible that altering biofilm architecture could increase diffusion of Tb through the biofilm, thereby increasing sensitivity to this agent. In support of this idea, a quorum-sensing mutant of P. aeruginosa that exhibited altered architecture was reported to be abnormally sensitive to SDS (Davies et al., Science 280(5361):295–298, 1998). However, the same mutant was as resistant to killing by the antibiotic ofloxacin as the wild type biofilm cells (Brooun et al., Antimicrob Agents Chemother. 44(3):640–6, 2000).
We utilized flow cells to analyze the architecture of the wild type and mutant strains. A flow cell allows a continuous supply of fresh medium to be delivered to a biofilm that is formed on the walls of a small, enclosed chamber. One side of this chamber is a glass cover slip, and the chamber can be mounted on to a microscope to allow for the non-destructive imaging of the biofilm. GFP-tagged wild type and 45E7 strains were inoculated into different chambers of a flow cell and the architecture of the biofilms produced by these strains was analyzed by epifluorescence microscopy. The reconstructed architecture of the wild-type and 45E7 mutant is shown in FIG. 1. This analysis showed that is no discernible difference in the architecture of these strains.
Currently, there are no standard methods for determining biofilm resistance to antimicrobial agents. Thus, we utilized two other assays of biofilm antibiotic resistance to demonstrate that the phenotype observed in the microtiter plate was robust and could be observed across a number of experimental models. We chose to analyze this mutant in flow cell and colony biofilm assays.
In order to document the sensitivity phenotype of the biofilms in the flow cell, the biofilm of the wild type and 45E7 strains were allowed to form. After the biofilm had developed for 24 hrs 0.2 mg/ml Tb was added to the medium. After 24 hours of exposure to Tb, flow through the cell was stopped and the BacLight viability stain was injected into the flow chambers. BacLight differentiates between cells with intact membranes (considered “live”) and those with damaged membranes (considered “dead”). After 15 minutes of staining, flow through the chamber was resumed and following a 15 minute wash the cells were examined by epifluorescent microscopy (FIG. 2). The left-hand panels show phase contrast images—there was no difference in biofilm architecture between these strains (see also FIG. 1). The center and right panel shows that there were more live than dead cells in the Tb-treated biofilm of the wild type strain. Conversely, there were more dead cells than live ones in the Tb-treated biofilm of the 45E7 mutant strain. This result confirmed the drug sensitivity phenotype first observed in the microtiter plate assay.
We also used the quantitative colony biofilm assay to document the 45E7 mutant phenotype. It has been reported that bacterial colonies develop some of the properties associated with biofilms, including increased resistance to biocides (Anderl et al., Antimicrob Agents Chemother. 44(7):1818–24, 2000; Stewart, P. S., Biotechnol Bioeng. 59(3):261–72, 1998). Colony biofilms were formed on polycarbonate filters for 48 hrs then transferred to solid media containing Tb. Viable cell numbers in the colony was determined after 4, 24 and 48 hours of exposure to Tb (FIG. 3). The 45E7 biofilm cells remained as resistant to the effects of Tb as the wild type at the first two time points assayed. However, at 48 hours, while the wild type biofilm cell viability was only reduced by 100-fold, no viable cells were detected for the 45E7 mutant. In the absence of Tb, there was difference in viability between the two strains tested. Taken together with the data presented above, we concluded that the 45E7 mutant is less resistant to the antimicrobial effects of Tb when growing in a biofilm.
The 45E7 Mutation is in PA1163, a Putative Glucosyltransferase
The transposon insertion carried by the 45E7 strain was cloned and the DNA flanking the transposon sequenced and compared to the published sequence of P. aeruginosa PAO1. The gene disrupted in 45E7, PA1163 is 58% identical to a Bradyrhizobium japonicum gene ndvB. The ndvB gene of Bradyrhizobium japonicum codes for a glucosyltransferase that is required for the syntheis of cyclic-β-(1,3), β-(1,6)-glucans (Bhagwat et al., J Bacteriol. 178(15):4635–42, 1996). Located in the periplasm and extrcellular media, cyclic glucans have been shown to play a role in growth in low osmotic media and in plant infection (Breedveld, M. W., and K. J. Miller, Microbiol Rev. 58(2):145–61, 1994). In B. japonicum, another gene, ndvC acts in concert with ndvB to form the β-(1,3), β-(1,6) linkages. ndvC mutants produce glucans with only β-(1,3) linkages (Bhagwat et al., Plant Physiol . 119(3):1057–64, 1999). Furthermore, in Sinorhizobium melioloti, the ndvA gene product is thought to be required for the export of cyclic glucans from the periplasm to the extracellular medium (Breedveld, M. W., and K. J. Miller. Microbiol Rev. 58(2):145–61, 1994). Upon investigation of the P. aeruginosa genome, we noticed that there is no ndvC homolog present, but there are three genes with  ̃50% homology to S. melioti ndvA. Thus, it seemed likely that P. aeruginosa produces periplasmic and extracellular β-(1,3)-glucans. To confirm that cyclic glucans were made by the wild type strain and that these glucans were altered or not present in the ndvB PA1163 mutant we characterized the periplasmic and extracellular polysaccharides produced by these strains. Ethanol extracts from both the periplasm and the extracellular medium of these strains were fractionated by gel filtration chromatography to estimate the molecular weight of the material (Wang et al., J Bacteriol. 181(15):4576–83, 1999). Fractons were assayed for polysaccharides using the colorometric anthrone-sulfuric acid method. The anthrone assay measures the total concentration of carbohydrate, or monosaccharide equivalents, in a sample (Loewus, F. A., Anal. Chem. 24:219, 1952). Anthrone-positive extracellular material from the wild type eluted from the sizing column in fractions that corresponded to a molecular weight (MW) of approximately 1500, while the mutant produced no anthrone positive fraction in the 100 MW range. In contrast, anthrone-positive material from the 45E7 mutant extracts eluted in the column void volume, indicates a MW of greater than 80,000, possibly indicating an aggregate of polysaccharides.
The material extracted from the periplasm was also fractionated by gel filtration chromatography and it was found that the anthrone-positive material produced by the wild type and mutant strains also differed (FIG. 4). While the wild type strain produced material that eluted across the molecular weight range of the column, the mutant strain lacked anthrone-positive material in fractions where cyclic glucans typically elute (Wang et al., J Bacteriol. 181(15): 4576–83, 1999).
Based on the current understanding of the roles of cyclic glucans in B. japonicum, S. meliloti and Agrobacterium tumefaciens, we envisioned three possible models to describe the role of these molecules in the development of resistance in biofilm populations. Cyclic glucans may be required to: i) maintain the osmotic balance within biofilms, ii) sequester antimicrobial agents in biofilm-grown cells, or iii) act as signaling molecules required for the development of resistance to antimicrobial agents.
To test the hypothesis that cyclic glucans are important for hypo-osmotic adaptation, we examined the wild type and -PA1163 strains for their ability to survive and grow in low osmotic strength medium. As a first step, we diluted overnight cultures into water and monitored the survival of the wild type and mutant strains over 24 hrs. There was no difference in the survival of these strains in water. We assessed the growth of both strains in liquid 1/10 strength minimal salts M63 medium (a hypo-osmotic medium compared to full strength M63) and on solid GYM media with no salt. The ndvB mutant of S. meliloti grows very slowly on GYM media, while the wild type shows no growth defect (Bhagwat et al., FEMS Microbiol Lett. 114(2): 139–44, 1993; Cangelosi et al., J Bacteriol. 172(4):2172–4, 1990; lelpi et al., J Biol Chem. 265(5):2843–5 1990). There was no difference in the growth of the wild type and PA1163 mutant of P. aeruginosa on these media, suggesting that PA1163 may not be involved in hypo-osmotic adaptation in P. aeruginosa. 
A number of reports suggest that cyclic glucans can bind or sequester a range of chemically unrelated compounds [reviewed in (Breedveld, M. W., and K. J. Miller. Microbiol Rev. 58(2):145–61, 1994)]. This suggested the possibility that glucans in the extracellular and/or periplasmic space might sequester antimicrobial agents and thus prevent them from entering into the cytoplasm of the bacterial cell. To test this idea, we utilized the putative cyclic glucan fractions isolated by gel filtration chromatography from the periplasm of the wild-type strain (see above). This material was incubated in the presence of Tb, then spotted on a filter disk placed on a freshly spread lawn of E. coli. Filter disks spotted with Tb alone, glucans alone, and water were also included as controls. Preliminary studies with the disk-diffusion assay indicated that glucan-treated Tb was decreased in its zone of killing as compared to Tb alone. Glucans had no antimicrobial activity at the concentrations used in these assays. These data indicate that the presence of cyclic glucans can decrease the antimicrobial activity of Tb, and is consistent with a role for glucans in the sequestering of antimicrobial agents.
PA1163 mRNA is Expressed in Biofilm Grown Cells, but not in Planktonic Cells
In order to investigate the expression pattern of PA1163 we used a continuous flow system to grow planktonic and biofilm bacteria. Total mRNA was harvested from both biofilm and planktonic cells and RT-PCR used to detect the presence of PA1163 transcript. In this study expression of rplU, a gene known to be expressed in both planktonic cells and biofilm grown cells, was used as a control. Chromosomal DNA was used to identify the expected size of the PA1163 mRNA. This study revealed that PA1163mRNA is expressed in biofilm grown cells and is undetectable in planktonic cells. These data indicate that PA1163 may be poorly expressed (or not expressed at all) under planktonic conditions. The fact that PA1163 appears to be expressed only in biofilm-grown cells is consistent with our model that PA1163 plays a role in biofilm-related antibiotic resistance.
P. aeruginosa PA1163 can Complement a ndvB S. meliloti Mutant
The Rm8519 ndvB mutant of S. meliloti exhibits a hypo-osmotic growth phenotype. In order to investigate whether P. aeruginosa PA1163 can complement this mutant, and is thus likely to encode a glucosyltransferase, we introduced a vector pSMC654 containing the P. aeruginosa PA1163 gene into the ndvB mutant of S. meliloti. As a control, wild type strain and the ndvB mutant of S. meliloti were transformed with empty vector pSW213 alone. The PA1163 containing vector (but not the empty vector) complemented the ndvB mutant of S. meliloti for its hypo-osmotic growth phenotype. Therefore, the PA 1163 gene of P. aeruginosa can functionally substitute for S. meliloti ndvB, strongly suggesting that P. aeruginosa PA1163 protein is a glucosyltransferase.
Wild-Type P. aeruginosa, but not PA1163 Mutants Produce Glucans.
We compared carbohydrates produced by wild-type P. aeruginosa to purified cyclic glucan from S. meliloti using chromatographic analysis. This analysis revealed that glucans produced by wild-type P. aeruginosa elute in same fractions as purified cyclic glucan from S. meliloti. Similarly eluting material was not detectable in carbohydrates produced by a P. aeruginosa PA1163 mutant. Moreover, analysis of the pooled glucan-containing fractions from the wild-type P. aeruginosa strain showed that glucose is the predominate sugar as judged by a glucose standard and consistent with their identification as glucans. The same fractions from the PA1163 mutant did not contain glucose.
Glucans Interact with Tb in vitro
If periplasmic glucans were indeed sequestering Tb, we predicted that these molecules should interact in vitro. To test this possibility, we examined in vitro interactions of purified glucans with Tb. Tb was loaded onto a C18 column and its elution profile was monitored by a bioassay on a lawn of sensitive bacteria. A zone of clearing indicated the presence of Tb in a fraction. Tb was detected in the column flow-through and first water wash, but not in any subsequent fractions. In contrast, when a crude periplasmic carbohydrate extracted from the wild type strain was pre-loaded onto the column, a portion of the Tb was retained on the column and eluted with 25% acetonitrile. Thus, the presence of the wild type extract on the column retarded the elution of Tb, suggesting that periplasmic glucans interacted with Tb.
To determine which components of the crude extract were responsible for the Tb retention on the C18 column, we performed the same experiment as above except the C-18 column was pre-loaded with partially pure glucan-containing fractions from a G-75 gel filtration sizing column. Tb was retained on the column pre-loaded with material from the wild type extract and eluted from the column with 25% acetonitrile. In contrast, no Tb activity was present in the 25% acetonitrile fraction from the column preloaded with the corresponding fractions isolated from the P. aeruginosa PA1163 mutant. Only the material present in glucan-containing fractions derived from the wild type interacted with and changed the chromatographic behavior of Tb.
Characterization of the 30B1 Mutant.
A second mutant strain defective in biofilm specific Tb resistance, designated 30B1, was isolated and characterized. Like 45E7, this strain grew as well as the wild type in liquid culture, formed a wild-type biofilm in the microtiter plates, and had an exponential phase planktonic MBC indistinguishable from the parent strain. This mutant is also less resistant to the antibiotics Gm and Cip. In all cases, the decrease in resistance of this mutant is less than the decrease observed for the 45E7 mutant. These results suggest that the functions disrupted in this strain debilitate biofilm-related antibiotic resistance via a different mechanism.







TABLE 2







Bioflim and planktonic resistance of the wild type and 45E7 mutant.












Tb
Gm
Cip














Strain
MBC-P
MBC-B
MBC-P
MBC-B
MBC-P
MBC-B





Wild-type
0.008
0.4
0.04
0.5 
0.004
0.05 


30B1
0.008
0.1
0.04
0.25
0.004
0.0125





Notes: MBC-P, MBC of planktonically grown cells; MBC-B, MBC of bioflim grown cells. All antibiotic concentrations are in mg/ml.






We also examined the architecture of this mutant and showed that it was identical to the wild-type strain as judged by the flow cell assay and analysis of the biofilms by fluorescence microscopy (data not shown).
The colony biofilm assay was also utilized to assess the antibiotic resistance of the 30B1 mutant strain as described above. As was observed for the 45E7 mutant, the 30B1 strain showed a marked decrease in resistance to Tb as compared to the wild-type strain (FIG. 5). After 48 hrs of exposure to Tb, the viability of the wild type had dropped  ̃100-fold, while there were no viable cells detected for the 30B1 mutant (a drop in viable count of  ̃109). This experiment confirms the results obtained in the microtiter dish assay.
The 30B1 Mutation is in PA1874
The transposon insertion carried by the 30B1 strain was cloned and the DNA flanking the transposon was sequenced and compared to the published sequence of P. aeruginosa PAO1. The open reading frame (ORF) disrupted by the transposon, PA1874, encodes a predicted outer membrane protein with sequence similarity to LapA of P. putida (42% similarity) and Bap of Staphylococcus aureus (46% similarity). Both of these proteins are important for biofilm development. LapA is required for the colonization of seeds by P. putida and Bap was identified in a screen for mutants unable to make a biofilm (Cucarella et al., J Bacteriol. 183(9):2888–2896, 2001; Espinosa-Urgel et al., J Bacteriol. 182(9):2363–2369, 2000).
In P. aeruginosa, PA1874 is the first gene in a predicted four gene operon that, in addition to PA1874, includes: PA1875, an OprN-like outer membrane protein that bears some similarity to outer membrane proteins in the RND family; PA1876, a protein that is similar to an ABC family ATPase; and PA1877, a protein that appears to be a ABC family membrane fusion protein.
As noted above, PA1875 is similar to OprN. The OprN protein is part of the MexEF-OprN multidrug efflux pump, a RND-type efflux pump which is involved in fluoroquinolone resistance (Nikaido, H. 1994. Prevention of drug access to bacterial targets: permeability barriers and active efflux. Science. 264(5157):382–8; Piddock, L. J. 1999. Mechanisms of fluoroquinolone resistance: an update 1994–1998. Drugs. 58(Suppl 2):11–8. Thus, the PA1874-PA1877 operon encodes components of both multi-drug efflux pumps and ABC transporters. Although other RND efflux pumps include an outer membrane protein and a membrane fusion protein, they do not typically include a ABC family cytoplasmic membrane-located ATPase and they do not typically require two outer membrane proteins (Poole, K., J Mol Microbiol Biotechnol. 3(2):255–64, 2001). Thus, the PA1874-PA1877 operon appears to encode anew type of hybrid efflux pump that combines features of a RND multidrug efflux pumps and ABC transporters.
Identification of Additional Hybrid Efflux Pumps
We analyzed the sequence of the P. aeruginosa genome in a effort to identify other genetic loci that resemble PA1874-PA1877. We identified two other genetic loci, PA4142-PA4143 and PA2389-PA2391, that are similar to the PA1874-PA1877 operon in both sequence and organization. Each of these loci appears to encode three, rather than four polypeptides. These loci encode putative hybrid efflux pumps that are predicted to play a role in biofilm resistance.
Table 3 summarizes information for each of the proteins in the three identified hybrid efflux pump operons. Putative expression control sequences upstream of PA1874,PA4142, and 2389 are shown in FIGS. 17, 18 and 19 respectively.







TABLE 3







Summary of Hybrid Efflux Pump Genes













Nucleotide





Proposed
and Protein
Nucleic Acid
Protein SEQ


Name
Function
Sequence
SEQ ID NO.
ID NO.





PA1874
OMP
FIG. 7
SEQ ID NO:3
SEQ ID NO:4


PA1875
OprN-like
FIG. 8
SEQ ID NO:5
SEQ ID NO:6



OMP (similar



to RND family



OMP)


PA1876
ABC family
FIG. 9
SEQ ID NO:7
SEQ ID NO:8



ATPase


PA1877
MFP
FIG. 10
SEQ ID NO:9
SEQ ID NO:10


PA4142
MFP
FIG. 11
SEQ ID NO:11
SEQ ID NO:12


PA4143
ABC family
FIG. 12
SEQ ID NO:13
SEQ ID NO:14



ATPase


PA4144
OprM-like
FIG. 13
SEQ ID NO:15
SEQ ID NO:16



OMP efflux



pump protein



(similar to



RND family



OMP)


PA2389
MFP
FIG. 14
SEQ ID NO:17
SEQ ID NO:18


PA2390
ABC family
FIG. 15
SEQ ID NO:19
SEQ ID NO:20



ATPase


PA2391

FIG. 16
SEQ ID NO:21
SEQ ID NO:22









The putative Hybrid Efflux Pump Encoded by PA4144-PA4146 Appears to Play a Role in Biofilm Resistance
In order to determine whether the putative hybrid efflux pump encoded by PA4144-PA4146) plays a role antibiotic resistance, we inserted a nucleotide sequence that includes PA4144-PA4146 into a medium copy plasmid pSMC32 and used the resulting vector pSMC51 to transform P. aeruginosa strain PA14. Neither the PA4144-PA4146 encoding vector nor the parent plasmid had any effect on the resistance of planktonic P. aeruginosa to Tb.
We also investigated the resistance of the transformed cells to Tb when grown as a biofilm. Interestingly, wild-type P. aeruginosa carrying the PA4144-PA4146 encoding vector became hypersensitive to antibiotics in the colony biofilm assay for reasons that are not clear, but may be due to the increased metabolic burden of carrying a plasmid (see FIG. 21). Therefore, we created a “synthetic sensitivity” to antibiotics by having the wild type P. aeruginosa strain carry a parent plasmid (no PA4144-PA4146 encoding sequences). As shown in FIG. 21, a P. aeruginosa strain carrying both this parent plasmid and the PA4144-PA4146 encoding vector regained a level of antibiotic resistance similar to the of an untransformed strain (no parent plasmid and no PA4144-PA4146 encoding vector). These indirect data suggest that the hybrid efflux pump encoded by PA4144-PA4146 has the ability to confer antibiotic resistance in biofilm-grown bacteria and supports our hypothesis that these novel, hybrid efflux pumps play a role in biofilm-related antibiotic resistance.
Identification of Additional Proteins Resembling PA1163
We used sequence homology searching to identify genes encoding proteins that are likely homologs. The proteins encoded by these genes, like ndvB, are expected to play a role in biofilm resistance. The genes are: B. japonicum ndvB (GenBank Accession No. AAC62210; FIG. 22; SEQ ID NO:27); Agrobacterium tumefaciens unannotated sequence (GenBank Accession No. NP 357541; FIG. 23; SEQ ID NO:28); Pseudomonas putida KT2440 (FIGS. 24A–24C; SEQ ID Nos:29 and 30); and a Pseudomonas syringae gene (FIGS. 25A–25C; SEQ ID Nos:31 and 32).
Uses of the Identified Genes
The data described herein suggest two novel mechanisms for biofilm-related antimicrobial resistance. We have shown that a mutant unable to acquire biofilm-related resistance to the antibiotic Tb is defective in glucan synthesis. The P. aeruginosa ndvB mutant had increased biofilm-related sensitivity to Gm and Cip. We propose that these glucans sequester Tb and thereby prevent access of this antibiotic to the cytoplasm of the bacteria. This observation is consistent with previous reports that glucans can bind a range of chemically distinct molecules (Breedveld, M. W., and K. J. Miller. Microbiol Rev. 58(2):145–61, 1994). The ability to bind a range of biocides is also consistent with the reported ability of biofilms to develop broad resistance to antimicrobial agents [reviewed in (Mah, T.-F., and G. A. O'Toole. TIMS 9:34–39,2001)].
Based on our data, we submit that compounds that modulate the expression of ndvB or the function of an NdvB polypeptide, such that there is a decrease in ndvB gene transcription, ndvB mRNA translation, or NdvB polypeptide function, are expected to promote a decrease in microbial resistance to antimicrobial agents, possibly due to the loss of, or lower levels of, glucan synthesis. Compounds which alter the activity of PA1163 can be identified using an assay for ndvB activity, e.g., the assay described by Bhagwat et al. (J. Bact. 178:4635–42, 1994). Compounds that modulate function of the identified homologs of ndvB are also expected to promote a decrease in microbial resistance to antimicrobial agents, possibly due to the loss of, or lower levels of, glucan synthesis. This decrease in resistance is predicted to occur in biofilms, but may also occur in other physiological states as well as in cells having genetic changes leading to increased resistance.
We have also identified a novel efflux pump that is required for full biofilm-related antibiotic resistance. This pump appears to be a hybrid between known efflux pumps of the RND superfamily and ABC transporters. Efflux pumps typically have broad substrate specificity, which is consistent with the decrease in resistance of the 30B1 mutant to Tb, Gm and Cip.
Compounds that decrease either the expression of PA1874 or one or more of the following: PA1875, PA1876, and PA1877, or the function of the corresponding polypeptides, such that there is a decrease in gene transcription, mRNA translation, or polypeptide function of one or more of PA1874, PA1875, PA1876, or PA1877 are expected to promote a decrease in microbial resistance to antimicrobial agents. Similarly, compounds that decrease either the expression of any of PA4142-PA4144 and PA2389-PA2391, or the function of the corresponding polypeptides, such that there is a decrease in gene transcription, mRNA translation, or polypeptide function of one or more of PA4142-PA4144 and PA2389-PA2391 are expected to promote a decrease in microbial resistance to antimicrobial agents. This decrease in resistance is predicted to occur in biofilms, but may also occur in other physiological states as well as in cells having genetic changes leading to increased resistance.
Compounds which alter the expression of one or more of the hybrid efflux pump genes described herein can be identified using a reporter construct in which a reporter gene is operably linked to an expression control region located upstream of PA1873, PA4142 or PA2389 (see Table 3). The reporter construct is introduced into a cell, e.g., bacterial cell such as a P. aeruginosa cell. The cell is exposed to a test compound and the expression of the reporter gene is monitored.
One method to further examine the function of the novel efflux pumps is to express the components of the efflux pump in a variety of cell types, prokaryotic and eukaryotic, and use it to screen for compounds which overcome (inhibit) the action of the efflux pump. Bacteria have developed several different mechanisms to overcome the action of antibiotics. These mechanisms of resistance can be specific for a molecule or a family of antibiotics, or can be non-specific and be involved in resistance to unrelated antibiotics. Several mechanisms of resistance can exist in a single bacterial strain, and those mechanisms may act independently or they may act synergistically to overcome the action of an antibiotic or a combination of antibiotics. Specific mechanisms include degradation of the drug, inactivation of the drug by enzymatic modification, and alteration of the drug target (B. G. Spratt, Science 264:388 (1994)). There are, however, more general mechanisms of drug resistance, in which access of the antibiotic to the target is prevented or reduced by decreasing the transport of the antibiotic into the cell or by increasing the efflux of the drug from the cell to the outside medium. Both mechanisms can lower the concentration of drug at the target site and allow bacterial survival in the presence of one or more antibiotics which would otherwise inhibit or kill the bacterial cells. Some bacteria utilize both mechanisms, combining a low permeability of the cell wall (including membranes) with an active efflux of antibiotics. (H. Nikaido, Science 264:382–388 (1994)).
Different pumps can efflux specifically a drug or group of drugs, such as the NorA system that transports quinolones, or Tet A that transports tetracyclines, or they can efflux a large variety of molecules, such as certain efflux pumps of P. aeruginosa. In general, efflux pumps have a cytoplasmic component and energy is required to transport molecules out of the cell. Some efflux pumps have a second cytoplasmic membrane protein that extends into the periplasm. At least some efflux pumps of P. aeruginosa have a third protein located in the outer membrane.
Efflux pumps are involved in antibiotic resistance since, in some cases, they can remove a significant fraction of the antibiotic molecules which manage to enter the cells, thereby maintaining a very low intracellular antibiotic concentration. To illustrate, P. aeruginosa laboratory-derived mutant strain 799/61 which does not produce any measurable amounts of efflux pump is 8 to 10 fold more susceptible to tetracycline and ciprofloxacin than the parent strain P. aeruginosa 799, which synthesizes efflux pumps. Also, null mutants of mexA, the cytoplasmic component of a P. aeruginosa efflux pump, are more susceptible to antibiotics than the wild type.
The physiological role of efflux pumps has not been clearly defined yet. They are involved in drug resistance but they also are involved in the normal physiology of the bacterial cell. The efflux pump coded in the mexA operon of P. aeruginosa has been shown to be regulated by the iron content of the medium, and it is co-regulated with the synthesis of the receptors of siderophores. Siderophores are molecules that are needed for bacterial growth under iron starvation conditions, such as during infection of an animal. They are synthesized in the cytoplasm and exported when the bacterial cell needs iron. Siderophores scavenge iron within the infected animal and return the iron to the microbe to be used for essential microbial processes. Since there is essentially no free iron in the bodies of animals, including the human body, the production of siderophores by infecting bacteria is an important virulence factor for the progress of the infection.
One aspect of this invention concerns the identification of compounds that are inhibitors of a hybrid efflux pump described herein. Such efflux pumps export substrate molecules from the cytoplasm in an energy-dependent manner, and the exported substrate molecules can include antibacterial agents or other antimicrobial agents. Such efflux pump inhibitors are useful, for example, for treating microbial infections by reducing the export of a co-administered antimicrobial agent or by preventing the export of a compound synthesized by microbes (e.g., bacteria) to allow or improve their growth. An example of reducing the export of such a compound is inhibiting iron availability for the microbe by reducing the export of siderophores. Thus, this invention provides methods to identify compounds that are efflux pump inhibitors.
One recent hypothesis to explain biofilm-related antibiotic resistance invoked the development of “persistors”, or a subset of bacteria that develop high level resistance to antimicrobial agents. As is the case for the development of biofilm architecture we propose that entry into this persistent state requires a specific set of genes and their gene products. The isolation of mutants defective in biofilm-related resistance, such as PA1163, supports the hypothesis that there is a distinct genetic basis for this biofilm-related resistance and our approach has begun to identify these components.
The resistance of biofilms to traditional antibiotic therapy in the clinical setting is an ongoing problem. Our invention, however, provides new strategies to block the development of this resistance by identifying the genes and gene products responsible for resistance. In addition to providing a means for inhibiting biofilms, we provide a co-therapeutic approach where traditional antibiotics are combined with a drug that interferes with biofilm-related resistance to render biofilms, and possibly related physiological states, more susceptible to treatment.

## Claims

1. A purified polypeptide comprising the amino acid sequence of SEQ ID NO:30 or SEQ ID NO:32.