US20090202516A1 - Inhibition and treatment of gastrointestinal biofilms - Google Patents

Inhibition and treatment of gastrointestinal biofilms Download PDF

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US20090202516A1
US20090202516A1 US12/368,259 US36825909A US2009202516A1 US 20090202516 A1 US20090202516 A1 US 20090202516A1 US 36825909 A US36825909 A US 36825909A US 2009202516 A1 US2009202516 A1 US 2009202516A1
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biofilm
amount
acid
glucan
glucanohydrolase
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Stephen F. Olmstead
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ProThera Inc
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Assigned to PROTHERA, INC. reassignment PROTHERA, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: OLMSTEAD, STEPHEN F.
Publication of US20090202516A1 publication Critical patent/US20090202516A1/en
Priority to US15/979,362 priority patent/US11078516B2/en
Priority to US17/362,524 priority patent/US20210332409A1/en
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/02—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving viable microorganisms
    • C12Q1/18—Testing for antimicrobial activity of a material
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/43—Enzymes; Proenzymes; Derivatives thereof
    • A61K38/46—Hydrolases (3)
    • A61K38/465—Hydrolases (3) acting on ester bonds (3.1), e.g. lipases, ribonucleases
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/43—Enzymes; Proenzymes; Derivatives thereof
    • A61K38/46—Hydrolases (3)
    • A61K38/47—Hydrolases (3) acting on glycosyl compounds (3.2), e.g. cellulases, lactases
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/43—Enzymes; Proenzymes; Derivatives thereof
    • A61K38/46—Hydrolases (3)
    • A61K38/48—Hydrolases (3) acting on peptide bonds (3.4)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/04—Drugs for disorders of the alimentary tract or the digestive system for ulcers, gastritis or reflux esophagitis, e.g. antacids, inhibitors of acid secretion, mucosal protectants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/90—Enzymes; Proenzymes
    • G01N2333/914—Hydrolases (3)
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value
    • G01N2500/04—Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)

Definitions

  • a “biofilm” is a well known phenomenon and may be defined as a population of prokaryotic cells growing on a surface and enclosed in a self-produced matrix of extracellular polymeric material, which mediates adhesion of the cells to each other and to surfaces. Biofilms are not simply passive assemblages of cells that are stuck to surfaces, but are structurally and dynamically complex biological systems. As compared with cells that are planktonic in nature, bacteria growing in biofilms exhibit a different phenotype with respect to growth rate and gene transcription. See http://en.wikipedia.org/wiki/Biofilm.
  • Biofilms have been responsible, for example, for the fouling of cooling-water towers, water pipelines, membrane units and food-processing plants. Biofilms are notoriously difficult to eradicate. Microbes in industrial biofilms are protected from antimicrobial chemicals, environmental bacteriophages, and phagocytic amoebae. (Donlan R M, Costerton J W. Biofilms: survival mechanisms of clinically relevant microorganisms. Clin Microbiol Rev 2002; 15167-293.)
  • biofilms may be involved in a significant percentage of human microbial infections (Potera C. Forging a link between biofilms and disease. Science 1999; 283:1837-8).
  • Parsek and Singh proposed four criteria for defining a biofilm etiology of an infection: the pathogenic bacteria are surface associated or adherent to a substratum; direct examination reveals bacteria in clusters, encased in a matrix of bacterial or host constituents; the infection is localized; and the infection is resistant to antibiotic therapy despite the antibiotic sensitivity of the constituent planktonic organisms (Parsek M R, Singh P K. Bacterial biofilms: an emerging link to disease pathogenesis. Annu Rev Microbiol 2003; 57:677-701.)
  • Biofilm infections can be involved in the etiology of dental caries, periodontal disease, cystic fibrosis (CF) airway infections, native valve endocarditis, chronic bacterial prostatitis, otitis media, and vaginal infections.
  • Biofilm microorganisms are also involved in implant-related infections, in which adherent microbial populations form on the surfaces of catheters, prosthetic heart valves, joint replacements, and other devices (Donlan R M. Biofilms and device-associated infections. Emerg Infect Dis 2001; 7:277-81.)
  • the intestinal tract provides a reservoir for many antibiotic-resistant biofilm bacteria, including Enterobacteriaceae species, Pseudomonas aeruginosa , and Acinetobacter species (Donskey C J. The role of the intestinal tract as a reservoir and source for transmission of nosocomial pathogens. Clin Infect Dis 2004; 39:219-26.)
  • the human opportunistic pathogen, Pseudomonas aeruginosa is a major cause of infection-related mortality among the critically ill patients, and carries one of the highest case fatality rates of all gram-negative infections. Although the lungs have been traditionally considered to be a major site of P.
  • aeruginosa infection among critically ill patients a significant number of these infections arise as a result of direct contamination of the airways by the gastrointestinal flora or by hematogenous dissemination from the intestines to the lung parenchyma. Effective methods for the inhibition, reduction and/or treatment of P. aeruginosa would have a significant impact for this condition.
  • Gastrointestinal biofilm-associated bacteria include Bacteroides ssp., Clostridium ssp., Fusobacterium ssp., Klebsiella ssp., Spirochaetes ssp., Pseudomonas aeriginosa, Escherichia coli, Helicobacter pylori, Bifidobacterium ssp., and gram-positive cocci.
  • compositions, medicaments, therapeutics, systems, methods, etc. are directed to the reduction of gastrointestinal biofilm(s) in the gut of animals.
  • the methods include screening for physiologically acceptable anti-biofilm compositions, including for example nutraceutical, therapeutic, or pharmaceutical compositions, comprising anti-biofilm enzymes and other components suitable for oral ingestion by mammals such as humans, and methods of making and using or administering such compositions.
  • the present compositions, methods, etc. are directed to screening digestive enzymes in biofilm models to identify useful enzymes and compositions for the physiologically acceptable anti-biofilm compositions, treatment methods, etc., discussed herein.
  • Such enzymes may be screened as single agents, mixtures of agents, or in combination with antimicrobial agents, chelating agents, lactoferrin, herbals or other components as desired.
  • the present physiologically acceptable anti-biofilm compositions, methods, etc. are also directed to the use of digestive enzymes for the inhibition and reduction of pathogenic biofilm in the gastrointestinal tract of humans.
  • physiologically acceptable anti-biofilm compositions, methods, etc. can be directed to the use of cellulases, hemicellulases, lysozyme, pectinases, amylases, DNase I, Serratia peptidase, and other hydrolases that are capable of digesting the exopolysaccharide and exoprotein matrix of biofilms.
  • the present physiologically acceptable anti-biofilm compositions, methods, etc. are also directed to oral physiologically acceptable anti-biofilm compositions for the inhibition and treatment of pathogenic gastrointestinal biofilms in humans.
  • the present physiologically acceptable anti-biofilm compositions, methods, etc. are directed to agents that are foodborne, waterborne or are nosocomial. Some embodiments are further directed to biofilm infections that are antibiotic-resistant and/or recurrent.
  • the physiologically acceptable anti-biofilm compositions, etc. may be used in conjunction with antibiotics or antimicrobials. In addition these physiologically acceptable anti-biofilm compositions may be used in patients whose biofilm infections have failed to respond to antibiotics or antimicrobials.
  • the present physiologically acceptable anti-biofilm compositions, methods, etc. are also directed to the inhibition and treatment of biofilm infections caused by bioterrorist agents.
  • Gastrointestinal biofilms in mammals have been implicated in a variety of possible diseases, either as causing such diseases or making them worse.
  • the present compositions, systems, methods, etc. are directed to the reduction of gastrointestinal biofilm(s) in the gut of animals.
  • the methods include inhibiting, treating, or reducing biofilms in the gastrointestinal system.
  • Biofilm devices such as the Calgary Biofilm Device (Ceri et al., 1999; U.S. Pat. No. 7,041,470) can be modified, for example, to be used in conjunction with the present methods, to identify physiologically acceptable anti-biofilm compositions, etc., to screen for enzymes that are (a) orally available; (b) generally recognized as safe (GRAS); (c) are known to or can be established to retain their activity during passage through the stomach; and (d) are active in disrupting biofilms in model systems. Other devices that are suitable for the study of biofilms afflicting humans may be used.
  • GRAS generally recognized as safe
  • Other devices that are suitable for the study of biofilms afflicting humans may be used.
  • a Calgary Biofilm Device provides for rapid and reproducible assay of biofilm susceptibilities to antibiotics using 96 equivalent biofilms in a standard 96-well plate (or other suitable number as desired), which biofilms are then exposed to the antibiotics under investigation.
  • screening biofilms are exposed to enzyme concentrations, etc., as discussed herein.
  • Biofilm formation can be, for example, followed by quantitative microbiology and scanning electron microscopy.
  • Bacterial growth on a gastrointestinal surface often involves the self-production of a polysaccharide-rich extracellular matrix that provides structural support for the formation of biofilm communities. Enzymes that disrupt the biofilm matrices of these organisms within the gastrointestinal tract are the subject of the methods, etc., herein.
  • the particular enzyme(s) to be used may be selected according to the properties, if known, of the specific biofilm to be removed, or a combination of several enzymes having different enzyme activities may be used.
  • the composition of the extracellular matrix is complex and variable among different bacterial species and even within the same species under different environmental conditions.
  • exopolysaccharides are a typical compound of the biofilm matrix, providing the framework into which microbial cells are inserted.
  • cellulose and ⁇ -1,6-linked N-acetylglucosamine appear to be the most common components of the biofilm matrix of many different bacteria.
  • the suitable, physiologically acceptable anti-biofilm compositions, etc. herein comprises an amount of anti-polymeric ⁇ -1,6-N-acetyl-D-glucosamine (poly- ⁇ -1,6-GlcNAc) agents to substantially disperse poly- ⁇ -1,6-GlcNAc and thus capable of significant biofilm degradation.
  • poly- ⁇ -1,6-GlcNAc anti-polymeric ⁇ -1,6-N-acetyl-D-glucosamine
  • such significant reduction means, if measured in vitro, a log reduction of 1, typically 1.5, or 3.0-3.8 or better. In vivo, such significant reduction can be substantial reduction of one or more symptoms associated with a biofilm infection, or even substantial elimination of one or more symptoms associated with a biofilm infection.
  • exemplary anti-GlcNAc-agents include a previously identified ⁇ -hexosaminidase and biofilm-dispersing enzyme of A.
  • actinomycetemcomitans DspB or dispersin B, which specifically hydrolyzes the glycosidic linkages of poly- ⁇ -1,6-GlcNAc and disrupts bacterial biofilm (Kaplan J B, Ragunath C, Ramasubbu N, Fine D H. 2003. Detachment of Actinobacillus actinomycetemcomitans biofilm cells by an endogenous ⁇ -hexosaminidase activity. J Bacteriol 2003; 185:4693-8).
  • Dispersin B cleaves ⁇ (1,6)-linked N-acetylglucosamine polymer using a catalytic machinery similar to other family 20 hexosaminidases which cleave ⁇ (1,4)-linked N-acetylglucosamine residues.
  • Dispersin B and similar hexosaminidases with activity in biofilms are suitable for use in the methods, physiologically acceptable anti-biofilm compositions, etc., discussed herein.
  • the anti-poly- ⁇ -1,6-GlcNAc agents can be used with, or instead of, cellulase, discussed further below, although typically they are used together.
  • the suitable, physiologically acceptable anti-biofilm compositions comprise a cellulase in an amount capable of significant biofilm degradation.
  • Such cellulases can have activity, against for example, cellulose in a salmonella biofilm or others.
  • Cellulase refers to a class of enzymes produced chiefly by fungi, bacteria, and protozoans that catalyze the hydrolysis of cellulose.
  • cellulases produced by other types of organisms such as plants and animals.
  • Cellulases that have been used as digestive enzymes are known to be acid-stable. These include but are not limited to cellulases from Aspergillus species. Several different kinds of cellulases are known, which differ structurally and mechanistically.
  • the EC number for this group of enzymes is EC 3.2.1.4.
  • the reaction catalyzed is the endohydrolysis of 1,4- ⁇ -D-glycosidic linkages in cellulose.
  • Other names for cellulase are: Endoglucanase, endo-1,4- ⁇ -glucanase, carboxymethyl cellulose, endo-1,4- ⁇ -D-glucanase, ⁇ -1,4-glucanase, ⁇ -1,4-endoglucan hydrolase, celludextrinase, avicelase.
  • the cellulase(s) herein are resistant to denaturation/inactivation at a pH range of 1.0 to 5.0 and 10 to 14, possesses hydrolytic activity across a pH span of 1 to 14, has effective hydrolytic activity within the gastric environment at a fasting pH of 1.0 to 3.0 and in the presence of food and other ingested material, and/or possesses effective hydrolytic activity at a pH of 6.5 to 7.5 encompassing physiologic ph in the small intestines and colon.
  • cellulases hemicellulases and other enzymes that may be used include the following: Deerland Enzymes, Kennesaw, Ga. (www.deerlandenzymes.com); National Enzyme Company (www.nationalenzyme.com), Specialty Enzymes (www.specialtyenzymes.com); and others.
  • the enzymes may be derived from any suitable source such as plant, bacterial, fungal or animal sources.
  • the physiologically acceptable anti-biofilm composition comprises cellulase, hemicellulase/pectinase complex, ⁇ -gluconase, acid protease, alkaline protease, and Serratia peptidase with at least one pharmaceutically acceptable carrier, diluents, excipients, buffers, or adjuvants.
  • pharmaceutically acceptable carriers or diluents, excipients, buffers, adjuvants, and the like are nontoxic to recipients at the dosages and concentrations employed.
  • the amount of cellulase per oral dose is about 100-300 CU, and typically about 200 CU; the amount of hemicellulase/pectinase complex is about 60-100 HSU, and typically about 80 HSU; the amount of ⁇ -gluconase is about 6-10 BGU, and typically about 8 BGU; the amount of acid protease is about 15-25 SAP, and typically about 20 SAP; and, the amount of alkaline protease is about 15-25 HUT, and typically about 20 HUT.
  • the amount of cellulase per oral dose ranges from 1 to 10,000 CU
  • the amount of hemicellulase/pectinase complex ranges from 1 to 8,000 HSU
  • the amount of ⁇ -gluconase ranges from 1 to 1000 BGU
  • the amount of acid protease ranges from 1 to 10,000 SAP
  • the amount of alkaline protease ranges from 1 to 40,000 HUT.
  • the physiologically acceptable anti-biofilm composition comprises cellulase, hemicellulase/pectinase complex, ⁇ -gluconase, acid protease, alkaline protease, Serratia peptidase, and any one or more of the following in an amount capable an amount capable of significant biofilm degradation: disaccharides, amylase, ⁇ -amylase, ⁇ -amylase, glucoamylase, endoglucanase, xylanase, lipase, lysozyme, any enzyme such as a protease, peptidase or protease/peptidase complex with dipeptidyl peptidase IV (DPP-IV) activity, chitosanase, bromelain, papain, ficin, kiwi protease, any plant-derived protease or proteinase, or phytase.
  • DPP-IV dipeptidyl
  • the physiologically acceptable anti-biofilm composition is composed of cellulase, hemicellulase/pectinase complex, ⁇ -gluconase, acid protease, alkaline protease, Serratia peptidase, and any one or more of the following specific enzymes in an amount capable of biofilm degradation: 1,2-1,3- ⁇ -D-mannan mannohydrolase, 1,3- ⁇ -D-xylanxylanohydrolase, 1,3- ⁇ -D-glucan glucanohydrolase, 1,3(1,3; 1,4)- ⁇ -D-glucan 3-glucanohydrolase, 1,3(1,3; 1,4)- ⁇ -D-glucan 3(4)-glucanohydrolase, 1,3-1,4- ⁇ -D-glucan 4-glucanohydrolase, 1,4- ⁇ -D-glucan glucanehydrolase, 1,4- ⁇ -D-glucohydrolase, 1,4-(1,3:
  • subtilisin is a serine protease produced by Gram-positive bacteria or fungi.
  • the amino acid sequences of a number of subtilisins have been determined, including at least six subtilisins from Bacillus strains, namely, subtilisin 168, subtilisin BPN, subtilisin Carlsberg, subtilisin DY, subtilisin amylosacchariticus, and mesentericopeptidase, one subtilisin from an actinomycetales, thermitase from Thermoactinomyces vulgaris , and one fungal subtilisin, proteinase K from Tritirachium album.
  • an exemplary lipase as discussed above can be a microbial lipase.
  • the lipase may be selected from yeast lipases, e.g., Candida , and bacterial lipases, e.g. Pseudomonas or Bacillus , lipases; or fungal, e.g., Humicola or Rhizomucor.
  • amylases useful in the methods, etc., herein include Bacillus amylases, e.g., Bacillus stearothermophilus amylase, Bacillus amyloliquefaciens amylase, Bacillus subtilis amylase or Bacillus licheniformis amylase or Aspergillus amylases, e.g. Aspergillus niger or Aspergillus oryzae amylase.
  • Bacillus amylases e.g., Bacillus stearothermophilus amylase, Bacillus amyloliquefaciens amylase, Bacillus subtilis amylase or Bacillus licheniformis amylase or Aspergillus amylases, e.g. Aspergillus niger or Aspergillus oryzae amylase.
  • pectinases belonging to the enzyme classes polygalacturonases (EC3.2.1.15), pectinesterases (EC3.2.1.11), pectin lyases (EC4.2.2.10) and hemicellulases such as endo-1,3- ⁇ -xylosidase (EC 3.2.1.32), xylan 1,4- ⁇ -xylosidase (EC 3.2.1.37) and ⁇ -L-arabinofuranosidase (EC 3.2.1.55).
  • a suitable source organism for pectinases may be Aspergillus niger or Aspergillus aculeatus.
  • Lysozyme also known as muramidase or N-acetylmuramide glycanhydrolase, is a 14.4 kilodalton enzyme (EC 3.2.1.17) that damages bacterial cell walls by catalyzing hydrolysis of 1,4- ⁇ -linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins. Lysozyme is found in saliva, tears, and polymorphonucleocytes and has known antibacterial activity.
  • the enzyme functions by attacking peptidoglycans (found in the cells walls of bacteria, especially Gram-positive bacteria) and hydrolyzing the glycosidic bond that connects N-acetylmuramic acid with the fourth carbon atom of N-acetylglucosamine.
  • Lysozyme has been used in the treatment of otitis media and sinusitis (U.S. Pat. No. 7,060,674).
  • Oral lysozyme compositions have been used in the treatment of various conditions in humans, including arthritis (U.S. Pat. No. 7,229,809).
  • DNase I deoxyribonuclease I
  • a phosphodiesterase capable of hydrolyzing polydeoxyribonucleic acid.
  • DNase I has been purified from various species to various degrees. DNase I, when inhaled, affects the capability of P. aeruginosa to form biofilms in the lungs in the initial development stages. DNase I hydrolyzes the DNA present in sputum/mucus of cystic fibrosis patients and reduces viscosity in the lungs, promoting improved clearance of secretions. Enzymes that are acid-stable are candidates for use in conjunction with the methods, physiologically acceptable anti-biofilm compositions, etc., discussed herein. DNase I activities are classifiable into three groups on the basis of their different tissue distributions of DNase I. DNase I of parotid type is secreted from the parotid gland and must pass through the very acidic conditions in the stomach.
  • physiologically acceptable anti-biofilm compositions, methods, etc., herein are to be taken by mouth, typically at least 1 hour before or 1 hour after a meal or consumption of food.
  • physiologically acceptable anti-biofilm compositions, methods, etc., herein are typically to be taken 2 to 4 times per day (other intervals may be appropriate in certain circumstances) and the regimen is typically to be followed for an extended period, for example at least about 1 or 2 months.
  • the enzyme preparation may be combined with a natural antimicrobial such as oil of oregano, berberine, or undecylenic acid or with a prescription antibiotic or antimicrobial.
  • the enzyme preparation may be combined with the oral intake of one or more probiotic microorganisms.
  • the World Health Organization defines probiotic organisms as live microorganisms that when administered in adequate amounts confer a health benefit on the host.
  • the enzyme preparation may be combined with one or more prebiotics.
  • a prebiotic is defined as “selectively fermented ingredients that allow specific changes, both in the composition and/or activity in the gastrointestinal microflora that confer benefits upon host well-being and health.” (Roberfroid M. Prebiotics: the concept revisited. J Nutr 2007; 137(3 Suppl 2):830S-7S.)
  • Methods related to the compositions, etc., herein include methods of screening, making and using, including for the manufacture of medicaments.
  • the methods include methods of screening for a physiologically acceptable anti-biofilm composition suitable for oral administration to a mammal while retaining effectiveness in the gut, the method comprising, providing a significant plurality of samples of a live target biofilm on at least one substrate; applying to each of the plurality of samples one of range of doses of a candidate anti-biofilm agent selected from the group comprising acid-stable cellulase and an anti-biofilm anti-polymeric ⁇ -1,6-N-acetyl-D-glucosamine (poly- ⁇ -1,6-GlcNAc) agent, under conditions
  • the samples of the target biofilm can grow absent a significant anti-biofilm effect due to the candidate anti-biofilm agent; and, determining whether each of the range of doses of candidate anti-biofilm agent inhibited growth of its respective sample.
  • the methods can further comprise screening both the anti-biofilm acid-stable cellulase and the anti-biofilm anti-poly- ⁇ -1,6-GlcNAc agent.
  • the anti-biofilm anti-poly- ⁇ -1,6-GlcNAc agent can be a hexosaminidase such as Dispersin B.
  • the methods can further comprise screening at least one of an acid-stable hemicellulase/pectinase complex, ⁇ -gluconase, acid protease, alkaline protease, or Serratia peptidase.
  • the amount of cellulase can be equivalent to a dose of about 100-300 CU, the amount of hemicellulase/pectinase complex can be about 60-100 HSU, the amount of ⁇ -gluconase can be about 6-10 BGU, the amount of acid protease can be about 15-25 SAP, and the amount of alkaline protease can be about 15-25 HUT.
  • the methods can also comprise screening at least one an acid-stable agent selected from the following: a disaccharide; amylase; ⁇ -amylase; ⁇ -amylase; glucoamylase; endoglucanase; xylanase; lipase; lysozyme; an enzyme with dipeptidyl peptidase IV (DPP-IV) activity; chitosanase; bromelain; papain; ficin; kiwi protease; any plant-derived protease or proteinase, or phytase.
  • an acid-stable agent selected from the following: a disaccharide; amylase; ⁇ -amylase; ⁇ -amylase; glucoamylase; endoglucanase; xylanase; lipase; lysozyme; an enzyme with dipeptidyl peptidase IV (DPP-IV) activity; chitosanas
  • the lipase can be a microbial lipase, such as from at least one of Candida, Pseudomonas, Bacillus, Humicola or Rhizomucor .
  • the amylase can be at least one of a Bacillus amylase or Aspergillus amylase.
  • the screen can comprise at least one pectinase that can be at least one of a polygalacturonase (EC3.2.1.15), pectinesterase (EC3.2.1.11), pectin lyase (EC4.2.2.10) or hemicellulase.
  • the pectinase can be at least one an Aspergillus niger pectinase or Aspergillus aculeatus pectinase.
  • the methods can further comprise screening at least one of the following: 1,2-1,3- ⁇ -D-mannan mannohydrolase, 1,3- ⁇ -D-xylanxylanohydrolase, 1,3- ⁇ -D-glucan glucanohydrolase, 1,3(1,3; 1,4)- ⁇ -D-glucan 3-glucanohydrolase, 1,3(1,3; 1,4)- ⁇ -D-glucan 3(4)-glucanohydrolase, 1,3-1,4- ⁇ -D-glucan 4-glucanohydrolase, 1,4- ⁇ -D-glucan glucanehydrolase, 1,4- ⁇ -D-glucan glucohydrolase, 1,4-(1,3:1,4)- ⁇ -D-glucan 4-glucanohydrolase, 1,4- ⁇ -D-glucan glucohydrolase, 1,4- ⁇ -D-xylan xylanohydrolase, 1,4- ⁇ -mannan mannanohydrolase, 1,5- ⁇ -L-arabinanohydro
  • the methods can further comprise screening an acid-stable subtilisin, an acid-stable DNAse I, oil of oregano, berberine, undecylenic acid, a prescription antibiotic, a prescription antimicrobial, a probiotic microorganism or a prebiotic.
  • the methods comprise inhibiting a gastrointestinal biofilm infection in a mammal, the method comprising: identifying the presence of the gastrointestinal biofilm infection, orally administering to the mammal a therapeutically effective amount of at least one anti-biofilm agent comprising an acid-stable cellulase or an anti-polymeric ⁇ -1,6-N-acetyl-D-glucosamine (poly- ⁇ -1,6-GlcNAc) agent in at least one pharmaceutically acceptable carrier, in an amount and for a time sufficient to cause significant biofilm degradation within the gastrointestinal system of the mammal.
  • the methods comprise administering one or more of the other aspects of the compositions, etc., herein.
  • the composition can be for use as an active therapeutic substance, for use in the manufacture of a medicament for inhibiting or treating a gastrointestinal biofilm in a mammal, or for manufacturing a medicament able to reduce symptoms associated with a gastrointestinal biofilm in a human patient, for example comprising combining a pharmaceutically effective amount of at least one of an anti-biofilm acid-stable cellulase or an anti-biofilm anti-polymeric ⁇ -1,6-N-acetyl-D-glucosamine (poly- ⁇ -1,6-GlcNAc) agent in an amount capable of significant biofilm degradation with at least one of a pharmaceutically acceptable carrier, adjuvant, excipient, buffer and diluent.
  • a pharmaceutically acceptable carrier adjuvant, excipient, buffer and diluent.
  • target biofilm organisms including both indigenous and biofilm infectious organisms are discussed below.
  • Enterococci although part of the normal flora of the human gastrointestinal tract, have been recognized as an important cause of nosocomial infection for over two decades and are commonly implicated in urinary tract infections, bacteremia, intra-abdominal and surgical wound infections, catheter-related infections, and endocarditis.
  • Staphylococcus aureus is a common pathogen associated with nosocomial infections. It can persist in clinical settings and gain increased resistance to antimicrobial agents through biofilm formation. Staphylococcus aureus is among the leading pathogens causing bloodstream infections able to form biofilms on host tissue and indwelling medical devices and to persist and cause disease. Infections caused by S. aureus are becoming more difficult to treat because of increasing resistance to antibiotics (e.g., vancomycin or methicillin-resistant Staphylococcus aureus ). In a biofilm environment particularly, microbes exhibit enhanced resistance to antimicrobial agents.
  • antibiotics e.g., vancomycin or methicillin-resistant Staphylococcus aureus
  • the human opportunistic pathogen, Pseudomonas aeruginosa is a major cause of infectious-related mortality among the critically ill patients, and carries one of the highest case fatality rates of all gram-negative infections.
  • the lungs have been traditionally considered to be a major site of P. aeruginosa infection among critically ill patients, a significant number of these infections arise as a result of direct contamination of the airways by the gastrointestinal flora or by hematogenous dissemination from the intestine to the lung parenchyma.
  • Pseudomonas aeruginosa causes severe infections in immunologically compromised patients and is a major pathogen in cystic fibrosis patients.
  • alginate-negative mutants of P. aeruginosa are also able to form nonmucoid biofilms, showing an architecture different from that of biofilms formed by alginate-overproducing mucoid P. aeruginosa (Nivens D E, Ohman D E, Williams J, Franklin M J. Role of alginate and its 0 acetylation in formation of Pseudomonas aeruginosa microcolonies and biofilms.
  • Alginate is not a significant component of the extracellular polysaccharide matrix of PA14 and PAO1 Pseudomonas aeruginosa biofilms. Proc Natl Acad Sci USA 2003; 100:7907-12.)
  • H. pylori is one of the more common human pathogens infecting 50% of the world's population. It is associated with duodenal ulcers, gastric ulcers, gastritis, and gastric carcinoma. Treatment of H. pylori is difficult involving multidrug regimens and lengthy treatment periods. There is a 10-20% relapse rate. Recent studies document the importance of biofilms in the pathogenesis of H. pylori disease. (Coticchia J M et al. Presence and density of Helicobacter pylori biofilms in human gastric mucosa in patients with peptic ulcer disease. J Gastrointest Surg. 2006; 10:883-9) An oral multienzyme formulation holds great promise to facilitate the elimination of H. pylori biofilm and the eradication of H. pylori pathogens thereby reducing the risk of gastritis, peptic ulcer disease, and gastric cancer.
  • the foodborne pathogen Listeria is the causative agent of listeriosis, a severe disease where the overt form has a severe mortality greater than 25%.
  • Listeria monocytogenes can survive and grow over a wide range of environmental conditions such as refrigeration temperatures, low pH and high salt concentration. This allows the pathogen to overcome food preservation and safety barriers, and pose a potential risk to human health.
  • Listeria monocytogenes may specifically be found in raw foods, such as unpasteurized fluid milk, raw vegetables, raw and cooked poultry. It has the ability to grow at low temperatures; thus, allowing it to grow in refrigerated foods.
  • Campylobacter jejuni is a species of curved, rod-shaped, Gram-negative microaerophilic, bacteria commonly found in animal feces. It is one of the most common causes of human gastroenteritis in the world. Food poisoning caused by Campylobacter species can be severely debilitating but is rarely life-threatening. It has been linked with subsequent development of Guillain-Barre syndrome (GBS), which usually develops two to three weeks after the initial illness. Contaminated food is a major source of isolated infections, with incorrectly prepared meat and poultry normally the source of the bacteria. Infection with C. jejuni usually results in enteritis, which is characterized by abdominal pain, diarrhea, fever, and malaise.
  • Campylobacter jejuni The major gastrointestinal pathogen Campylobacter jejuni is shown to exist as three forms of monospecies biofilm in liquid culture. (Joshua G W, Guthrie-Irons C, Karlyshev A V, Wren B W. Biofilm formation in Campylobacter jejuni. Microbiology 2006; 152(Pt 2):387-96.)
  • Bacillus anthracis is a Gram-positive, endospore-forming bacterium and is the aetiological agent of pulmonary, gastrointestinal and cutaneous anthrax. In endemic areas in which humans and livestock interact, chronic cases of cutaneous anthrax are commonly reported.
  • biofilms have been characterized in other pathogenic and non-pathogenic Bacillus species, including Bacillus cereus and Bacillus subtilis , respectively.
  • B. anthracis readily forms biofilms which are inherently resistant to commonly prescribed antibiotics.
  • Yersiniosis is an infectious disease caused by a bacterium of the genus Yersinia . In the United States, most human illness is caused by one species, Y. enterocolitica . Infection with Y. enterocolitica occurs most often in young children. Common symptoms in children are fever, abdominal pain, and diarrhea. Gastrointestinal symptoms are common in both the acute and chronic states of yersiniosis. Infection is most often acquired by eating contaminated food, especially raw or undercooked pork products. Drinking contaminated unpasteurized milk or untreated water can also transmit the infection.
  • Yersinia pestis the causative agent of bubonic plague, is transmitted to rodents and humans by the bites of fleas whose proventriculi are blocked by a dense mass of the biofilm bacteria.
  • the blockage starves the flea and stimulates it to bite repeatedly in search of blood meals, thus spreading the bacteria to new hosts.
  • Biofilm models using Caenorhabditis elegans may be used to identify enzymes that kill Yersinia biofilms (Styer K L, Hopkins G W, Bartra S S, Plano G V, Frothingham R, Aballay A. Yersinia pestis kills Caenorhabditis elegans by a biofilm-independent process that involves novel virulence factors. EMBO reports 2005; 10:992-7.)
  • Humans are generally infected in one of three ways: eating or drinking something that is contaminated with Brucella , breathing in the organism (inhalation), or having the bacteria enter the body through skin wounds.
  • eating or drinking something that is contaminated with Brucella
  • breathing in the organism breathing in the organism (inhalation)
  • having the bacteria enter the body through skin wounds The most common way to be infected is by eating or drinking contaminated milk products.
  • Salmonella enterica a foodborne pathogen that causes salmonellosis, is caused by the ingestion of bacteria that invade the intestinal epithelium and multiply there. Salmonella enterica is known to form biofilms, and its attachment to, and growth on, eukaryotic cells is facilitated by exopolysaccharides (Ledeboer & Jones, 2005). Most persons infected with Salmonella develop diarrhea, fever, and abdominal cramps 12 to 72 hours after infection. The illness usually lasts 4 to 7 days, and most persons recover without treatment. However, in some persons the diarrhea may be so severe that the patient needs to be hospitalized. In these patients, the Salmonella infection may spread from the intestines to the blood stream, and then to other body sites and can cause death unless the person is treated promptly.
  • Shigella sonnei also known as “Group D” Shigella
  • Shigellosis is an infectious disease caused by a group of bacteria called Shigella .
  • Most who are infected with Shigella develop diarrhea, fever, and stomach cramps starting a day or two after they are exposed to the bacterium.
  • Some Shigella bacteria have become resistant to antibiotics.
  • a second type, Shigella flexneri , or “group B” Shigella accounts for almost all of the rest.
  • Other types of Shigella continue to be important causes of disease in the developing world.
  • Shigella dysenteriae type 1 causes deadly epidemics there.
  • Salmonella enterica serovar Typhi causes typhoid fever, an enteric fever that is potentially fatal.
  • Asymptomatic carriers may carry bacteria in the gallbladder.
  • Salmonella typhi lives only in humans. Persons with typhoid fever carry the bacteria in their bloodstream and intestinal tract. In addition, a small number of persons, called carriers, recover from typhoid fever but continue to carry the bacteria. Both ill persons and carriers shed S. typhi in their feces (stool). Salmonella typhi is transmitted in contaminated food, water and beverages.
  • a system was recently developed to analyze salmonella biofilm formation on glass coverslips (Prouty A M, Schwesinger W H, Gunn J S. Biofilm formation and interaction with the surfaces of gallstones by Salmonella spp. Infect Immun 2002; 70:2640-9.)
  • Enterotoxigenic Escherichia coli targets the small intestine where the barrier effect of the autochthonous microflora is low due to higher acidity and peristaltic movements in this region. This organism adheres to and colonizes the mucus in order to elicit a pathogenic effect (Knutton S, Lloyd D R, Candy D C, McNeish A S. In vitro adhesion of enterotoxigenic Escherichia coli to human intestinal epithelial cells from mucosal biopsies. Infect Immun 1984; 44:514-8.) This means that the pathogen and/or its toxins can readily adhere to exposed eneterocytes and invade the host.
  • Vibrio cholerae is a Gram-negative, facultative pathogen that is the causative agent of cholera, a devastating diarrheal disease that affects millions of people in the developing world each year; it survives in aqueous reservoirs, probably in the form of biofilms.
  • Invasive intestinal amebiasis caused by Entamoeba histolytica , is initiated with attachment of trophozoites to the colonic mucous layer, mucous disruption and/or depletion, and adherence to and cytolysis of host epithelial and inflammatory cells.
  • a current working model of intestinal amebiasis suggests that the microenvironment of the host intestine, particularly intestinal mucins and the bacterial biofilm, may influence the behavior of pathogenic amebae. Enzymes that disrupt bacterial biofilm will be useful in the inhibition and treatment of amebiasis.
  • the multienzyme formulation was tested in vitro against Escherichia coli O157:H7 , Kelbsiella pneumoniae ATCC 4352, Candida paratropicalis ATCC 99916, and Candida albicans SJ2083133. Although Candida albicans forms significant biofilms in vivo, it is not a predictable former of biofilms in vitro, but it was incorporated in the experiment because of its clinical importance.
  • Sterile 96-well microtiter plates were prepared under a laminar flow hood. Each plate included sterility controls, growth controls, and antibiotic challenge well. Gentamycin was used for the bacteria and amphotericin B for the Candida in concentration ranges from 1024 mcg/mL to 1 mcg/mL. Organisms were tested using exposure time points of 24 hours. One plate was assessed per organism per time point. Triplicate samples were used to assess the impact of the multienzyme formulation on biofilm formation.
  • MIC Planktonic minimal inhibitory concentration
  • MBC minimal bacteriocidal concentration
  • MBEC Minimum biofilm eradication concentration results were determined following the 24 hour incubation from the MBEC panels using the plate reader in conjunction with Log 10 reduction data. Turbidity was assessed visually in the wells of the recovery plate. Alternatively, a microtiter plate reader was used to obtain optical density measurements at 630 nm (OD 630 ). Clear wells (OD 630 ⁇ 0.1) are evidence of biofilm eradication.
  • the MBEC is defined as the minimum concentration of antibiotic that inhibits growth of the biofilm.
  • Experiment 2 assessed the above multienzyme formulation without and with 125 mg of Disodium ethylene diamine tetraacetic acid for antibiofilm activity against Staphylococcus aureus ATCC 29213 and Staphylococcus aureus MRSA U of C #18. Growth medium and conditions were TSB/TSA, aerobic, and 35 ⁇ 2° C. The experimental design and conditions were as described above for experiment 1.
  • Staphylococcus aureus ATCC 29213 The MIC, MBC and MBEC for the multienzyme formulation were found to have no cut-off points at the tested concentrations. The multienzyme formulation had antibiofilm activity at all but the lowest tested concentrations. The log reductions versus growth controls (GC) were significant at the P ⁇ 0.05 level. The data are tabulated below:
  • Staphylococcus aureus ATCC 29213 The MBEC for the multienzyme formulation with EDTA was found to have no cut-off point at the tested concentrations.
  • the MBC for multienzyme/EDTA was observed to have the cut-off point at 3.13 mg/mL and the MIC for multienzyme/EDTA was observed to have the cut-off point at 1.56 mg/mL.
  • the log reduction for multienzyme/EDTA much greater than the log reduction for the multienzyme formulation and at a much lower concentration for multienzyme/EDTA showing that multienzyme/EDTA has a much greater effect the eradication of the bacterial biofilm. The data are tabulated below.
  • Staphylococcus aureus MRSA 399 The MIC, MBC and MBEC for the multienzyme formulation were found to have no cut-off point at the tested concentrations. The multienzyme formulation exhibited antibiofilm activity across a range of concentrations although the activity was inconsistent. Variability among the triplicate samples is noted. The data are tabulated below.
  • Staphylococcus aureus MRSA 399 The MBEC for the multienzyme formulation with EDTA was found to have no cut-off point at the tested concentrations. The MIC and MBC for the multienzyme formulation with EDTA were observed to have the cut-off point at 1.56 mg/mL. The multienzyme formulation with EDTA more potent and more effective in the eradication of the bacterial biofilm compared to the multienzyme since the multienzyme formulation with EDTA's largest log reduction is at a lower concentration than the multienzyme's largest log reduction. The observation that the enzyme/EDTA for MIC and MBC activities indicates significant antimicrobial as well as antibiofilm properties. The data are tabulated below.

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