EP3149190A1 - Identification de nouvelle activité contre la persistance de borrelia burgdorferi - Google Patents

Identification de nouvelle activité contre la persistance de borrelia burgdorferi

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Publication number
EP3149190A1
EP3149190A1 EP15788973.4A EP15788973A EP3149190A1 EP 3149190 A1 EP3149190 A1 EP 3149190A1 EP 15788973 A EP15788973 A EP 15788973A EP 3149190 A1 EP3149190 A1 EP 3149190A1
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European Patent Office
Prior art keywords
bacteria
amino
burgdorferi
culture
agent
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EP15788973.4A
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German (de)
English (en)
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EP3149190A4 (fr
Inventor
Ying Zhang
Jie Feng
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Johns Hopkins University
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Johns Hopkins University
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Publication of EP3149190A1 publication Critical patent/EP3149190A1/fr
Publication of EP3149190A4 publication Critical patent/EP3149190A4/fr
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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
    • C12Q1/04—Determining presence or kind of microorganism; Use of selective media for testing antibiotics or bacteriocides; Compositions containing a chemical indicator therefor
    • C12Q1/06—Quantitative determination
    • 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
    • A61K31/33—Heterocyclic compounds
    • A61K31/335—Heterocyclic compounds having oxygen as the only ring hetero atom, e.g. fungichromin
    • A61K31/365—Lactones
    • A61K31/366—Lactones having six-membered rings, e.g. delta-lactones
    • 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
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/41—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with two or more ring hetero atoms, at least one of which being nitrogen, e.g. tetrazole
    • A61K31/4164—1,3-Diazoles
    • A61K31/4178—1,3-Diazoles not condensed 1,3-diazoles and containing further heterocyclic rings, e.g. pilocarpine, nitrofurantoin
    • 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
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/54—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one sulfur as the ring hetero atoms, e.g. sulthiame
    • A61K31/542—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one sulfur as the ring hetero atoms, e.g. sulthiame ortho- or peri-condensed with heterocyclic ring systems
    • A61K31/545—Compounds containing 5-thia-1-azabicyclo [4.2.0] octane ring systems, i.e. compounds containing a ring system of the formula:, e.g. cephalosporins, cefaclor, or cephalexine
    • A61K31/546—Compounds containing 5-thia-1-azabicyclo [4.2.0] octane ring systems, i.e. compounds containing a ring system of the formula:, e.g. cephalosporins, cefaclor, or cephalexine containing further heterocyclic rings, e.g. cephalothin
    • 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
    • A61K31/65—Tetracyclines
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/04—Peptides having up to 20 amino acids in a fully defined sequence; Derivatives thereof
    • A61K38/12—Cyclic peptides, e.g. bacitracins; Polymyxins; Gramicidins S, C; Tyrocidins A, B or C
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
    • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
    • 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
    • C12Q1/04—Determining presence or kind of microorganism; Use of selective media for testing antibiotics or bacteriocides; Compositions containing a chemical indicator therefor
    • 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
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00—Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64—Fluorescence; Phosphorescence
    • G01N21/6428—Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes"
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00—Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64—Fluorescence; Phosphorescence
    • G01N21/6428—Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes"
    • G01N2021/6439—Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" with indicators, stains, dyes, tags, labels, marks
    • G01N2021/6441—Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" with indicators, stains, dyes, tags, labels, marks with two or more labels
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00—Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64—Fluorescence; Phosphorescence
    • G01N21/645—Specially adapted constructive features of fluorimeters
    • G01N21/6456—Spatial resolved fluorescence measurements; Imaging
    • G01N21/6458—Fluorescence microscopy
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • Lyme disease is a multisystem disease caused by the spirochetal bacterium Borrelia burgdorferi (Meek et al, 1996; Strieker et al, 201 1). The disease is transmitted by tick vectors that can be spread by rodents, reptiles, birds and deer (Strieker et al, 2011 ; Radolf et al, 2012). In the United States, the number of Lyme disease cases has doubled in the last 15 years (Orloski et al., 2000; Bacon et al., 2008) and is estimated to be about 300,000 cases each year (Centers for Disease Control, 2014).
  • Lyme disease is considered the most common tick-borne disease in the United States and Europe (Bacon et al., 2008; Armed Forces Health Surveillance; 2001-2012; CDC, Lyme Disease, 2014).
  • the clinical manifestations of early Lyme disease are most often characterized by an erythema migrans rash often accompanied by flu-like symptoms.
  • An inflammatory arthritis or neurological dysfunction can be frequent sequelae of untreated infection.
  • B. burgdorferi is capable of a complex life style in vitro characterized by multiple pleomorphic forms including spirochetal, spheroplast (or L-form), cyst or round body (RB), and microcolony forms (Diterich et al., 2003; Brorson et al, 2009; Sapi et al, 2012; Miklossy et al, 2008; Alban et al, 2000; Hodzic et al, 2008).
  • RB forms appear as coccoid, membrane-bound atypical variants of B. burgdorferi, forming under experimental stress conditions, such as starvation, oxidative stress, pH variations, heating, or antibiotic treatment in culture (Brorson et al., 2009; Murgia and Cinco, 2004; Brorson and Brorson, 1997; Kersten et al, 1995).
  • the RB forms which have lower metabolism and resist diverse stresses, might be a protective mechanism to overcome adverse environmental conditions (Murgia and Cinco, 2004; Brorson et al., 2009).
  • the presently disclosed subject matter provides a method for viability assessment of spirochetal organisms, such as from the Borrelia genus, and more preferably, the Borrelia burgdorferi species, and related organisms.
  • the presently disclosed subject matter provides a method for assessing the viability of bacteria from the Borrelia genus, the method comprising: (a) establishing a bacterial culture comprising isolated bacteria from the Borrelia genus; (b) incubating the bacterial culture with a staining mixture comprising: (i) a first agent which emits fluorescence of a first color that is indicative of live bacterial cells in the culture, and (ii) a second agent which emits fluorescence of a second color that contrasts from the first color and is indicative of dead bacterial cells in the culture; and (c) calculating a ratio of the intensity of emitted fluorescence of the first color to the intensity of emitted fluorescence the second color; and (d) assessing the viability of the bacteria in the culture, wherein the ratio calculated in (c) is indicative of the percentage of live bacteria in the culture.
  • the presently disclosed subject matter provides a method for assessing the susceptibility of bacteria from the Borrelia genus to at least one antibiotic agent, the method comprising: (a) establishing a bacterial culture comprising isolated bacteria from the Borrelia genus; (b) incubating the culture under suitable conditions for bacterial growth to occur with: (i) at least one dose of at least one antibiotic agent; and (ii) a staining mixture comprising a first agent which emits fluorescence of a first color that is indicative of live bacteria in the culture, and a second agent which emits fluorescence of a second color that contrasts from the first color and is indicative of dead bacteria in the culture, wherein a ratio of the intensity of emitted fluorescence of the first color to the intensity of emitted fluorescence of the second color is indicative of the percentage of live bacteria in the culture; and (c) assessing the susceptibility of bacteria from the Borrelia genus to at least one antibiotic agent by calculating the ratio in (b)(ii) after
  • the bacteria are Borrelia burgdorferi.
  • the method is performed in a high-throughput format, such as for drug screens.
  • the presently disclosed subject matter provides a method for identifying a candidate agent that is capable of inhibiting growth or survival of bacteria from the Borrelia genus, the method comprising: (a) establishing a culture comprising isolated bacteria from the Borrelia genus; (b) contacting the culture with a test agent; (c) assessing a viability of the bacteria in the culture in the presence of the test agent as compared to the viability of the bacteria in a control culture which lacks the test agent, wherein assessing the viability of the bacteria in the culture comprises: (i) incubating the culture with a staining mixture comprising a first agent which emits fluorescence of a first color that is indicative of live bacteria, and a second agent which emits fluorescence of a second color that contrasts from the first color and is indicative of dead bacteria; (ii) calculating
  • the presently disclosed subject matter provides a kit forscreening for at least one agent that is capable of inhibiting growth or survival of bacteria from the Borrelia genus, the kit comprising isolated non-replicating persister forms of Borrelia burgdorferi bacteria and reagents for performing a SYBR Green I/Propidium iodide viability assay.
  • the presently disclosed subject matter provides a kit for assessing the viability and sensitivity of B. burgdorferi cultures for at least one agent (current Lyme disease antibiotics or any new agents) that is capable of inhibiting growth or survival of bacteria from the Borrelia genus, the kit comprising B.
  • reagents for performing a SYBR Green I/Propidium iodide assay and optionally at least one test agent.
  • the presently disclosed subject matter provies a kit for screening at least one candidate agent that is capable of inhibiting growth or survival of bacteria from the Borrelia genus, the kit comprising: (a) a population of isolated bacteria comprising bacteria from the Borellia genus or a culture thereof; (b) a staining mixture comprising: (i) a first agent which emits fluorescence of a first color that is indicative of live bacterial cells, and (ii) a second agent which emits fluorescence of a second color that contrasts from the first color and is indicative of dead bacterial cells, wherein when the staining mixture is incubated with the bacteria population or culture thereof a calculated ratio of the intensity of emitted fluorescence of the first color to the intensity of emitted fluorescence the second color is indicative of the percentage of live bacteria in the population or culture thereof; and (c) instructions for using the bacteria in (a) and the staining mixture in (b) to screen for at least one candidate agent that is capable of inhibiting growth or survival of
  • the presently disclosed subject matter provides a method for inhibiting the growth and/or survival of bacteria from the Borrelia genus, the method comprising contacting bacteria from the Borrelia genus with an effective amount of: (a) at least one compound selected from the group consisting of daptomycin, artemisinin, ciprofloxacin, sulfacetamide, sulfamethoxypyridazine, nifuroxime, fosfomycin, chlortetracycline, sulfathiazole, clofazimine, cefmenoxime,
  • cefoperazone carbomycin, cefotiam, cefepime, amodiaquin, fosfomycin and streptomycin; (b) at least one compound selected from the group consisting of daunomycin 3-oxime; dimethyldaunomycin; daunorubicin; 9, 10-anthracenedione, 1- hydroxy-4-[[2-[(2-hydroxyethyl)amino]ethyl]amino]-; anthracene-9, 10-dione, 1,5- bis[3-[[(2-hydroxyethyl)amino] propyl]amino]-9,10-dihydro-; nogalamycin; pyronin B; N-allyl-2-(methylthio)[l,3]thiazolo[5,4-d]pyrimidin-7-amine; pyrromycin;
  • rhodomycin A chaetochromin; 9, 10-anthracenedione, l,4-dihydroxy-2-[[2-[(2- hydroxyethyl)amino]ethyl]amino]-; prodigiosin; mitomycin; nanaomycin; 9-hydroxy- 2-(2-piperidinylethyl)ellipticinium acetate; N-[3-(2-pyridyl)isoquinolin-l-yl]-2- pyridinecarboxamidine; naphthalene- 1 ,4-dione, 2-chloro-5,8-dihydroxy- 3-(2- methoxyethoxy)-; 9H-thioxanthen-9-one, l-[[2-(dimethylamino)ethyl]amino]-7- hydroxy-4-methyl-,monohydriodide; dactinomycin; emodin; (5,8-dihydroxy-l,4
  • the presently disclosed subject matter provides a method for treating Lyme disease in a subject in need thereof, the method comprising administering to a subject an effective amount of: (a) at least one compound selected from the group consisting of daptomycin, artemisinin, ciprofloxacin, sulfacetamide, sulfamethoxypyridazine, nifuroxime, fosfomycin, chlortetracycline, sulfathiazole, clofazimine, cefmenoxime, cefoperazone, carbomycin, cefotiam, cefepime, amodiaquin, fosfomycin and streptomycin; (b) at least one compound selected from the group consisting of daunomycin 3-oxime; dimethyldaunomycin; daunorubicin; 9, 10-anthracenedione, 1 -hydroxy -4-[[2-[(2-hydroxyethyl)amino]ethyl]amino]-
  • prodigiosin mitomycin; nanaomycin; 9-hydroxy-2-(2-piperidinylethyl)ellipticinium acetate; N-[3-(2-pyridyl)isoquinolin-l-yl]-2-pyridinecarboxamidine; naphthalene- 1,4- dione, 2-chloro-5,8-dihydroxy- 3-(2-methoxyethoxy)-; 9H-thioxanthen-9-one, l-[[2- (dimethylamino)ethyl]amino]-7-hydroxy-4-methyl-,monohydriodide; dactinomycin; emodin; (5,8-dihydroxy-l,4-dioxo-l,4-dihydronaphthalene-2,3-diyl)dimethanediyl dicarbamate; 1 -phenazinecarboxamide, N-[2-(dimethylamino)ethyl
  • a second compound other than the first compound selected from the group consisting of daptomycin, amoxicillin, cefuroxime, ceftriaxone, miconazole, doxycycline, carbenicillin, clofazimine, artemisinin, ciprofloxacin, sulfacetamide, sulfamethoxypyridazine, sulfachlorpyridazine, nifuroxime, nitrofurantoin, fosfomycin, chlortetracycline, sulfathiazole, clofazimine, chlortetracycline, cefmenoxime, cefmetazole, cefoperazone, carbomycin, cefotiam, cefepime, amodiaquin, fosfomycin, streptomycin, daunomycin 3-oxime;
  • the presently disclosed subject matter provides a method for treating Lyme disease in a subject in need thereof, the method comprising: (a) administering to the subject an effective amount of a combination of at least two agents comprising: (i) at least one agent that inhibits growth and/or survival of replicating forms of bacteria from the Borrelia genus; and (ii) at least one agent that inhibits growth and/or survival of non-replicating persister forms of bacteria from the Borrelia genus.
  • FIG. 1 shows representative morphological changes of Borrelia cells following treatment with antibiotics
  • FIG. 2 shows a comparison of methods for assaying B. burgdorferi viability in a 96-well plate
  • FIG. 3 shows a linear relationship between the percentage of live B.
  • FIG. 4 shows the B. burgdorferi B31 strain with commonly used viability assays MTT, XTT, fluoroscein diacetate assay (FDA), the commercially available LIVE/DEAD BacLight assay, and the presently disclosed SYBR Green I/PI assay;
  • FIGS. 5A-5D show the B. burgdorferi B31 strain observed with: (A) the fluorescent microscopy LIVE/DEAD BacLight stain; (B) SYBR Green/PI stain; (C) FDA stain; and (D) the B. burgdorferi biofilm stained by SYBR Green/PI;
  • FIG. 6 shows a SYBR Green/PI assay showing correlation with direct microscope counting in an antibiotic exposure (1. Samples were stained with LIVE/DEAD BacLight kit);
  • FIG. 7 shows a representative drawing of the Yin- Yang model of bacterial persisters and latent infections where it is proposed to target both growing and non- growing bacterial populations for more effective treatment of difficult to cure or persistent bacterial infections and even cancer (Zhang, 2014);
  • FIGS. 8A-8C show: (A) a growth curve of B. burgdorferi strain B31 in vitro; (B) representative images of log phase (3 day culture) and stationary phase (7 day culture) of the B. burgdorferi B31 strain observed with fluorescent microscopy using SYBR Green I/PI stain; the arrows indicate multiple morphological forms of B.
  • FIG. 9 shows the screening of a FDA-approved drug library (2,000 compounds) on stationary phase Borrelia persisters. In vitro activity of some effective antibiotics against stationary phase B. burgdorferi (cultured for 7 days) is shown;
  • FIGS. 10A-10D show representative images of the stationary phase of B. burgdorferi strain B3 Itreated by: (A) daptomycin; (B) cefoperazone; (C) tetracycline; and (D) drug- free control. Treatment was followed by staining with SYBR Green I PI;
  • FIG. 1 1 shows representative images of the stationary phase of B. burgdorferi strain B31 treated by carbomycin (left) and clofazimine (right);
  • FIG. 12 shows antibiotic minimum inhibitory concentrations (MICs) of some persister-active antibiotics for B. burgdorferi strain B31 ;
  • FIGS. 13A-13C show representative images of: (A) 3-day-old log; (B) 7-day - old stationary; and (C) 10-day-old stationary phase B. burgdorferi cultures.
  • the B. burgdorferi cultures of varying ages were stained with SYBR Green I/PI assay and observed under the microscope (400 x magnification).
  • the arrows indicate the spirochete (s), round body (r), and microcolony (m) forms of B. burgdorferi in stationary phase cultures;
  • FIG. 14 shows the effect of drugs (50 ⁇ g/mL) and combinations on stationary phase Borrelia. Susceptibility of stationary phase B. burgdorferi to drugs alone and their combinations after 5 days treatment. G/R: Green/Red ratio. Bracketed values: microscope counting percentages of residual viable cell. Dox: doxcycline; Amox: amoxillin; Cef-P: cefoperazone; Cef-T:ceftriaxone; MTZ: metronidazone; CFZ: clofazimine; MCZ: miconazole; PMB: polymyxin B; FIG. 15 shows representative drug combinations against Borrelia biofilm. Images captured with epi-fluorescence inverted microscope (20X magnification). Drug concentration, 50 ⁇ g/mL;
  • FIG. 16 shows the activity of representative drug combinations against Borrelia biofilm. Fluorescence intensity and area of image were calculated by Image Pro Plus software;
  • FIGS. 17A-17B show the effect of antibiotics alone and in combinations on aggregated microcolony form and planktonic forms of B. burgdorferi.
  • Stationary phase B. burgdorferi culture (10-day old) was treated with 10 ⁇ g/mL drugs (labeled on the image) for 7 days followed by staining by SYBR Green I/PI assay.
  • Green cells indicate live cells whereas red cells indicate dead cells:
  • MC B. burgdorferi aggregated microcolony
  • PT planktonic form as observed by fluorescence microscopy at 400 x magnification; and
  • B susceptibility of the B.
  • burgdorferi microcolony form to antibiotics and antibiotic combinations was assessed by fluorescence microscopy at 200 x magnification.
  • the luminance of an individual RB is much weaker than that of a microcolony, which made the individual cells hard to observe when the microcolonies were being examined.
  • FIGS. 18A-18I show subculture (15 days) of 10-day-old 5. burgdorferi stationary phase culture treated with different antibiotics alone or in combinations. Representative images were taken with fluorescence microscopy (400 x
  • FIGS. 19A-19D show microscopy demonstrating round body formation in the presence of amoxicillin and subsequent reversion to spirochetal form of B.
  • FIG. 20 shows exposure of 5-day old spirochetes and amoxicillin-induced round body form of B. burgdorferi (5 days) to 50 ⁇ doxycycline, cefuroxime, and ceftriaxone for 5 days. The percentages of residual live cells were determined by
  • FIGS. 21A-21I show representative images of amoxicillin-induced round body form of B. burgdorferi (6- day old culture induced with 50 ⁇ g/mL amoxicillin for 72 hours) treated with different antibiotics (50 ⁇ ) for 7 days followed by staining with
  • FIGS. 22A-22P show the effect of antibiotics alone or in combinations on stationary phase B. burgdorferi microcolonies. Stationary phase culture of B.
  • burgdorferi (10-day old) was treated with 10 ⁇ g/mL drugs alone or in combinations (labeled on the image) for 7 days followed by staining with SYBR Green I PI assay.
  • Green cells indicate live cells whereas red cells indicate dead cells.
  • Dox doxycycline; CefP, cefoperazone; Art, Artemisinin; Dap, daptomycin; CefM, cefmetazole; Sep, sulfachlorpyridazine;
  • FIGS. 23A-23I show subculture (20 days) of the amoxicillin-induced round body form of B. burgdorferi (6-day old culture induced with 50 ⁇ g/mL amoxicillin for
  • FIG. 24 shows representative images of stationary phase B. burgdorferi treated with different compounds (50 ⁇ ) followed by staining with SYBR Green I PI assay.
  • DOX doxycycline
  • AMO amoxicillin
  • DAP daptomycin
  • DAU daunomycin
  • NOG nogalamycin
  • PYR pyrromycin
  • RHO Rhodomycin A
  • CHA chaetochromin
  • PRO prodigiosin
  • MIT mitomycin
  • NAN nanaomycin
  • DAC DAC
  • FIG. 25 shows representative images of stationary phase B. burgdorferi strain B31 treated with different compounds (20 ⁇ ) followed by staining with SYBR Green I/PI assay.
  • DOX doxycycline
  • DAP daptomycin
  • DAU doxycycline
  • daunomycin Nogalamycin
  • PYR pyrromycin
  • RHO Rhodomycin A
  • CHA chaetochromin
  • PRO prodigiosin
  • NAN nanaomycin.
  • the presently disclosed subject matter relates to methods for assessing the viability of bacteria (e.g., from the Borrelia genus, e.g., replicating and/or non- replicating persister forms of B. burgdorferi), methods for assessing the susceptibility of bacteria to candidate antibiotic agents, methods for screening for at least one agent that inhibits the growth or survival of bacteria, methods for inhibiting the growth and/or survival of bacteria, methods of treating Lyme disease, and related
  • compositions and kits that can be used to perform the methods.
  • the presently disclosed subject matter provides a method for assessing the viability of bacteria from the Borrelia genus, the method comprising: (a) establishing a bacterial culture comprising isolated bacteria from the Borrelia genus; (b) incubating the bacterial culture with a staining mixture comprising: (i) a first agent which emits fluorescence of a first color that is indicative of live bacterial cells in the culture, and (ii) a second agent which emits fluorescence of a second color that contrasts from the first color and is indicative of dead bacterial cells in the culture; and (c) calculating a ratio of the intensity of emitted fluorescence of the first color to the intensity of emitted fluorescence the second color; and (d) assessing the viability of the bacteria in the culture, wherein the ratio calculated in (c) is indicative of the percentage of live bacteria in the culture.
  • the presently disclosed subject matter provides a new SYBR Green I/propidium iodide (PI) (also termed SYBR Green/PI) assay based on a green fluorescence to red fluorescence ratio for rapid viability assessment of bacteria, such as those from the Borrelia genus.
  • PI SYBR Green I/propidium iodide
  • This assay is superior to other assays commonly used for measuring the viability and for rapid drug susceptibility testing of B. burgdorferi, such as the current commercially available LIVE/DEAD BacLight viability assay (Invitrogen, Carlsbad, CA).
  • the term "viability assay” as used herein refers to an assay to determine the ability of cells to maintain or recover viability, such as the ability to grow.
  • the presently disclosed subject matter provides a method for assessing the viability of bacteria from the Borrelia genus, the method comprising: (a) obtaining a culture comprising bacterial cells from the Borrelia genus; (b) performing a viability assay of the bacterial cells in the culture by using a SYBR Green I/Propidium Iodide assay based on a ratio of green fluorescence, indicative of live bacterial cells, to red fluorescence, indicative of dead bacterial cells, comprising: (i) mixing the culture with a staining mixture comprising SYBR Green I and propidium iodide; (ii) allowing the culture and staining mixture to incubate in the dark; (iii) determining the fluorescence intensity of the culture and staining mixture at 535 nm, which measures green fluorescence, and 635 nm, which measures red fluorescence; and (iv) calculating the ratio of green fluorescence to red fluorescence; and wherein
  • the first color is green and the second color is red or orange.
  • the first agent is SYBR Green I and the second agent is propidium iodide.
  • the SYBR Green I is present in the culture in a concentration range of between about O. lx and about lOOx and propidium iodide is present in the culture in a range of between about 0.1 mM and about 5 mM.
  • the concentration of SYBR Green I in the culture is lOx and the concentration of propidium iodide is 2mM.
  • the culture further comprises a BSK-H medium.
  • the step of incubating the culture with the mixture is performed for approximately 15 minutes. In further embodiments, the step of incubating is performed in the dark.
  • Borrelia is a genus of bacteria of the Spirochete phylum.
  • the Borrelia burgdorferi sensu lato complex includes at least 18 genospecies.
  • Non-limiting examples of bacteria in this genus include d, burgdorferi, B. garinii, B. afzelii, B. americana, B. carolinensis, B. lusitaniae, B. japonica, B. miyamotoi and B. sinica.
  • the bacteria are Borrelia burgdorferi
  • the Borrelia burgdorferi comprise a morphological form selected from the group consisting of a spirochete form, a spheroplast form, a cystic or round body form, a microcolony form, a biofilm-like and biofilm form, and combinations thereof.
  • the method is performed in a high-throughput format, e.g., for drug screening.
  • a high-throughput format e.g., for drug screening.
  • the methods can be used without a washing step and for high- throughput screens. That is, the methods can be used to assess viability, susceptibility of bacteria to antibiotics, and in drug screening directly in a high-throughput manner in the absence of washing.
  • the high-throughput format uses at least one multi-well microplate.
  • suitable multi-well microplates include, without limitation, a 6-well microplate, a 24-well microplate, a 96-well microplate, a 384-well microplate, and a 1536-well microplate.
  • the multi-well microplate comprises a 96-well microplate.
  • the presently disclosed subject matter provides a method for assessing the susceptibility of bacteria from the Borrelia genus to at least one antibiotic agent, the method comprising: (a) establishing a bacterial culture comprising isolated bacteria from the Borrelia genus; (b) incubating the culture under suitable conditions for bacterial growth to occur with: (i) at least one dose of at least one antibiotic agent; and (ii) a staining mixture comprising a first agent which emits fluorescence of a first color that is indicative of live bacteria in the culture, and a second agent which emits fluorescence of a second color that contrasts from the first color and is indicative of dead bacteria in the culture, wherein a ratio of the intensity of emitted fluorescence of the first color to the intensity of emitted fluorescence of the second color is indicative of the percentage of live bacteria in the culture; and (c) assessing the susceptibility of bacteria from the Borrelia genus to at least one antibiotic agent by calculating the ratio in (b)(ii)
  • the presently disclosed subject matter provides a method for screening for a compound that is capable of inhibiting bacteria from the Borrelia genus, the method comprising: (a) obtaining a stationary phase bacterial culture that comprises bacterial cells from the Borrelia genus; (b) contacting the culture with a test compound; (c) performing a viability assay of the bacterial cells in the culture by using a SYBR Green I/Propidium Iodide assay based on a ratio of green fluorescence, indicative of live bacterial cells, to red fluorescence, indicative of dead bacterial cells, comprising: (i) mixing the culture with a staining mixture comprising SYBR Green I and propidium iodide; (ii) allowing the culture and staining mixture to incubate in the dark; (iii) determining the fluorescence intensity of the culture and staining mixture at 535 nm, which measures green fluorescence, and 635 nm, which measures red fluorescence; (i
  • the method further comprises determining a minimum inhibitory concentration breakpoint for at least one antibiotic agent.
  • the first color is green and the second color is red or orange.
  • the first agent is SYBR Green I and the second agent is propidium iodide.
  • the concentration of SYBR Green I in the culture is about lOx and the concentration of propidium iodide is about 2mM.
  • the culture further comprises a BSK-H medium.
  • the bacteria are Borrelia burgdorferi.
  • the Borrelia burgdorferi comprise a morphological form selected from the group consisting of a spirochete form, a spheroplast form, a cystic or round body form, a microcolony form, a biofilm-like and biofilm form, and combinations thereof.
  • the method is performed in a high-throughput format.
  • the high-throughput format uses at least one multi-well microplate.
  • the multi-well microplate comprises a 96-well microplate.
  • the presently disclosed subject matter provides a method for identifying a candidate agent that is capable of inhibiting growth or survival of bacteria from the Borrelia genus, the method comprising: (a) establishing a culture comprising isolated bacteria from the Borrelia genus; (b) contacting the culture with a test agent; (c) assessing a viability of the bacteria in the culture in the presence of the test agent as compared to the viability of the bacteria in a control culture which lacks the test agent, wherein assessing the viability of the bacteria in the culture comprises: (i) incubating the culture with a staining mixture comprising a first agent which emits fluorescence of a first color that is indicative of live bacteria, and a second agent which emits fluorescence of a second color that contrasts from the first color and is indicative of dead bacteria; (ii) calculating a ratio of the intensity of emitted fluorescence of the first color to the intensity of emitted fluorescence the second color, wherein the ratio is indicative of the percentage
  • the bacteria are Borrelia burgdorferi.
  • the culture comprises a stationary phase culture.
  • the stationary phase culture comprises non-replicating persister cells.
  • the stationary phase culture comprises morphological forms selected from the group consisting of round bodies, planktonic, and bio film.
  • the first color is green and the second color is red or orange.
  • the first agent is SYBR Green I and the second agent is propidium iodide.
  • the concentration of SYBR Green I in the culture is about lOx and the concentration of propidium iodide is about 2mM.
  • the culture further comprises a BSK-H medium.
  • the method is performed in a high-throughput format.
  • the high-throughput format uses at least one multi-well microplate.
  • the multi-well microplate comprises a 96-well microplate.
  • the method includes conducting a microscopic counting rescreen to confirm that at least one test agent is a candidate agent for inhibiting growth or survival of bacteria.
  • the terms “inhibit”, “inhibits”, or “significant decrease” means to decrease, suppress, attenuate, diminish, or arrest, for example the growth and/or survival of bacteria in a culture or in a subject, by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or even 100% compared to an untreated control culture or subject.
  • Inhibiting "survival" of bacteria in this context refers to killing bacteria or reducing live bacterial cell count. In some embodiments, the growth of the bacteria is inhibited by more than approximately 50%.
  • the percentage of live bacterial cells in the culture after the treatment with the test compound is less than approximately 50% compared to the percentage of live bacterial cells in the control under identical conditions, but in the absence of the test compound.
  • the stationary phase bacterial culture comprises non-replicating persister cells.
  • the term "significant increase” means an increase by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or even 100%.
  • test compound can be any compound or drug that is desirable to test for inhibitory activity, especially for anti- persister activity.
  • anti-persister activity means that the compound has inhibitory activity against those bacterial cells that might still persist in a culture or subject after contact or administration with a course of antibiotics.
  • the persistent bacteria may evade host immune clearance and result in chronic persistent infection in a subject.
  • the test compound may be a known compound, such as an identified drug found to be effective in at least one disease or disorder, or may be an unknown compound that is not known to be effective in any disease or disorder.
  • the test compound is a known compound that has been approved by a health regulatory agency (e.g., FDA or EMA) for an indication other than treating chronic persistent Lyme disease.
  • a health regulatory agency e.g., FDA or EMA
  • the test compound is a compound that is known to exhibit antibiotic activity against bacteria other than those from the Borellia genus.
  • the test compound is a known compound that has not previously been reported to exhibit antibiotic activity against non-replicating persister forms of bacteria.
  • the method is performed in a high-throughput format.
  • high-throughput it is meant that many samples, such as test compounds, can be tested at one time.
  • the high-throughput format uses at least one 96-well plate.
  • the ordinarily skilled artisan will appreciate that larger or smaller microplates can be used in a high-throughput format to carry out a method of the present disclosure.
  • bacteria culture refers to bacteria growing in a medium conducive for growth of those bacteria.
  • the bacterial culture can be found in any type of container, such as a flask, a tube, a microwell plate, and the like.
  • bacteria have different phases of growth. When a population of bacteria first enters a high-nutrient environment that allows growth, the cells need to adapt to their new environment. The first phase of growth is the lag phase, a period of slow growth when the cells are adapting to the high-nutrient environment and preparing for fast growth.
  • the lag phase has high biosynthesis rates, as proteins necessary for rapid growth are produced.
  • the second phase of growth is the log phase, also known as the logarithmic or exponential phase, in which the bacteria undergo rapid exponential growth.
  • the third phase of growth is the stationary phase and is caused by depleted nutrients.
  • a bacterial culture in "stationary phase” means that the bacteria in the culture have an approximately equal growth rate and death rate.
  • the term “growing forms” of bacteria generally refers to bacteria that are in lag or log phase and not in stationary phase.
  • the stationary phase bacterial culture has been grown for approximately 7 days.
  • the stationary phase bacterial culture comprises non-replicating persister cells. By “non- replicating persister cells,” it is meant bacterial cells that enter a state in which they stop replicating and are able to tolerate antibiotics.
  • kits for practicing the methods of the presently disclosed subject matter.
  • a presently disclosed kit contains some or all of the components, reagents, supplies, and the like to practice a method according to the presently disclosed subject matter.
  • the term "kit” refers to any intended any article of manufacture (e.g., a package or a container) comprising bacteria from the Borrelia genus and an effective amount of reagents for performing a presently disclosed assay.
  • the kit may also include a set of particular instructions for practicing the methods of the presently disclosed subject matter.
  • the presently disclosed subject matter provides a kit for screening for a compound that is capable of inhibiting bacteria from the Borrelia genus, the kit comprising Borrelia bacterial cells and reagents for performing a presently disclosed assay.
  • the presently disclosed subject matter provides a kit for screening for at least one agent that is capable of inhibiting growth or survival of bacteria from the Borrelia genus, the kit comprising isolated non- replicating persister forms of Borrelia burgdorferi bacteria and reagents for performing a SYBR Green LPropidium iodide viability assay.
  • the presently disclosed subject matter provides a kit for screening at least one candidate agent that is capable of inhibiting growth or survival of bacteria from the Borrelia genus, the kit comprising: (a) a population of isolated bacteria comprising bacteria from the Borellia genus or a culture thereof; (b) a staining mixture comprising: (i) a first agent which emits fluorescence of a first color that is indicative of live bacterial cells, and (ii) a second agent which emits fluorescence of a second color that contrasts from the first color and is indicative of dead bacterial cells, wherein when the staining mixture is incubated with the bacteria population or culture thereof a calculated ratio of the intensity of emitted fluorescence of the first color to the intensity of emitted fluorescence the second color is indicative of the percentage of live bacteria in the population or culture thereof; and (c) instructions for using the bacteria in (a) and the staining mixture in (b) to screen for at least one candidate agent that is capable of inhibiting growth or survival of bacteria
  • the kit further comprises at least one test agent to screen for its ability to inhibit the growth or survival of bacteria from the Borrelia genus.
  • the kit further comprises instructions for contacting the population of bacteria or population thereof with at least one test agent.
  • the kit further comprises instructions for incubating the staining mixture with the population of bacteria or culture thereof.
  • the kit further comprises instructions for assessing the viability of the bacteria in the population or culture thereof.
  • the kit further comprises instructions for calculating a ratio of the intensity of emitted fluorescence of the first color to the intensity of emitted fluorescence the second color.
  • the calculated intensity ratio in is indicative of the percentage of live bacteria in the population or culture thereof after a period of exposure to at least one test agent.
  • the bacteria are Borrelia burgdorferi.
  • the culture comprises a stationary phase culture comprising non-replicating persister cells.
  • the stationary phase culture comprises at least one morphological form selected from the group consisting of round bodies, planktonic, biofilm and combinations thereof.
  • the first agent emits green fluorescence and the second agent emits red or orange fluorescence.
  • the first agent is SYBR Green I and the second agent is propidium iodide.
  • the kit further comprises instructions for using SYBR Green I in the screen at a concentration of about lOx and using propidium iodide in the screen at a
  • the presently disclosed subject matter provides a kit for assessing the viability and sensitivity of B. burgdorferi cultures for at least one agent (current Lyme disease antibiotics or any new agents) that is capable of inhibiting growth or survival of bacteria from the Borrelia genus, the kit comprising B.
  • reagents for performing a SYBR Green I/Propidium iodide assay and optionally at least one test agent.
  • the presently disclosed subject matter provides methods for killing, inhibiting, and/ or preventing the growth of bacterial cells.
  • the presently disclosed subject matter provides a method for inhibiting the growth and/or survival of bacteria from the Borrelia genus, the method comprising contacting bacteria from the Borrelia genus with an effective amount of: (a) at least one compound selected from the group consisting of daptomycin, artemisinin, ciprofloxacin, sulfacetamide, sulfamethoxypyridazine, nifuroxime, fosfomycin, chlortetracycline, sulfathiazole, clofazimine, cefmenoxime, cefoperazone, carbomycin, cefotiam, cefepime, amodiaquin, fosfomycin and streptomycin; (b) at least one compound selected from the group consisting of daunomycin 3-oxime; dimethyldaunomycin; daunorubicin; 9, 10-
  • prodigiosin mitomycin; nanaomycin; 9-hydroxy-2-(2-piperidinylethyl)ellipticinium acetate; N-[3-(2-pyridyl)isoquinolin-l-yl]-2-pyridinecarboxamidine; naphthalene- 1,4- dione, 2-chloro-5,8-dihydroxy- 3-(2-methoxyethoxy)-; 9H-thioxanthen-9-one, l-[[2- (dimethylamino)ethyl]amino]-7-hydroxy-4-methyl-,monohydriodide; dactinomycin; emodin; (5,8-dihydroxy-l,4-dioxo-l,4-dihydronaphthalene-2,3-diyl)dimethanediyl dicarbamate; 1 -phenazinecarboxamide, N-[2-(dimethylamino)ethyl
  • a second compound other than the first compound selected from the group consisting of daptomycin, amoxicillin, cefuroxime, ceftriaxone, miconazole, doxycycline, carbenicillin, clofazimine, artemisinin, ciprofloxacin, sulfacetamide, sulfamethoxypyridazine, sulfachlorpyridazine, nifuroxime, nitrofurantoin, fosfomycin, chlortetracycline, sulfathiazole, clofazimine, chlortetracycline, cefmenoxime, cefmetazole, cefoperazone, carbomycin, cefotiam, cefepime, amodiaquin, fosfomycin, streptomycin, daunomycin 3-oxime;
  • the compounds in (c) (ii) and (d) (iii) can be any currently used first-line treatment for Lyme disease.
  • the presently disclosed method comprises administering any combination of the compounds in (a), (b), (c), and (d), e.g., at least two compounds comprising a first compound selected from (a), (b), (c) and (d), and a second compound other than the first selected from (a), (b), (c) and (d), at least three compounds comprising a first compound selected from (a), (b), (c) and (d), a second compound other than the first compound selected from (a), (b), (c) and (d), and a third compound other than the first or second compound selected from (a), (b), (c) and (d), etc.
  • At least one compound in (b) is selected from the group consisting of daunomycin 3-oxime, dimethyldaunomycin, daunorubicin, 9, 10- anthracenedione, 1 -hydroxy -4-[[2-[(2-hydroxyethyl)amino]ethyl]amino]-, anthracene- 9, 10-dione, l,5-bis[3-[[(2-hydroxyethyl)amino] propyl]amino]-9,10-dihydro-, and nogalamycin.
  • the combination of at least two compounds in (c) is daptomycin and doxycycline.
  • the combination of at least two compounds in (c) is daptomycin and cefoperazone.
  • the combination of at least three compounds in (d) is daptomycin, doxycycline, and cefoperazone. In still further embodiments, the combination of at least three compounds in (d) is daptomycin, doxycycline, and sulfamethoxypyridazine. In other embodiments, the combination of at least three compounds in (d) is daptomycin, doxycycline, and clofazamine. In still other embodiments, the combination of at least three compounds in (d) is daptomycin, doxycycline, and carbencillin. In further embodiments, the combination of at least three compounds in (d) is cefoperazone, doxycycline, and clofazamine.
  • the combination of at least three compounds in (d) is cefoperazone, doxycycline, and sulfamethoxypyridazine. In other embodiments, the combination of at least three compounds in (d) is cefoperazone, doxycycline, and miconazole.
  • the bacteria are Borrelia burgdorferi. In other embodiments, the bacteria comprise replicating forms of Borrelia burgdorferi, non- replicating persister forms of Borrelia burgdorferi, and combinations of replicating forms of Borrelia burgdorferi, non-replicating persister forms of Borrelia
  • the bacteria comprise a morphological form of Borrelia burgdorferi selected from the group consisting of round bodies, planktonic, and biofilm.
  • the contacting occurs in vitro or in vivo.
  • contacting refers to any action that results in at least one compound of the presently disclosed subject matter physically contacting at least one bacterial cell or the environment in which at least one bacterial cell resides (e.g., a culture medium).
  • the presently disclosed subject matter provides methods for treating Lyme disease, for example in a subject that has post-treatment Lyme disease syndrome (PTLDS) and/or antibiotic refractory Lyme arthritis. It has been found that an effective amount of particular antibiotics in combination with an effective amount of at least one other particular antibiotic is able to kill non- replicating persister cells. In other embodiments, the method inhibits a bacterial infection in a subject, such as a Borrelia burgdorferi infection.
  • PTLDS Lyme disease syndrome
  • the presently disclosed subject matter provides a method for treating Lyme disease in a subject in need thereof, the method comprising administering to a subject an effective amount of: (a) at least one compound selected from the group consisting of daptomycin, artemisinin, ciprofloxacin, sulfacetamide, sulfamethoxypyridazine, nifuroxime, fosfomycin, chlortetracycline, sulfathiazole, clofazimine, cefmenoxime, cefoperazone, carbomycin, cefotiam, cefepime, amodiaquin, fosfomycin and streptomycin; (b) at least one compound selected from the group consisting of daunomycin 3-oxime; dimethyldaunomycin; daunorubicin; 9, 10-anthracenedione, l-hydroxy-4-[[2-[(2- hydroxyethyl)amino]ethyl]a
  • the compounds in (c) (ii) and (d) (iii) can be any currently used first-line treatment for Lyme disease.
  • the presently disclosed method comprises administering any combination of the compounds in (a), (b), (c), and (d).
  • At least one compound in (b) is selected from the group consisting of daunomycin 3-oxime, dimethyldaunomycin, daunorubicin, 9, 10- anthracenedione, 1 -hydroxy -4-[[2-[(2-hydroxyethyl)amino]ethyl]amino]-, anthracene- 9, 10-dione, l,5-bis[3-[[(2-hydroxyethyl)amino] propyl]amino]-9,10-dihydro-, and nogalamycin.
  • the combination of at least two compounds in (c) is daptomycin and doxycycline.
  • the combination of at least two compounds in (c) is daptomycin and cefoperazone.
  • the combination of at least three compounds in (d) is daptomycin, doxycycline, and cefoperazone. In other embodiments, the combination of at least three compounds in (d) is daptomycin, doxycycline, and
  • the combination of at least three compounds in (d) is daptomycin, doxycycline, and clofazamine. In further embodiments, the combination of at least three compounds in (d) is daptomycin, doxycycline, and carbencillin. In still further embodiments, the combination of at least three compounds in (d) is cefoperazone, doxycycline, and clofazamine. In some embodiments, the combination of at least three compounds in (d) is cefoperazone, doxycycline, and sulfamethoxypyridazine. In other embodiments, the combination of at least three compounds in (d) is cefoperazone, doxycycline, and miconazole.
  • the bacteria are Borrelia burgdorferi. In other embodiments, the bacteria comprise replicating forms of Borrelia burgdorferi, non- replicating persister forms of Borrelia burgdorferi, and combinations of replicating forms of Borrelia burgdorferi, non-replicating persister forms of Borrelia
  • the bacteria comprise a morphological form of Borrelia burgdorferi selected from the group consisting of round bodies, planktonic, and biofilm.
  • the subject has, or is suspected of having, post-treatment Lyme disease syndrome (PTLDS) and/or antibiotic refractory Lyme arthritis.
  • PTLDS post-treatment Lyme disease syndrome
  • the presently disclosed subject matter provides a method for treating Lyme disease in a subject in need thereof, the method comprising: (a) administering to the subject an effective amount of a combination of at least two agents comprising: (i) at least one agent that inhibits growth and/or survival of replicating forms of bacteria from the Borrelia genus; and (ii) at least one agent that inhibits growth and/or survival of non-replicating persister forms of bacteria from the Borrelia genus.
  • the method further comprises one or more steps selected from the group consisting of: (b) obtaining from the subject a biological sample comprising one or more morphological forms of bacteria from the Borrelia genus; (c) isolating at least one of the morphological forms of the bacteria; (d) culturing the isolated bacteria; and (e) assessing the susceptibility of the cultured bacteria to the at least one agent that inhibits the growth and/or survival of replicating forms of bacteria, the at least one agent that inhibits the growth and/or survival of non-replicating persister forms of bacteria, or both.
  • At least one agent that inhibits growth and/or survival of replicating forms of bacteria is selected from the group consisting of a beta-lactam, an antibiotic that damages DNA, and an energy inhibitor.
  • at least one agent that inhibits the growth and/or survival of replicating forms of bacteria is incubated in vitro with a culture comprising non-replicating persister forms of bacteria from the Borrelia genus, at least one agent that inhibits growth and/or survival of replicating forms of bacteria inhibits the growth and/or survival of less than 25 percent of the population of non-replicating persister bacteria in the culture.
  • At least one agent that inhibits the growth and/or survival of replicating forms of bacteria is selected from the group consisting of doxycycline, cefoperazone, carbenicillin, clofazimine, and combinations thereof.
  • at least one agent that inhibits the growth and/or survival of non- replicating persister forms of bacteria is an anthraquinone-containing compound.
  • At least one agent that inhibits the growth and/or survival of non-replicating persister forms of bacteria is incubated in vitro with a culture comprising non-replicating persister forms of bacteria from the Borrelia genus, the at least one agent that inhibits growth and/or survival of the non-replicating persister forms of bacteria inhibits the growth and/or survival of greater than about 50 percent of the population of non-replicating persister forms of bacteria in the culture. In some embodiments, at least one agent inhibits the growth and/or survival of greater than about 75 percent of the population of non-replicating persister forms of bacteria in the culture.
  • At least one agent inhibits the growth and/or survival better than the current antibiotics used for Lyme disease, such as doxycycline, amoxicillin, cefuroxime or ceftriaxone, metronidazole, tinidazole, and combinations thereof.
  • at least one agent that inhibits the growth and/or survival better than the current antibiotics used for Lyme disease can be determined using the presently disclosed methods.
  • At least one agent that inhibits the growth and/or survival of non-replicating persister forms of bacteria is selected from the group consisting of daptomycin, artemisinin, ciprofloxacin, sulfacetamide,
  • sulfamethoxypyridazine nifuroxime, fosfomycin, chlortetracycline, sulfathiazole, clofazimine, cefmenoxime, cefoperazone, carbomycin, cefotiam, cefepime, amodiaquin, fosfomycin and streptomycin; daunomycin 3-oxime;
  • the bacteria are Borrelia burgdorferi. In other embodiments, the bacteria comprise replicating forms of Borrelia burgdorferi, non- replicating persister forms of Borrelia burgdorferi, and combinations of replicating forms of Borrelia burgdorferi, non-replicating persister forms of Borrelia
  • the bacteria comprise a morphological form of Borrelia burgdorferi selected from the group consisting of round bodies, planktonic, and biofilm.
  • antibiotic refers to a compound that has the ability to kill or inhibit the growth of bacteria, particularly bacteria of the Borrelia genus.
  • 'beta-lactam or “beta-lactam antibiotic” refers to an antibiotic with a beta-lactam ring as part of its core structure, such as penicillin and penicillin derivatives (penams), cephalosporins (cephems), monobactams, and carbapenems. Many of these antibiotics work by inhibiting bacterial cell wall biosynthesis.
  • the subject has, or is suspected of having, post- treatment Lyme disease syndrome (PTLDS) and/or antibiotic refractory Lyme arthritis.
  • PTLDS post- treatment Lyme disease syndrome
  • the subject treated by the presently disclosed methods in their many embodiments is desirably a human subject, although it is to be understood that the methods described herein are effective with respect to all vertebrate species, which are intended to be included in the term "subject.”
  • a "subject" can include a human subject for medical purposes, such as for the treatment of an existing disease, disorder, condition or the prophylactic treatment for preventing the onset of a disease, disorder, or condition or an animal subject for medical, veterinary purposes, or developmental purposes.
  • Suitable animal subjects include mammals including, but not limited to, primates, e.g., humans, monkeys, apes, gibbons, chimpanzees, orangutans, macaques and the like; bovines, e.g., cattle, oxen, and the like; ovines, e.g., sheep and the like; caprines, e.g., goats and the like; porcines, e.g., pigs, hogs, and the like; equines, e.g., horses, donkeys, zebras, and the like; felines, including wild and domestic cats; canines, including dogs; lagomorphs, including rabbits, hares, and the like; and rodents, including mice, rats, guinea pigs, and the like.
  • primates e.g., humans, monkeys, apes, gibbons, chimpanzees, orangutans, macaques and the like
  • an animal may be a transgenic animal.
  • the subject is a human including, but not limited to, fetal, neonatal, infant, juvenile, and adult subjects.
  • a "subject” can include a patient afflicted with or suspected of being afflicted with a disease, disorder, or condition.
  • Subjects also include animal disease models (e.g., rats or mice used in experiments, and the like).
  • the term "effective amount” refers to the amount of antibiotic or compound required to inhibit or kill a bacterial cell.
  • the term "effective amount,” as in “a therapeutically effective amount,” of a therapeutic agent refers to the amount of the agent necessary to elicit the desired biological response.
  • the effective amount of an agent may vary depending on such factors as the desired biological endpoint, the agent to be delivered, the composition of the pharmaceutical composition, the target tissue or cell, and the like.
  • the term "effective amount” refers to an amount sufficient to produce the desired effect, e.g., to reduce or ameliorate the severity, duration, progression, or onset of a disease, disorder, or condition, or one or more symptoms thereof; prevent the advancement of a disease, disorder, or condition, cause the regression of a disease, disorder, or condition; prevent the recurrence, development, onset or progression of a symptom associated with a disease, disorder, or condition, or enhance or improve the prophylactic or therapeutic effect(s) of another therapy.
  • the disease, disorder, or condition is Lyme disease.
  • the terms “treat,” treating,” “treatment,” and the like are meant to decrease, suppress, attenuate, diminish, arrest, the underlying cause of a disease, disorder, or condition, or to stabilize the development or progression of a disease, disorder, condition, and/or symptoms associated therewith.
  • the terms “treat,” “treating,” “treatment,” and the like, as used herein can refer to curative therapy, prophylactic therapy, and preventative therapy.
  • Consecutive treatment, administration, or therapy can be consecutive or intermittent. Consecutive treatment, administration, or therapy refers to treatment on at least a daily basis without interruption in treatment by one or more days. Intermittent treatment or
  • treatment refers to treatment that is not consecutive, but rather cyclic in nature.
  • Treatment according to the presently disclosed methods can result in complete relief or cure from a disease, disorder, or condition, or partial amelioration of one or more symptoms of the disease, disease, or condition, and can be temporary or permanent.
  • treatment also is intended to encompass prophylaxis, therapy and cure.
  • the term “combination” is used in its broadest sense and means that a subject is administered at least two agents, for example an antibiotic, and one or more antibacterial agents. More particularly, the term “in combination” refers to the concomitant administration of two (or more) active agents for the treatment of a, e.g., single and multiple disease states with heterogeneous bacterial populations consisting of growing and non-growing or any in between bacterial cells..
  • the active agents may be combined and administered in a single dosage form, may be administered as separate dosage forms at the same time, or may be administered as separate dosage forms that are administered alternately or sequentially on the same or separate days.
  • the active agents are combined and administered in a single dosage form.
  • the active agents are administered in separate dosage forms (e.g., wherein it is desirable to vary the amount of one, but not the other).
  • the single dosage form may include additional active agents for the treatment of the disease state.
  • the compounds described herein can be administered alone or in combination with adjuvants that enhance stability of the compounds, facilitate administration of pharmaceutical compositions containing them in certain embodiments, provide increased dissolution or dispersion, increase inhibitory activity, provide adjunct therapy, and the like, including other active ingredients.
  • such combination therapies utilize lower dosages of the conventional therapeutics, thus avoiding possible toxicity and adverse side effects incurred when those agents are used as monotherapies.
  • the timing of administration of the compounds can be varied so long as the beneficial effects of the combination of these agents are achieved.
  • the phrase "in combination with” refers to the administration of a compound, and at least one additional therapeutic agent, such as an antibiotic or other compound, either simultaneously, sequentially, or a combination thereof. Therefore, a subject administered a combination of a compound and at least one additional therapeutic agent, can receive the compound and at least one additional therapeutic agent at the same time (i.e., simultaneously) or at different times (i.e., sequentially, in either order, on the same day or on different days), so long as the effect of the combination of both agents is achieved in the subject.
  • agents administered sequentially can be administered within 1, 5, 10, 30, 60, 120, 180, 240 minutes or longer of one another. In other embodiments, agents administered sequentially, can be administered within 1, 5, 10, 15, 20 or more days of one another.
  • the compound and at least one additional therapeutic agent are administered simultaneously, they can be administered to the subject as separate pharmaceutical compositions, each comprising either a compound or at least one additional therapeutic agent, or they can be administered to a subject as a single pharmaceutical composition comprising both agents.
  • the effective concentration of each of the agents to elicit a particular biological response may be less than the effective concentration of each agent when administered alone, thereby allowing a reduction in the dose of one or more of the agents relative to the dose that would be needed if the agent was administered as a single agent.
  • the effects of multiple agents may, but need not be, additive or synergistic.
  • the agents may be administered multiple times.
  • the two or more agents when administered in combination, can have a synergistic effect.
  • “synergistic,” “synergistically” and derivations thereof, such as in a “synergistic effect” or a “synergistic combination” or a “synergistic composition” refer to circumstances under which the biological activity of a combination of a compound and at least one additional therapeutic agent is greater than the sum of the biological activities of the respective agents when administered individually.
  • Synergy can be expressed in terms of a "Synergy Index (SI)," which generally can be determined by the method described by F. C. Kull et al, Applied Microbiology 9, 538 (1961), from the ratio determined by:
  • SI Synergy Index
  • Q A is the concentration of a component A, acting alone, which produced an end point in relation to component A;
  • Q a is the concentration of component A, in a mixture, which produced an end point
  • Q B is the concentration of a component B, acting alone, which produced an end point in relation to component B;
  • Qb is the concentration of component B, in a mixture, which produced an end point.
  • a "synergistic combination” has an activity higher that what can be expected based on the observed activities of the individual components when used alone.
  • a “synergistically effective amount" of a component refers to the amount of the component necessary to elicit a synergistic effect in, for example, another therapeutic agent present in the composition.
  • the term "about,” when referring to a value can be meant to encompass variations of, in some embodiments, ⁇ 100% in some embodiments ⁇ 50%, in some embodiments ⁇ 20%, in some embodiments ⁇ 10%, in some embodiments ⁇ 5%, in some embodiments ⁇ 1%, in some embodiments ⁇ 0.5%, and in some embodiments ⁇ 0.1% from the specified amount, as such variations are appropriate to perform the disclosed methods or employ the disclosed compositions.
  • Borrelia burgdorferi strain B31 was obtained from the American Type Tissue Collection. Borrelia burgdorferi was cultured in BSK-H medium (HiMedia Laboratories Pvt. Ltd.), with 6% rabbit serum (Sigma-Aldrich, St. Louis, MO). All culture media were filter-sterilized by 0.2- ⁇ filter. Cultures were incubated in sterile 50-mL closed conical tubes (BD
  • Microscopy techniques Specimens were examined on a Nikon Eclipse E800 microscope equipped with differential interference contrast (DIC) and epi-fluorescent illumination, and recorded with a Spot slider color camera.
  • Cell proliferation assays were performed by directly counting using a bacterial counting chamber (Hausser Scientific Partnership, Horsham, PA) and DIC microscopy.
  • DIC differential interference contrast
  • Antibiotics and FDA-approved drug library Doxycycline, amoxicillin, metronidazole, clofazimine, ketoconazole, miconazole, aspirin, polymyxin B (PMB), and sulfamethoxazole (SMX) (all purchased from Sigma-Aldrich) were dissolved in appropriate solvents (Clinical and Laboratory Standards Institute, 2007) to form stock solutions. All the antibiotic stocks were filter-sterilized by a 0.2- ⁇ filter. The stocks then were pre-diluted into 500- ⁇ pre-diluted stocks and stored at -20 °C.
  • Each drug in the Johns Hopkins Clinical Compound Library (JHCCL) (Chong et al, 2006) was made into 10-mM stock solutions with DMSO. The stock solutions were arrayed in a total of 24 96-well plates, leaving the first and the last columns in each plate for controls. Each solution in these master plates was diluted with PBS to make 500- ⁇ pre-diluted plates. The first and the last columns in each pre-diluted plate were included as blank controls, doxycycline control, and amoxicillin control. The pre-diluted drug plates were sealed and stored at -20 °C.
  • Antibiotic susceptibility test To qualitatively determine the effect of the antibiotics, 10 ⁇ ⁇ of each compound from the pre-diluted plate or pre-diluted stock was added to the B. burgdorferi culture in the screening plate. The final volume per well was adjusted to 100 ⁇ . The plates were sealed and placed in a 33 °C incubator for 7 days.
  • SYBR Green I/PI assay was used as described in a previous study (Feng, Wang, Shi, et al, 2014).
  • SYBR Green I 10,000 x stock, Invitrogen, Carlsbad, CA
  • 30 ⁇ ⁇ propidium iodide (20 mM, Sigma-Aldrich) was mixed with 30 ⁇ ⁇ propidium iodide (20 mM, Sigma-Aldrich) into 1.0 mL of sterilized dH 2 0 and mixed thoroughly. Staining mixture (10 ⁇ ) was added to each well and mixed thoroughly. The plates at room temperature were incubated in the dark for 15 minutes.
  • the fluorescence intensities at 535 nm (green emission) and 635 nm (red emission) were measured for each well of the screening plate using a HTS 7000 plus Bio Assay Reader (PerkinElmer Inc.,
  • B. burgdorferi suspensions live and 70% isopropyl alcohol-killed
  • five different proportions of live:dead cells (0: 10, 2:8, 5:5, 8:2, 10:0) the mixture was added in wells of a 96-well plate.
  • SYBR Green I7PI reagent was then added to each of the five samples and the green/red fluorescence ratios for each proportion of live/dead B. burgdorferi were measured using a HTS 7000 plus Bio Assay Reader as described above.
  • the regression equation and regression curve of the relationship between the percentage of live bacteria and green/red fluorescence ratios were obtained with least-square fitting analysis. The regression equation was used to calculate the percentage of live cells in each well of the screening plate. Some effective candidates were further confirmed by epi- fluorescence microscope counting.
  • MIC determination The standard microdilution method was used to determine the antibiotic minimum inhibitory concentration (MIC) that would inhibit visible growth of B. burgdorferi after a 72-hour incubation period (Sapi et al, 2011 ; Dever et al, 1992; Boerner et al, 1995). B. burgdorferi cells (1 x 10 5 ) were inoculated into each well of a 96-well microplate containing 90 ⁇ ⁇ fresh BSK-H medium per well.
  • FIG. 1 Representative morphological changes of Borrelia cells following treatment with some currently used antibiotics is shown in FIG. 1. During the log phase, the Borrelia cells treated with amoxicillin and doxycycline adopt cystic or round body forms. During the stationary phase, the Borrelia cells treated with the same antibiotic adopt a spirochete form.
  • FIG. 4 shows the B. burgdorferi B31 strain with commonly used viability assays MTT, XTT, fluoroscein diacetate assay (FDA), the commercially available LIVE/DEAD BacLight assay, and the presently disclosed SYBR Green I/PI assay.
  • the SYBR Green I/PI assay had a less than 10% error and could be completed in approximately 20 minutes.
  • FIGS. 5A-5D show the B. burgdorferi B31 strain observed with: (A) the fluorescent microscopy LIVE/DEAD BacLight stain; (B) SYBR Green/PI stain; (C) FDA stain; and (D) the B. burgdorferi biofilm stained by SYBR Green/PI.
  • the SYBR Green/PI assay showed correlation with direct microscope counting with antibiotic exposure (FIG. 6).
  • FIG. 7 shows a representative drawing of the Yin- Yang model of bacterial persisters and latent infections (Zhang, 2014).
  • the Yin-Yang model depicts a dynamic and complex bacterial population consisting of growing (Yang, in red) and non-growing populations (Yin, in black) which are in varying metabolic states in continuum and can interconvert.
  • growing population Yang
  • non-growing or slowly growing persisters Yin
  • the persister population is again heterogeneous and composed of various sub-populations in continuum and includes a varying hierarchy of persisters.
  • isoniazid kills growing bacteria (Yang)
  • rifampin RAF
  • PZA pyrazinamide
  • Persisters not killed by antibiotics could revert to replicating forms (reverters) and cause relapse.
  • the current Lyme disease antibiotics doxycycline and amoxicillin or ceftriaxone only kill the growing Borrelia burgdorferi bacteria (Yang) and have little or no activity for dormant non- growing Borrelia burgdorferi persisters (Yin).
  • the Yin-Yang model proposes targeting both replicating and non-replicating cells for better treatment of both persistent bacterial infections, including Lyme disease.
  • persister active drugs or antibiotics such as daptomycin, clofazimine, cefoperazone, carbomycin, sulfa drugs, and/or quinolones
  • Lyme disease antibiotics such as doxycycline, amoxicillin and/or ceftriaxone, which are active against the growing Borrelia burgdorferi bacteria (Yang) for more effective treatment of all forms of Lyme disease, especially the chronic and persistent forms of the disease.
  • B. burgdorferi culture was grown in BSK-H medium for 7 days, and cell number was determined by microscope counting at different time points.
  • the B. burgdorferi growth reached peaks (5 x 10 7 spirochetes/mL) after 5-6 days.
  • the microscope counts of cell density remained relatively constant until 11 days of incubation (FIG. 8A).
  • the ratio of round bodies and biofilm-like colonies significantly increased in the stationary phase B. burgdorferi culture (FIG. 8B).
  • These stationary phase cultures may represent a mixed population of different morphological forms.
  • burgdorferi stationary phase culture of 7 days was chosen as a persistence model to screen for drugs.
  • bResidual viable B. burgdorferi was assayed by epifluorescence microscope counting.
  • Residual viable B. burgdorferi was calculated according to the regression equation and ratio of Green/Red fluorescence obtained by SYBR Green I/PI assay.
  • FIG. 1 Representative images are shown of the stationary phase of B. burgdorferi strain B3 Itreated by daptomycin, cefoperazone, and tetracycline (FIGS. 10A-10D), as well as carbomycin and clofazimine (FIG. 1 1).
  • Some of these compounds may block protein synthesis.
  • macrolides have greater activity than penicillin or ceftriaxone for B. burgdorferi persisters.
  • Carbomycin, a macrolide showed higher activity against B. burgdorferi than other macrolides, such as erythromycin.
  • Other compounds may damage DNA and/or energy, such as clofazimine.
  • Compounds also might block DNA synthesis.
  • sulfa drugs such as sulfameter and sulfisoxazole, were effective against stationary phase B. burgdorferi, while sulfamethoxazole also exhibited a low MIC ( ⁇ 0.2 ⁇ g/mL).
  • the presently disclosed subject matter provides a rapid and convenient viability assay (e.g., SYBR Green I/PI) that is suitable for high-throughput screening for identifying new drugs and for rapidly evaluating antibiotic susceptibility of B. burgdorferi (Feng, Wang, Shi, et al, 2014).
  • a FDA- approved compound library was screened for activity against non-replicating persisters of B. burgdorferi. A number of drug candidates were identified that have activity for Borrelia persisters.
  • Daptomycin is a lipopeptide antibiotic used in the treatment of infections caused by Gram-positive organisms.
  • the presently disclosed data showed daptomycin had the highest activity against stationary phase B. burgdorferi persisters among all the active hits. Daptomycin could disrupt multiple aspects of bacterial cell membrane function. It inserts into the membrane, and creates pores that allow cells to leak ions, which causes rapid depolarization, resulting in a loss of membrane potential and bacterial cell death (Pogliano et al, 2012).
  • the B. burgdorferi cells treated by daptomycin showed almost all red fluorescence as spirochetes (FIG. 10A) after staining. This result indicated the daptomycin could disrupt the cell membrane of B.
  • Macrolides and ketolides were chosen as candidate antibiotics for clinical therapy of Lyme disease in previous studies (Hunfeld and Brade, 2006).
  • carbomycin a 16-membered macrolide
  • the MIC data showed carbomycin also was effective against multiplying B. burgdorferi.
  • Treatment of B. burgdorferi with beta-lactams was commonly used therapy in a clinical setting (Hunfeld and Brade, 2006). Beta-lactams might induce round-body propagules of B.
  • Cefoperazone a third generation cephalosporin, appears to be the best beta- lactam antibiotic against stationary phase B. burgdorferi, followed by some second generation cephalosporins, such as cefotiam, cefmetazole and cefonicid.
  • first generation cephalosporins showed very limited activity against stationary phase B. burgdorferi. It has been found that the activities of cephalosporins against stationary phase B. burgdorferi did not completely fit with the classic generation grouping of these antibiotics according to their spectrum of activity against Gram-negative and Gram-positive bacteria. This observation is probably related to the differences of B. burgdorferi from common gram-negative or gram-positive bacteria (Bergstrom and Zuckert, 2010). Although beta-lactamase inhibitor tazobactam had a limited effect on multiplying B.
  • the optimized combination of beta-lactams and lactamase inhibitor has good activity against B. burgdorferi persistence.
  • Tetracycline antibiotics especially doxycycline, are used in clinic settings as frontline drugs for Lyme disease. These antibiotics have lower MIC values (Hunfeld and Brade, 2006) and have good activity on multiplying B. burgdorferi. Interestingly, it was found that tetracycline had higher activity against stationary phase B.
  • B. burgdorferi than doxycycline. It was observed that most cells were round-body propagules in the stationary phase B. burgdorferi treated by tetracycline (FIG. IOC). B. burgdorferi could form different morphological shapes in stationary phase or under adverse conditions, while tetracycline antibiotics might be ineffective on some morphological cells, such as round bodies (cysts) cells (Sapi et al, 2011).
  • Clofazimine was originally developed for the treatment of tuberculosis, although now it is commonly used for the treatment of leprosy (Arbiser and
  • burgdorferi persisters were identified from existing drugs used for treating other diseases or conditions. These drugs include daptomycin, clofazimine, carbomycin, sulfa drugs like sulfamethoxazole and certain cephalosporins, such as cefoperazone.
  • daptomycin clofazimine
  • carbomycin sulfa drugs like sulfamethoxazole
  • cephalosporins such as cefoperazone.
  • strain, media and culture The strain, media, and culture were obtained and used as in Example I.
  • Antibiotics Doxycycline (Dox), amoxicillin (Amo), cefoperazone (CefP), clofazimine (Cfz), miconazole (Mcz), polymyxin B (Pmb), sulfamethoxazole (Smx), daptomycin (Dap), carbomycin (magnamycin A), vancomycin, nisin, carbencillin, ofloxacin, tigecycline, hydroxychloroquine, rifampin, and clarithromycin (Sigma- Aldrich) were dissolved in suitable solvents (Clinical and Laboratory Standards Institute, 2007) to obtain stock solutions. The antibiotic stocks were filter-sterilized by 0.2- ⁇ filter except clofazimine, which was dissolved in DSMO
  • Microscopy techniques Specimens were examined on a Nikon Eclipse E800 microscope equipped with differential interference contrast (DIC) and epi- fluorescence illumination, and recorded with a Spot slider color camera.
  • Cell proliferation assays were performed by direct counting using a bacterial counting chamber (Hausser Scientific Partnership) and DIC microscopy. SYBR Green I/PI assay was performed to assess the viability of B. burgdorferi. The ratio of live
  • Image Pro-Plus software was applied for measuring the biomass (fluorescence intensity) of different forms (spirochetes, round body, and microcolony) of B. burgdorferi as previously described (Shopov and Williams, 2000).
  • Antibiotic exposure assay To qualitatively determine the effect of antibiotics, 10 of each compound from the pre-diluted plate or pre-diluted stock was added to stationary phase B. burgdorferi culture in the 96-well plate. The final volume per well was adjusted to 100 ⁇ ⁇ at a concentration of 10 ⁇ g/mL for each antibiotic. Plates were sealed and placed in a 33°C incubator for 7 days. The SYBR Green II PI viability assay was used to assess the live and dead cells after antibiotic exposure as described (Feng, Wang, Shi, et al, 2014).
  • the regression equation and regression curve of the relationship between percentage of live bacteria and green/red fluorescence ratios was obtained.
  • the regression equation was used to calculate the percentage of live cells in each well of the 96-well plate.
  • Subculture of antibiotic-treated B. burgdorferi to assess viability of the organisms Seven-day-old B. burgdorferi culture (1 * 10 7 spirochetes/mL) (500 ⁇ ) was treated with drugs or drug combinations in Eppendorf tubes. After incubation at 33 °C for 7 days without shaking, the cells were collected by centrifugation and rinsed with 1 mL fresh BSK-H medium followed by resuspension in 500 fresh BSK-H medium without antibiotics.
  • B. burgdorferi culture possesses different proportions of morphological variants including round body and microcolony forms as the culture ages: As shown in a previous study (Feng, Wang, Shi, et al, 2014), the stationary phase culture was enriched with morphological variants, such as round body form and biofilm-like aggregated microcolony, form in increasing proportions in contrast to individual spirochetes found in log phase culture (FIG. 13). To more accurately assess the proportion of different morphological variant forms, representative images of each sample taken from cultures of different ages were examined to measure the percentage of different morphological forms of B. burgdorferi (Table 2). It was found that the log phase (3-day-old) B. burgdorferi culture consisted almost entirely of spirochetal form (96%), with few round body form (4%) and no aggregated microcolony form (FIG. 13 A). In the 7-day-old stationary phase culture of B.
  • FIG. 13B When B. burgdorferi stationary phase culture was cultured for 10 days, the percentage of the microcolony form increased to 64%, and the spirochetal form and the round body form were 20% and 16%, respectively (FIG. 13C).
  • Persister frequencies in log phase and stationary phase cultures Because B. burgdorferi does not form colonies easily on agar plates, the conventional method to assay persister frequency after antibiotic exposure by calculating the percentage of bacteria killed by a bacteriocidal antibiotic cannot be applied to B. burgdorferi.
  • the frequency of B. burgdorferi persisters in log phase and stationary phase cultures was assessed using the SYBR Green I/PI viability assay after exposure of the cultures to antimicrobials.
  • E. coli culture was used as a control after exposure to antibiotics to validate the SYBR Green I/PI viability assay for persister frequency assessment.
  • the persister frequency of the log phase E. coli culture with exposure to 50 ⁇ g/mL amoxicillin for 3 hours was 4.4% for the SYBR Green I/PI assay and 0.9% for the CFU assay (Table 1).
  • the persister frequencies of B was assessed using the SYBR Green I/PI viability assay after exposure of the cultures to antimicrobials.
  • E. coli culture was used as a control after exposure to antibiotics to validate the SYBR Green I/PI viability assay for persister frequency assessment.
  • the persister frequency of the log phase E. coli culture with exposure to 50 ⁇ g/mL amoxicillin for 3 hours was 4.4% for the SYBR
  • Microcolony form is more tolerant to antibiotics than free-living spirochetal and round body forms: Previous studies showed that the stationary phase B.
  • FIG. 14 shows the effect of drugs (50 ⁇ g/mL) and combinations on stationary phase Borrelia.
  • FIG. 15 shows some promising drug combinations against Borrelia biofilm.
  • FIG. 16 shows the activity of drug combinations against Borrelia biofilm.
  • burgdorferi persisters as shown by the presence of significant numbers of red cells (dead cells) mixed with some green cells (viable cells) in the microcolony (FIG. 17A, Panel h).
  • the other persister active drug cefoperazone (Feng, Wang, Shi,et al, 2014) had weaker activity than daptomycin since it had some activity for the planktonic form cells (52% cells were green cells), but little activity for the microcolony form of persisters where most of the microcolony cells remained as green (live) cells (FIG. 17A, Panel e).
  • doxycycline had the least activity against stationary phase B.
  • Daptomycin (10 ⁇ g/mL) alone could not eliminate the microcolonies by itself
  • daptomycin in combination with doxycycline or beta- lactams was very effective against B. burgdorferi planktonic persisters and also against microcolonies (Table 2, FIG. 17B).
  • daptomycin in combination with doxycycline or cefoperazone produced better bacteriocidal activity for the microcolony form than either of these agents alone or drug combinations without daptomycin, such as doxycycline + cefoperazone or even doxycycline + cefoperazone + sulfamethoxazole, as shown by more red cells (dead cells) being produced after daptomycin drug combinations (FIG.
  • burgdorferi persisters were Dox + either CefP or miconazole or sulfamethoxazole (Table 3).
  • clofazimine showed good activity against stationary phase B. burgdorferi persisters when combined with doxycycline and cefoperazone (Table 3). It is worth noting that the activity of carbenicillin, vancomycin, ofloxacin, clarithromycin, tigecycline, nisin, and hydroxychloroquine when combined with doxycycline only marginally enhanced doxycycline activity and their anti-persister activities were not as effective as when they were combined with daptomycin (Table 3).
  • this drug combination could eliminate not only planktonic stationary phase B. burgdorferi persisters (spirochetal and round body forms), but also the more resistant biofilm-like microcolonies (Table 4, FIG. 18). Subculturing the sample treated with this drug combination showed no sign of any detectable organisms by microscopy (detection limit ⁇ 10 5 ) even after 15 days of subculture (Table 4, FIG. 18i). These findings indicate that the microcolony structures are not eliminated by doxycycline, amoxicillin, persister active drugs alone, two drug combinations or even some three drug combinations, but could be eradicated by the drug combination of doxycycline, cefoperazone and daptomycin.
  • B. burgdorferi assayed by epi-fluorescence microscope counting was calibrated using E. coli as a control.
  • the log phase culture was obtained by subculture of a stationary phase culture at 1 :50 dilution for 3 days in BSK medium.
  • Persister frequency calculated by epi-fluorescence microscope counting after SYBR Green I/PI viability staining.
  • washed bacterial cells was subcultured in 1 mL fresh BSK-H medium for 7 days and 15 days.
  • G/R ratio Green/Red fluorescence ratio
  • Dox doxycycline
  • CefP cefoperazone
  • Cfz clofazimine
  • Dap daptomycin
  • Green/Red fluorescence ratios were obtained by microplate reader after SYBR Green I/PI staining. Each value is the mean of three replicates.
  • B. burgdorferi persisters It was found that it is more effective to kill B. burgdorferi persisters by drug combination than single antibiotic, but bacteriocidal activity depended on the particular antibiotics used (Table 3). It is interesting to note that despite the persister active antibiotics, such as the lipopeptide daptomycin and beta- lactam cefoperazone themselves, were quite active against planktonic B. burgdorferi persisters (both spirochetal and round body forms), they were unable to eradicate the more resistant microcolony form when used alone or even in combination (FIG. 17). Previous studies showed that tinadazole, metronidazole, and tigecycline were more active against B.
  • tigecycline was the most active antibiotic against the round body form compared with tinadazole and metronidazole in that study (Sapi et al, 201 1), it was found that by itself tigecycline was not very effective at killing the biofilm-like microcolonies (Table 3).
  • daptomycin in combination with doxycycline and cefoperazone or carbencillin was able to completely eradicate the most resistant microcolonies (FIG. 17), and this was further confirmed by subculture studies, which showed lack of any growth (FIG. 18). While various drug combinations showed improved activity against stationary phase B. burgdorferi persisters, daptomycin combinations had the best activity among drug combinations against persisters (Table 3). The only non-daptomycin regimens that were close to daptomycin combinations contained cefoperazone (FIG. 17, Table 3). Unexpectedly, other antibiotics, such as sulfamethoxazole, clofazimine and miconazole, also had more activity against stationary phase B.
  • burgdorferi persisters in combination with doxycycline and cefoperazone. These drugs are not currently used as antibiotics for treatment of Lyme disease clinically (CDC, Post-Treatment Lyme Disease Syndrome, 2014; Hunfeld and Brade, 2006). Although sulfa drugs are bacteriostatic when used alone for growing bacteria, they could kill non-growing round body or aggregated microcolony form of B. burgdorferi during long-term treatment. Clofazimine with high anti-persister activity improved the combination with daptomycin or daptomycin plus doxycycline (Table 3), which may be due to its multiple mechanisms of action including membrane destabilization, reactive oxygen species production, and inhibition of membrane energy metabolism in M. tuberculosis (Xu et al, 2012). It also was found that miconazole, an imidazole antifungal drug, had high activity against B.
  • burgdorferi persisters when combined with doxycycline and cefoperazone (Table 2).
  • Miconazole has been shown to alter the integrity of lipid membrane (Vanden Bossche et al, 1989) and therefore may facilitate the penetration of other drugs, such as doxycycline and cefoperazone, for improved activity against B. burgdorferi persisters (Table 3).
  • microcolonies which is consistent with the proposition to use drugs targeting both growing and non-growing microbial populations for improved treatment of persistent infections (Zhang, 2014).
  • B. burgdorferi spirochetes could develop morphological variants as in vitro cultures age or are subjected to adverse conditions (Feng, Wang, Shi, et al, 2014; Brorson et al, 2009; Alban et al, 2000; Sapi et al, 201 1; Murgia and Cinco, 2004).
  • the proportions of these variants have not been well characterized over time in culture conditions.
  • the percentages of morphological variants were determined as they transitioned from spirochetes to progressively round body form to then microcolony form as log phase culture grew to stationary phase (7- 10 days) (FIG. 13).
  • persister frequencies vary according to the antibiotic used, with the more effective antibiotic ceftriaxone having a lower persister frequency than amoxicillin (Table 2), a finding that is consistent with previous studies (Zhang, 2014; Lu and Zhang, 2007). It remains to be determined if there are differences in persistence of B. burgdorferi strains and if the high persister frequencies in B. burgdorferi strains are associated with recalcitrance to antibiotic therapies.
  • burgdorferi persisters with increasing antibiotic tolerance as the culture ages from log phase to stationary phase with morphological changes from spirochetal form to round body and microcolony forms.
  • Persister frequencies in log phase B. burgdorferi culture ranged 5.8-9.6% depending on the antibiotic as measured by SYBR Green I/propidium iodide (PI) viability stain and microscope counting, but the corrected log phase B. burgdorferi persister frequencies were at 1-2% using E. coli as a control.
  • drug combinations were studied using previously identified drugs from an FDA- approved drug library with high activity against B. burgdorferi persisters.
  • daptomycin-containing drug combinations were the most effective at killing B. burgdorferi persisters.
  • daptomycin was the common element in the most active regimens against persisters when used with doxycycline plus either beta-lactams (cefoperazone or carbenicillin) or energy inhibitor (clofazimine).
  • beta-lactams cefoperazone or carbenicillin
  • clofazimine energy inhibitor
  • Daptomycin plus doxycycline and cefoperazone eradicated the most resistant microcolony form of B. burgdorferi persisters and did not yield viable spirochetes upon subculturing, suggesting durable killing of these persisting forms, which was not achieved by any other two or three drug
  • B. burgdorferi strain B31 was obtained from American Type Tissue Collection. B. burgdorferi and was cultured in BSK-H media (HiMedia Laboratories Pvt. Ltd.), with 6% rabbit serum (Sigma-Aldrich, Co). All culture media were filter-sterilized by 0.2 ⁇ filter. Cultures were incubated in sterile 50 mL closed conical tubes (BD Biosciences, California, USA) at 33°C without antibiotics.
  • B. burgdorferi spirochetes (1 x 10 5 spirochetes/ml) were cultured in BKS-H medium for 6 days without shaking. After the 6-day incubation, amoxicillin at a final concentration of 50 ⁇ g/mL was added to the culture for round body form induction. After 72 h induction at 33°C, the round body forms of B.
  • the round body cells (100 ⁇ ) were transferred to 96-well tissue culture microplates for evaluation of the effects of antibiotic treatment.
  • Microscopy techniques Specimens were examined on a Nikon Eclipse E800 microscope equipped with differential interference contrast (DIC) and epi- fluorescence illumination, and recorded with a Spot slider color camera.
  • Cell proliferation assays were performed by direct counting using a bacterial counting chamber (Hausser Scientific Partnership, PA, USA) and DIC microscopy.
  • DIC differential interference contrast
  • the ratio of live (green) and dead (red) B. burgdorferi was calculated by counting the cells using a bacterial counting chamber and epi- fluorescence microscopy.
  • Antibiotics and FDA drug library Doxycycline, metronidazole, cefmetazole, roliteracycline, sulfachlorpyridazine, artemisinin, cefoperazone, daptomycin (Sigma- Aldrich) were dissolved in suitable solvents (Wikler and Ferraro, 2008) to form stock solutions.
  • the antibiotic stocks were filter-sterilized by 0.2 ⁇ filter. Then the stocks were pre-diluted into 500 ⁇ pre-diluted stocks and stored at -20°C.
  • Each drug in the JHCCL FDA-approved drug library was made to 10 mM stock solutions with DMSO.
  • the stock solutions were arrayed in a total of 24 96-well plates, leaving the first and the last columns in each plate as controls.
  • Each solution in these master plates was diluted with PBS to make 500 ⁇ pre-diluted working stock plates.
  • the first and the last columns in each pre-diluted plate were set as blank controls, doxycycline control, and amoxicillin control.
  • the pre-diluted drug stock plates were sealed and stored at -20°C.
  • Antibiotic susceptibility test To qualitatively determine the effect of antibiotics, 10 ⁇ ⁇ of each compound (final concentration 50 ⁇ ) from the pre-diluted plate or pre-diluted stock was added to round body form or stationary phase B.
  • SYBR Green II PI viability assay was used to assess the live and dead cells after antibiotic exposure as described (Feng, Wang, Shi, et al, 2014). Briefly, 10 ⁇ ⁇ of SYBR Green I (10,000 x stock, Invitrogen) was mixed with 30 ⁇ ⁇ propidium iodide (PI, 20 mM, Sigma-Aldrich) into 1.0 ml of sterile dH ⁇ O. Then, 10 ⁇ ⁇ staining mixture was added to each well and mixed thoroughly.
  • PI propidium iodide
  • the plates were incubated at room temperature in the dark for 15 minutes followed by plate reading at excitation wavelength at 485 nm and the fluorescence intensity at 535 nm (green emission) and 635 nm (red emission) in microplate reader (HTS 7000 plus Bio Assay Reader, PerkinElmer Inc., USA). With least-square fitting analysis, the regression equation and regression curve of the relationship between percentage of live and dead bacteria as shown in green/red fluorescence ratios was obtained. The regression equation was used to calculate the percentage of live cells in each well of the 96-well plate.
  • Beta-lactam antibiotics are the most commonly used frontline drugs for the treatment of Lyme disease, but intriguingly could induce spirochetal B. burgdorferi to form round bodies which are resistant to Lyme antibiotics (Brorson et al, 2009; Sapi et al, 2011).
  • the optimal conditions for induction of round body form were assessed. It was found that 6-day or older culture could not be induced to round body form completely with even 100 ⁇ g/ml amoxicillin (FIG. 19D).
  • the effective hits were selected as having residual viable cell ratios below that of the amoxicillin control. Hit compounds were selected for further rescreens, followed by microscope counting to verify the screening results. Epi-fluorescence microscope counting further validated the effective drug candidates by the SYBR Green I/PI assay (data not shown). Of the 1582 FDA-approved drugs tested, 23 drugs were found to have higher activity against the round body form of B. burgdorferi than doxycycline (Table 5).
  • cefmenoxime in order of decreasing activity, had better activity than the known round body active antibiotic metronidazole or tinidazole (Table 5).
  • Antimalarial drug artemisinin showed high activity against the round body form of B. burgdorferi.
  • ciprofloxacin (28% residual live cells) was the most active among quinolone drugs levofloxacin 41%, norfloxacin 41%, and moxifloxacin 49% (not shown).
  • chlortetracycline, meclocycline and rolitetracycline were more active than doxycycline (42% residual live cells) against the round body forms (Table 5).
  • Ciprofloxacin 28% 6.30 6.04 6.20 0.0108
  • the line above tinidazole refers to antibiotics used to treat Lyme disease.
  • bResidual viable B. burgdorferi was calculated according to the regression equation and ratios of Green/Red fluorescence obtained by SYBR Green I/PI assay.
  • cp-values of standard i-test were calculated for the select antibiotic treated samples in comparison with the amoxicillin treated sample as a control.
  • dBold type indicates the 11 drug candidates that had better activity against the round body forms than metronidazole or tinidazole in order of decreasing activity.
  • B. burgdorferi culture was treated with 10 ⁇ / ⁇ drugs or their combinations for 7 days.
  • Residual viable B. burgdorferi was calculated according to the regression equation and ratio of Green/Red fluorescence obtained by SYBR Green I/PI assay as described (Feng, Wang, Shi, et al., 2014). Direct microscopy counting was employed to rectify the results of the SYBR Green I/PI assay. Residual viable percentages less than 30% are shown in bold text and the best drug combinations without daptomycin are underlined.
  • the three drug combinations e.g., doxycycline+daptomycin+ either cefoperazone or artemisinin or sulfachlorpyridazine did not show any sign of growth as no visible spirochetes were observed, whereas other drug combinations all had visible live spirochetes under the microscope (data not shown).
  • the 20-day subculture there were about 8x 10 6 spirochetes in the control sample and about 5* 10 6 spirochetes in doxycycline-treated samples (Table 7). Daptomycin alone, or two drug combinations
  • doxycycline+daptomycin+artemisinin or sulfachlorpyridazine significantly reduced the number of spirochetes with very few spirochetes being visible after the 20-day subculture (FIG. 23).
  • the daptomycin in combination with doxycycline and cefoperazone still showed the best activity which killed all round body form of B. burgdorferi persisters with no viable spirochetes observed after the 20-day subculture (FIG. 23).
  • Amoxicillin induced round body form B. burgdorferi culture (500 ⁇ ⁇ ) was treated with 10 ⁇ g/mL drugs alone or drug combinations for 7 days. Then, 50 ⁇ , of washed bacterial cells was subcultured in 1 mL fresh BSK-H medium for 10 days and 20 days, respectively and examined by microscopy.
  • BSK-H medium 1 mL fresh BSK-H medium for 10 days and 20 days, respectively and examined by microscopy.
  • Green/Red fluorescence ratios were obtained by microplate reader after SYBR Green I/PI staining. Each value is the mean of three replicates.
  • B. burgdorferi as a persister form could survive in adverse conditions including antibiotic exposure in vitro and are found in chronic Lyme neuroborreliosis in vivo (Brorson and Brorson, 1998; Miklossy et al, 2008). As shown in previous studies (Brorson and Brorson, 1997; Murgia and Cinco, 2004; Brorson and Brorson, 1998) and also in this study, the round body form of B. burgdorferi could still reproduce and revert to spirochetes under suitable conditions upon removal of the stress during subculture. The B.
  • burgdorferi round body form shows lower metabolic activity and is tolerant to antibiotics (Brorson et al, 2009; Kersten et al, 1995; Barthold et al., 2010).
  • metronidazole, tinidazole and tigecycline were reported to have certain activity against the round body form, they were not able to completely eradicate these persister forms (Sapi et al, 2011).
  • no good antibiotics against the round body form of B. burgdorferi are available (Brorson et al, 2009; Barthold et al, 2010).
  • daptomycin still remains the most active drug against the round body form of B. burgdorferi persisters. Daptomycin killed most planktonic round body form of B. burgdorferi (FIG. 2 Id). It is possible that daptomycin preferentially acts on the membrane of the round body form of B. burgdorferi that is different from the membrane of actively growing spirochetal form and thus making it particularly active for the persister forms.
  • Daptomycin is known to disrupt the membrane structure and cause rapid
  • the antimalarial activity of artemisinin might involve endoperoxide activation by free ferrous iron from haemoglobin digestion by malaria parasites (Wells et al., 2009).
  • the content of ferrous iron or haemoglobin is very low in the B. burgdorferi culture, so the activation of endoperoxide might not be the main mechanism of artemisinin activity against B. burgdorferi round body forms.
  • the study in yeast is noted in which artemisinin impairs the membrane structure and causes depolarization of the mitochondrial membrane (Wang, Huang, et al, 2010; Li et al., 2005).
  • artemisinin may have a similar mechanism of action of disrupting the bacterial membrane as the basis for its high activity against the round body form of B. burgdorferi. It is noteworthy that artemisinin has been used for treating Lyme co-infections and found to be effective clinically. The reason that artemisinin is effective was interpreted to be due to its action against Babesia co-infection, but it is quite likely that the clinical efficacy of artemisinin may at least partly be due to its activity against the round body form of B. burgdorferi persisters as shown in this study.
  • sulfonamide antibiotics such as sulfacetamide, sulfamethoxypyridazine and sulfaquinoxaline.
  • sulfonamide antibiotics have also been identified in the previous drug screen against stationary phase persisters and showed low MICs ( ⁇ 0.2 ⁇ g/ml) (Feng, Wang, Shi, et al, 2014).
  • the sulfonamides inhibit utilization of PABA required for the synthesis of folic acid, which results in the blockade of several enzymes needed for synthesis of DNA and methionine, glycine, and formylmethionyl-transfer-R A. It is worth noting that sulfachloropyridazine as the analogue of sulfamethoxypyridazine also showed good activity against stationary phase B. burgdorferi (residual viable cells is about 38%) and, when combined with daptomycin and doxycycline, showed remarkable activity against stationary phase B. burgdorferi (residual viable cells is about 8%) (Table 6). It is believed that further studies on metabolic changes of the round body form of B. burgdorferi could help understand the mechanism by which sulfonamide acts against B. burgdorferi persisters.
  • Ciprofloxacin as a fluoroquinolone has shown activity against B. burgdorferi in vitro and could kill the inoculum with 16 ⁇ g/mL MBC (41.5 ⁇ ) after 72 h (Kraiczy et al., 2001). It has been presently disclosed that ciprofloxacin was the most active fluoroquinolone against the round body form of B. burgdorferi among other quinolones, but ciprofloxacin was not identified to have activity against B. burgdorferi stationary phase persisters in the previous screen
  • Vancomycin is a glycopeptide antibiotic acting on the cell wall rather than acting on the cell membrane like daptomycin. Good activity of vancomycin was not found against amoxicillin treated round bodies, though it showed relatively good activity against stationary phase B. burgdorferi in the previous drug screen (Feng, Wang, Shi, et al, 2014). This might be due to cell wall deficiency of the round body form induced by amoxicillin.
  • this study represents the first high-throughput drug screens against the round body form of B. burgdorferi persisters and identified a number of FDA-approved antibiotics that show excellent activity against such forms.
  • some interesting drug candidates were identified that are preferentially active against the round body form of persisters, including artemisinin, ciprofloxacin, nifuroxime, fosfomycin, chlortetracycline, and some sulfa drugs which were found to be active against the round body form for the first time.
  • These round body effective drugs in appropriate combinations can be used to eliminate the persistence phenomenon and improve the treatment of persistent forms of Lyme disease, including antibiotic refractory Lyme arthritis and PTLDS.
  • B31 Bacterial strain, media and culture: Borrelia burgdorferi strain B31 (ATCC 35210) was obtained from American Type Tissue Collection. B. burgdorferi was cultured in BSK-H medium (HiMedia Laboratories Pvt. Ltd.), with 6% rabbit serum (Sigma-Aldrich). All culture media were filter-sterilized by 0.2 ⁇ filter. Cultures were incubated in sterile 50 rnL closed conical tubes (BD Biosciences, California, USA) at 33°C without antibiotics. Based on a previous study that demonstrated the antibiotic tolerance of the stationary phase cultures, 7 day old stationary phase B. burgdorferi cultures enriched in persisters were chosen for drug screens in 96-well microtiter plates as described (Feng, Wang, Shi, et al, 2014).
  • Microscopy techniques Specimens were examined on a Zeiss Axiolmager M2 microscope equipped with differential interference contrast (DIC) and
  • Antibiotics and the NCI chemical compound library Antibiotics including doxycycline, amoxicillin, and daptomycin were purchased from Sigma-Aldrich and dissolved in appropriate solvents (Clinical and Laboratory Standards Institute, 2007) to form stock solutions. All the antibiotic stocks were filter-sterilized by 0.2 ⁇ filter. Then the stocks were diluted into 500 ⁇ pre-diluted stocks and stored at -20°C.
  • NCI compound library collection consisting of diversity set V (Moody et al, 1978), mechanistic diversity set II (DTP-Mechanistic Set Information, 2015) and the natural products set III (DTP-Natural Products Set Information, 2015), was kindly supplied by National Cancer Institute Developmental Therapeutic Program's Open Compound Repository.
  • These NCI compound libraries were prepared in 1 mM stock solutions with DMSO in 96-well plates leaving the first and the last columns in each plate for controls, which included DMSO blank controls, doxycycline control, and amoxicillin control. The pre-diluted drug plates were sealed and stored at -20°C.
  • the fluorescence intensities at 535 nm (green emission) and 615 nm (red emission) were measured for each well of the screening plate using SpectraMax M2 Microplate Reader (Molecular Devices Inc., USA). Some effective candidates were further confirmed by epifluorescence microscopy as described (Feng, Wang, Zhang, et al, 2014).
  • MIC determination The standard microdilution method was used to determine the minimum inhibitory concentration (MIC) that would inhibit visible growth of B. burgdorferi after a 72 hours incubation period (Sapi et al, 2011 ; Dever et al, 1992; Boerner et al, 1995).
  • B. burgdorferi cells (1 x 10 5 ) were inoculated into each well of a 96-well microplate containing 90 ⁇ ⁇ fresh BSK-H medium per well. Each diluted compound (10 ⁇ ,) was added to the culture. All experiments were run in triplicate. The 96-well plate was sealed and placed in an incubator at 33°C for 5 days. Cell proliferation was assessed using the SYBR Green I/PI assay and a bacterial counting chamber after the incubation as described (Feng, Wang, Shi, et al, 2014).
  • daptomycin was found to have the highest activity against B. burgdorferi persisters among all the candidate drugs. Although daptomycin could almost eradicate B. burgdorferi persisters at 50 ⁇ , this drug concentration is quite high for clinical use, and in addition, daptomycin generally has to be used intravenously, which is not convenient to administer.
  • NCI compound library collection has three compound libraries: the diversity set IV compound library (1593 compounds), the mechanistic set II library (816 compounds), and the natural product set III library (117 compounds), for a total of 2526 compounds. These compounds are chosen based on structural diversity from more than 250,000 natural products and synthetic compounds (Open Repository Collection of Synthetics and Pure Natural Products, 2014). By screening this NCI compound library collection, new anti-persister compounds were identified that were not found in the previous screens (Feng, Wang, Shi, et al., 2014). These new persister active hits can be used for a treatment for Lyme disease.
  • dimethyldaunomycin, daunomycin, NSC299187, NSC363998 and nogalamycin showed the highest activities (residual viable cells from 6% to 15%) against stationary phase B. burgdorferi persisters. These six compounds showed higher activity than daptomycin (18% residual viable cells).
  • another five anthraquinone compounds, pyrromycin, rhodomycin A, NCS316157, emodin, and NSC156516 also showed good activity against stationary phase B. burgdorferi persisters (residual viable cells 21% to 50%).
  • pyronin B a xanthene compound highlighted itself as having a good activity (residual viable cells 19%) against stationary phase B. burgdorferi persisters.
  • chaetochromin a bis-naphtho-y-pyrone compound, showed good activity with 22% residual viable cells.
  • Mitomycin an aziridine-containing benzoquinone antitumour drug, showed reasonably good activity with 25% residual viable cells.
  • NCS224124 had relatively good activity against stationary phase B. burgdorferi persisters.
  • a polypeptide antibiotic dactinomycin also had relatively high activity against B. burgdorferi persisters (residual viable cells 30%).
  • 11 clinically used drugs (daunomycin 3-oxime, dimethyldaunomycin, daunomycin, nogalamycin, pyrromycin, chaetochromin, prodigiosin, mitomycin, nanaomycin and dactinomycin), 19 non-medicinal compounds also were found that showed good activity against stationary phase B. burgdorferi persisters to varying levels (Table 8, FIG. 24).
  • NSC number is a numeric identifier for substances submitted to the National Cancer Institute (NCI).
  • Residual viable B. burgdorferi was calculated according to the regression equation and ratio of Green/Red fluorescence obtained by SYBR Green I/PI assay as described (Feng, Wang, Shi, et al., 2014).
  • NSC299187 Another anthraquinone compound, NSC299187, showed relatively high MIC (3.26-6.52 ⁇ g/ml) although it had excellent anti-persister activity (residual viable cells 13%). It was also noted that prodigiosin (nitrogen-containing aromatic rings compound), mitomycin (aziridine-containing benzoquinone), nanaomycin (1,4-naphthoquinone) and dactinomycin (polypeptide antibiotic) had very good activity against replicating B. burgdorferi with low MICs ( ⁇ 0.2, ⁇ 0.21, 0.76- 1.57, ⁇ 0.78 ⁇ g/ml, respectively).
  • pyronin B and chaetochromin were less potent against growing B. burgdorferi with relatively high MICs (1.8-3.6, 2.74-5.47 ⁇ g/ml, respectively) but had excellent anti-persister activity.
  • Daptomycin at 50 ⁇ has shown strong activity against stationary phase B. burgdorferi persisters in a previous study (Feng, Wang, Shi, et al, 2014), but it could not kill the microcolony form B. burgdorferi persisters at lower concentration such as 10 ⁇ g/ml (Feng et al. 2015, in press).
  • stationary phase B. burgdorferi persisters with 20 ⁇ drug concentration (about 10 ⁇ g/ml for most compounds and 32 ⁇ g/ml for daptomycin).
  • Most residual viable percentage of stationary phase B. burgdorferi increased with the decrease of drug concentration (Table 10, FIG.
  • burgdorferi persisters using the NCI compound library collection. From the 2526 compounds in three NCI compound libraries, 237 compounds were found to have higher activity against B. burgdorferi persisters than doxycycline or amoxicillin, from which the top 30 active hits were confirmed by microscopy rescreen. The use of the mechanistic compound library helped to identify the anthraquinone (anthracycline) class of drugs that have high activity against B. burgdorferi persisters. It is interesting to note that more than one third of the 30 most active compounds possess an anthraquinone (also called anthracenedione or dioxoanthracene) structure. The top 6 active compounds, daunomycin 3-oxime, dimethyldaunomycin, daunomycin
  • NCS156516 had weak anti-persister activity and showed 50% residual viable (green) cells (FIG. 24). Thus confirmation is needed in assessing compounds that have red color and have activity against B. burgdorferi persisters by careful microscopic examination, using low concentration of compounds and subculture studies.
  • Anthraquinones are a class of naturally occurring phenolic compounds isolated from Streptomyces and have diverse medical uses including anti-cancer, antimalarial, and laxatives.
  • Anthracycline antibiotics such as daunomycin, nogalamycin, pyrromycin and rhodomycin A, were used in chemotherapy of some cancers, especially for several specific types of leukemia (Tan et al., 1967). It has been reported that anthracycline drugs have antibacterial activity against 5 * . aureus, and the MICs of daunomycin and doxorubicin are 8-32 ⁇ g/ml and 0.12-0.5 ⁇ g/ml, respectively (Zhu et al, 2005).
  • Daunomycin did not show bactericidal activity for Gram-negative bacteria Pseudomonas aeruginosa, Klebsiella pneumoniae and E. coli (Moody et al, 1978). This study is the first to demonstrate the activity of this class of compounds active against both growing and non-growing forms of Gram-negative B. burgdorferi. However, the mechanisms of action of this class of anthraquinone compounds against B. burgdorferi are unclear and remain to be determined.
  • Anthracycline antibiotics could inhibit DNA and RNA synthesis by inserting into base pairs of the DNA/RNA strand (Mizuno et al., 1975).
  • anthracycline antibiotics could stabilize the topoisomerase II complex and prevent dissociation of topoisomerase II from its nucleic acid substrate, leading to DNA damage and blocking DNA transcription and replication as well as producing reactive oxygen species, which could damage mitochondria and lead to cardiotoxicity as side effects (Jensen et al, 1993; Pommier et al, 2010).
  • the sugar moiety of daunomycin plays a critical role in determining its anticancer activity (Zhu et al, 2005).
  • 1,4- naphthoquinones such as nanaomycin, NCS659997 and NCS224124, showed high activity against stationary phase B. burgdorferi persisters.
  • 1,4-naphthoquinone has an analogue molecular skeleton similar to anthraquinone. Nanaomycin may interfere with the function of the bacterial cell membrane and interact with the respiratory chain of bacteria (Hayashi et al, 1982), and such mode of action may explain its activity against B. burgdorferi persisters.
  • chaetochromin a bis-naphtho-y-pyrone produced by several species of chaetomium, also showed high activity against stationary phase B.
  • Bis-naphtho-y-pyrones have a broad-range of biological activities such as inhibition of ATP synthesis in mitochondria, cells proliferation inhibition, triacylglycerol synthesis inhibition, and antimicrobial activity (Lu et al, 2014).
  • Bis- naphtho-y-pyrones were active against various bacteria such as S. aureus, E. coli and M. tuberculosis, with MIC values ranging from 2 to 50 ⁇ g/ml (Lu et al, 2014).
  • prodigiosin is a secondary metabolite of Serratia marcescens and is well known to have antibacterial, antifungal, antiprotozoal, antimalarial, immunosuppressive and anticancer activities (Williamson et al., 2007).
  • Mitomycin shows its activity as a DNA crosslinker through its aziridine functional group and crosslinks the complementary strands of the DNA double helix to cause the death of a bacterial cell (Szybalski and Iyer, 1964; Tomasz, 1995). The activity of mitomycin against B. burgdorferi persisters may also be due to its DNA crosslinking activity.
  • Dactinomycin is a polypeptide antitumor antibiotic isolated from soil bacteria Streptomyces (Hollstein, 1974) and is known to bind DNA and interfere with DNA replication (Hollstein, 1974), and also inhibit RNA transcription (Sobell, 1985).
  • NCS311153 were found to be effective against stationary phase B. burgdorferi persisters to a varying extent. These newfound interesting compounds have more anti-persister activity than current Lyme antibiotics and may be explored in the future as leads for further drug development and mechanism study for bacterial persistence.
  • anthracycline class of compounds and antibiotics along with some other compounds, including prodigiosin, mitomycin, nanaomycin and dactinomycin, have been identified as having excellent activity against B. burgdorferi persisters.
  • the structure activity relationship and mechanisms of action of the anthracycline/anthraquinone class of compounds against B. burgdorferi persisters should be addressed in future studies. Drug combination studies with the
  • Brorson, O., and Brorson, S.H Transformation of cystic forms of Borrelia burgdorferi to normal, mobile spirochetes. Infection 1997, 25: 240-246. Brorson, O. and Brorson, S.H. In vitro conversion oiBorrelia burgdorferi to cystic forms in spinal fluid, and transformation to mobile spirochetes by incubation in BSK-H medium. Infection 1998, 26: 144-150.
  • Eucaryotic cells protect Borrelia burgdorferi from the action of penicillin and ceftriaxone but not from the action of doxycycline and erythromycin. Antimicrob. Agents Chemother. 1996, 40(6): p. 1552-1554.
  • Li, Y. and Zhang, Y. PhoU is a persistence switch involved in persister formation and tolerance to multiple antibiotics and stresses in Escherichia coli.
  • Tan, C, et al Daunomycin, an antitumor antibiotic, in the treatment of neoplastic disease. Clinical evaluation with special reference to childhood leukemia. Cancer 1967;20(3):333-53.
  • Wormser, G.P., et al The clinical assessment, treatment, and prevention of Lyme disease, human granulocytic anaplasmosis, and babesiosis: clinical practice guidelines by the Infectious Diseases Society of America. Clin. Infect. Dis. 2006, 43 : 1089-1 134.

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Abstract

La présente invention concerne des procédés, des compositions et des kits pour l'évaluation de la viabilité de bactéries du genre Borrelia, l'évaluation de la sensibilité aux antibiotiques de bactéries du genre Borrelia et l'identification de composés présentant une activité contre la persistance de bactéries du genre Borrelia. L'invention concerne également des procédés pour l'inhibition de la croissance et/ou la survie de bactéries du genre Borrelia et pour le traitement de la maladie de Lyme chez un sujet.
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