Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
DETAILED ACTION
This is a US national phase of PCT/EP2022/066238, filed June 14, 2022, with
foreign application EP21305813.4, filed June 14, 2021.
Applicant's Preliminary amendment filed December 13, 2023 is acknowledged.
Claims 1-55 are canceled.
Claims 56-70 are newly added and pending.
Election/Restrictions
Applicant’s election without traverse of species: 1) PVDF membrane, 2) xanthene-based dye, MB660R, 3) Alicyclobacillus, in the reply filed on July 28, 2026 is acknowledged.
Claim 63 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim.
Claims 56-62 and 64-70 are under examination.
Drawings
The drawings are objected to because the drawings are labeled “Figure” instead of “FIG.”. See MPEP 608.02 V. DRAWING STANDARDS (u):
(u) Numbering of views.
(1) The different views must be numbered in consecutive Arabic numerals, starting with 1, independent of the numbering of the sheets and, if possible, in the order in which they appear on the drawing sheet(s). Partial views intended to form one complete view, on one or several sheets, must be identified by the same number followed by a capital letter. View numbers must be preceded by the abbreviation "FIG." Where only a single view is used in an application to illustrate the claimed invention, it must not be numbered and the abbreviation "FIG." must not appear.
(2) Numbers and letters identifying the views must be simple and clear and must not be used in association with brackets, circles, or inverted commas. The view numbers must be larger than the numbers used for reference characters.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The use of the terms, MB660R, DRAQ5, Cytrak Orange, Alexa Flour 350, Pacific Blue, Cy5, BODIPY 500/510, Alexa Flour 405, Cascade Blue, Seta 650, Seta 375, Setau 647, SeTau 488, Alexa Flour 488, ATTO 647, Hoechst dye, Eosin, Methylene Blue, Raka Ray agar, MICA, DIAMIDEX, which are trade names or marks used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 56-62 and 64-70 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 56-62 and 64-70 recite a method for detecting or enumerating a microorganism or group of microorganisms of interest comprising contacting a sample containing said microbes with a solid growth medium and with at least one fluorescent dye, incubating under conditions and at a sufficient time to form microcolonies, then detecting or enumerating microcolonies emitting a fluorescent signal. Claims 57, 60-62, and 64-66 recite a membrane filter is used to concentrate the sample in the method. The breadth of the claims encompasses any type of sample, any microorganism, any fluorescent dye, and any membrane filter. The inventions of claims 58-59, 61-62, 64, 66-67, and 69-70 require the use of the invention of claims 56-57, 60, 65, and 68, and therefore are likewise rejected as failing to comply with the written description requirement.
The specification defines ‘microorganism’ as a bacterium, an archaebacterium, or a microscopic fungus, such as a bacterium, a yeast (i.e. unicellular microscopic fungus) or a mold (i.e. multicellular and filamentous microscopic fungus). The specification discloses the microorganisms of interest may belong to thermophilic acidophilic bacteria, acetic acid bacteria, lactic acid bacteria, anaerobic bacteria, aerobic mesophilic bacteria, Gram-negative bacteria, yeasts and molds, heterotrophic bacteria, and lists species from the genera recited in claim 69.
The specification defines ‘samples’ as obtained from a liquid (e.g. water, fruit juices, beer, wine, biological fluids such as urine), a solid (e.g. food, pharmaceutical or cosmetic products, medical devices or any solid surfaces) or a gas (e.g. air), and in particular, the sample can be a liquid sample or a liquified sample. Microorganisms may also be extracted from different surfaces or devices using any method known by the skilled person such as swabbing methods, friction methods, e.g. using wipes, printing methods, e.g. by agar contact method, rinsing or immersion methods, or sonication methods, in particular to dislodge biofilms.
The specification defines ‘fluorescent dyes’ as a chemical compound that can re-emit light upon light excitation, and discloses that the fluorescent dye is not a fluorogenic substrate, i.e. a substrate which produces a fluorescent substance after a reaction with an enzyme or a group of enzymes of a microorganism, is not linked to a functional moiety which is able to specifically recognize a microorganism or a group of microorganisms, such as an antibody, does not restrict growth of microorganisms of interest, is not encapsulated, e.g. in liposomes or lipid vesicles, is not a DNA and/or RNA intercalating agent, and is not sulforhodamine B, a Hoechst dye, rhodamine B, neutral red, bromothymol blue, eosin, methylene blue, amphotericin B nor Nile Red. The specification discloses the fluorescent dye can be xanthene-based dyes, acridine dyes, anthracene-based dyes, coumarin-based dyes, cyanine based dyes, dipyrromethene-based dyes, naphthalene-based dyes, pyrene-based dyes, squaraine-based dyes, squaraine rotaxane-based dyes and 4',6-diamidino-2-phenylindole (DAPI), and combinations thereof, and lists specific examples recited in claim 70.
The specification discloses the membrane filter can be made of mixed cellulose esters (MCE), polyvinylidene difluoride (PVDF), nitrocellulose, polytetrafluoroethylene, polycarbonate or nylon, more preferably is made of MCE or PVDF. The specification discloses the microfiltration membrane filter having pore sizes smaller than the target microorganisms, preferably not greater than 0.45µm pore size.
To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. See, e.g., Moba, B.V. v. Diamond Automation, Inc., 325 F.3d 1306, 1319, 66 USPQ2d 1429, 1438 (Fed. Cir. 2003); Vas-Cath, Inc. v. Mahurkar, 935 F.2d at 1563, 19 USPQ2d at 1116.
In analyzing whether the written description requirement is met for genus claims, it is first determined whether a representative number of species have been described by their complete structure. In the instant case, the specification merely gives working examples of the combinations of microorganisms, fluorescent dyes, and membrane filters disclosed in Table 1 that are useful in the detection of microorganisms (pgs. 78-83), and the working examples utilize only ‘liquid samples’. While the genus of samples, microorganisms, fluorescent dyes, and membrane filters, encompasses a large number of variants that have the same activity in kind and the genus encompasses a large number of variants that have a different structure, the specification does not describe the complete structure of a representative number of species of the large genus of samples, microorganisms, fluorescent dyes, and membrane filter variants or functional equivalents thereof.
Next, then, it is determined whether a representative number of species have been sufficiently described by other relevant identifying characteristics, specific features, and functional attributes that would distinguish different members of the claimed genus. In the instant case, the only identifying characteristic of ‘membrane filter’ is the passage of nutrients through the filter during incubation allows the growth of organisms in the form of microcolonies, on the upper surface of the membrane, the only other identifying characteristic of ‘microorganism’ is microorganisms or groups of microorganisms that can be grown in a culture device, and in particular on a suitable solid growth medium, i.e. culturable microorganisms, and the only other identifying characteristic of ‘fluorescent dye’ may be membrane-permeable, and stain the inner side of the microorganisms or may be just adsorbed on the outer surface of the microorganisms. Such broad limitations cannot be an identifying characteristic for the claimed diverse genus of samples, microorganisms, fluorescent dyes, and membrane filter variants since by Applicant’s definition of variant or functional equivalent thereof all members of the claimed genus will have that characteristic.
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 58-60, 65, and 70 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 58 recites: The method according to claim 56, wherein step a) “may” comprise a1) contacting a sample suspected of containing said microorganism or group of microorganisms with at least one fluorescent dye, and a2) contacting, in a container, said sample with a solid growth medium containing nutrients to support growth of said microorganism or group of microorganisms, steps a1) and a2) being carried out simultaneously or sequentially, in any order. The phrase “may comprise” renders the scope of the claim unclear because it is uncertain whether steps a1) and a2) are required further limitations of the claimed method, or steps a1) and a2) are merely optional and not required.
Claims 59-60 are likewise rejected as being dependent on an indefinite claim.
Claim 65 recites that “the membrane filter is removed from the solid growth medium and microcolonies thereon are detected and/or enumerated in step c)”. The term “thereon” is indefinite because it is unclear whether “thereon” refers to the membrane filter or solid growth medium, thus is indefinite.
Claim 70 contains the trademark/trade name MB660R, DRAQ5, Cytrak Orange, Alexa Flour 350, Pacific Blue, Cy5, BODIPY 500/510, Alexa Flour 405, Cascade Blue, Seta 650, Seta 375, Setau 647, SeTau 488, Alexa Flour 488, ATTO 647. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe various fluorescent dyes and, accordingly, the identification/description is indefinite.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 56, 58, and 67-70 are rejected under 35 U.S.C. 102(a)(1)(a)(2) as being anticipated by Sum et al. (WO 2017/146648 A1, cited in IDS filed 12/13/2023, hereinafter “Sum”).
Regarding claims 56 and 58, Sum teaches a method for detecting β-hemolytic pathogens in a sample. The method comprises: (a) adding a sample suspected of containing a beta-hemolytic pathogen to a growth medium containing sterically-stabilized liposomes comprising an encapsulated fluorophore to form a test assay mixture; (b) incubating the test assay mixture for a period of time sufficient for the beta-hemolytic pathogen, if present, to form a population of test cells and to cause lysis of the sterically-stabilized liposomes to release the fluorophore into the assay mixture for assimilation into the population of test cells; (c) detecting the fluorescence of the population of test cells; and (d) comparing the amount of fluorescence of the population of test cells with the amount of fluorescence of a population of control cells. See [0012]. A sample suspected of containing a beta-hemolytic pathogen is added to the solid growth medium described herein to form an assay mixture. See [0046]. The population of test cells is one or more test colonies and the population of control cells is one or more control colonies. See Sum Claim 6. The incubation is in wells of a well plate (container). See Sum Claim 12. Sum teaches the ability of liposomes to distinguish beta hemolytic bacteria from alpha- and gamma-hemolytic bacteria via direct microscopic visualization of beta-hemolytic colonies on agar [0063]. Colonies were visualized at 10x magnification on a Zeiss Axiovert 200M microscope. For fluorescence visualization, colonies were excited with UV light (365 nm) and the resulting emission (LP at 395 nm) was captured with a CoolSnap HQ CCD camera [0077].
Although Sum is silent that ‘microcolonies’ were visualized in the method, the instant specification defines ‘microcolonies’ as colonies which have grown for several hours or days depending on the microorganism and which are invisible or barely visible with the naked eye, and the surface of the growth medium, or the membrane filter, may be periodically microscopically monitored for growth using a fluorescent microscope or another suitable system (pg. 89, lines 11-22), therefore the method taught by Sum detecting the fluorescent colonies with a microscope and HQ CCD camera would inherently detect ‘microcolonies’.
Regarding claim 67, The medium is directly supplemented with selective agents of choice including, but not limited to, antibiotics, salts, bile salts, dyes, tellurite and charcoal [0052].
Regarding claims 68 and 70, Sum teaches fluorescent dyes including DAPI, acridine orange, and rhodamine. See [0043] & [0053]. For visualization of co-cultured beta-hemolytic S. pyogenes or S. aureus with alpha- hemolytic S. pneumoniae colonies, the procedure was similar as above except colonies were probed with anti-S'. pneumoniae antibodies to identify S. pneumoniae colonies. Briefly, after incubation, the cover slip was removed, and the gel was washed once with lx PBS pH 7.4. Next, the gel was blocked with 5% bovine serum albumin (BSA, A4503, Sigma- Aldrich) for three hours and probed with mouse anti-S1. pneumoniae (1 :50, 8437-5208, AbD Serotec) overnight. The antibodies were removed, washed thrice with lx PBS pH 7.4 for one hour and then probed again with an Alexa Fluor 488 conjugated goat anti-mouse antibody (1 :200, A1 1029, Life Technologies) overnight. The secondary antibodies were removed and washed thrice with lx PBS pH 7.4 for one hour. All washing and probing steps were done in a humidified chamber at room temperature. Colonies were visualized with a 5x magnification lens on a Zeiss Axiovert 200M microscope. For fluorescence visualization, colonies were excited with UV or blue light (365 nm or 488 ran) and the emission (BP 445/50nm, BP 525/50 ran) was captured using a CoolSnap HQ CCD camera. See [0077].
Regarding claim 69, Sum (p. 26 and Table 1) teaches the bacterial strains detected in the method are Streptococcus pyogenes and Bacillus cereus [0036], Staphylococcus aureus, Clostridium perfringens, and E. coli [0020], which are species of the genera recited in the claim.
Thus, claims 56, 58, and 67-70 are anticipated by Sum et al.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 57, 59-60, and 65-66 are rejected under 35 U.S.C. 103 as being unpatentable over Sum as applied to claims 56, 58, and 67-70 above, and further in view of Mates et al. (Microbios, 1988, 53, pgs. 161-165, cited in IDS filed 12/13/2023, hereinafter “Mates”).
Sum’s teachings pertaining to claims 56, 58, and 67-70 are discussed above.
Sum teaches a method wherein beta-hemolysis was rapidly detected in broth by observation of a fluorescent signal at least 26 fold above baseline [0065], thus Sum implicitly teaches a method wherein the microorganisms in the sample are contacted with the fluorescent dye before contacting the sample with a solid growth medium, though does not teach the step of a2) recited in claim 59.
Sum also does not teach the microorganisms are concentrated on a membrane filter before contacting with the solid growth medium and fluorescent dye.
Regarding claim 57, 59 and 60, Mates teaches a method for counting Escherichia coli in sea water using a membrane filter procedure, following filtration the membrane filter is incubated on mFC agar medium (abstract). Mates teaches the in situ test for determination of E. coli is carried out by transferring the membrane filter to nutrient agar (solid growth medium) containing 4,methyl-umbiliferyl-B-D glucuronide (MUG) (abstract). After a 3h incubation period, the E. coli colonies are detected by fluorescence (abstract).
Regarding claim 65, Mates teaches the blue colonies representing fecal coliforms were marked on the filter which was aseptically transferred to plates containing the MUG media, followed by incubation for 3 h at 35°C when all the blue colonies lost their color; the E. coli colonies were identified by their ability to hydrolyze MUG producing a fluorogenic compound which was visualized under long wavelength UV light (pg. 162, para 4).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of Sum by contacting microorganisms with the fluorescent dye in a sample (i.e. broth), then concentrating the microorganisms on a membrane filter before contacting the microorganisms with the solid growth medium, and then transferring said membrane filter with the microcolonies thereon to be detected and/or enumerated by emitting the fluorescent signal as taught by Mates. One of ordinary skill in the would have been motivated to modify the method by concentrating the microorganisms on a membrane filter from the sample (i.e. broth), transferring the filter to the solid growth medium to grow microcolonies, and detecting the fluorescent signal from the microcolonies thereon with a fluorescent microscope, in order to enable rapid identification of fluorescing microcolonies with shorter incubation times, since Sum teaches bacteria mixed with the fluorophore in the broth generated the quickest detection time ranging from 1-10 CFUs [0065], thus concentrating on a filter with further plating on solid growth medium, would enable rapid detection and enumeration of the microbes of interest.
Regarding claim 66, Sum teaches direct microscopic visualization of beta-hemolytic colonies on agar, wherein colonies were visualized at 10x magnification on a Zeiss Axiovert 200M microscope, and fluorescence visualization was performed with colonies excited with UV light (365 nm) and the resulting emission (LP at 395 nm) was captured with a CoolSnap HQ CCD camera [0063, 0077].
Claims 61-62 and 64 are rejected under 35 U.S.C. 103 as being unpatentable over Sum and Mates as applied to claims 57, 59-60, and 65-66 above, and further in view of Zhang et al. (Journal of Membrane Science, 618 (2021) 118741, pgs. 1-9, hereinafter “Zhang”).
As described above, Sum in view of Mates teach a modified method for detecting microorganisms by contacting a sample with a fluorescent dye and concentrating on a membrane filter, and contacting on a solid growth medium, then detecting and/or enumerating the fluorescent colonies.
Neither Sum nor Mates teaches the membrane filter is polyvinylidene fluoride (PVDF).
However, Zhang teaches a food functional membrane for simultaneous exclusion and inactivation of Alicyclobacillus acidoterrestris in apple juice (title). Zhang teaches a multi-stage modification by immobilizing polydopamine and nisin microspheres onto the polyvinylidene difluoride (PVDF) membrane. In comparison with pristine polyvinylidene difluoride (PVDF) membrane, the modified membrane surface showed promoted performance in terms of hydrophilicity, water flux and the rejection of A. acidoterrestris (abstract). Zhang teaches a fluorescence-based cell assay was utilized for detecting the bacterial viability on the membrane surface, wherein the membrane coupons with a size of 1 cm × 1 cm were collected after microfiltration process with A. acidoterrestris contaminated apple juice (sample) as the feed; the membrane coupons were stained by 4′ -6-diamidino-2-phenylindole (DAPI, 5 μg/mL) and propidium iodide (PI, 1 μg/mL) in the dark at 4◦C for 10 min and the bacterial cells were then observed by a fluorescence microscope (pg. 3, sec. 2.5). In Figure 6, Zhang teaches retention of A. acidoterrestris on the membrane surface of live DAPI stained cells in fluorescent micrographs (pg. 7).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date to further modify Sum’s method as modified by Mates, by concentrating bacteria in a liquid sample on a membrane filter comprising PVDF that efficiently retains bacteria, as taught by Zhang, before contacting the bacteria-concentrated PVDF membrane with a solid growth medium and at least one fluorescent dye, for detection/enumeration with fluorescent imaging by a fluorescent microscope. One of ordinary skill in the art would have been motivated to utilize a PVDF membrane taught by Zhang in the modified method taught by Sum and Mates, as this membrane has high retention of bacterial cells during the filtration process according to the Standard Test Method for Determining Bacterial Retention of Membrane Filters Utilized for Liquid Filtration, and can be easily modified to exclude or inactivate certain bacteria, and the potential reusability of a modified membrane was proven by different membrane cleaning methods including water flushing and chemical cleaning, as taught by Zhang (pg. 2, sec. 2.2; pg. 8, sec. 4).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA EDWARDS whose telephone number is (571)270-0938. The examiner can normally be reached M-F 8am-5pm EST.
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/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/JESSICA EDWARDS/
Examiner, Art Unit 1657
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