DETAILED ACTION
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 .
Election/Restrictions
Applicant's election with traverse of Group I (claims 1-8 and 11-14) in the reply filed on 06/19/2025 (and the supplemental response filed on 08/11/2025) is acknowledged.
The traversal is on the grounds that the special technical feature of the claimed invention is not disclosed by Wang et al. Specifically, applicant asserts that Wang “does not specifically or inherently require the use of a metabolic marker including a fluorescent D-type amino acid metabolic marker” (Remarks, 8/11/2025, p. 9, par. 3) and “the proper special technical feature may include the bacteria to be tested being metabolically labeled with fluorescent D-type amino acid metabolic markers to evaluate the metabolic activity of bacteria in the growth process according to their fluorescence intensity or changes in intensity; and adding a fluorescent D-type amino acid metabolic marker to the bacteria to be tested for culture to label the bacteria to be tested” (Id.).
This is not found persuasive because the Examiner disagrees that applicant’s proposed special technical feature is the proper special technical feature of the claimed inventions. A group of inventions is considered linked to form a single general inventive concept when there is a technical relationship among the inventions that involves at least one common or corresponding special technical feature. The expression “special technical feature” is defined as meaning those technical features that define the contribution which each claimed invention, considered as a whole, makes over the prior art (MPEP § 1893.03(d)). Because applicant’s asserted features are not reflected in both inventions, there is no requirement that Wang et al. actually used the fluorescent D-type amino acid metabolic marker nor is there any requirement that such composition is used to evaluate the metabolic activity of bacteria or to metabolically label a bacterium. Although these components may be a consideration when determining the novelty and nonobviousness of the claimed invention, the prior art does not need to disclose the exact invention which is being claimed. Instead, the prior art must disclose the linking feature. To that end, the only structure that links Group II to Group I is the fluorescent D-type amino acid metabolic marker (note that the kit of Group II does not even require the additional buffer, diluent, carrier, culture plate, or culture dish by virtue of the “and/or” language in line 2 of claim 9). Thus, the linking feature in the groups of inventions has been appropriately identified as the fluorescent D-type amino acid metabolic marker and this feature is clearly described in Wang et al.
For at least this reason, the requirement is still deemed proper and is therefore made FINAL.
Claims 9-10 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Claims 1-8 and 11-14 are directed to the elected invention and have been examined on their merits.
Priority
The present application is a § 371 National Stage Entry of PCT/CN2021/083051 (filed on 03/25/2021) and claims priority to foreign applications CN202110295193.8 (filed on 03/19/2021) and CN202010263592.1 (filed on 04/07/2020).
Information Disclosure Statement
It is noted that there is a listing of references in paragraphs [0123]-[0136] of the specification. The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Drawings
The drawings are objected to for the following minor informalities:
Figures 2-10, 26-27, and 29-30 contain text which is smaller than the minimum required text size. The drawing standards require numbers, letters, and reference characters in drawings to be a least 0.32 cm (1/8 inch; 0.125 inches) in height (37 CFR 1.84(p)(3)).
Figures 3-10 and 28-29 are not presented in sufficient quality to be readable when reproduced. All drawings must be made by a process which will give them satisfactory reproduction characteristics. Every line, number, and letter must be durable, clean, black (except for color drawings), sufficiently dense and dark, and uniformly thick and well-defined (37 CFR 1.84(l)).
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 disclosure is objected to for the following reasons:
The specification contains unitalicized taxonomic names. In general, the names of taxonomic genera and species should be italicized. Unitalicized taxonomic names are noted in paragraphs [0023]-[0039], [0048], [0051]-[0052], [0066], [0072], [0090], [0105], and [0116].
Appropriate correction is required.
Claim Objections
Claim 1 is objected to because the word “Preferably” should not be capitalized as it is not the beginning of a sentence nor is it a proper noun.
Claim 2 is objected to because although it is clear that applicant is attempting to limit the structure of the fluorescent D-type amino acid metabolic marker recited in line 5 of claim 1, the phrase “characterized in that” should be replaced with a “wherein” clause in order to promote readability.
For example, claim 2 may be amended to read:
“The method for evaluating the metabolic activity of bacteria according to claim 1,
wherein the fluorescent D-type amino acid metabolic marker is a D-type amino acid or a derivative thereof covalently modified by a fluorescent group; and
wherein the fluorescent D-type amino acid metabolic marker includes a D-type amino acid fluorescent probe of….”.
Moreover, the conjunction “or” should be removed from line 6 because it precedes the second to last element and not the last element (which is also preceded by the conjunction “or”).
Additionally, the article “a” should be inserted before “D-type amino acid fluorescent probe” in the final element of the list of acceptable fluorescent probes.
Claim 2 is further objected to because the abbreviation “Cy5” should be defined when first used in the claims. For example, the claim may be amended to read “Cyanine 5 (Cy5)”.
Claim 3 is objected to because the phrase “which is characterized in that” should be replaced with a “wherein” clause in order to promote readability of the claim.
Claim 3 is further objected to because the list of R1 groups should be separated by commas and joined by the conjunction “or”.
Claim 4 is objected to because the list of R1 groups should be separated by commas and joined by the conjunction “or”.
Claim 4 is further objected to because the word “wherein” should be added before “the fluorescent D-type amino acid metabolic marker is used” in line 2.
Claim 5 is objected to because the phrase “A detection method for antimicrobial susceptibly test” is grammatically incorrect. The word “test” should be amended to “testing” or the article “an” should be inserted before “antimicrobial”.
Claim 5 is further objected to because the article “a” should be added before “blood sample” in line 10.
Claim 5 is further objected to because although it is clear that the “fluorescent markers” in lines 4-5 refer to the fluorescent D-type amino acid metabolic markers, the phrase “fluorescent markers” should be replaced with the full antecedent term (“fluorescent D-type amino acid metabolic markers”).
Claim 6 is objected to because a hyphen should be added between “co” and “cultured” to form the word “co-cultured”.
Claim 7 is objected to because the word “The” (line 2) should not be capitalized as it is not the beginning of a sentence nor is it a proper noun.
Claim 13 is objected to because the phrase “which is characterized in that” should be replaced with a “wherein” clause in order to promote readability of the claim.
Claim 14 is objected to because the phrase “which is characterized in that” should be replaced with a “wherein” clause in order to promote readability of the claim.
Appropriate correction is required.
Claim Interpretation
Claim 1 recites a “preferable” limitation. Description of examples or preferences is properly set forth in the specification rather than the claims (MPEP § 2173.05(d)). If stated in the claims, examples and preferences may lead to confusion over the intended scope of a claim (Id.). In this claim, it is clear that the limitation “the specific step comprises adding a fluorescent D-type amino acid metabolic marker to the bacteria to be tested for culture to label the bacteria to be tested” is strictly optional because it is clearly introduced as “preferable”. As such, a rejection under 35 U.S.C. § 112(b) has not been made for definiteness with respect to this particular aspect of the claim (however, a rejection has been made below for other reasons).
Because this portion of the claim imparts no patentable weight, it is suggested that the “preferable” language be removed from the claim and the preferences instead be set forth in the specification.
Claims 3 and 11 use similar “preferable” language and these limitations have been interpreted as strictly optional as well.
Throughout the claims, applicant has used the phrase “which is characterized in that”. This phrase is considered to be descriptive of the intended effect of the method but the claims are indefinite (as discussed below) because it is unclear what actual active, positive steps are performed in the claimed methods. Where appropriate, claim rejections have been made over the portions of the claims which are considered to be indefinite.
For example: claim 1 is characterized in that the bacteria to be tested are metabolically labeled with fluorescent D-type amino acid metabolic markers to evaluate the metabolic activity of bacteria in the growth process according to their fluorescence intensity or changes in fluorescence intensity. This claim does not actually require an active step of “metabolically labeling the bacteria to be tested” but merely states why the bacteria “are labeled” (i.e., they are labeled to evaluate the metabolic activity of bacteria in the growth process according to their fluorescence intensity or changes in fluorescence intensity). The claim does not distinctly describe how this labeling is performed nor does the claim actually require that any labeling is performed (e.g., the bacteria used in the claim could be reasonably interpreted to be previously labeled bacteria which are used for the recited purpose). Moreover, the claim describes the purpose of the metabolic labeling (“to evaluate the metabolic activity of bacteria in the growth process”) but does not actually require a step of “evaluating the metabolic activity of bacteria in the growth process”.
Accordingly, these portions of the claims are not considered to impart patentable weight for the purpose of determining novelty and non-obviousness. Similar language is used throughout the other pending claims. As appropriate, rejections have been made for definiteness in order to ensure that the claims distinctly define the metes and bounds of applicant’s methods and, as appropriate, the prior art teachings have been applied to the claims as written.
Claim Suggestions
In the interest of compact prosecution, it is recommended that the claims be rewritten to distinctly define the methods using conventional claim language such as by using a preamble, a transitional phrase, and specific active verbs to perform the claimed method (e.g., reciting “culturing” instead of “for culture” or “evaluating” instead of “to evaluate”). The claims have been examined for prior art purposes according to what effect the claims purport to achieve but it is not possible to examine some of the claims for the specific steps contained therein because there are none. A sample claim structure has been presented below which may assist in making the appropriate corrections. Applicant is not required to use this exact claim structure but any future amendment should ensure that the claims distinctly define the specific concrete steps used in the claimed methods.
A method for… [comprising/consisting essentially of/consisting of]:
[step 1];
[step 2];
[step 3](etc.);
wherein;
wherein; and
wherein.
Claim Rejections - 35 USC § 112
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.
Claims 1-4 and 11 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, regards as the invention.
Claim 1 is indefinite because it contains vague language which renders the scope of the claim unclear for the following reasons.
First, claim 1 recites that the method is characterized in that the bacteria to be tested are metabolically labeled with fluorescent D-type amino acid metabolic markers to evaluate the metabolic activity of bacteria in the growth process according to their fluorescence intensity or changes in fluorescence intensity (emphasis added). It is unclear if this portion of the claim recites an active step (i.e., an active step of “metabolically labeling with fluorescent D-type amino acid metabolic markers”) or merely describes the intended effect of the method (i.e., describes why the method involves fluorescent D-type amino acid metabolic markers).
For example, this limitation can be interpreted to mean that the method (1) in some way involves metabolically labeled bacteria for the purpose of evaluating the metabolic activity of bacteria in the growth process or (2) requires a positive, delineating step of actually metabolically labeling the bacterium. In other words, this portion of the claim can be reasonably interpreted to only recite what the method is and why it is performed but does not state how the method is actually performed.
The only clearly defined active step in this claim is adding a fluorescent D-type amino acid metabolic marker to the bacteria to be tested for culture to label the bacteria to be tested but this step is contained within a “preferable” limitation, which as discussed in the “Claim Interpretation” section of the action is strictly optional.
In the interest of compact prosecution, it is noted that even the “preferable” portion of the claim is considered to be indefinite because it refers to “the specific step” but, as discussed above, there is no “specific step”. Therefore, there is no antecedent basis for the term “the specific step”. And although applicant is encouraged to not use “preferable” language in the claims, if such a limitation is desired, the claim should at least define a “specific step” or the generic terminology (“specific step”) should be replaced to distinctly reference a previously set forth step. For example, if applicant introduces a step of “metabolically labeling”, then the “specific step” should refer to “the metabolic labeling”.
Finally, the “preferable” step recites “adding a fluorescent D-type amino acid metabolic marker to the bacteria to be tested for culture to label the bacteria to be tested” (emphasis added). The latter portion of the claim does not distinctly recite an active step of “culturing” and instead also recites an intended effect occurring downstream of the “adding” step without necessarily requiring this effect. In other words, the method may use the addition “for culture” but that doesn’t mean that there is actually any culturing step.
The claim as written merely describes why the bacteria must be metabolically labeled but does not actually require any evaluation to occur. Therefore, this limitation does not impart any manipulative difference on the claim because it describes an evaluation step which does not necessarily have to occur.
The claim is further made unclear because the claim is drafted without any transitional phrases or indentation which would help distinctly define the claimed process. Applicant is reminded that “where a claim sets forth a plurality of elements or steps, each element or step should be separated by a line indentation” (37 CFR 1.75(i)). The claim’s lack of separation and indentation of potential steps causes further confusion in the interpretation of the claims.
Interpretation: Because, for the reasons discussed above, the claimed method does not have any clear meaning or active steps, a prior art rejection cannot be made over claim 1. In the interest of compact prosecution, the relevant prior art teachings have been presented below.
Claims 2-3 depend from claim 1 and do not clarify the meaning of the claim. Rather, these claims merely limit the fluorescent D-type amino acid metabolic marker.
Interpretation: Because, for the reasons discussed above, the claimed method does not have any clear meaning or active steps, a prior art rejection cannot be made over claims 2-3. In the interest of compact prosecution, the relevant prior art teachings have been presented below.
Claim 4 is considered to be an improper “use” claim. Attempts to claim a process without setting forth any steps involved in the process generally raises an issue of indefiniteness under 35 U.S.C. § 112(b)(MPEP § 2173.05(q)). In this case, it is not clear how the “D-type amino acid metabolic marker” is actually “used” because the claim does not set forth any active, positive steps delimiting how this use is actually practiced.
Moreover, it is not clear what applicant means by “the fluorescent D-type amino acid metabolic marker is used from D-alanine or its derivatives” (emphasis added). If applicant intends for portion of the claim to be limiting the D-type amino acid metabolic marker to D-alanine or its derivatives, it is recommended that applicant amend this portion of the claim to read “…wherein the fluorescent D-type amino acid metabolic marker is fluorescent D-alanine or its derivatives, and its structural formula is:…”. Merely stating that a composition is “used” is not sufficient to clearly define a claim.
Interpretation: Because, for the reasons discussed above, the claimed method does not have any clear meaning or active steps, a prior art rejection cannot be made over claim 4. In the interest of compact prosecution, the relevant prior art teachings have been presented below.
Claim 5 recites the bacterial solution and the sample solution and there is no antecedent basis for these terms. Because a bacterial solution and a sample solution have not been clearly established in the claims, it is unclear what solutions applicant is referencing.
Suggestion: In the interest of compact prosecution, it is recommended that the article “the” be replaced with “a” in order to appropriately introduce these solutions. For example, the claim can be amended to read “…to co-culture a bacterial solution or a sample solution to be tested”. Alternatively, the claim may be amended to introduce “a bacterial solution” or a “sample solution to be tested” earlier in the claim.
Interpretation: For the purpose of applying prior art, the claim has been interpreted as meaning “a bacterial solution” and “a sample solution”.
Similarly, the claim references obtaining “the signal intensity of fluorescent markers”. There is no antecedent basis for this term.
Suggestion: Similar correction may be made (i.e., replacing “the” with “a”). Alternatively, if multiple intensities are measured, the phrase “the signal intensity” should be replaced with “one or more signal intensities”. This is an important consideration because applicant’s methods may involve “real time” detection, which necessarily involves measurement of a signal intensity at more than one time point.
Moreover, claim 5 refers to “the minimum inhibitory concentration of the antibiotic to be tested”. There is no antecedent basis for either of these terms. Although minimum inhibitory concentration (MIC) is an inherent property of an antibiotic, it varies with each bacterium to be tested. Accordingly, it is not clear which MIC is being referenced. Similarly, the claims make no previous reference to an “antibiotic”. Instead, they refer to an antibiotic solution. Therefore, it is not clear what antibiotic is being tested.
Claim 5 is further rejected because it limits “the sample liquid to be tested” with no clear antecedent basis for this term. It is not clear what “sample liquid to be tested” is being limited. For example, applicant contemplates the use of “the bacterial solution” or “the sample solution to be tested”. It is not clear if these solutions are distinct from “the sample liquid” or how the sample liquid is related to the above terms.
Suggestion: If applicant intends for this phrase to be referring to the original sample used in the antimicrobial susceptibility test, the phrase should be introduced earlier in the claim. As discussed above, these claims should contain active language and clear delineated steps.
Interpretation: It is interpreted that this limitation refers to “a sample liquid to be tested”.
Applicant is reminded that words such as “the” or “said” are typically used to refer to a previously established term and any new terminology should generally be preceded by phrases such as “a”, “an”, “one or more”, etc. in order to properly identify when a new element is being added to a claim versus when a reference is being made to a previously set forth element. See MPEP § 2173.05(e).
Finally, claim 5 limits the sample liquid to be tested to be alveolar lavage fluid and blood sample with positive blood culture. This phrase could be interpreted to mean that the sample liquid must contain both components (i.e., must be an alveolar lavage and blood) by virtue of the conjunction “and” or could mean that the sample could contain either component.
Interpretation: For the purpose of applying prior art, the latter (broader) interpretation has been applied.
Claims 7 and 12 are rejected as indefinite because they recite two “final concentration” ranges. Lines 2-4 read “the final concentration of the fluorescent D-type amino acid metabolic marker is 0.01-5 mM and the final concentration of the fluorescent D-type amino acid metabolic marker is 0.1-1 mM”. It is not clear which range is the actual “final concentration”.
Interpretation: In the interest of compact prosecution, the claims have been examined for prior art purposes under the broader range.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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 5-8 and 12-14 are rejected under 35 U.S.C. 103 as being unpatentable over Stern et al. (WO 2018/119439 A1) in view of Wang et al. (Nature Communications, 2019, Vol. 1317, pages 1-7; cited in IDS filed on 09/30/2022).
Stern et al. (hereinafter Stern) teaches rapid antimicrobial susceptibility testing ([0002]). Specifically, Stern teaches metabolic growth assays comprising (a) addition of a metabolic probe to a plurality of chambers; (b) an assay incubation period under conditions promoting microbial growth; and (c) obtaining of one or more of an absorbance, fluorescent, luminescent, and electrochemical signal measurement ([0027]). Additionally, Stern teaches a method of determining antimicrobial susceptibility of one or more microorganisms comprising performing a growth assay comprising incubating a suspension of a microorganism in the presence of one or more antimicrobials without a metabolic probe present, introducing a metabolic probe in an aqueous-miscible solvent after the incubation of the one or more microorganisms and determining antimicrobial susceptibility of the one or more microorganisms based on relative microorganism growth ([0014]).
Regarding claim 5, Stern teaches a method of determining antimicrobial susceptibility (i.e., a detection method for an antimicrobial susceptibility test)([0014]). Stern’s method comprises performing a growth assay comprising incubating a suspension of a microorganism in the presence of one or more antimicrobials without a metabolic probe present, introducing a metabolic probe in an aqueous-miscible solvent after the incubation of the one or more microorganisms and determining antimicrobial susceptibility of the one or more microorganisms based on relative microorganism growth ([0014]). Because Stern’s method is an antimicrobial susceptibility assay, it necessarily judges the antibacterial effect. This conclusion is supported by par. [0012] which states that the test can determine susceptibility, minimum inhibitory concentration or qualitative susceptibility. And because the test uses metabolic probes, it is necessarily for evaluating bacterial metabolic activity.
With respect to the requirement that the method is characterized by the use of fluorescent D-type amino acid metabolic markers, Stern provides a litany of potential metabolic probes in pars. [0202]-[0222] including by incorporating “well known” probes in other related publications ([0203]). Stern differs because it does not disclose or incorporate fluorescent D-type amino acid metabolic markers.
Nonetheless, Wang et al. (hereinafter Wang) teaches that the past decade has witnessed a great leap forward in our understanding of the diverse physiological and pathological functions of the gut microbiota (p. 2, left col., par. 1). Wang teaches that one reason for poor knowledge of the fate of fecal microbiota transfer bacteria is the absence of a feasible method to track the transplanted microbiotas and evaluate their viabilities (Id.). Wang envisions that tracking transplanted microbiota by fluorescent imaging would be a promising strategy if one could fluorescently label the microbiota (Id.). Wang teaches that analogs of D-amino acids (DAAs) with fluorophore side chains (FDAAs) have been developed for metabolic labeling of bacterial peptidoglycans (PGNs) and PGNs are ubiquitous among most bacteria, which use DAAs as essential building blocks (p. 2, right col., par. 1). Thus, Wang developed a sequential tagging with DAA-based metabolic probe (STAMP) strategy for fluorescent tracking and assessing the viabilities of transplanted microbiotas (p. 2, right col., par. 2). Wang states that STAMP exploits the fact that FDAAs are metabolically incorporated into PGNs only in living bacteria and therefore, only the living bacteria incorporate the pre- and post-transplant FDAAs (Id.).
Because Stern provides the use of metabolic probes and teaches hundreds of probes which would be suitable for the antimicrobial susceptibility assay (thus teaching that the particular probe is not particularly important) and because Wang teaches an improved metabolic probe which is advantageously only incorporated into living bacteria, it would have been obvious to have simply substituted the generic metabolic probes taught by Stern with the fluorescent D-type amino acid metabolic markers taught by Wang. The result of the substitution would have been predictable because Wang demonstrates the usefulness of FDAAs as metabolic probes for assessing viability of bacteria and the only modification required is that the probes are used to assess antimicrobial susceptibility rather than post-transplantation viability. And, as discussed above, it would have been particularly advantageous to substitute Stern’s generic probes for Wang’s FDAAs because Wang teaches their selective incorporation into only viable cells which would advantageously be expected to improve the accuracy of the viability assay. This obviousness is based upon the “Simple Substitution of One Known Element for Another to Obtain Predictable Results” rationale set forth in KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395-97 (2007).
With respect to the requirement that the markers are used with an antibiotic solution to co-culture the bacterial solution or the sample solution to be tested, as discussed above, Stern teaches the addition of the metabolic probe to the one or more bacteria which contains one or more antimicrobials. As such, Stern teaches the use of the markers and antibiotic solution to co-culture the bacterial solution or sample solution to be tested.
With respect to the requirement that the method involves detecting and obtaining a signal intensity of fluorescent markers, as discussed above, Stern’s method involve incubating the fluorescent marker and obtaining fluorescence signal measurement ([0027], [0070], and [0256]). Stern teaches that “the intensity of the signal is proportional to the amount of live bacteria in the culture solution and therefore is indicative of the growth” ([0382]). Thus, Stern’s methods clearly involve detecting and obtaining a signal intensity of the fluorescent markers and this signal is related to the growth rate and metabolic activity of bacteria.
With respect to the requirement that the fluorescence signal intensity is analyzed to obtain the minimum inhibitory concentration of the antibiotic to be tested to obtain the antibacterial result, as discussed above, Stern teaches that the metabolic probe assay is used to determine a minimum inhibitory concentration or QSR ([0233]).
With respect to the requirement that the sample liquid to be tested is alveolar lavage fluid and blood sample with positive blood culture, Stern teaches that the microorganisms can be derived from biological samples and exemplary biological samples can include blood or bronchoalveolar lavage ([0316]). The position that “alveolar lavage” and “bronchoalveolar lavage” are the same is supported by Example 5 of applicant’s specification which describes an antimicrobial test of “alveolar lavage fluid” ([0093]) using “bronchoalveolar lavage fluid” ([0094]). Stern also teaches that the sample can be a positive blood culture ([0244]).
For at least these reasons, claim 5 is obvious over Stern in view of Wang.
Regarding claim 6, as discussed above, Stern in view of Wang renders obvious the detection method of claim 5.
Stern teaches the addition of the metabolic probe to the one or more bacteria which contains one or more antimicrobials. As such, Stern teaches that the method includes a sample solution to be tested (the one or more bacteria) which is mixed with antibiotic solution (the one or more antimicrobials) and a metabolic probe and then co-cultured to obtain the fluorescent labeling signal intensity.
With respect to the method being performed at a specific time and/or in real time, Stern teaches obtaining the fluorescence after an incubation period ([0027]). Stern’s incubation period is from about 2 to 18 hours ([0028]). Because this observation happens after incubating the metabolic probe with the bacteria for an assay incubation period (i.e., the co-culturing period), it occurs “at a specific time”.
Alternatively, Stern renders obvious observation at “a specific time” because any time at which the assay is performed is a “specific time” under the BRI of the term.
Regarding claims 7 and 12, as discussed above, Stern in view of Wang renders obvious the detection method of claims 5 and 6.
The instant claims limit the final concentration of the FDAA metabolic marker. As discussed in the 35 U.S.C. § 112(b) section of this action, these claims are examined for a final concentration of 0.01-5 mM. Wang teaches the use of certain concentrations of FDAA metabolic markers. Specifically, Wang teaches that TADA probes can be used in “much lower concentration[s]” such as 1 mM and this causes less disturbances to the bacteria in the microbiota while still achieving “strong fluorescent labeling” (p. 3, right col., par. 2). As such, because it was previously known that low concentrations such as 1 mM were sufficient to achieve strong fluorescent labeling, it would have been obvious to have used a concentration such as 1 mM, which falls within the recited range (and notably, within the narrower claimed range as well).
Alternatively, it would have been obvious to have routinely experimented with various concentration ranges of FDAA metabolic markers in order to optimize the fluorescent labeling. A person having ordinary skill in the art would have had a reasonable expectation of success because the prior art previously recognized FDAA metabolic markers as suitable for labeling viable bacteria and taught that various concentrations of FDAA markers can be used with strong fluorescent labeling (Id.). Generally, differences in concentration will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical (MPEP § 2144.05(II)(A)). There is no evidence of record that the “final concentration” range recited in this claim elicits any critical result.
Claims 7 and 12 further require that the antibiotic solution adopts gradient concentration. As discussed previously, Stern teaches the assay can be used for determining minimum inhibitory concentration. A person having ordinary skill in the art would understand that such a test necessarily requires a gradient concentration. For example, Stern teaches that “as is known to those skilled in the art [antimicrobial susceptibility test] platforms can yield minimum inhibitory concentration results” and “according to CLSI Microbiology standards, an MIC of a given antibiotic for a given species and strain of a microorganism can be defined as the lowest concentration of the antibiotic in two-fold dilution series that inhibits growth of the microorganism” ([0192]). Additionally, in order to produce MIC results, dilution series can be required for each antimicrobial” and these assays are commonly performed in cartridges and/or microplates, which enable parallel testing of different antimicrobials at different concentrations ([0193]). Thus, Stern’s method (and any MIC-establishing protocol) necessarily uses an antimicrobial gradient concentration.
With respect to the structure of the D-type amino acid metabolic marker, as discussed above, Stern in view of Wang renders obvious the use of D-type amino acid metabolic markers in the detection method. Wang teaches labeling bacteria with TADA and Cy5ADA. Wang teaches that TADA comes from D-alanine (TAMRA-amino-D-alanine)(p. 3, left col., par. 2). Moreover, Wang teaches the development of three probes (TADA, TADA-amide, and TADA-ester). As such, Wang teaches the method wherein the fluorescent D-type amino acid metabolic marker is a D-type amino acid covalently modified by a fluorescent group and the fluorescent D-type amino acid metabolic marker is a D-type alanine fluorescent probe; wherein the fluorescent D-type amino acid metabolic marker comprises TAMRA DAA.
Thus, claims 7 and 12 are obvious over Stern in view of Wang.
Regarding claims 8 and 13-14, as discussed above, Stern in view of Wang renders obvious the detection method of claims 5-7. Stern teaches that exemplary antimicrobials can include penicillins, cephalosporins, aminoglycosides, tetracyclines, macrolides, and sulfonamides ([0309]).
Pertinent Prior Art
A prior art rejection has not been made over claims 1-4 and 11 because, as discussed in the 35 U.S.C. § 112 section above, the claims are so indefinite that they do not permit examination for prior art purposes. In the interest of compact prosecution, it is noted that Wang and Stern provide the following teachings, which may be relevant to future claims.
Wang teaches labeling bacteria with TADA and Cy5ADA. Wang teaches that TADA comes from D-alanine (TAMRA-amino-D-alanine)(p. 3, left col., par. 2). Moreover, Wang teaches the development of three probes (TADA, TADA-amide, and TADA-ester) which possess the R1 groups recited in the claims (p. 3, Fig. 2a; Replicated below). As seen below, the TADA, TADA-amide, and TADA-esters all contain tetra-methylrhodamine (i.e., a fluorescent group) on R2.
PNG
media_image1.png
437
1010
media_image1.png
Greyscale
As such, Wang teaches the method wherein the fluorescent D-type amino acid metabolic marker comes from D-alanine or its derivatives and its structural formula is that which is recited in claim 4.
And although Wang does not teach that the method is for using a fluorescent D-type amino acid metabolic marker for evaluating susceptibility testing, Stern teaches that phenotypic antimicrobial susceptibility testing (AST) of microorganisms is critical for informing physicians of appropriate therapeutic regimens ([0003]). Stern teaches a method for determining antimicrobial susceptibility of one or more microorganisms comprising performing a plurality of different assays sharing an incubation period ([0008]). In some aspects, Stern teaches introduction of a metabolic probe in a solvent and determining antimicrobial susceptibility of the one or more microorganisms based on relative microorganism growth ([0014]).
Thus, because Wang teaches a metabolic probe which can be used to assess the viability of bacterial cells in vitro and in vivo and because Stern teaches that metabolic probes can be used in order to assess antimicrobial susceptibility, it would have been obvious to have modified Wang’s method such that the fluorescent D-type amino acid metabolic markers are used to determine antimicrobial susceptibly. There would have been a reasonable expectation of success because the modified method relies on the shared principle taught by Wang that the FDAAs are exclusively incorporated into viable bacterial cells. Thus, the method would also have been expected to work when the purpose of the method is modified to evaluating antimicrobial susceptibility testing.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to GRANT C CURRENS whose telephone number is (571)272-0053. The examiner can normally be reached Monday - Thursday: 7:00-5:00.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Adam Weidner can be reached at (571)272-3045. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/GRANT C CURRENS/Examiner, Art Unit 1651