DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
This application is the national stage of PCT/KR2021/014293, filed 15 October 2021, claiming foreign priority to KR10-2020-0142045 (filed 29 October 2020) and KR10-2021-0130787 (filed 01 October 2021). The International Search Report issued in the PCT application has been received and reviewed. Certified translations of the foreign priority documents have not been provided, and the effective filing date of the claimed invention is that of the PCT application, i.e., 15 October 2021.
Election/Restrictions
Applicant’s election without traverse of Group III (claims 8-12 and 14-15) in the reply filed on 14 October 2025 is acknowledged.
Claims 1-4 and 18-25 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 14 October 2025.
Applicant’s election of the species of (a) SosA protein and (b) vancomycin in the reply filed on 14 October 2025 is also acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)). Upon further consideration, the requirement of (a) to elect either mRNA or protein is withdrawn; accordingly, all of claims 8-12 and 14-15 are under consideration herein (with claim 9 under consideration as directed to vancomycin).
Nucleotide and/or Amino Acid Sequence Disclosures and Figures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). See in particular Figure 7. Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
As the Figures are otherwise acceptable, and as replacement of Figure 7 is not required if Applicant provides a substitute specification as described above, the Figures have been accepted (however correction is required with regard to the above noted issue).
Claim Interpretation
Regarding the limitation “preparation for measuring an mRNA expression level of the sosA gene or an expression level of the SosA protein” (see independent claim 8, and see also claim 10), it is noted that the specification at paragraph 37 (page 7) states that:
The preparation for measuring the mRNA expression level of the sosA gene is an antisense oligonucleotide, primer pair, or probe that specifically binds to an mRNA of the sosA, and the preparation for measuring the expression level of the SosA protein is an oligopeptide, monoclonal antibody, polyclonal antibody, chimeric antibody, ligand, peptide nucleic acid (PNA), or aptamer that specifically binds to the SosA protein.
With regard to the recitation in independent claim 8 of the language “Staphylococcus aureus having a sosA gene or a SosA protein expressed” (as well as the language “the Staphylococcus aureus having the sosA gene or the SosA protein expressed”), it is noted that in view of the teachings of the disclosure (see, e.g., paragraphs 9-10 and 17), as well as the recitation in claim 8 of the use of a “preparation for measuring an mRNA expression level of the sosA gene or an expression level of the SosA protein”, the claim is interpreted as embracing detecting expression of the sosA gene and/or the resulting expressed SosA protein, but not merely the detection of “Staphylococcus aureus having a sosA gene”.
Claim Rejections - 35 USC § 112(b)/second paragraph
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 8-12 and 14-15 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.
Claims 8-12 and 14-15 are indefinite over the recitation in claim 8 of the limitation “determining that the Staphylococcus aureus having the sosA gene or the SosA protein expressed has susceptibility to the antibiotic”, because it is unclear what is required by this language, and how it relates to the prior recited method step. The claims require “diagnosing susceptibility of Staphylococcus aureus to an antibiotic” via a method comprising “detecting Staphylococcus aureus having a sosA gene or a SosA protein expressed by treating a biological sample isolated from a patient infected with Staphylococcus aureus with the antibiotic and a preparation for measuring an mRNA expression level of the sosA gene or an expression level of the SosA protein” (followed by the above noted “determining”). While it is clear that the claims require detection of S. aureus exhibiting sosA gene/SosA protein expression, the nature of what is required by the “determining” is unclear; some persons of ordinary skill in the art would reasonably interpret this language as reciting a mental step/activity in which a conclusion is formed regarding the S. aureus based upon the result of the active “detecting”, while other such persons would (also reasonably) interpret this language as referring to performing further/additional active steps aimed at determining susceptibility of the bacterium. As there are thus multiple reasonable interpretations of the claim language having different meanings and boundaries, further clarification is required.
Claim 10 (dependent from claim 8) recites the limitation "the antibody specifically binding to the SosA protein" at lines 2-3. There is insufficient antecedent basis for this limitation in the claim, as such an antibody is not previously referenced. Further, as there is no prior reference to/requirement for this type of antibody, is unclear how the following claim language in lines 3-4 limits the claims.
Claim 11 (dependent from claim 8) recites the limitation "the detecting of Staphylococcus aureus having the SosA protein expressed on its surface" at lines 1-2, and “the antibody specifically binding to the SosA protein” at lines 2-3. There is insufficient antecedent basis for these limitations in the claims, as there is no prior reference in the claims to such a specific type of “detecting”, or to such a type of antibody.
Claim 11 is also indefinite over the language following the above referenced “the detecting…on its surface”, because it is unclear how this language further limits what is claimed. First, as there is no prior reference to such a type of “detecting”, it is unclear what activity is being further limited. Second, the language “comprises developing of the antibody specifically binding to the SosA protein” is unclear, as there is no prior reference to such an antibody, and as it is unclear what types actions/steps might be encompassing by “developing” such an antibody (given the various and disparate possible meanings of “developing”). Third, regarding “further treating with a fluorescent material”, the claim fails to specify what is being “further treated”. Accordingly, further clarification of several issues is required.
Claim 12 (dependent form claim 8) recites the limitation "the fluorescent material" in line 1. There is insufficient antecedent basis for this limitation in the claim, as the claims do not previously refer to or require a “fluorescent material”. Further, it is unclear how claim 12 further limits claim 8, given the lack of prior reference to such a material.
Claim 12 is also indefinite over the recitation of the language “the fluorescent material is a green fluorescent protein (GFP), yellow fluorescent protein (YFP), blue fluorescent protein (BFP), or red fluorescent protein (RFP) and any other biologically usable fluorescent material”, because it is unclear how the language “and any other biologically usable fluorescent material” further limits the alternative(s) being claim. More particularly, this language may reasonable be interpreted as imparting a further limitation on only the final alternative of the claim (requiring “red fluorescent protein (RFP) and any other biologically usable fluorescent material”), or on all the listed alternatives (i.e., requiring that any of GFP, YFP, BFP, or RFP must further include “any other biologically usable fluorescent material”); additionally, some persons of ordinary skill in the art might interpret the claims as simply being grammatically incorrect, and intended to encompass the separate use of “any other biologically usable fluorescent material”. Further clarification is therefore required.
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.
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.
Claim(s) 8-12 and 14-15 are rejected under 35 U.S.C. 103 as being unpatentable over Institut Pasteur Korea (KR 10-1779038 [Sept 2017]; cited in IDS) (“IPK”) in view of Sass et al (Current Opinion in Microbiology 16:522 [2013]; cited herein) and Bojer et al (Molecular Microbiology 112(4):1116 [Aug 2019]; cited herein). With regard to the IPK reference, it is noted that the copy of the document provided by Applicant with the IDS does not include page numbers; the numbering referenced below corresponds to the actual page number(s) of the (45 page) cited document.
Independent claim 8 (from which claims 9-12 and 14-15 depend) is directed to a method “of diagnosing susceptibility of Staphylococcus aureus to an antibiotic” comprising “detecting Staphylococcus aureus having a sosA gene or a SosA protein expressed by treating a biological sample isolated from a patient infected with Staphylococcus aureus with the antibiotic and a preparation for measuring an mRNA expression level of the sosA gene or an expression level of the SosA protein” and “determining that the Staphylococcus aureus having the sosA gene or the SosA protein expressed has susceptibility to the antibiotic”.
IPK teaches methods of determining/predicting susceptibility of S. aureus to an antibiotic comprising measuring expression levels of a gene or protein that serves as a biomarker for such susceptibility, in particular the S. aureus small membrane protein, or “SMP” (see entire reference, particularly page 6). Among preferred embodiments taught by IPK are method in which S. aureus present in a biological sample separated from an “infection patient” is “processed” in presence of the antibiotic, and the expression level of SMP (mRNA and/or protein) measured; see entire reference, particularly pages 6-9. IPK teaches that their methods allow for determination of antibiotic susceptibility, providing the further benefits of properly treating a patient with the correct antibiotic (as well as avoiding misuse of antibiotics); see, e.g., pages 10-11.
IPK thus disclose methods meeting the requirements of claim 8, with the exception of teaching sosA/SosA as a biomarker for use in such antibiotic susceptibility testing/screening.
Sass et al teach that genes/proteins involved in bacterial cell division are considered “a potential target pathway for antibiotic treatment” (see entire reference, particularly page 522, left column), and that employing antibiotics to inhibit cell division (including both novel therapies and known antibiotics, including in combination therapies) is proving to be “a promising strategy to counteract important human pathogens” (page 528, right column, “Conclusions”).
Bojer et al teach that SosA, encoded by the sosA gene, is an inhibitor of S. aureus cell division, i.e., a protein of the type taught by Sass et al (i.e., involved in S. aureus cell division); see entire reference, particularly the Abstract and page 1118, left column). Bojer et al state that one aim of their study of the function of sosA/SosA is “the development of new antimicrobials targeting the cell division machinery in S. aureus” (see page 1118, left column; see also page 1126).
In view of the teachings of Sass et al and Bojer et al, 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 have modified the methods of IPK so as to have substituted sosA/SosA for SMP, and thereby to have performed methods meeting all limitations of the instant claims. Given Sass et al’s teachings regard the applicability of cell division genes/proteins as potential antibiotic targets, and Bojer et al’s teachings that sosA/SosA is such a gene/protein – as well as Bojer et al’s specific teaching that an aim of their research related to sosA/SosA is in development of antimicrobial therapy – an ordinary artisan would have been motivated to have made such a modification for the benefit of detecting affects of vancomycin on sosA/SosA expression in a biological sample of a patient infected with S. aureus (for the further benefit of establishing vancomycin susceptibility of that patient and/or the relationship of sosA/SosA to vancomycin susceptibility). It is noted that claim 8 as written is indefinite with regard to what is required by the language “determining that the” S. aureus…has susceptibility” (as discussed above); further, based upon at least one reasonable interpretation of the claim language, this “determining” is simply an instructional limitation added to a method suggested by the art, i.e., non-functional descriptive material that need not be given patentable weight when comparing the claims to the prior art (see MPEP 2111.05). Thus, the teachings of the cited art need not disclose any specific association between sosA/SosA and vancomycin susceptibility in order to suggest all that is required by the claims. Further, given the detailed guidance of IPK regarding the general practice of their methods, as well as the specific teachings of Bojer et al regarding sosA/SosA, an ordinary artisan would have had a reasonable expectation of success in practicing such methods.
With further regard to claim 9, vancomycin is among the preferred antibiotics taught by IPK, such that IPK in view of Sass et al and Bojer et al suggest what is claimed (see, e.g., page 6 and page 16 bridging to page 17). Regarding claims 10-12, it is noted that these claims are not clearly further limiting of claim 8 and/or are limiting of only one possible embodiment (without the claims clearly requiring that embodiment), such that nothing more than what is required by claim 8 is clearly required by these claims. However, it is also noted that IPK teaches measurement of target protein expression levels via the use of specific antibodies (see, e.g., page 8) as well as the use of fluorescent reporters in such methods (see, e.g., page 9); additionally, while not required by the present claim language, Bojer et al teach a specific antibody meeting the requirements 10 (see page 1128, right column, “Western blot analysis”, noting that the antibody of Bojer et al includes instant SEQ ID NO: 7). Regarding dependent claims 14-15, IPK disclose a variety of techniques meeting the requirements of these claims, and thus suggest their use in the methods suggested by IPK in view of Sass et al and Bojer et al; see, e.g., page 8 bridging to page 9 of IPK.
Accordingly, all of claims 8-12 and 14-15 are obvious over IPK in view of Sass et al and Bojer et al.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 8-12 and 14-15 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Independent claim 8 is drawn to a method of “diagnosing susceptibility of Staphylococcus aureus to an antibiotic” concluding with a step/activity of “determining that the Staphylococcus aureus having the sosA gene or the SosA protein expressed has susceptibility to the antibiotic”. While such a “determining” may potentially involve active/manipulative steps of determining antibiotic susceptibility, the claim as written also embraces, e.g., forming a conclusion regarding susceptibility based on the results of the prior “detecting”, which is an activity that may be performed entirely in the human mind, i.e., an abstract idea. Further, the recitation of “diagnosing” in the preamble also embraces such purely mental activities. This judicial exception is not integrated into a practical application because the “detecting” of the claim is a data gathering step that does not add a meaningful limitation to the method as it constitutes insignificant extra-solution activity. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the “detecting” of the claim encompasses well-understood, routine, and conventional activity as of Applicant’s effective filing date. More particularly, detection of expression (including of mRNA and/or protein) of S. aureus genes in response to antibiotics (and using “preparations” as set forth in claim 8) is exemplified by, e.g., IPK (cited and discussed above). While it is noted that IPK does not disclose measuring sosA, they do disclose the use of “preparations” usable in such measuring/detecting, and it is also noted that alterations S. aureus in gene expression resulting from exposure to an antibiotic are a natural phenomenon, i.e., another type of judicial exception (JE). An inventive concept cannot be furnished by a judicial exception (i.e., a law of nature/natural phenomenon/abstract idea) itself (see MPEP 2106.05(I)).
With further regard to dependent claim 9, the claim recites a variety of well-known antibiotics with respect to which data is gathered; nothing amounting to a practical application of a JE, or something “significantly more” than a JE, is added.
Regarding dependent claims 10-12, none of these claims is clearly further limiting of claim 8, and/or the claims are limiting of one possible alternative without requiring that alternative; thus, nothing amounting to either a practical application, or something “significantly more” than a JE, is added. Regarding claims 14-15, while these claims recite further requirements with regard to the “detecting” of the claim, they set forth broad categories of techniques/methods for gathering data, rather than any type of application/implementation of a JE, and nothing “significantly more” than a JE is added (as all of the various methodologies correspond to well-understood, routine, and conventional activities).
Accordingly, none of claims 8-12 and 14-15 is directed to patent eligible subject matter.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DIANA B JOHANNSEN whose telephone number is (571)272-0744. The examiner can normally be reached Monday-Friday, 7:30 am-3:30 pm EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Winston Shen can be reached at (571) 272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/DIANA B JOHANNSEN/Primary Examiner, Art Unit 1682