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 without traverse of serovar Infantis, SEQ ID NO: 17, 18, and 47, as well as the combination of primer pair species recited which amplify only the serovars and the probes from claim 13 of SEQ ID NO: 31-56 in the reply filed on 11/10/2025 is acknowledged.
Claims are free of the art insofar as they require SEQ ID NO: 17, 18, or 47. Methods which use this primer pair and probe are novel and unobvious. Additional species have not been rejoined because they lack unity of invention with the elected species and improper Markush group members as discussed herein.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 9 rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. The claim recites with or without an enrichment culture which covers all possible options, and therefore fails to further limit claim 8. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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 5, 8-14, 18 and 19 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 5 is indefinite because it is not clear if “the primer pair” must comprise one of the pairs listed (example: SEQ ID NO: 1 and 2) or if the primer pair could comprise any two nucleotide sequences selected from the listing of sequences (SEQ ID NO: 1 and 3, for example). Consistent with the specification, the first interpretation is adopted for this Office action. Furthermore, when the claim recites “and a combination thereof” this is unclear because it is unclear how “the primer pair” (a pair is two) could comprise a combination of 28 primers. That would no longer be “the primer pair.” Claim 18 is similarly indefinite.
Claim 12 is indefinite when it recites “primer pairs comprise nucleotide sequences of” because it is not clear if this is mean to be a Markush group listing of alternatives from which primer pairs must be selected, or if all 28 primers (i.e. 17 primer pairs) must be included in the plurality. Furthermore, it is not clear if “sequences of” is open or closed language with regard to the length of the sequences of the primers, or even if fragments of the primers would be encompassed. The use of the phrase “sequences of” raises this issue. Claims 13 and 19 are similarly indefinite when it recites “probes comprise sequences of.” For claim interpretation, consistent with the specification and remarks filed 11/10/2025, the claims are interpreted in this office action as requiring all sequences, and should be amended to clarify this. For example, primer pairs comprise the sequences recited in SEQ ID NO: 1-28.
Claim 8 recites “a plurality of fluorescently-labeled primer pairs selective for all Salmonella serovars” and it is unclear what this limitation means. First, it is unclear what “selective” for all serovars means. Does each primer pair in the reaction have to be selective for a different serovar and the totality of the primer pairs in the reaction have to amplify every serovar? Second it is unclear what “all serovars” means when interpreted in light of the specification. All serovars of interest? All serovars that might be expected in a sample? If it is meant to be a subset (of interest or expected) this is also indefinite absent a definition of the subset. There are thousands of Salmonella serovars, and when describing the instantly claimed embodiment (which is disclosed in para 23 of the specification) the specification states “representative Salmonella serotype include but are not limited to” a recited list of serotypes. This is not a limiting definition of what “all serovars” means. The word “all” us used to refer to the whole quantity or extent of a particular group or thing. It is unclear here, however if “all Salmonella serovars” means every Salmonella serovar (i.e. thousands) or fewer, such as “all” of a particular group or subset. Since the specification falls far short of mentioning all possible Salmonella serovars, it appears that this phrase may be a translation error or is intended to mean all of a subset of serovars of interest.
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 8-14 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.
This rejection is written to address the interpretation that “an amplification reaction on the total DNA using a plurality of fluorescently-labeled primer pairs selective for all Salmonella serovars” means that multiple primer pairs are added to a single reaction mixture and are able to amplify every possible Salmonella serovar. The plain language of the claim suggests this meaning. However, the specification does not demonstrate possession of such a method.
The specification demonstrates a multiplex amplification where primers specific for 13 different Salmonella serovars are included, as well as a primer pair generic to all Salmonella and a primer pair for a positive control (see p. 16, line 5). This is a single embodiment which amplifies 13 serovars. However, there are thousands of Salmonella serovars (Yang et al, p. 2 1st column). The specification does not demonstrate possession of an assay which uses a plurality of primer pairs selective for all Salmonella serovars that were discovered before the filing date, and also not for those yet to be discovered, which even though not yet discovered are would still be encompassed within “all” serovars. There is a high level of unpredictability with regard to the structure of the primers and oligonucleotide probes used in the claimed assay, particularly considering the claim requirement that “an amplification reaction” uses primers to amplify the target. The primers must be functional together in an amplification reaction and specific to each of 2600 different serovars. There is no guidance in the specification as to how to accomplish this. Although methods for selecting oligonucleotides with specificity are known, the knowledge in the prior art of how to go about attempting to develop the claimed method does not correlate to a structural description of the oligonucleotide necessary to practice the claimed method. Therefore, having considered this, it is concluded that the specification fails to satisfy the written description requirement of 35 USC 112, first paragraph.
Claim Rejections – Improper Markush Grouping
Claims 5, 6, 18, and 19 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of different SEQ ID NO primer pairs and probes is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: the different molecules do not share a common structure or function, as each primer pair and probe is directed to amplification and detection of a unique serovar or group of sequences.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
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.
Claim(s) 1, 2, 3, 4, 7, 8, 9, 11, and 14 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by JP2021036802A.
A translation of the reference is provided in the file with JP2021036802.
The reference teaches a method that comprises
obtaining a sample (¶0096)
extracting DNA therefrom (¶0050, 0096)
performing an amplification reaction on the DNA using at least one fluorescently-labeled primer pair selective for the at least one Salmonella sp. Serovar to generate fluorescently-labeled serovar amplicons (¶0097-98);
hybridizing the fluorescently-labeled serovar DNA amplicons to a plurality of nucleic acid probes each having a sequence corresponding to a sequence determinant in the Salmonella sp. Serovar DNA and each attached to a microarray (¶0054, (¶0101);
washing the microarray at least once (¶0102); and
imaging the microarray to detect at least one fluorescent signal from the fluorescently-labeled serovar DNA amplicons, thereby detecting the at least one Salmonella sp. Serovar in the sample (¶0055, 0102). Thus, the reference anticipates claim 1.
With regard to claim 8, insofar as the claim is meant to require primers selective for “all” serovars “of interest” the reference teaches a multiplex amplification to amplify all of the target serovars.
With regard to claims 2 and 9, the reference teaches that the sample is a primary enrichment of a sample matrix. That is, here the “sample matrix” is the original bacterial samples (¶0092-95) and the “primary enrichment of a sample matrix” sample matrix after culturing to enrich the bacteria (¶0096).
With regard to claims 3 and 4 and 11, the reference the detected Salmonella enterica, and included detecting serovar Infantis (¶0088).
With regard to claims 7, the “subject” is a culture, thus the sample is obtained from a subject (¶0096). With regard to claim 14, The reference further teaches the method can be employed for testing for Salmonella in livestock products, foods and the environment (¶0054).
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.
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) 15-17 and 20-22 is/are rejected under 35 U.S.C. 103 as being unpatentable over JP2021036802A.
A translation of the reference is provided in the file with JP2021036802.
The reference teaches a method that comprises
obtaining a sample (¶0096)
extracting DNA therefrom (¶0050, 0096)
performing an amplification reaction on the DNA using at least one fluorescently-labeled primer pair selective for the at least one Salmonella sp. serovar and a generic Salmonella sp. marker to generate fluorescently-labeled serovar amplicons (¶0097-98);
hybridizing the fluorescently-labeled serovar DNA amplicons to a plurality of nucleic acid probes each having a sequence corresponding to a sequence determinant in the Salmonella sp. Serovar DNA and each attached to a microarray (¶0054, (¶0101);
washing the microarray at least once (¶0102); and
imaging the microarray to detect at least one fluorescent signal from the fluorescently-labeled serovar DNA amplicons, thereby detecting the at least one Salmonella sp. Serovar in the sample (¶0055, 0102).
With regard to claims 16 and 17, the reference the detected Salmonella enterica, and included detecting serovar Infantis (¶0088).
Regarding claim 20, the generic Salmonella sp. target is invA (¶0039).
The reference does not teach obtaining a selective media enrichment of a food matrix associated with the food product.
The reference does teach culturing bacteria prior to nucleic acid extraction, and (¶0096) the reference teaches the disclosed method can be employed for testing for Salmonella in livestock products, foods and the environment (¶0054). The reference teaches that the sample is a primary enrichment of a sample matrix. That is, here the “sample matrix” is the original bacterial samples (¶0092-95) and the “primary enrichment of a sample matrix” sample matrix after culturing to enrich the bacteria (¶0096).
Regarding claim 21, the reference teaches testing “livestock products” which are “a product from a farm animal” recited in the claim (¶0054). Regarding claim 22, to be a food product that is a “livestock product” some level of processing is inherently required, so the “livestock product” is considered a “processed food product.
It would have been prima facie obvious to have modified the method taught in “Test 4” of the reference so to have substituted the bacteria test cultures with cultured samples from animal livestock food products. One would have been motivated to do so by the express teaching of the reference that the disclosed methods are for testing livestock products, which are food products.
Claim(s) 10 is/are rejected under 35 U.S.C. 103 as being unpatentable over JP2021036802A in view of Katchman et al. (Journal of AOAC INTERNATIONAL, 105(5), 2022, 1390–1407).
The teachings of JP2021036802A as they are relevant to claims 8 and 9, from which claim 10 depends are given previously in this office action and are fully incorporated here.
Katchman et al. does not teach wherein the sample matrix is processed without an enrichment culture, and the sample comprises a rinsate or a swab of the sample matrix. Katchman teaches using microarray technology to detect Salmonella species from sample matrices without enrichment. The reference teaches obtaining environmental swabs of four sample matrices (p. 1391, 1st column). The method employed for detection by Katchman et al. included amplification with fluorescent primers and detection via microarray, p. 1393-1394.
It would have been obvious to have modified the method taught by JP2021036802A by using a swabbed sample without enrichment as taught by Katchman. One would have been motivated to do so in order to provide a method that is simple to use for detection of Salmonella on environmental matrices.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Juliet Switzer whose telephone number is (571)272-0753. The examiner can normally be reached Monday to Thursday, 8:00 AM-3:30 PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, 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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Juliet Switzer
Primary Examiner
Art Unit 1682
/JULIET C SWITZER/Primary Examiner, Art Unit 1682