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 .
Status of the application
This application is a 371 of PCT/IB2021/054614 05/26/2021. Accordingly, the priority date is 05/26/2021. Claims 1-42 are pending. Under 37 CFR 1.475(a) applicants have elected without traverse Group I, claims 1-28, drawn to a method of detection/quantification Listeria monocytogenes, Salmonella spp. and Shiga toxin-producing Escherichia coli in a sample.
Election for examination
Applicants elect as species, the SEQ ID NO: 13 and SEQ ID NO: 8 as a forward primer and reverse primer and primer SEQ ID NO: 19 as to the central linker region. Claims 1-4, 6-7, 9-12, 17, 22, 24-25, 27-28 read on the species elected for examination. Accordingly, claims 5, 8, 13-16, 18-21, 23 and 26 are withdrawn from further consideration as not drawn to the elected invention.
Information Disclosure Statement
Applicant information disclosure statement filed 11/24/2023 is in compliance with 37 CFR 1.97 and 1.98 and has been considered.
Claim Interpretation
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. Phillips v. AWH Corp., 415 F.3d l303, 75 USPQ2d l321 (Fed. Cir. 2005), "During patent examination, the pending claims must be 'given their broadest reasonable interpretation consistent with the specification.' " As pointed out in In re Mott, 190 U.S.P.Q. 536 (CCPA 1975), "Claims must be given broadest reasonable construction their language will permit in ex parte prosecution, and applicant who uses broad language runs the risk that others may be able to support the same claim with a different disclosure." The term “derivatives or combinations thereof” is found through the specification and the claims but it is not defined. Because the term is not expressly defined in the specification the meaning ascribed thereto is given the ordinary and customary meaning in light of the specification under BRI.
When considering the ordinary and customary meaning in light of the specification, as applied to sequences, the person of skill in the art would consider this term to comprise:
a sequence with substitutions, insertions, or deletions,
a sequence with a certain percentage identity,
a functionally equivalent sequence,
a chemically modified sequence, or
any other bounded class of variants.
The term “derivatives” is recited in the specification as follows:
primer set for L. monocytogenes “selected from SEQ ID No. 1 to 6, its derivatives, or combinations thereof”
probe set for L. monocytogenes “selected from SEQ ID No. 22 to 25, its derivatives, or combinations thereof”
primer set for STEC “selected from SEQ ID No. 7 to 12, its derivatives, or combinations thereof”
probe set for STEC “selected from SEQ ID No. 26 to 29, its derivatives, or combinations thereof”
primer set for Salmonella spp. “selected from SEQ ID No. 13 to 18, its derivatives, or combinations thereof”
probe set for Salmonella spp. “selected from SEQ ID No. 30 to 33, its derivatives, or combinations thereof”
internal control forward primer set “selected from SEQ ID No. 1, 3, 5, 7, 9, 11, 13, 15, and 17, its derivatives, or combinations thereof”
internal control reverse primer set “selected from SEQ ID No 2, 4, 6, 8, 10, 12, 14, 16, and 18, its derivatives, or combinations thereof”
internal control probe set “selected from SEQ ID No. 34 to 35, its derivatives, or combinations thereof”
Accordingly, a derivative or combination of a sequence is considered to encompass any sequence that functions for the intended purpose.
The term “Salmonella-type bacteria” is cited in claim 22, but it is not defined. Because the term is not expressly defined in the specification, (there are no instances of the phrase Salmonella-type in the specification) the meaning ascribed thereto is given the ordinary and customary meaning in light of the specification under BRI. The term “Salmonella-type bacteria” is not a formal, standardized term of art in microbiology or medical terminology. It is informal shorthand used in casual or descriptive contexts to refer to bacteria that are similar to or share characteristics with Salmonella, but it is not a precise taxonomic or clinical category. The genus Salmonella includes over 2,500 serotypes, with Salmonella enterica and Salmonella bongori being the main species. Accordingly, the term is considered to encompass any bacteria within the 2500 serotypes.
35USC 112(b)
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 1-28 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 1 is indefinite because it contains reference to a previous step not present in the claim. Claim 1 recites steps (e) through (h), but step (h) refers “to the concentration used in (a)”. No step (a) appears in claim 1 or in any other claims. As written, the claim does not particularly point out and distinctly claim the subject matter regarded as the invention. As claims 2-28 depend directly or indirectly from claim 1, they too are 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. A claim should not be rejected over prior art just because it is indefinite. Ionescu, 222 USPQ at 540 (citing Steele). Although a claim that is indefinite because it is susceptible to more than one interpretation may be rejected over prior art, an examiner should not base a prior art rejection on a claim interpretation that is not reasonable.
Additionally, claim 24 refers to where the Cq value, obtained by qPCR in Step b) then “and validating it by the value for I.C. signal obtained in step d) is similarly indefinite as neither steps b) nor d) are recited in claim 1.
35 USC 112(a)
Written Description
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 18-23, and 25-27 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.
“[T]he purpose of the written description requirement is to ‘ensure that the scope of the right to exclude, as set forth in the claims, does not overreach the scope of the inventor’s contribution to the field of art as described in the patent specification.”’ Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1353–54 (Fed. Cir. 2010) (en banc). Whether the disclosure of a patent satisfies the written description requirement is a question of fact. See id. at 1351.
The test for sufficiency of the written description support is “whether the disclosure of the application relied upon reasonably conveys to those skilled in the art that the inventor had possession of the claimed subject matter as of the filing date sought.” Id.
This “possession” test “requires an objective inquiry into the four corners of the specification from the perspective of a person of ordinary skill in the art.” Id. Possession shown by evidence “outside of the specification is not enough,” and “a description that merely renders the invention obvious does not satisfy the requirement.” Id. at 1352. Instead, it is the specification itself that must demonstrate possession. Id.
For example, in Hyatt v. Dudas, 492 F.3d 1365, 1371 (Fed. Cir. 2007), the examiner made a prima facie case by clearly and specifically explaining why applicant’s specification did not support the particular claimed combination of elements, even though applicant’s specification listed each and every element in the claimed combination. The court found the "examiner was explicit that while each element may be individually described in the specification, the deficiency was a lack of adequate description of their combination" and, thus, "[t]he burden was then properly shifted to the [inventor] to cite to the examiner where adequate written description could be found or to make an amendment to address the deficiency." Id.; see also Novozymes A/S v. DuPont Nutrition Biosciences APS, 723 F.3d 1336, 1349 (Fed. Cir. 2013) (explaining that each claim must be taken “as an integrated whole rather than as a collection of independent limitations” and the specification must be viewed prospectively, based on PHOSITA knowledge at the time, not in hindsight); Flash-Control, LLC v. Intel Corp., -- Fed. Appx. --, 2021 WL 2944592, *4 (Fed. Cir. July 14, 2021) (“A patent owner cannot show written description support by picking and choosing claim elements from different embodiments that are never linked together in the specification.”); Stored Value Solutions, Inc. v. Card Activation Techs., 499 Fed.App’x 5, 13-14 (Fed. Cir. 2012) (non-precedential) (Finding inadequate written support for claims drawn to a method of processing debit purchase transactions requiring three separate authorization codes because "the written description [did] not contain a method that include[d] all three codes" and "[e]ach authorization code is an important claim limitation, and the presence of multiple authorization codes in [the claim] was essential".) Just as in Hyatt, Applicant has not demonstrated sufficiently how the Specification supports the particular combination of limitations identified by the Examiner recited in the selected claims.
In this specific case, the claims recite primer sequences selected from listed SEQ ID NOs “its derivatives, or combinations thereof,” but the specification does not reasonably convey possession of the full scope of those derivative sequences or combinations thereof as claimed.
The specification describes certain specific primer sequences by SEQ ID NO and discloses a limited number of specific chimeric embodiments, including full-length sequences. However, the specification does not define “derivatives”, nor identify structural boundaries for what constitutes a derivative sequence, and does not provide representative examples or a meaningful roadmap showing possession of the full scope of all primer/probe derivatives encompassed by the claims. Likewise, the specification does not adequately describe possession of the claimed “combinations thereof” across the full breadth of the recited sequence selections.
Accordingly, the disclosure as filed does not reasonably demonstrate that applicant was in possession of the full scope of the claimed derivative and combination subject matter on the filing date.
Claims 22 and 23 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.
Claim 22 recites the limitation of “Salmonella-type bacteria,” however, the specification does not define the meaning and it is not a common term of art. As noted above there are over 2500 serotype of bacteria identified as Salmonella bacteria. Accordingly, the disclosure as filed does not reasonably demonstrate that applicant was in possession of the full scope of the claimed derivative and combination subject matter on the filing date.
Prior art
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.
Before the application of prior art, the examiner is charged with determining the state of the prior art. The landmark case defining how to evaluate the state of the prior art is Graham v. John Deere Co., 383 U.S. 1 (1966). In this ruling, the U.S. Supreme Court established the foundational "Graham Factors" used to determine whether an invention is non-obvious under 35 U.S.C. § 103:
Determining the scope and content of the prior art (identifying the state of existing technology at the time of the invention).
Assessing the differences between the prior art and the claimed invention.
Establishing the level of ordinary skill in the pertinent art.
Evaluating secondary considerations (commercial success, long-felt but unresolved needs, and failure of others).
In addition to the Graham factors the following case law is instructive as to how the determination of what constitutes a proper evaluation and rejection over the prior art.
In KSR Int'l Co. v. Teleflex Inc. (2007): Reaffirmed Graham and clarified that combining elements of prior art can render an invention obvious if there is a flexible, common-sense rationale for doing so.
In Helsinn Healthcare S.A. v. Teva Pharmaceuticals USA, Inc. (2019): Addressed what qualifies as prior art, holding that secret or confidential commercial sales prior to filing still trigger the "on-sale bar" under 35 U.S.C. § 102.
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 1, 2–4, 17, 22, 24–25, and 27–28 are rejected under 35 U.S.C. § 103 as being unpatentable over Carloni et al. in view of Kawasaki, WO2015044472, Chen et al, and Petrucci et al.
Carloni et al. teach a multiplex molecular platform for simultaneous detection and quantification of three foodborne pathogens; Escherichia coli O157, Salmonella spp., and Listeria monocytogenes in food samples using multiplex magnetic capture hybridization (mMCH) and multiplex real-time PCR. Carloni et al. expressly teaches standard-curve-based quantification and Chen teaches IAC-based validation of qPCR/qRT-PCR results (pp. 736–738). The assay combines DNA extraction and real-time PCR which is described by Carloni et al. having widely described in the prior art. Kawasaki et al. describes multiplex PCR method was developed for simultaneous detection of Salmonella spp., Listeria monocytogenes, and Escherichia coli O157:H7 in meat samples in which agreement was obtained for the results of multiplex PCR and the conventional culture method, which suggests that the multiplex PCR is a reliable and useful method for rapid screening of meat products for Salmonella spp., L. monocytogenes, and E. coli O157:H7 contamination. (Abstract.) Accordingly, the concept of simultaneously detection of these food born pathogen was well known and perfected in the art.
Turning back to Carloni et al., these authors taught in 2010 the simultaneous quantification of each bacterium (736, last paragraph before Material and Methods). Carloni et al. further describes that the multipathogen FLUO kit detects Salmonella in the Green channel, L. monocytogenes in the Red channel, E. coli O157 in the Orange channel, and an Internal Amplification Control (IAC) in the Yellow channel, and further teaches standard-curve quantification (p 737, left bottom). However, neither Carloni et al. or Kawasaki et al teach adding an internal control comprising a chimeric polynucleotide to the multiplex assay, however, this concept was taught by WO2015044472.
WO2015044472 teaches a “designed a chimeric type IAC” having a heterologous DNA sequence flanked by the hybridization sites of the primer pairs used for qRTi-PCR amplification. See, pp. 39–40, paras. WO2015044472 further explains construction of the QIAC by progressively adding primer annealing sites to an internal fragment of the Eucalyptus globulus cinnamoyl-CoA reductase gene and ligating the resulting approximately 360 bp insert into a vector. (pp. 177–182).
The suggestion to include an internal control is also taught by Chen et al. who evidences that qPCR and qRT-PCR assays for foodborne pathogen detection should include an internal amplification control to monitor PCR inhibition in complex food matrices and to reduce false-negative results. (Chen, pp. 40–41, section 2.2.) However, the simultaneous detection of Shiga toxin-producing bacteria by this combination of prior art is not taught but was well within the ordinary skill in the art as taught by Petrucci et al.
Petrucci et al. taught detection of Shiga toxin-producing bacteria by RPA using specific primers to identify different stx1 genes by targeting stx1/stx2 in food matrices using rapid amplification and lateral-flow readout. (pp. 2–4 and pp. 6–10.)
It would have been obvious to a person of ordinary skill before the effective filing date of the present claimed invention, in view of the known problem of PCR inhibition and false negatives in complex food matrices as taught by Carloni et al., Petrucci et al and Chen et al., to incorporate the chimeric internal control concept of WO2015044472 into a host/vector and to employ that control in the multiplex food-pathogen detection workflow of Carloni et al. Such a modification would have predictably provided a known control source that could be introduced with the sample and used to validate the assay, thereby reducing false negatives and monitoring the combined processing and amplification steps in food-sample analysis.
Claims 1, 2–4, 17, 22, 24–25, and 27–28 are rejected under 35 U.S.C. 103 as being unpatentable over Carloni et al. in view of Kawasaki, WO2015044472, Chen et al, and Petrucci et al. further in view of as applied to claims 1, 2–4, 17, 22, 24–25, and 27–28 above, and further in view of Lowe et al., Chellapandi et al. and Malorny et al.
Applicants elected sequences ID No: 13, 8 and 19 for examination purposes. Sequence ID No: 19, is described as directed to the central region to internal control. Seq ID No: 13 is described as the forward primer for Salmonella species and Seq ID NO: 8 is described as a primer that bind reverse Shiga toxin-producing Escherichia coli (STEC). In view of the limitation, “derivatives or combinations” as set forth in the claims, these sequences and those that can be derived therefrom were well known in the art. For example, Chellapandi et al. disclose SEQ ID NO; 8 of the instant invention as part of a greater sequence and as deposited under NCBI Genbank Accession NO: KX832336 to KX832345 showing 100% sequence identity to gatcattttc attacccgta cca of the instant invention. Similarly, Malorny et al. disclose SEQ ID NO: 13, cggactcacc aggagattac, as part of a larger sequences, as deposited under NCBI as accession no AY578070 which is 100% identical to the instant invention. While this prior art does not disclose the use of these sequences are used as primer or probes the generation of primers and probes from known sequences is well taught by the Lowe et al. None of the references cited teach determining the pathogen concentration based on the elected sequences, but given that the prior art teaches the used of primers and chimeric control sequences in which the each is modified as a “derivatives or combination thereof” the prior art of record makes the use of any such sequence a derivative or combination thereof the claimed sequences. Accordingly, It would have been obvious to a person of ordinary skill before the effective filing date of the present claimed invention.
Accordingly, it would have been obvious to a person of ordinary skill before the effective filing date of the present claimed invention, in view of the known sequences corresponding to each species to used the method of Lowe et al. to derived primers thereto
Conclusion
No Claim is allowed.
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GARY BENZION, Ph.D.
Supervisory Patent Examiner
Art Unit 1681
/GARY BENZION/Supervisory Patent Examiner, Art Unit 1681
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