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 .
Claims 1-5, 7-11, 13-17, 19-23, 25-27, 32-33 and 35 are pending. Claims 1, 20-23 and 25 are being examined on the merits. Claims 2-5, 7-11, 13-17, 19, 26-27, 32-33 and 35 are withdrawn.
Election/Restrictions
Applicant’s election of Group I (claims 1-5, 7-11, 13-17, 19-23 and 25) and Species (F) in the reply filed on September 2, 2025 is 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)).
Claims 26-27, 32-33 and 35 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Claims 2-5, 7-11 and 13-19 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on September 2, 2025.
The requirement is still deemed proper and is therefore made FINAL.
Information Disclosure Statement
The Information Disclosure Statement submitted June 6, 2024 has been considered, as has each of the two Information Disclosure Statements submitted July 26, 2023.
Nucleotide and/or Amino Acid Sequence Disclosures
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 specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Specifically, sequence identifiers are missing in paras. 174 (last two sequences), 175 (last 2 sequences), and 180 (last two sequences),
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, 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.
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 1, 20-21 and 25 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more.
Eligibility is considered in light of MPEP 2106 III, which incorporates the 2019 Revised Patent Subject Matter Eligibility Guidance (2019 PEG) published on January 17, 2019 (84 Fed. Reg. 50) and clarified in the October 2019 Update.
As can be seen in the MPEP 2106 III Figure, eligibility analysis requires one to address the following questions: (i) Step 1 – Is the claim directed to one of the four statutory categories (i.e., process, machine, manufacture or composition of matter); (ii) Step 2A – Is the claim directed to a judicial exception (i.e., a natural phenomenon, law of nature or abstract idea); and (iii) Step 2B – does the claim recite additional elements that amount to significantly more than the judicial exception. In addition, as can be seen in the MPEP 2106.04 II Figure, Step 2A is a two-prong inquiry, with Prong One asking whether the claims recite a judicial exception (i.e., an abstract idea, natural phenomenon or law of nature) and Prong Two asking whether the claims recite additional elements that integrate the judicial exception into a practical application.
In this case, as to Step 1, claims 1, 20-21 and 25 are directed to one of the four statutory categories since they are drawn to a composition of matter.
The analysis cannot be streamlined, so the claims are considered with respect to Step 2A.
With respect to Prong One of Step 2A, claims 1, 20-21 and 25 recite a judicial exception. Specifically, the primers/probes are a product of nature (i.e., a natural phenomenon). The claims require primers/probes that each specifically bind to a particular OXA or rRNA gene. It is not clear that these primers exist in nature, but these oligonucleotides, are, nevertheless, judicial exceptions because they are derived from naturally occurring nucleic acids (see citations in conjunction with the prior art rejections below) and possess no structural or functional differences relative to their naturally occurring counterpart. For example, the oligonucleotides are not required to include a label or non-naturally occurring nucleotides, nor do they have functions not possessed by naturally occurring nucleic acids. As well, MPEP 2164.04(b)(i) identifies isolated nucleic acids having no structural or functional differences from naturally occurring nucleic acids as an example of a patent-ineligible natural product.
In addition, as discussed in MPEP 2016.04(b)(II), “[P]roduct of nature exceptions include both naturally occurring products and non-naturally occurring products that lack markedly different characteristics from any naturally occurring counterpart.” See Ambry Genetics, 774 F.3d at 760, 113 USPQ2d at 1244. In this case, the claimed oligonucleotides have no functional differences relative to their naturally occurring counterparts since both the claimed and naturally occurring molecules hybridize to complementary nucleic acids.
In view of the foregoing, claims 1, 20-21 and 25 clearly recite a judicial exception. With respect to Prong Two of Step 2A, the claims do not recite additional elements that integrate the judicial exceptions into a practical application for the following reason. In particular, the claims do not require any components other than the judicial exceptions. In addition, to the extent that the term “kit” in the preamble is construed to require something additional, such as assembling the various oligonucleotides into container(s), this also constitutes insignificant extra-solution activity as described in the 2019 PEG and MPEP 2106.05(g).
Thus, the answer to step 2A is “Yes, the claims are directed to a judicial exception,” and the analysis moves to Step 2B, which asks if the additional elements in the claim amount to significantly more than the judicial exception.
In this case, claims 1, 20-21 and 25 do not include additional elements that are sufficient to amount to significantly more than the judicial exception because claims 1, 20-21 and 25 need not have any components other than the recited oligonucleotides. In addition, assembling nucleotides into kits was routinely taught in the art prior to the effective filing date of the claimed invention (e.g., see Torres (WO 2017/218789 A1): paras. 11, 34). Therefore, an additional element of a kit is not non-routine or unconventional.
In view of the foregoing, claims 1, 20-21 and 25 are rejected under 35 U.S.C. 101 as being drawn to a judicial exception without significantly more.
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.
Claims 1, 23 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Torres1 (WO 2017/218789 A1) in view of GenBank Accession No. MF594724.1 (Acinetobacter pittii strain 1-1175 OXA-143 family carbapenem-hydrolyzing class D beta-lactamase-like protein (blaOXA) gene, partial cds, 2018) and An (US 2003/0050470).
Regarding independent claim 1 and dependent claims 23 and 25, Torres teaches
primer/probe kits for detecting various antibiotic resistance genes including, e.g., beta-lactamase genes such as OXA (paras. 10-11). Torres teaches that the probes can be labeled with various labels, including, e.g., a FRET pair (para. 35).
Regarding instant SEQ ID NOs: 322-323 and 324 (labeled)/364 (unlabeled), these sequences correspond with 100% homology to the following positions on GenBank Accession No. MF594724.1: 140-165, 382-406 (reverse complement) and 312-336, respectively.
Further, An teaches “[v]arious probes and primers can be designed around the disclosed nucleotide sequences. Primers can be of any length, but, typically, are 10-20 bases in length. By assigning numeric values to a sequence, for example, the first residue is 1, the residue is 2, etc., an algorithm defining all primers can be proposed:
n to n+y
where n is an integer from 1 to the last number of the sequence and y is the length of the primer minus 1 (9 to 19), where n+y does not exceed the last number of the sequence. Thus, for a 10-mer, the probes correspond to bases 1 to 10, 2 to 11, 3 to 12 … and so on. For a 15-mer, the probes correspond to bases 1 to 15, 2 to 16, 3 to 17 … and so on” (paras. 65-67).
Therefore, An not only teaches designing primers or probes based on a known sequence, but also teaches an algorithm for defining all possible primers and probes of a given length based on a known sequence. In this respect, An teaches that all possible subsequences of a known sequence could be considered as a primer or probe for that sequence. While An is discussing sequences having to do with prostate, bladder and breast cancer (e.g., abstract), the ordinary artisan would have recognized that the principles of designing primers and probes based on a disclosed nucleotide sequence would have applied to any nucleotide sequence under study.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious to practice the Torres method with primer/probe kits, and modify the primer/probe kits to arrive at the instantly claimed invention. Torres teaches the use of primer/probe kits, and teaches that the probes can be labeled. Torres also teaches the significance of detecting the OXA gene. One of ordinary skill in the art would have been motivated to modify the Torres primer/probe kits to optimize the primers/probes and the probe labels for a particular assay using the GenBank Accession Nos. and the teachings of An, and would have had an expectation of success, as such modifications are well known in the art.
Claim 21 is rejected under 35 U.S.C. 103 as being unpatentable over Torres (WO 2017/218789 A1) in view of GenBank Accession No. MF594724.1 (Acinetobacter pittii strain 1-1175 OXA-143 family carbapenem-hydrolyzing class D beta-lactamase-like protein (blaOXA) gene, partial cds, 2018) and An (US 2003/0050470), as applied to claim 1 above, and further in view of GenBank Accession No. JN358191.1 (Uncultured bacterium clone 4_D_061373_0176_0934 16S ribosomal RNA gene, partial sequence, 2011).
Regarding dependent claim 21, Torres teaches that the kit further comprises instant SEQ
ID NOs: 79-80, 76-77 and 370 (Torres SEQ ID NOs: 79-80, 76-77 and 30, respectively). Torres also teaches detecting rRNA as a control (para. 59).
Regarding instant SEQ ID NOs: 340 (labeled)/369 (unlabeled), these sequences correspond with 100% homology to nucleotides 24-47 of GenBank Accession No. JN358191.1, which corresponds to bacterial 16S rRNA.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious to further modify the modified Torres primer/probe kits, to include a probe that detects rRNA. Torres teaches detecting rRNA as a control gene. One of ordinary skill in the art would have been motivated to modify the Torres primer/probe kits to optimize the primers/probes and the probe labels, and to incorporate appropriate control reagents for a particular assay, using the GenBank Accession Nos. and the teachings of An, and would have had an expectation of success, as such modifications are well known in the art.
Claims 1, 23 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Torres (WO 2017/218789 A1) in view of GenBank Accession No. MG254523.1 (Acinetobacter baumannii strain KK-AB:12 class D beta-lactamase OXA-24 (blaOXA gene), blaOXA-24 allele, partial cds, 2018) and An (US 2003/0050470).
Regarding independent claim 1 and dependent claims 23 and 25, Torres teaches
primer/probe kits for detecting various antibiotic resistance genes including, e.g., beta-lactamase genes such as OXA (paras. 10-11). Torres teaches that the probes can be labeled with various labels, including, e.g., a FRET pair (para. 35).
Regarding instant SEQ ID NOs: 328-329 and 330 (labeled)/365 (unlabeled), these sequences correspond with 100% homology to the following positions on GenBank Accession No. MG254523.1: 158-183, 390-411 (reverse complement) and 329-357, respectively.
Further, An teaches “[v]arious probes and primers can be designed around the disclosed nucleotide sequences. Primers can be of any length, but, typically, are 10-20 bases in length. By assigning numeric values to a sequence, for example, the first residue is 1, the residue is 2, etc., an algorithm defining all primers can be proposed:
n to n+y
where n is an integer from 1 to the last number of the sequence and y is the length of the primer minus 1 (9 to 19), where n+y does not exceed the last number of the sequence. Thus, for a 10-mer, the probes correspond to bases 1 to 10, 2 to 11, 3 to 12 … and so on. For a 15-mer, the probes correspond to bases 1 to 15, 2 to 16, 3 to 17 … and so on” (paras. 65-67).
Therefore, An not only teaches designing primers or probes based on a known sequence, but also teaches an algorithm for defining all possible primers and probes of a given length based on a known sequence. In this respect, An teaches that all possible subsequences of a known sequence could be considered as a primer or probe for that sequence. While An is discussing sequences having to do with prostate, bladder and breast cancer (e.g., abstract), the ordinary artisan would have recognized that the principles of designing primers and probes based on a disclosed nucleotide sequence would have applied to any nucleotide sequence under study.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious to practice the Torres method with primer/probe kits, and modify the primer/probe kits to arrive at the instantly claimed invention. Torres teaches the use of primer/probe kits, and teaches that the probes can be labeled. Torres also teaches the significance of detecting the OXA gene. One of ordinary skill in the art would have been motivated to modify the Torres primer/probe kits to optimize the primers/probes and the probe labels for a particular assay using the GenBank Accession Nos. and the teachings of An, and would have had an expectation of success, as such modifications are well known in the art.
Claim 21 are rejected under 35 U.S.C. 103 as being unpatentable over Torres (WO 2017/218789 A1) in view of GenBank Accession No. MG254523.1 (Acinetobacter baumannii strain KK-AB:12 class D beta-lactamase OXA-24 (blaOXA gene), blaOXA-24 allele, partial cds, 2018) and An (US 2003/0050470), as applied to claim 1 above, and further in view of GenBank Accession No. JN358191.1 (Uncultured bacterium clone 4_D_061373_0176_0934 16S ribosomal RNA gene, partial sequence, 2011).
Regarding dependent claim 21, Torres teaches that the kit further comprises instant SEQ
ID NOs: 79-80, 76-77 and 370 (Torres SEQ ID NOs: 79-80, 76-77 and 30, respectively). Torres also teaches detecting rRNA as a control (para. 59).
Regarding instant SEQ ID NOs: 340 (labeled)/369 (unlabeled), these sequences correspond with 100% homology to nucleotides 24-47 of GenBank Accession No. JN358191.1, which corresponds to bacterial 16S rRNA.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious to further modify the modified Torres primer/probe kits, to include a probe that detects rRNA. Torres teaches detecting rRNA as a control gene. One of ordinary skill in the art would have been motivated to modify the Torres primer/probe kits to optimize the primers/probes and the probe labels, and to incorporate appropriate control reagents for a particular assay, using the GenBank Accession Nos. and the teachings of An, and would have had an expectation of success, as such modifications are well known in the art.
Claims 1, 23 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Torres (WO 2017/218789 A1) in view of GenBank Accession No. KT148593.1 (Acinetobacter baumannii strain IPTSP-UFG:ABs:51(2207) class D beta-lactamase OXA-58 (OXA-58), gene, partial CDS, 2015) and An (US 2003/0050470).
Regarding independent claim 1 and dependent claims 23 and 25, Torres teaches
primer/probe kits for detecting various antibiotic resistance genes including, e.g., beta-lactamase genes such as OXA (paras. 10-11). Torres teaches that the probes can be labeled with various labels, including, e.g., a FRET pair (para. 35).
Regarding instant SEQ ID NOs: 331-332 and 333 (labeled)/366 (unlabeled), these sequences correspond with 100% homology to the following positions on GenBank Accession No. KT148593.1: 75-97, 364-386 (reverse complement) and 162-190, respectively.
Further, An teaches “[v]arious probes and primers can be designed around the disclosed nucleotide sequences. Primers can be of any length, but, typically, are 10-20 bases in length. By assigning numeric values to a sequence, for example, the first residue is 1, the residue is 2, etc., an algorithm defining all primers can be proposed:
n to n+y
where n is an integer from 1 to the last number of the sequence and y is the length of the primer minus 1 (9 to 19), where n+y does not exceed the last number of the sequence. Thus, for a 10-mer, the probes correspond to bases 1 to 10, 2 to 11, 3 to 12 … and so on. For a 15-mer, the probes correspond to bases 1 to 15, 2 to 16, 3 to 17 … and so on” (paras. 65-67).
Therefore, An not only teaches designing primers or probes based on a known sequence, but also teaches an algorithm for defining all possible primers and probes of a given length based on a known sequence. In this respect, An teaches that all possible subsequences of a known sequence could be considered as a primer or probe for that sequence. While An is discussing sequences having to do with prostate, bladder and breast cancer (e.g., abstract), the ordinary artisan would have recognized that the principles of designing primers and probes based on a disclosed nucleotide sequence would have applied to any nucleotide sequence under study.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious to practice the Torres method with primer/probe kits, and modify the primer/probe kits to arrive at the instantly claimed invention. Torres teaches the use of primer/probe kits, and teaches that the probes can be labeled. Torres also teaches the significance of detecting the OXA gene. One of ordinary skill in the art would have been motivated to modify the Torres primer/probe kits to optimize the primers/probes and the probe labels for a particular assay using the GenBank Accession Nos. and the teachings of An, and would have had an expectation of success, as such modifications are well known in the art.
Claim 21 are rejected under 35 U.S.C. 103 as being unpatentable over Torres (WO 2017/218789 A1) in view of GenBank Accession No. KT148593.1 (Acinetobacter baumannii strain IPTSP-UFG:ABs:51(2207) class D beta-lactamase OXA-58 (OXA-58), gene, partial CDS, 2015), as applied to claim 1 above, and further in view of GenBank Accession No. JN358191.1 (Uncultured bacterium clone 4_D_061373_0176_0934 16S ribosomal RNA gene, partial sequence, 2011).
Regarding dependent claim 21, Torres teaches that the kit further comprises instant SEQ
ID NOs: 79-80, 76-77 and 370 (Torres SEQ ID NOs: 79-80, 76-77 and 30, respectively). Torres also teaches detecting rRNA as a control (para. 59).
Regarding instant SEQ ID NOs: 340 (labeled)/369 (unlabeled), these sequences correspond with 100% homology to nucleotides 24-47 of GenBank Accession No. JN358191.1, which corresponds to bacterial 16S rRNA.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious to further modify the modified Torres primer/probe kits, to include a probe that detects rRNA. Torres teaches detecting rRNA as a control gene. One of ordinary skill in the art would have been motivated to modify the Torres primer/probe kits to optimize the primers/probes and the probe labels, and to incorporate appropriate control reagents for a particular assay, using the GenBank Accession Nos. and the teachings of An, and would have had an expectation of success, as such modifications are well known in the art.
Claims 1, 23 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Torres (WO 2017/218789 A1) in view of GenBank Accession No. JQ342836.1 (Acinetobacter baumannii strain PKS19 class D beta-lactamase gene, partial cds, 2012) and An (US 2003/0050470).
Regarding independent claim 1 and dependent claims 23 and 25, Torres teaches
primer/probe kits for detecting various antibiotic resistance genes including, e.g., beta-lactamase genes such as OXA (paras. 10-11). Torres teaches that the probes can be labeled with various labels, including, e.g., a FRET pair (para. 35).
Regarding instant SEQ ID NOs: 334-335 and 336 (labeled)/367 (unlabeled), these sequences correspond with 100% homology to the following positions on GenBank Accession No. JQ342836.1: 84-104, 549-569 (reverse complement) and 107-136, respectively.
Further, An teaches “[v]arious probes and primers can be designed around the disclosed nucleotide sequences. Primers can be of any length, but, typically, are 10-20 bases in length. By assigning numeric values to a sequence, for example, the first residue is 1, the residue is 2, etc., an algorithm defining all primers can be proposed:
n to n+y
where n is an integer from 1 to the last number of the sequence and y is the length of the primer minus 1 (9 to 19), where n+y does not exceed the last number of the sequence. Thus, for a 10-mer, the probes correspond to bases 1 to 10, 2 to 11, 3 to 12 … and so on. For a 15-mer, the probes correspond to bases 1 to 15, 2 to 16, 3 to 17 … and so on” (paras. 65-67).
Therefore, An not only teaches designing primers or probes based on a known sequence, but also teaches an algorithm for defining all possible primers and probes of a given length based on a known sequence. In this respect, An teaches that all possible subsequences of a known sequence could be considered as a primer or probe for that sequence. While An is discussing sequences having to do with prostate, bladder and breast cancer (e.g., abstract), the ordinary artisan would have recognized that the principles of designing primers and probes based on a disclosed nucleotide sequence would have applied to any nucleotide sequence under study.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious to practice the Torres method with primer/probe kits, and modify the primer/probe kits to arrive at the instantly claimed invention. Torres teaches the use of primer/probe kits, and teaches that the probes can be labeled. Torres also teaches the significance of detecting the OXA gene. One of ordinary skill in the art would have been motivated to modify the Torres primer/probe kits to optimize the primers/probes and the probe labels for a particular assay using the GenBank Accession Nos. and the teachings of An, and would have had an expectation of success, as such modifications are well known in the art.
Claim 21 are rejected under 35 U.S.C. 103 as being unpatentable over Torres (WO 2017/218789 A1) in view of GenBank Accession No. JQ342836.1 (Acinetobacter baumannii strain PKS19 class D beta-lactamase gene, partial cds, 2012), as applied to claim 1 above, and further in view of GenBank Accession No. JN358191.1 (Uncultured bacterium clone 4_D_061373_0176_0934 16S ribosomal RNA gene, partial sequence, 2011).
Regarding dependent claim 21, Torres teaches that the kit further comprises instant SEQ
ID NOs: 79-80, 76-77 and 370 (Torres SEQ ID NOs: 79-80, 76-77 and 30, respectively). Torres also teaches detecting rRNA as a control (para. 59).
Regarding instant SEQ ID NOs: 340 (labeled)/369 (unlabeled), these sequences correspond with 100% homology to nucleotides 24-47 of GenBank Accession No. JN358191.1, which corresponds to bacterial 16S rRNA.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious to further modify the modified Torres primer/probe kits, to include a probe that detects rRNA. Torres teaches detecting rRNA as a control gene. One of ordinary skill in the art would have been motivated to modify the Torres primer/probe kits to optimize the primers/probes and the probe labels, and to incorporate appropriate control reagents for a particular assay, using the GenBank Accession Nos. and the teachings of An, and would have had an expectation of success, as such modifications are well known in the art.
Claims 1, 23 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Torres (WO 2017/218789 A1) in view of GenBank Accession No. KY439042.1 (Acinetobacter baumannii strain Yazd-32 beta-lactamase OXA-23 (blaOXA23) gene, partial cds, 2017), GenBank Accession No. KU310908.1 (Acinetobacter baumannii carbapenemas M1-like (OXA-23) gene, partial sequence, 2016) and An (US 2003/0050470).
Regarding independent claim 1 and dependent claims 23 and 25, Torres teaches
primer/probe kits for detecting various antibiotic resistance genes including, e.g., beta-lactamase genes such as OXA (paras. 10-11). Torres teaches that the probes can be labeled with various labels, including, e.g., a FRET pair (para. 35).
Regarding instant SEQ ID NOs: 337 and 339 (labeled)/368 (unlabeled), these sequences correspond with 100% homology to the following positions on GenBank Accession No. KY439042.1: 115-138 and 154-177, respectively.
Regarding instant SEQ ID NO: 338, this sequence corresponds with 100% homology to the following positions on GenBank Accession No. KU310908.1: 7-60 (reverse complement).
Further, An teaches “[v]arious probes and primers can be designed around the disclosed nucleotide sequences. Primers can be of any length, but, typically, are 10-20 bases in length. By assigning numeric values to a sequence, for example, the first residue is 1, the residue is 2, etc., an algorithm defining all primers can be proposed:
n to n+y
where n is an integer from 1 to the last number of the sequence and y is the length of the primer minus 1 (9 to 19), where n+y does not exceed the last number of the sequence. Thus, for a 10-mer, the probes correspond to bases 1 to 10, 2 to 11, 3 to 12 … and so on. For a 15-mer, the probes correspond to bases 1 to 15, 2 to 16, 3 to 17 … and so on” (paras. 65-67).
Therefore, An not only teaches designing primers or probes based on a known sequence, but also teaches an algorithm for defining all possible primers and probes of a given length based on a known sequence. In this respect, An teaches that all possible subsequences of a known sequence could be considered as a primer or probe for that sequence. While An is discussing sequences having to do with prostate, bladder and breast cancer (e.g., abstract), the ordinary artisan would have recognized that the principles of designing primers and probes based on a disclosed nucleotide sequence would have applied to any nucleotide sequence under study.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious to practice the Torres method with primer/probe kits, and modify the primer/probe kits to arrive at the instantly claimed invention. Torres teaches the use of primer/probe kits, and teaches that the probes can be labeled. Torres also teaches the significance of detecting the OXA gene. One of ordinary skill in the art would have been motivated to modify the Torres primer/probe kits to optimize the primers/probes and the probe labels for a particular assay using the GenBank Accession Nos. and the teachings of An, and would have had an expectation of success, as such modifications are well known in the art.
Claim 21 are rejected under 35 U.S.C. 103 as being unpatentable over Torres (WO 2017/218789 A1) in view of GenBank Accession No. KY439042.1 (Acinetobacter baumannii strain Yazd-32 beta-lactamase OXA-23 (blaOXA23) gene, partial cds, 2017), GenBank Accession No. KU310908.1 (Acinetobacter baumannii carbapenemas M1-like (OXA-23) gene, partial sequence, 2016), as applied to claim 1 above, and further in view of GenBank Accession No. JN358191.1 (Uncultured bacterium clone 4_D_061373_0176_0934 16S ribosomal RNA gene, partial sequence, 2011).
Regarding dependent claim 21, Torres teaches that the kit further comprises instant SEQ
ID NOs: 79-80, 76-77 and 370 (Torres SEQ ID NOs: 79-80, 76-77 and 30, respectively). Torres also teaches detecting rRNA as a control (para. 59).
Regarding instant SEQ ID NOs: 340 (labeled)/369 (unlabeled), these sequences correspond with 100% homology to nucleotides 24-47 of GenBank Accession No. JN358191.1, which corresponds to bacterial 16S rRNA.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious to further modify the modified Torres primer/probe kits, to include a probe that detects rRNA. Torres teaches detecting rRNA as a control gene. One of ordinary skill in the art would have been motivated to modify the Torres primer/probe kits to optimize the primers/probes and the probe labels, and to incorporate appropriate control reagents for a particular assay, using the GenBank Accession Nos. and the teachings of An, and would have had an expectation of success, as such modifications are well known in the art.
Claims 1, 20, 23 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Torres (WO 2017/218789 A1) in view of GenBank Accession No. MF594724.1 (Acinetobacter pittii strain 1-1175 OXA-143 family carbapenem-hydrolyzing class D beta-lactamase-like protein (blaOXA) gene, partial cds, 2018), GenBank Accession No. MG254523.1 (Acinetobacter baumannii strain KK-AB:12 class D beta-lactamase OXA-24 (blaOXA gene), blaOXA-24 allele, partial cds, 2018), GenBank Accession No. KT148593.1 (Acinetobacter baumannii strain IPTSP-UFG:ABs:51(2207) class D beta-lactamase OXA-58 (OXA-58), gene, partial CDS, 2015), GenBank Accession No. JQ342836.1 (Acinetobacter baumannii strain PKS19 class D beta-lactamase gene, partial cds, 2012), GenBank Accession No. KY439042.1 (Acinetobacter baumannii strain Yazd-32 beta-lactamase OXA-23 (blaOXA23) gene, partial cds, 2017), GenBank Accession No. KU310908.1 (Acinetobacter baumannii carbapenemas M1-like (OXA-23) gene, partial sequence, 2016) and An (US 2003/0050470).
Regarding independent claim 1 and dependent claims 20, 23 and 25, Torres teaches
primer/probe kits for detecting various antibiotic resistance genes including, e.g., beta-lactamase genes such as OXA (paras. 10-11). Torres teaches that the probes can be labeled with various labels, including, e.g., a FRET pair (para. 35).
Regarding instant SEQ ID NOs: 322-323 and 324 (labeled)/364 (unlabeled), these sequences correspond with 100% homology to the following positions on GenBank Accession No. MF594724.1: 140-165, 382-406 (reverse complement) and 312-336, respectively.
Regarding instant SEQ ID NOs: 328-329 and 330 (labeled)/365 (unlabeled), these sequences correspond with 100% homology to the following positions on GenBank Accession No. MG254523.1: 158-183, 390-411 (reverse complement) and 329-357, respectively.
Regarding instant SEQ ID NOs: 331-332 and 333 (labeled)/366 (unlabeled), these sequences correspond with 100% homology to the following positions on GenBank Accession No. KT148593.1: 75-97, 364-386 (reverse complement) and 162-190, respectively.
Regarding instant SEQ ID NOs: 334-335 and 336 (labeled)/367 (unlabeled), these sequences correspond with 100% homology to the following positions on GenBank Accession No. JQ342836.1: 84-104, 549-569 (reverse complement) and 107-136, respectively.
Regarding instant SEQ ID NOs: 337 and 339 (labeled)/368 (unlabeled), these sequences correspond with 100% homology to the following positions on GenBank Accession No. KY439042.1: 115-138 and 154-177, respectively.
Regarding instant SEQ ID NO: 338, this sequence corresponds with 100% homology to the following positions on GenBank Accession No. KU310908.1: 7-60 (reverse complement).
Further, An teaches “[v]arious probes and primers can be designed around the disclosed nucleotide sequences. Primers can be of any length, but, typically, are 10-20 bases in length. By assigning numeric values to a sequence, for example, the first residue is 1, the residue is 2, etc., an algorithm defining all primers can be proposed:
n to n+y
where n is an integer from 1 to the last number of the sequence and y is the length of the primer minus 1 (9 to 19), where n+y does not exceed the last number of the sequence. Thus, for a 10-mer, the probes correspond to bases 1 to 10, 2 to 11, 3 to 12 … and so on. For a 15-mer, the probes correspond to bases 1 to 15, 2 to 16, 3 to 17 … and so on” (paras. 65-67).
Therefore, An not only teaches designing primers or probes based on a known sequence, but also teaches an algorithm for defining all possible primers and probes of a given length based on a known sequence. In this respect, An teaches that all possible subsequences of a known sequence could be considered as a primer or probe for that sequence. While An is discussing sequences having to do with prostate, bladder and breast cancer (e.g., abstract), the ordinary artisan would have recognized that the principles of designing primers and probes based on a disclosed nucleotide sequence would have applied to any nucleotide sequence under study.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious to practice the Torres method with primer/probe kits, and modify the primer/probe kits to arrive at the instantly claimed invention. Torres teaches the use of primer/probe kits, and teaches that the probes can be labeled. Torres also teaches the significance of detecting the OXA gene. One of ordinary skill in the art would have been motivated to modify the Torres primer/probe kits to optimize the primers/probes and the probe labels for a particular assay using the GenBank Accession Nos. and the teachings of An, and would have had an expectation of success, as such modifications are well known in the art.
Prior Art
Regarding dependent claim 22, Torres teaches that the kit further comprises instant SEQ ID NOs: 58 and 264 (Torres, 58 and 264, respectively). However, at least SEQ ID NO. 350 is not known in the art. Thus, claim 22 is free of the art.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1, 20, 23 and 25 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 3-5 and 14 of copending Application No. 19/485,594 (hereinafter, the ‘594 application).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Although the claims at issue are not identical, they are not patentably distinct from each other because the ‘594 application claim 3 teaches kits for identifying OXA, wherein the kit comprises one or more primers/probes, including SEQ ID NOs. 322-323 and 328-329, and probes 364/324, 365/330, 366/333, 367/336 and 368/339. The ‘594 application claim 4 teaches probe 369/340. The ‘594 application claim 5 teaches SEQ ID NOs. 331-332, 334-335 and 337-338. The ‘594 application claim 14 teaches probes comprising a label.
Thus, these claims of the ‘594 application teach all of the limitations of at least some embodiments of instant claims 1, 20, 23 and 25, albeit in different embodiments.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious to modify the ‘594 application primer/probe kits to arrive at the instantly claimed invention. The ‘594 application teaches primer/probe kits for detecting the OXA gene, and teaches that the probes can be labeled. One of ordinary skill in the art would have been motivated to modify the ‘594 application primer/probe kits to optimize the primers/probes and the probe labels for a particular assay, and would have had an expectation of success, as such modifications are well known in the art.
Claims 20-21 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 10-11 of copending Application No. 19/485,294 in view of Torres (WO 2017/218789 A1).
This is a provisional nonstatutory double patenting rejection.
The ‘594 application claims 10-11 teach kits comprising SEQ ID NOs: 58, 264 and 349-
353, and the ‘594 application claim 4 teaches SEQ ID NOs: 76-77 and 340. In addition, Torres teaches that the kit further comprises instant SEQ ID NOs: 79-80 and 370 (Torres SEQ ID NOs: 79-80 and 30, respectively).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious to modify the ‘594 application primer/probe kits to add primers/probes of Torres to arrive at the instantly claimed invention. The ‘594 application teaches primer/probe kits for detecting the OXA gene, and teaches that the probes can be labeled. One of ordinary skill in the art would have been motivated to modify the ‘594 application primer/probe kits to optimize the primers/probes and the probe labels for a particular assay, and would have had an expectation of success, as such modifications are well known in the art.
Conclusion
Claims 1, 20-23 and 25 are being examined and are rejected. No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CAROLYN GREENE whose telephone number is (571)272-3240. The examiner can normally be reached M-Th 7:30-5:30 EST.
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, Gary Benzion can be reached at 571-272-0782. 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.
/CAROLYN L GREENE/Examiner, Art Unit 1681
1 Torres was cited in the Information Disclosure Statement submitted July 26, 2023.