FINAL 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 action is responsive to the Amendments and Response filed 06 July 2026. Claims 1, 3, 5-9, 11-12, 14-16, and 24 have been amended, claims 4, 10, and 13 have been canceled, and claims 31-32 have been added. All prior rejections of claims 4, 10, and 13 are moot in view of the cancelation of those claims. Claims 25-26 remain withdrawn, and claims 1, 3, 5-9, 11-12, 14-16, 21, 24, 28, and 31-32 remain/are under consideration herein. Applicant’s amendments and arguments have been thoroughly reviewed, and have overcome the following objections/rejections set forth in the prior Office action:
The objections to the specification (including regarding the presence of hyperlinks and the issue identified regarding missing SEQ ID Nos), in view of Applicant’s filing of a substitute specification (date of 07 July 2026);
The improper Markush grouping rejection, in view of Applicant’s amendments to each of the independent claims;
Several rejections under 35 USC 112(b), in view of Applicant’s clarifying amendments (although some claims remain rejected as indefinite for the reasons given below);
The rejection of claim 8 and claims dependent therefrom under 35 USC 112(d), in view of Applicant’s clarifying amendments (although it is noted that claim 12, dependent from claim 8, is now rejected under 35 USC 112(d) for reasons given below);
The rejections of claims under 35 USC 103 in view of the amendment of claim 1 to require a method comprising “contacting the nucleic acids or the at least one amplicon with a SNP variant polynucleotide probe” meeting the structural and functional requirements now specified in independent claim 1, with the claim further requiring “detecting specific hybridization of the SNP variant polynucleotide probe to the nucleic acids or to the at least one amplicon, thereby detecting a CC8 Clade”;
The rejection of claims 3 and 5 and claims dependent therefrom under 35 USC 101, in view of the amendment of each of claims 3 and 5 to add the limitation “wherein the SNP variant polynucleotide probe comprises a non-naturally occurring fluorescent label or is immobilized on” the surface of a microarray (claim 3)/the surface of a solid support (claim 5); and
The rejections of some (but not all) claims on the grounds of nonstatutory double patenting in view of Applicant’s amendments (specifically, claims 3, 5-6, and 9 now recite/require SEQ ID NO: 3; claims 8, 11, and 28 now recite/require SEQ ID NO: 4; and claims 15-16 recite/require use of SEQ ID NOS 1 and 2 (or recited portions thereof), with new claim 32 also requiring SEQ ID NOS 1-2).
Claims 1, 3, 5, 7, 9, 12, 14-16, 21, 24, 31, and 32 remain/are rejected for the reasons given below, which include new grounds of rejection necessitated by Applicant’s amendment. Any rejections and/or objections not reiterated in this action have been withdrawn. This action is FINAL.
Claims 6, 8, 11, and 28 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Election/Restrictions
Applicant’s election without traverse of “methods and products directed to the single ‘CC8 Clade’ SNP variant, corresponding to variant sequences SEQ ID Nos: 34, 35, and 3; reference sequences SEQ ID NO: 36, 37, and 4; and the primer pair SEQ ID NO: 1 and SEQ ID NO: 2” in the reply filed on 06 February 2026 is again acknowledged.
Claims 25-26 remain 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 06 February 2026.
Claims 1, 3, 5-9, 11-12, 14-16, 21, 24, 28, 31, and 32 are under consideration herein as directed to the elected species identified above.
Claim Rejections - 35 USC § 112(b)/second paragraph
THE FOLLOWING INCLUDES NEW GROUNDS OF REJECTION NECESSITATED BY APPLICANT’S AMENDMENTS:
Claims 3, 5, 9, 12, 14-16, and 32 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 3 and 9 are indefinite over the recitation in claim 3 of the limitation “specifically hybridizes to the CC8-associated A allele represented by SEQ ID NO: 3 and does not hybridize to the corresponding non-CC8-associated G allele represented by SEQ ID NO: 4”, with dependent claim 9 being additionally indefinite over the recitation of analogous language referring to a reference polynucleotide probe and corresponding SEQ ID NOs. While the language “specifically hybridizes to….and does not hybridize to…” is sufficiently clear as recited in Applicant’s method claims (given that those claims involve active steps in which hybridize does/does not occur), the language as used in the present product claims is vague, given that the same probe structures would be expected to hybridize under some conditions and not under others. The specification recites potential use of the term “specifically hybridizes to” in reference to a variety of different types of hybridization conditions (see, e.g., paragraph 44 of the published application), and these claims do not recite, e.g., the type of hybridization conditions under which the required properties of “specifically hybridizing” and “not hybridizing” occur (and do not otherwise make clear how such language affects the boundaries of what is being claimed). Further clarification is therefore needed.
Claims 5 and 32 are indefinite over the recitation in claim 5 of the limitation “specifically hybridizes to the CC8-associated A allele represented by SEQ ID NO: 3 and does not hybridize to the corresponding non-CC8-associated G allele represented by SEQ ID NO: 4”. Again, while the language “specifically hybridizes to….and does not hybridize to…” is sufficiently clear as recited in Applicant’s method claims (given that those claims involve active steps in which hybridize does/does not occur), the language as used in the present product claims is vague, given that the same probe structures would be expected to hybridize under some conditions and not under others. The specification recites potential use of the term “specifically hybridizes to” in reference to a variety of different types of hybridization conditions (see, e.g., paragraph 44 of the published application), and these claims do not recite, e.g., the type of hybridization conditions under which the required properties of “specifically hybridizing” and “not hybridizing” occur (and do not otherwise make clear how such language affects the boundaries of what is being claimed). Further clarification is therefore needed.
Claim 12 is indefinite because it is unclear how/whether the claim further limits amended claim 8, from which it depends. Claim 8 has been amended to recite a probe “comprising SEQ ID NO: 4…” and to delete the recitation of SEQ ID NOS 36-37; however, claim 12 continues to recite SEQ ID NO 36 or SEQ ID NO: 37. It is not clear whether claim 12 requires, e.g., further steps employing SEQ ID NOS 36-37, whether the claim is an attempt to recite an alternative to SEQ ID NO: 4 (such that the claim is no longer properly further limiting of claim 8), etc. Further clarification is required, and it is noted that the claim is also rejected under 35 USC 112(d), below.
Claims 14-16 are indefinite over the recitation in claim 14 (from which claims 15-16 depend) of the language “wherein the optional amplification step (b) is performed and comprises contacting the nucleic acid or the amplicon…”. While it is noted that the reference to “the optional amplification step (b)” has been interpreted as referring to the “optionally amplifying” of b) of claim 1 (despite the lack of prior use of the term “step”), there is insufficient antecedent basis in amended claim 1 for the limitations “the nucleic acid” and “the amplicon”. Accordingly, further clarification is required.
Claim Rejections - 35 USC § 112(d)/fourth paragraph
THE FOLLOWING INCLUDES NEW GROUNDS OF REJECTION NECESSITATED BY APPLICANT’S AMENDMENTS:
Claim 12 is 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. As discussed above, given Applicant’s amendments to claim 8, claim 12 is indefinite and no longer clearly further limiting of 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.
Claim Rejections - 35 USC § 102
THE FOLLOWING INCLUDES NEW GROUNDS OF REJECTION NECESSITATED BY APPLICANT’S AMENDMENTS:
Claim(s) 3, 5 and 9 remain rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by Reeve et al (WO9947706A1 [Sept 1999]; previously cited).
Reeve et al teach compositions, including arrays, comprising all possible “N mer” oligonucleotides or subsets thereof “where N is preferably from 5 to 10, particularly 8 or 9” (see entire reference, particularly pages 4-5; quotation from page 5, lines 10-11). As the instant claims (see text of independent claims 3 and 5) continue to embrace probes including “a reverse complement” (i.e., any reverse complement of any length) of a recited SEQ ID NO, the population of Nmers disclosed by Reeve et al includes oligonucleotides meeting the structural requirements of the claims. With further regard to claim 3 and claim 9, Reeve et al teach embodiments of their invention in which their Nmers are labeled (see, e.g., page 4, lines 13-19), meeting the requirements of the embodiment of a labeled probe, and Reeve et al also teach an embodiment in which each Nmer “is immobilized at a spaced location” on a support/array, meeting the requirements of this embodiment. With further regard to dependent claim 9, the population of Nmers of Reeve et al also include Nmers meeting the structural requirements of the probes of this claim, as the claim again broadly recites “a reverse complement” (i.e., any reverse complement). With further regard to independent claim 5, Reeve et al also teach kits comprising their arrays and/or combinations of all possible N-mers (see, e.g., claim 11 of Reeve et al).
Reeve et al thus anticipate claims 3, 5 and 9.
The Reply of 06 July 2026 traverses the prior rejection of claims under 35 USC 102 on the following grounds. Applicant argues that Reeve does not teach or suggest all features of the amended claims, noting that Reeve teach “sequencing by hybridization libraries rather than specific CC8-diagnostic probes (Reply page 14). Applicant urges that the “SNP variant polynucleotide probe of the instant invention is used for lineage typing of CC8 strains in a detection assay”, and further that a “library of five- to ten-mers cannot disclose, and cannot “comprise”, the claimed nineteen-nucleotide SEQ ID NO: 3”, or probes requiring the other features of the claims (Reply page 15).
These arguments have been thoroughly considered but are not persuasive.
First, it is noted that the claims are not limited to the specific probe of SEQ ID NO: 3, but are rather directed to one or more probes or a microarray comprising such probes (and in the case of claim 5, a kit comprising such products). Thus, the claims embrace any compositions/kits including probes meeting the requirements specified in the claims, which also clearly include “a reverse complement” of the recited sequences; additionally, given the open transitional language “comprising” any other probes and materials may be present in the claimed compositions. Accordingly, the products actually being claimed are much broader in scope that the preferred embodiments referenced in applicant’s arguments (and it is noted that the prior art has been applied with regard to compositions comprising a probe that is “a reverse complement” of the recited sequence(s), not the full-length sequence of SEQ ID NO: 3; i.e., Applicant’s arguments apply to a different embodiment embraced by the claims that is not the subject of the rejection). Additionally, with regard to the issue of the use of the claimed probes in a particular “detection assay”, the claims rejected herein are directed to products, not methods that require the products to be employed in any particular way. Thus, this argument is also non-persuasive. Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
Double Patenting
THE FOLLOWING INCLUDES NEW GROUNDS OF REJECTION NECESSITATED BY APPLICANT’S AMENDMENTS:
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, 7, 12, 14, and 21 remain rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. 11,572,591. Although the claims at issue are not identical, they are not patentably distinct from each other for the following reasons.
Initially, it is reiterated that the species elected for consideration herein includes SEQ ID NOS 34-37 and 1-4; however, the claims under consideration recite additional alternatives that may potentially be eligible for later rejoinder (and it is particularly noted that withdrawn claims 25-26 continue to recite additional SEQ ID NOS). The ‘591 claims are directed to methods employing combinations of SEQ ID NOS that include sequences of the instant elected species. As was previously noted, species including SEQ ID NOS elected herein were rejoined when the application issuing as the ‘591 patent was allowed, such that the instant rejection is not barred. It is also noted that claim 12 continues to be rejected herein to the extent that it does not properly depend from claim 8 (see the above rejections under 35 USC 112(b) and 35 USC 112(d)).
Instant claim 1 and claims dependent therefrom are directed to methods of detecting an S. aureus CC8 strain in which probes/primers corresponding to SEQ ID NOS recited in the claims (and structurally related sequences) are employed, with the instant claims recited the elected species of SEQ ID NOS 34-37 and 1-4, but also additional alternative sequences (including SEQ ID NOS 58-59 and other sequences recited in the ‘591 claims). The ‘591 claims are similarly directed to methods of detecting an S. aureus CC8 strain, reciting the use of combinations of sequences including the instantly elected SEQ ID NOS 34-37. As the methods of the instant claims and those of the ‘591 patent recite analogous steps of obtaining nucleic acids, optionally amplifying the nucleic acids, contacting the nucleic acids or an amplicon with probes as set forth in the claims, and detecting specific hybridization to achieve detection, the instantly rejected claims are either anticipated by the ‘591 claims (in the cases in which SEQ ID NOS 34-37 are recited/used in probe combinations set forth in the ‘591 claims, such as in ‘591 claims 4-5 and 20), or obvious over the ‘591 claims (in view of the recitation in both sets of claims of the use of corresponding probes in analogous method steps). With further regard to instant claim 14, while the ‘591 claims do not recite the use of primers, this claim remains indefinite, such that the claim is obvious over the ‘591 claims at least for the reasons that apply to instant claim 1. Regarding claim 21, while the ‘591 claims do not reference the use of bacterial colonies, as the claims are drawn to method of detection of bacteria (S. aureus), i.e., a type of target that is typically grown/propagated in a manner known to produce bacterial colonies, the testing of such a target sample type would have been prima facie obvious to one of ordinary skill in the art as of Applicant’s effective filing date over the ‘591 claims. Accordingly, none of claims 1, 7, 12, 14, and 21 is patentably distinct from the ‘591 claims.
Claims 24 and 31 remain/are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. 11,572,591 in view of Mothershed et al (Clinica Chimica Acta 363:206-220 [2006]; cited herein).
Regarding claim 24 and 31, which are method claims dependent from independent claim 1, it is reiterated that instant claim 1 is directed to methods of detecting an S. aureus CC8 strain in which probes/primers corresponding to SEQ ID NOS recited in the claims (and structurally related sequences) are employed, with the instant claims recited the elected species of SEQ ID NOS 34-37 and 1-4, but also additional alternative sequences (including SEQ ID NOS 58-59 and other sequences recited in the ‘591 claims). The ‘591 claims are similarly directed to methods of detecting an S. aureus CC8 strain, reciting the use of combinations of sequences including the instantly elected SEQ ID NOS 34-37. As the methods of the instant claims and those of the ‘591 patent recite analogous steps of obtaining nucleic acids, optionally amplifying the nucleic acids, contacting the nucleic acids or an amplicon with probes as set forth in the claims, and detecting specific hybridization to achieve detection, the instantly rejected claims 24 and 31 lack obviousness over the ‘591 claims alone only because claim 24 recites the further activity of “administering an effective amount” of one of the antibiotics recited in the claim, while claim 31 requires a polynucleotide probe that is labeled.
Mothershed et al provide an overview of recent advances (as of the publication date of 2006) “in nucleic acid-based methods to detect bacteria” (see entire reference, particularly the Abstract). Mothershed et al teach that “hundreds of nucleic acid-based bacterial detection tests have been published in the literature” (Abstract) and that several “PCR and hybridization tests are commercially available for specific organism detection” (Abstract); among the products disclosed by Mothershed et al are multiple types of kits for S. aureus detection (see, e.g., Table 1 and page 213, right column). Mothershed et al teach that such assays and products have advantages including facilitating rapid and reliable specific pathogen detection with low detection limits, which may further facilitate “faster and improved patient treatment and potentially shorter hospital stays”, as well as better control of outbreaks and nosocomial infections (page 207, both columns). Among the types of PCR and hybridization based tests taught by Mothershed et al are those in which probes are labeled to facilitate detection (see page 207 right column, page 209 both columns, page 211, right column bridging to page 212 left column).
In view of the teachings of Mothershed 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 the ‘591 claims so as to have prepared and employed labeled probes (as required by new claim 31). An ordinary artisan would have been motivated to have made such modifications for the benefits of facilitating more rapid detection of S. aureus by a practitioner, as well as for the potential additional benefits of improved improving patient treatment and infection/outbreak control, as suggested by Mothershed et al. With further regard to claim 24, as Mothershed et al teach that a benefit of rapid bacterial detection is improved patient treatment (as discussed above) as well as detection of antibiotic resistance and subtyping (see page 207, right column), an ordinary artisan would have been further motivated to have followed testing as suggested by the ‘591 claims in view of Mothershed et with a step of administering a well-known, appropriately selected antibiotic treatment (inclusive of an antibiotic as set forth in claim 24). Accordingly, claims 24 and 31 are not patentably distinct from the ‘591 claims in view of Mothershed et al.
The Reply of 06 July 2026 traverses the prior nonstatutory double patenting rejection on the grounds that “the allowable scope of the pending claims has not yet been determined”, further requesting that the “rejections be held in abeyance until the remaining rejections are resolved” (further noting that Applicant is “prepared to file an appropriate terminal disclaimer” if necessary).
As these arguments are non-persuasive with regard to the merits of the rejections, and as a terminal disclaimer has not been filed, the claims identified above remain rejected for the reasons indicated (although it is noted that, as was also indicated above, the rejections of some claims have been overcome by Applicant’s amendments).
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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
