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 Amendment filed 29 August 2025. Claims 6-7 have been amended and claims 1-5 have been canceled. Claims 8-13 remain withdrawn, and claims 6-7 remain pending and under consideration herein. It is noted that all prior rejections of claims 1-5 are moot in view of the cancelation of those claims. Applicant’s amendments and arguments have been thoroughly reviewed, and have overcome the following objections/rejections set forth in the prior Office action:
The objection to the specification, in view of Applicant’s filing of a substitute specification (in which active hyperlinks were removed);
The objection to the Drawings (in view of Applicant’s filing of a replacement Figure); and
Some rejections under 35 USC 112(b), in view of Applicant’s amendments (although it is noted that the claims remain rejected under 35 USC 112(b) for the reasons given below).
Claims 6-7 remain rejected for the reasons given below, which include new grounds of rejection necessitated by Applicant’s amendments. Any rejections and/or objections not reiterated in this action have been withdrawn. This action is FINAL.
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 Group I and of the species of “each SNP combination” in the reply filed on April 21, 2025 is again acknowledged.
Claims 8-13 remain withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on April 21, 2025.
Claim Interpretation
Regarding claims 6-7, the claim 6 limitation “administering metronidazole to the subject when the category of Clostridium difficile clade2 strain comprises said Category 1, administering moxiflaxacin and/or metronidazole to the subject when the category of Clostridium difficile strain comprises said Category 2, or administering vancomycin to the subject when the category of Clostridium difficile strain comprises said Category 3” includes three possible alternative conditional/contingent steps. While it is noted that the references in the second and third alternatives are interpreted as referring to the previously recited C. difficile clade2 strains (despite the fact that only the first alternative actually recites clade2), as claim 6 as written does not in fact require an outcome in which one of the recited three “Categories” is necessarily found to be present (see also the indefiniteness rejections below) – and given the recitation of the language “administering….when” as noted above – the claims are interpreted as requiring one of the recited “administering” steps only “when” one of Categories 1/2/3 is unambiguously identified (such that the broadest reasonable interpretation of the claim does not in fact require any of the three recited “administering” steps). As previously noted (in the prior Office action), the broadest reasonable interpretation of a method including contingent/conditional limitations “requires only those steps that must be performed and does not include steps that are not required to be performed because the condition(s) precedent are not met” (see MPEP 2111.04(II)).
Claim Rejections - 35 USC § 112(b)/second paragraph
THE FOLLOWING INCLUDES NEW GROUNDS OF REJECTION NECESSITATED BY APPLICANT’S AMENDMENTS:
Claims 6-7 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 6-7 are indefinite over the recitation in independent claim 6 of the limitation “Group 3:….., wherein the genomic base positions are based on Clostridium difficile CD196 (NC_013315.1) as a reference genome”, for several reasons. First, there is insufficient antecedent basis for the limitation “the genomic base positions”, as while the claim previously refers to “at least one genomic base position from at least two groups..”, and lists a variety of specific positions corresponding to multiple different Groups, the term “genomic base positions” is not previously employed. Given the placement of the “wherein” clause within the recitation of “Group 3”, the reference to “the genomic base positions” may reasonably be interpreted as an attempt to refer to and further limit only the previously listed positions for “Group 3”; alternatively, the language may be interpreted as an attempt to further limit the “at least one genomic base position from at least two groups” (however the present claim language does not make sufficiently clear what “genomic positions” are being referenced and further limited). Additionally, with regard to the recitation “CD196 (NC_013315.1)”, it is not clear how the parenthetic material further limits what is claimed, i.e., whether this a requirement of the claimed invention or not. Furthermore, as the information/data associated with such database accession numbers is subject to change over time – i.e., is fluid rather than fixed and definite - to the extent that the recitation of “NC_013315.1” limits the claim, the manner in which it does so is not clear. Accordingly, further clarification is required with regard to what further limitations are imparted by the language of this “wherein” clause.
Claims 6-7 are indefinite over the recitation in independent claim 6 of the limitation “identifying whether the Clostridium difficile clade2 strain Clostridium difficile clade2 strain from the subject belongs to Category 1, Category 2 or Category 3 according to the base information”, because while the claim subsequently recites what various individual bases at different positions indicate, it is not clear from the claim language how a specific category is to actually be assigned to a subject, particularly with regard to instances when results are in conflict with regard to what “Category” appears to be present in a sample. While some possible outcomes embraced by the claims would be expected to have a clear outcome – specifically, in instances when all “base information” consistently corresponds to a single “Category” – the language of claim 6 does not indicate what would be considered sufficient for “identifying” a strain exhibiting characteristics of multiple categories (as would reasonably be expected when testing samples from an infected subject, particularly a subject being treated with antibiotics; it is also reiterated that clarity is lacking regarding the genomic base position numbering in the claims, such that inconsistent results with regard to “Category” typing would be expected in the context of the present claims). Additionally, the language “identifying whether the…strain…belongs to” one of the recited Categories appears to potentially encompass outcomes in which no such identification is necessarily made (although this is not clear from the language of the claims). Further clarification is therefore required.
Claim 7 is indefinite over the recitation of the limitation “the site” (see line 2), as there is insufficient antecedent basis for this term in the claims (as it is noted that claim 6 has been amended such that it not longer refers to, e.g., “a site of at least one SNP marker”). Clarification is therefore required with regard to how claim 7 further limits claim 6 as amended.
Claim Rejections - 35 USC § 102
THE FOLLOWING INCLUDES NEW GROUNDS OF REJECTION NECESSITATED BY APPLICANT’S AMENDMENTS:
Claim(s) 6-7 remain rejected under 35 U.S.C. 102(a)(1) as being anticipated by Bletz et al (Journal of Clinical Microbiology 56(6):e01987-17 [online 04 April 2018]; previously cited), with regard to dependent claim 7, as evidenced by Simner et al (Journal of Clinical Microbiology 56(9):e00472-18 [online 05 July 2018]; previously cited).
It is reiterated that the specification teaches that the genomic base position(s) of the claims are identified by reference to the (known and published) C. difficile strain CD196 reference genome (see, e.g., page 13 of the specification, including Table 1 and paragraph 54).
Bletz et al teach genome-wide typing of C. difficile via methods including whole genome sequencing and analysis of resulting sequences (see entire reference). It is noted that Bletz et al also teach that C. difficile was “recently renamed Clostridiodes difficile” (establishing that there are two different known prior art names for this bacterium), and further disclose use of the same NCBI accession number (NC_013315) for the genome of the “well characterized reference strain” C. difficile CD196 that is taught by Applicant (see, e.g., page 2 and Table 1 of Bletz et al, noting the disclosure of Bletz et al that CD196 is a clade 2 bacterium), and of the existence and use of the C. difficile cgMLST nomenclature database (www.cgmlst.org) (see page 8 of Bletz et al).
In addition to teaching the analysis of CD196 and other known C. difficile genome sequences as references (see again page 2 including Table 1), Bletz et al teach the analysis of numerous additional C. difficile genomes, including obtaining sequences electronically as well as via whole genome sequencing (see entire reference, particularly the Materials and Methods at pages 2-4, including Table 2, noting the analysis of isolates of all 5 clades disclosed in Table 2). The methods of Bletz et al include all required limitations of Applicant’s claims 6-7, and therefore anticipate the claims. Bletz et al disclose obtaining isolates/strains to be identified and characterized via their methodology, inclusive of whole genome sequencing of some strains/isolates, and categorizing the isolates/strains using the determined sequences (and it is noted that whole genome sequencing inherently achieves obtaining “base information” with respect to each “genomic base position” of Applicant’s claims, corresponding to the elected species); it is particularly noted that Bletz et al disclose obtaining several samples acquired from subjects infected with a C. difficile strain, inclusive of clade2 strains (see again pages 2-4 including Table 2). As the instant claims do not clearly require any particular outcome with regard to the recited “identifying”, and include “administering” steps that are also conditional/contingent and not clearly required based on the present claim language (as discussed above), the claims require nothing beyond what is disclosed by Bletz et al. Regarding dependent claim 7, while Bletz et al do not recite the use of amplifying and sequencing, the teachings of Simner et al establish that Bletz et al’s disclosure of whole genome sequence via the combination of Nextera XT chemistry and Illumina MiSeq (as taught by Bletz et al at page 4) inherently comprises such activities (see in particular page 3 of Simner et al). Thus, Bletz et al also anticipate claim 7.
The Reply of 29 August 2025 traverses the prior rejection of claims under 35 USC 102 on the grounds that the amended claims require determining classification of clade2 C. difficile and use of the “classification result to guide therapeutic selection in order to avoid severe drug resistance” (Reply page 9). While this argument has been thoroughly considered it is not persuasive given what is actually required by the language of the amended claims (as discussed above). It is particularly noted that the claims as presently written do not clearly require/recite classification of a subject and an associated/resultant treating/administering of the subject (as discussed above), and that the amended claims remain rejected on the grounds stated above.
THE FOLLOWING INCLUDES NEW GROUNDS OF REJECTION NECESSITATED BY APPLICANT’S AMENDMENTS:
Claims 6-7 remain rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Independent claim 6 as amended recites “identifying whether the Clostridium difficile clade2 strain Clostridium difficile clade2 strain from the subject belongs to Category 1, Category 2 or Category 3 according to the base information”; as such mental categorization of information may be performed entirely in the human mind, the claim is directed to an abstract idea (i.e., a judicial exception [JE]).
The JE of the claims is not integrated into a practical application because the only required active steps (the “obtaining” of a sample and the “obtaining” of base information therefrom) are data gathering steps that do not add a meaningful limitation to the method as they are insignificant extra-solution activity; there is no required application/implementation of the JE of the claims. While it is noted that independent claim 6 recites a method of “treating a subject” and includes the recitation of possible “administering”/treating activities, the claim language is indefinite and these steps as written are conditional/contingent rather than required (as discussed above). When the broadest reasonable interpretation of a claim encompasses both statutory and non-statutory embodiments, then the claim is directed to subject matter not eligible for patent protection (see MPEP 2106.03(II)). The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the active steps of obtaining a strain (or sample comprising a strain) to be identified, and obtaining “base information” in that strain, whether considered alone or in combination, clearly correspond to well-known, routine, and conventional activity as of Applicant’s effective filing date; see, e.g., Bletz et al (cited/discussed above), as well as Suzuki et al (Gut Pathog 9:70 [2017]; cited herein) and/or Zhou et al (Journal of Clinical Microbiology 52(12):4260 [Dec 2014]; cited in IDS). Dependent claim 7 sets forth broadly recited, and well-understood, routine, and conventional data gathering steps, as amplification with primers “adapted to” amplify a target region, and sequencing, were clearly well-known steps to obtain sequencing information at the time of Applicant’s invention; further, such activities are directed to the gathering of data/information (i.e., insignificant extrasolution activity), rather than an application of a JE. Thus, neither claim 6 nor dependent claim 7 is directed to patent eligible subject matter.
The Reply of 29 August 2025 traverses the prior rejection of claims under 35 USC 101 on the grounds that claims 6-7 “include a step of ‘administering’ a therapeutic to a subject under any cases, and are thus directed to a patent eligible subject matter” (Reply page 9). This argument has been thoroughly considered but is not persuasive because the claims cannot reasonably be interpreted as requiring that an “administering’ occur “under any cases” based on the present claim language (as is discussed above in the rejections applied to amended claim 6-7).
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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/DIANA B JOHANNSEN/Primary Examiner, Art Unit 1682
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