DETAILED ACTION Applicant's response, filed 8/25/2025, has been fully considered. 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. Prosecution Note Please note that since the previous Office action, the application has been transferred to Examiner Leverett. Priority This application filed 12/01/2022 is a National Stage entry of PCT/ JP2021 /014475, with an International Filing Date of 04/05/2021 , and claims foreign priority to 2020-096551, filed 06/03/2020 . T he claims are therefore examined as filed on 06/03/2020 , the effective filing date. In future actions, the effective filing date of one or more claims may change, due to amendments to the claims, or further review of the priority application(s). Election/Restrictions Claim s 5-8 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention , there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 08/25/2025 . Applicant’s election without traverse of claims 1-4 , and the combination of genes in claim 2, in the reply filed on 08/25/2025 is acknowledged. Claim Status Claims 1-8 are pending. Claims 1 and 3 are objected to. Claims 5-8 are withdrawn. Claims 1-4 are directed to the elected invention. Claims 1-4 are examined. Claims 1-4 are rejected. Specification The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see claims 3-4 and 7-8, and specification [012-13, 17-18, 28, 31, and 41]) . Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. Claim Objections Claim 1 is objected to because of the following informalities: Line 6 of claim 1 should read “ [[a]] software for comparing the sequence information instead of “a software…” In claim 3 , the space in the database name should be removed so that the claim reads “ mlstdb.NTM ” instead of “ mlstdb . NTM” Appropriate correction is required. Claim Rejections - 35 USC § 112 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 appl icant regards as his invention. Claims 1-4 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 recites “wherein the multiple gens are selected from the group consisting of 184 genes shown in Table 1.” The claim is indefinite b ecause the tables and/or the content within the tables is not recited in the claim. MPEP § 2173.05(s) explains that where possible, claims are to be complete in themselves. Incorporation by reference to a specific figure or table "'...is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience.' Ex parte Fressola , 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993) (citations omitted) .” It is not clear that claim 1 constitutes "exceptional circumstances." As one option to overcome this rejection, the genes referenced in Table 1 may be recited in the claim. Alternatively, the entire table might be copied into the claim. Claims 2 -4 are also indefinite as they depend from claim 1 and do not resolve the above issue s . Claims 3 and 4 also contain the trademark/trade names “ mlstdb . NTM (https://github.com/ ymatsumoto / mlstverse.Mycobacterium.db ) ” and “ mlstverse (https://github.com/ ymatsumoto / mlstverse ) ”, respectively. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA), second paragraph. See Ex parte Simpson , 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe online databases that may be later updated and, accordingly, the identification/description is indefinite. 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 1-4 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of mental processes, without significantly more. The MPEP at MPEP 2106 sets forth steps for identifying eligible subject matter: (1) Are the claims directed to a process, machine, manufacture or composition of matter? ( 2A )(1) Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea? ( 2A )(2) Do the claims recite additional elements that integrate the judicial exception into a practical application? ( 2B ) If the claims recite a judicial exception and do not integrate the judicial exception, do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception? With regard to step (1) ( Are the claims directed to a process, machine, manufacture or composition of matter? ): Yes. The claims are directed to one of the statutory classes. Claims 1-4 are directed to a machine product (a system comprising a sequencing device, database and software ) . With regard to step ( 2A )(1) ( Do the claims recite a judicially recognized exception?): Yes. Claims 1-4 recite the abstract ideas of processing data using mental steps and mathematical concepts, and observing the processed data. Claims that recite nothing more than abstract ideas, natural phenomena, or laws of nature are not eligible for patent protection (see MPEP 2106.04). Abstract ideas include mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (including procedures for collecting, observing, evaluating, and organizing information (See MPEP 2106.04(a)(2)). In particular, these abstract ideas include but are not limited to: Comparing sequence information of multiple genes with sequence information stored in a database (mental process; the human mind is capable of comparing sequencing data to data stored in a database; claim 1) Selecting from known NTM stored in a database, species or subspecies of NTM having the most similar sequence information to the sequence information of NTM in a specimen (mental process; the human mind is capable of making a selection of data based on a similarity, and comparing data to determine a similarity; claim 1) Therefore, the claims recite elements that constitute one or more judicial exceptions. With regard to step ( 2A )(2) ( Do the claims recite additional elements that integrate the judicial exception into a practical application? ): No. Claim 1 and its dependents recite the additional element s of a system comprising a sequencing device for acquiring information, a database for storing information, and software for performing the abstract idea, and claims 3-4 further define the database and software. While the claims recite the additional element of acquiring data using a sequencer, and storing that data in a database , such steps that only amount to necessary data gathering without any technical details of how the data is obtained or stored that integrate the judicial exception, are insignificant extrasolution activities that do not add a meaningful limitation to the claims (see MPEP 2106.05(g)). As a result, the judicial exception is not integrated into a practical application. In addition , w hile claims recite elements related to the use of computers , they do not provide any specific details by which the system performs or carries out the judicial exception listed in step ( 2A )(1), nor do they provide any details of how specific structures of the system are used to implement these functions. The judicial exception is therefore not integrated into a practical application because the generically recited computer elements do not add a meaningful limitation to the abstract idea, as they amount to simply implementing the abstract idea on a computer (see MPEP 2106.05(f)) . Because the claims do not recite any additional elements that integrate the judicial exception into a practical application, the claims as a whole are directed to an abstract idea. With regard to step ( 2B ) ( Do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception? ): No. The claims recite an abstract idea with additional elements; however, these additional elements are implied general computer elements added to abstract ideas, and non-particular instructions to apply the abstract idea by linking it to a field of use or extrasolution activity (see MPEP 2106.05(f-h)). General computer elements used to perform an abstract idea do not provide an inventive concept, and similarly, non-particular instructions to gather or store data do not provide an inventive concept. Non-particular instructions to gather data using non-specific sequencing methods and store data are also considered well-understood, routine and conventional activities (see MPEP 2106.05(d), which indicates that limitations such as “Receiving or transmitting data over a network” from Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 , “Storing and retrieving information in memory” from Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015) ; OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93 , and “amplifying and sequencing nucleic acid sequences, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014) are recognized as conventional activities) . The claims therefore do not include additional elements that are sufficient to amount to significantly more than the judicial exception. As a result, the claims as a whole do not provide an inventive concept. Claim Rejections - 35 USC § 103 In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis ( i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status. 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. Claim Rejection Claims 1-4 are rejected under 35 U.S.C. 103 as being unpatentable over KIM 201 8 “Identification of nontuberculous mycobacteria using multilocous sequence analysis of 16S rRNA, hsp65 , and rpoB ” (Cited on the IDS filed 12/01/2022) in view of FEDRIZZI 2017 “Genomic characterization of Nontuberculous Mycobacteria.” Claim Interpretation and Scope and Contents of Prior Art Claim 1 recites a system for identifying species or subspecies of non-tuberculous mycobacteria (NTM) in a specimen using MLST (multi-locus sequence typing), comprising: a sequencing device for acquiring sequence information of multiple genes in the genomic sequence of NTM present in the specimen; a database for storing sequence information of multiple genes in known NTM; and a software for comparing the sequence information of the multiple genes acquired by the sequencing device with the sequence information of the multiple genes stored in the database to select, from the known NTM stored in the database, species or subspecies of NTM having most similar sequence information to the sequence information of NTM in the specimen. With respect to these limitations, KIM teaches a system and method for identifying species of NTM from clinical isolates using MLST , in which isolates were sequenced and the sequencing information compared to sequences of NTM for 16S rRNA, hsp65 , and rpoB target genes that were collected from GenBank and constructed into a database; the species were identified based on the most similar sequences (Abstract). Claim 1 also recites the limitation wherein the multiple genes are selected from the group consisting of 184 genes shown in Table 1 (specifically, the genes recited in claim 2 as elected by the Applicant following restriction). Claim 2 recites that these genes include 30S ribosome S1 to S21 ( rpsA to rpsU ), 50S ribosome L1 to L36 ( rplA to rplF , rplI to rplU , rpmA to rpmJ ), 5S ribosome RNA ( rrf ), 16S ribosome RNA ( rrs ), 23S ribosome RNA ( rrl ), rpoB , groEL2 , gyrB , inhA , tlyA , katG , pncA , erm, eis , and embB . With respect to these limitations, KIM teaches that the genes included16S rRNA, hsp65 , and rpoB , but does not include the rest of the genes listed in claim 2. However, FEDRIZZI teaches whole-genome sequencing of 44 NTM species, identification and alignment of 243 fully conserved genes (Abstract, Fig 1), while also determining gene presence/absence and unique gene families for the species (Fig 2). It would there be obvious to one of ordinary skill in the art to compare any number/combination of these known genes that differ between species in improving the accuracy of determining the species of NTM. Claim 3 recites the limitation wherein the database is mlstdb.NTM (https://github.com/ymatsumoto/mlstverse.Mycobacterium.db). KIM does not teach the use of the specific database “ mlstdb.NTM ”, however this database is not patentably distinct from the database described in KIM, which is equivalent in function, as it is a database storing NTM sequence information for comparison to query sequences ( pg 2 col 1). As such, it would be obvious to one of ordinary skill to store NTM sequence data in the database of KIM or other such database. Claim 4 recites the limitation wherein the software is mlstverse (https://github.com/ymatsumoto/mlstverse). KIM also does not teach the use of the specific software mlstverse , however this software is not patentably distinct from the software/analysis used in KIM, which is equivalent in function, as it aligns the sequences and calculates an identity score based on the comparison to determine NTM species ( pg 2 par 4-6). As such, it would be obvious to one of ordinary skill to compare NTM sequence data using the software of KIM or other such software. Resolving Ordinary Skill in the Art and Obviousness Rationale A teaching, suggestion, or motivation in the prior art would have led one of ordinary skill in the art to modify or combine the prior art to arrive at the claimed invention. Specifically, a person of ordinary skill in NTM identification and sequence analysis would have been motivated to combine the teachings of KIM with the teachings of FEDRIZZI , in order to achieve the claimed invention , because comparison of multiple genes across the whole genome allows to determining diversity within a genus such that a species can be accurately placed in a phylogenic analysis ( pg 2) , and result s in more accurate determination of a species when comparing a query NTM to a database of known species in the phylogeny . A person of ordinary skill would reasonably expect success from combining these teachings, as both KIM and FEDRIZZI teach methods of analyzing and comparing sequences across multiple NTM species and across multiple genes . Therefore, the claims at issue would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention as there is both a reason to modify or combine the prior art, and a reasonable expectation of success (see MPEP 2143.02 (I)). Conclusion Any inquiry concerning this communication or earlier communications from the examiner should be directed to FILLIN "Examiner name" \* MERGEFORMAT MARY C LEVERETT whose telephone number is FILLIN "Phone number" \* MERGEFORMAT (571)272-5494 . The examiner can normally be reached FILLIN "Work Schedule?" \* MERGEFORMAT 8:00am - 5:00pm M-Th . 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, FILLIN "SPE Name?" \* MERGEFORMAT Karlheinz R. Skowronek can be reached at FILLIN "SPE Phone?" \* MERGEFORMAT (571) 272-9047 . 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. / M.C.L ./ Examiner, Art Unit 1687 /Karlheinz R. Skowronek/ Supervisory Patent Examiner, Art Unit 1687