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 .
DETAILED ACTION
Claims 1, 5, 7, 9-12, 14, 19-20, 24, 26-28, 41-42, 45, and 52 are pending. Claims 19-20, 24, 26-28, 41-42, and 45 are withdrawn. Claim 4, 6, 8, 13, 15, 17-18, 21-23, 25, 29-40, 43-44, and 46-51 were cancelled previously. Claims 2-3, and 16 are newly cancelled. Claims 1, 5, 7, 9-12, 14, and 52 are under examination on their merits.
Response to Arguments
Applicant's arguments filed 7/20/2026 have been fully considered but they are not persuasive.
Applicant argues against the rejection of claims under 35 U.S.C. 103 on the grounds that Mao does not use β-lactamase for its ability to degrade antibiotics. Applicant argues that engineering microbes to degrade therapeutically administered antibiotics in a subject would be antithetical to Mao's stated purpose of treating intestinal
infections (Arguments, bottom two paragraphs on page 9). Applicant argues the expression of an enzyme that degrades therapeutic antibiotics in a subject is counterproductive to the treatment of a detected infection in Mao (Arguments, page 10, first full paragraph).
In response, these arguments are not persuasive. Mao is in the field of administering antibiotics to treat infections. As such, Mao would also have considered the secondary impacts of administering antibiotics (i.e. antibiotic resistance). Thus, Mao would have considered applying the microorganism comprising the β-lactamase for other purposes related to administering antibiotics. Kokai-Kun teaches a recombinant β-lactamase that degrades β-lactam antibiotics and has been formulated to be administered orally to patients receiving intravenous β-lactam antibiotics including cephalosporins (Abstract). Therefore, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to replace the β-lactamase of Mao with the recombinant beta-lactamase SYN-004 of Kokai-Kun in order to engineer the Lactococcus lactis of Mao to degrade unmetabolized antibiotics excreted into the intestines and thus protect the gut microbiome from disruption by antibiotics.
Applicant argues the secondary consideration of unexpected results: the composition expressing a split β-lactamase enzyme protected mice from infection and loss of diversity in the gut microbiota and maintains colonization resistance against infection in 100% of the treated mice. The treated mice carry a smaller burden of antimicrobial resistance genes (Arguments, paragraph 2 on page 10).
In response, these results are not unexpected in light of the prior art. First, Brevnova teaches reducing horizontal gene transfer of a functional protein by separately encoding domains of the protein on at least two spatially distinct nucleic acid sequences, where each individual domain alone is non-functional, but co-expression of the encoded domains results in their association to form a functional protein (Abstract). Second, Harmoinen (A novel enzymic therapy, targeted recombinant beta-lactamase, in the prevention of antibiotic-induced adverse effects on gut microbiota. Diss. Helsingin yliopisto, 2004) teaches orally treating mice with pills containing freeze-dried recombinant β-lactamase to prevent antibiotic-induced adverse effects on gut microbiota (Title, bottom paragraph on page 35, bottom two paragraphs on page 36). Administering the β-lactamase preserves fecal colonization resistance in mice administered piperacillin (page 34, first paragraph of section 7.1.4 and page 49, second paragraph of section 8.6). Therefore, none of Applicant’s results are unexpected.
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 applicant regards as his invention.
(New Rejection Necessitated by Amendment) Claims 5, 7, and 12 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 5 recites the limitation "first nucleic acid construct" in lines 1-2 and “second nucleic acid construct” in line 4. There is insufficient antecedent basis for this limitation in the claim.
Claims 7 and 12 are rejected for depending from a rejected base claim and not rectifying the source of indefiniteness discussed above.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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.
The following rejections are necessitated by the amendment.
Claims 1, 5, 7, 9, and 14 are rejected under 35 U.S.C. 103 as being unpatentable over Mao et al. (US 2018/0328923 A1; cited on the IDS filed on 6/31/2023) in view of Kokai-Kun et al. (International journal of toxicology 35.3 (2016): 309-316), and Brevnova et al. (US 2017/0204401A1; cited on the IDS filed on 6/31/2023) as evidenced by Pandey et al. (2023 website).
Regarding claim 1, Mao teaches an engineered Lactococcus lactis comprising a β-lactamase ([0093]) to detect the presence of other microorganisms, such as pathogenic V. cholerae using an in vitro colorimetric assay ([0094]). Mao also teaches an engineered Lactococcus lactis that activates expression of a target gene, such as a gene encoding an antimicrobial peptide, by detecting the quorum-sensing molecule CAI-1 produced by Vibrio cholerase ([0081] and [0087]). Mao teaches pharmaceutical compositions comprising any of the engineered microorganisms ([0070]).
Mao does not teach that the Lactococcus lactis is engineered to degrade an antibiotic in the mammalian gut.
Mao does not teach the composition is a pill, tablet, capsule, or sachet.
Kokai-Kun teaches that antibiotics exposure causes dysbiosis and can result in antibiotic-associated diarrhea as well as the emergence of opportunistic pathogens such as Clostridium difficile (page 66, Introduction, paragraph bridging left and right column). Kokai-Kun teaches SYN-004, which is a recombinant β-lactamase that degrades β-lactam antibiotics and has been formulated to be administered orally to patients receiving intravenous β-lactam antibiotics including cephalosporins (Abstract). Mao formulates SYN-004 as a capsule (page 310, left column, Materials and Methods, Test Article, paragraph 1). SYN-004 is intended to degrade unmetabolized antibiotics excreted into the intestines and thus has the potential to protect the gut microbiome from disruption by these antibiotics (Abstract). Kokai-Kun administers SYN-004 to beagle dogs and suggests advancing SYN-004 into human clinical trials (Abstract). Both dogs and humans have mammalian guts.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to replace the beta-lactamase of Mao with the recombinant beta-lactamase SYN-004 of Kokai-Kun in order to engineer the Lactococcus lactis of Mao to degrade unmetabolized antibiotics excreted into the intestines and thus protect the gut microbiome from disruption by antibiotics. It would have been further obvious to formulate the engineered bacteria as a capsule for oral delivery per the teaching of Kokai-Kun. The person of ordinary skill in the art would have had a reasonable expectation of success in replacing Mao’s beta-lactamase with the beta-lactamase of Kokai-Kun and formulating the composition as a capsule.
Mao and Kokai-Kun do not teach that the microorganism is also engineered to reduce the likelihood of horizontal transmission of its engineered antibiotic-degrading capacity by encoding the enzyme in first and second parts on separate, first and second nucleic acid sequences, wherein neither sequence on its own encodes the active antibiotic-degrading enzyme, and wherein both parts of the enzyme are needed to provide antibiotic-degrading activity.
Brevnova teaches reducing horizontal gene transfer of a functional protein by separately encoding domains of the protein on at least two spatially distinct nucleic acid sequences, where each individual domain alone is non-functional, but co-expression of the encoded domains results in their association to form a functional protein (Abstract). Brevnova teaches that the domains are encoded by sequences on two different polynucleotides, such as two plasmids ([0007]). In some embodiments, the protein is an enzyme ([0012]). In other embodiments, the protein confers resistance to antibiotics such as amoxicillin, ampicillin, and penicillin ([0048]), which are all beta-lactams as evidenced by Pandey (middle of page 2, top third of page 3). Brevnova teaches that the different domains of the protein associate via protein binding motifs ([0014] and Fig. 4).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to further modify the engineered bacterium of Mao modified by Kokai-Kun by separately encoding the β-lactamase into two parts, each part adjacently fused to a protein binding motif and on a different plasmid, per the teaching of Brevnova in order to reduce the likelihood of horizontal gene transfer. The person of ordinary skill in the art would have had a reasonable expectation of success in applying the teaching of Brevnova to the engineered bacterium of Mao modified by Kokai-Kun.
Regarding claims 5 and 7, the protein binding motifs fused to each β-lactamase fragment would have specifically bound the two β-lactamase fragments produced by the engineered microorganism of Mao modified by Kokai-Kun (see Brevnova Fig. 4, which shows the protein binding motifs adjacent to the nucleotide sequence encoding each protein domain). Thus, the two protein binding motifs promote the physical interaction of the first and second parts of the enzyme and reconstitution of the beta-lactamase (antibiotic-degrading) enzymatic activity.
Regarding claim 9, SYN-004 is a β-lactamase (Kokai-Kun Abstract).
Regarding claim 14, Mao teaches that Lactococcus lactis is a lactic acid bacterium (Mao [0034]).
Claims 10 and 52 are rejected under 35 U.S.C. 103 as being unpatentable over Harmoinen (A novel enzymic therapy, targeted recombinant beta-lactamase, in the prevention of antibiotic-induced adverse effects on gut microbiota. Diss. Helsingin yliopisto, 2004) in view of Kaushal et al. (International journal of pharmaceutics 312.1-2 (2006): 90-95) and Brevnova et al. (US 2017/0204401A1; cited on the IDS filed on 6/31/2023) as evidenced by Pandey et al. (2023 website).
Harmoinen teaches orally treating mice with freeze-dried recombinant β-lactamase to prevent antibiotic-induced adverse effects on gut microbiota (Title, bottom paragraph on page 35, and bottom two paragraphs on page 36). The recombinant β-lactamase is the PenP protein (a penicillinase) of Bacillus licheniformis 749/C (second to last paragraph on page 36). Harmoinen teaches formulating the purified oral β-lactamase as a pellet (“pill”): see 7.2.2 Oral drug substances bottom paragraph on page 36).
Harmoinen does not teach a microorganism engineered to express the recombinant β-lactamase.
Kaushal teaches L. lactis comprising β-lactamase from Bacillus cereus (page 91, left column, 2.1 Material, paragraph 1). Kaushal teaches that L. lactis increases the transportation of β-lactamase through Caco-2 monolayer and almost doubles the transportation rate as compared to the solution form (page 91, left column, paragraph 2).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to express the β-lactamase of Harmoinen in L. lactis for more efficient delivery of the β-lactamase. The person of ordinary skill in the art would have been motivated by the teaching of Kaushal, who suggests that L. lactis is an efficient vehicle for the delivery of protein therapeutics. It would have been further obvious to formulate the recombinant L. lactis in a pill for efficient oral delivery.
Harmoinen and Kaushal do not teach that the microorganism is also engineered to reduce the likelihood of horizontal transmission of its engineered antibiotic-degrading capacity by encoding the enzyme in first and second parts on separate, first and second nucleic acid sequences, wherein neither sequence on its own encodes active antibiotic-degrading enzyme, and wherein both parts of the enzyme are needed to provide antibiotic-degrading activity.
Brevnova teaches reducing horizontal gene transfer of a functional protein by separately encoding domains of the protein on at least two spatially distinct nucleic acid sequences, where each individual domain alone is non-functional, but co-expression of the encoded domains results in their association to form a functional protein (Abstract). Brevnova teaches that the domains are encoded by sequences on two different polynucleotides, such as two plasmids ([0007]). In some embodiments, the protein is an enzyme ([0012]). In other embodiments, the protein confers resistance to antibiotics such as amoxicillin, ampicillin, and penicillin ([0048]), which are all beta-lactams as evidenced by Pandey (middle of page 2, top third of page 3). Brevnova teaches that the different domains of the protein associate via protein binding motifs ([0014] and Fig. 4).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to further modify the engineered bacterium of Harmoinen modified by Kaushal by separately encoding the β-lactamase into two parts, each part adjacently fused to a protein binding motif and on a different plasmid, per the teaching of Brevnova in order to reduce the likelihood of horizontal gene transfer. The person of ordinary skill in the art would have had a reasonable expectation of success in applying the teaching of Brevnova to the engineered bacterium of Harmoinen modified by Kaushal.
Harmoinen’s orally delivered β-lactamase is the PenP protein of Bacillus licheniformis 749/C (Harmoinen second to last paragraph on page 36) rather than a TEM-1 β-lactamase.
However, Harmoinen also teaches that TEM-1 type β-lactamases is the most commonly isolated β-lactamase from human clinical isolates and produced by both Gram-positive and Gram-negative bacteria (bottom paragraph on page 24).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to replace the PenP protein of Bacillus licheniformis 749/C with a TEM-1 β-lactamase as they are art-recognized equivalents for the same purpose: they are both β-lactamases. See MPEP 2144.06(II): substituting equivalents known for the same purpose. The person of ordinary skill in the art would have had a reasonable expectation of success in the substitution.
Regarding claim 52, Harmoinen teaches freeze-drying the purified β-lactamase (second to last paragraph on page 36),
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to lyophilize the L. lactis of Harmoinen modified by Kaushal and Brevnova. The person of ordinary skill in the art would have been motivated by the teaching of Harmoinen, who suggests freeze-drying the β -lactamase. The person of ordinary skill in the art would have had a reasonable expectation of success.
Allowable Subject Matter
Claim 11 is 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 following is a statement of reasons for the indication of allowable subject matter: the prior art does not teach a microorganism engineered to express TEM β lactamase encoded in first and second parts, on separate, first and second nucleic acid sequences, wherein the first nucleic acid sequence encodes β lactamase fragment (BLF) 1, comprising SEQ ID NO: 1 or 3, and the second nucleic acid sequence encodes BLF 2, comprising SEQ ID NO: 5 or 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 CANDICE LEE SWIFT whose telephone number is (571)272-0177. The examiner can normally be reached M-F 8:00 AM-4:30 PM (Eastern).
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, Louise Humphrey can be reached at (571)272-5543. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/CANDICE LEE SWIFT/Examiner, Art Unit 1657
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