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 .
The preliminary amendment to the claims submitted on 4/15/2024 is entered. Claims 1-14 are examined on the merits.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 4/15/24 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
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 1-11 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of U.S. Patent No. 10,918,680. Although the claims at issue are not identical, they are not patentably distinct from each other because the patented invention is drawn to:
1. A method of treating of an infection in a mammal in need thereof, comprising administering to the mammal infected with an Escherichia coli (E. coli) strain an antibacterial composition in an amount effective to treat said E. coli infection, wherein said composition comprises at least two distinct bacteriophages having lytic activity to said E. coli strain, said at least two distinct bacteriophages being selected from the bacteriophages having a genome comprising a nucleotide sequence selected from any one of SEQ ID NOs: 1 to 15 or a sequence having at least 99% identity thereto.
2. The method of claim 1, wherein the composition comprises at least three distinct bacteriophages selected from the bacteriophages having a genome comprising a nucleotide sequence selected from any one of SEQ ID NOs: 1 to 15 or a sequence having at least 99% identity thereto.
3. The method of claim 1, wherein the composition comprises a combination of all of the bacteriophages BP539, BP700, BP753, BP814, BP953, BP954, BP970, BP1002, BP1151, BP1155, BP1168, BP1176, BP1197, BP1226 and BP1229 comprising the nucleotide sequence of SEQ ID NOs: 1 to 15, respectively.
4. The method of claim 1, wherein the composition is lytic against antibiotic-resistant E. coli strains.
5. The method of claim 1, wherein the composition is lytic against more than 90% of all bacterial strains of EcoR collection.
6. The method of claim 1, wherein the composition further comprises a pharmaceutically acceptable excipient or carrier.
7. The method of claim 1, wherein the composition is a liquid, semi-liquid, solid or lyophilized formulation.
8. The method of claim 1, wherein the composition comprises between 10.sup.e2 and 10.sup.e12 PFU of bacteriophage.
9. A method for improving the condition of a mammal by modifying the microbial flora, comprising administering to the mammal an effective amount of an antibacterial composition, wherein said composition comprises at least two distinct bacteriophages having lytic activity to an Escherichia coli (E. coli) strain, said at least two distinct bacteriophages being selected from the bacteriophages having a genome comprising a nucleotide sequence selected from any one of SEQ ID NOs: 1 to 15 or a sequence having at least 99% identity thereto and said microbial flora comprises said E. coli strain.
10. A method for decontaminating a material, comprising exposing the material to an amount of an antibacterial composition effective to decontaminate said material, wherein said composition comprises at least two distinct bacteriophages having lytic activity to an Escherichia coli (E. coli) strain, said at least two distinct bacteriophages being selected from the bacteriophages having a genome comprising a nucleotide sequence selected from any one of SEQ ID NOs: 1 to 15 or a sequence having at least 99% identity thereto.
11. An antibacterial composition comprising at least two distinct bacteriophages having lytic activity to an Escherichia coli (E. coli) strain and a pharmaceutically acceptable excipient or carrier, said at least two distinct bacteriophages being selected from the bacteriophages having a genome comprising a nucleotide sequence selected from any one of SEQ ID NOs: 1 to 15 or a sequence having at least 99% identity thereto and said pharmaceutically acceptable excipient or carrier comprising a preservative in an amount effective to preserve the activity of the bacteriophages.
12. The composition of claim 11, comprising at least three distinct bacteriophages selected from the bacteriophages having a genome comprising a nucleotide sequence selected from any one of SEQ ID NOs: 1 to 15 or a sequence having at least 99% identity thereto.
13. The composition of claim 11, comprising a combination of all 15 of said bacteriophages.
14. The composition of claim 11, which is a liquid, semi-liquid, solid or lyophilized formulation.
Therefore, patented invention anticipates the instant invention.
Claims 1-14 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-13 of U.S. Patent No. 11,957,724. Although the claims at issue are not identical, they are not patentably distinct from each other because the patented invention is drawn to:
1. An antibacterial composition comprising at least one bacteriophage having lytic activity to an Escherichia coli (E. coli) strain and a pharmaceutically acceptable excipient or carrier, said at least one bacteriophage being selected from the bacteriophages having a genome comprising a nucleotide sequence selected from any one of SEQ ID NOs: 1 to 15 or a sequence having at least 99% identity thereto, and said pharmaceutically acceptable excipient or carrier comprising a preservative in an amount effective to preserve the activity of the bacteriophage.
2. The composition of claim 1, comprising at least one of the bacteriophages BP539, BP700, BP753, BP814, BP953, BP954, BP970, BP1002, BP1151, BP1155, BP1168, BP1176, BP1197, BP1226 and BP1229 comprising the nucleotide sequence of SEQ ID NOs: 1 to 15, respectively.
3. The composition of claim 1, which is lytic against antibiotic-resistant E. coli strains.
4. The composition of claim 1, which is lytic against more that 90% of all bacterial strains of EcoR collection.
5. The composition of claim 1, which is a liquid, semi-liquid, solid or lyophilized formulation.
6. The composition of claim 1, which comprises between 10.sup.e2 and 10.sup.e12 PFU of bacteriophage.
7. The composition of claim 1, wherein the bacteriophage has lytic activity to a pathogenic E. coli strain, and wherein the bacteriophage (i) is specific for E. coli (ii) is active against antibiotic-resistant E. coli strains, and (iii) has a productive lytic effect (“PLE”) below 15.
8. A method of treatment of an infection in a mammal in need thereof, comprising administering to the mammal infected with an Escherichia coli (E. coli) strain an antibacterial composition in an amount effective to treat the E. coli infection, wherein said composition comprises at least one bacteriophage having lytic activity to the E. coli strain, said at least one bacteriophage being selected from the bacteriophages having a genome comprising a nucleotide sequence selected from any one of SEQ ID NOs: 1 to 15 or a sequence having at least 99% identity thereto.
9. A method for improving the condition of a mammal by modifying the microbial flora thereof, comprising administering to the mammal an effective amount of an antibacterial composition, wherein said composition comprises at least one bacteriophage having lytic activity to an Escherichia coli (E. coli) strain, said at least one bacteriophage being selected from the bacteriophages having a genome comprising a nucleotide sequence selected from any one of SEQ ID NOs: 1 to 15 or a sequence having at least 99% identity thereto, and said microbial flora comprises the E. coli strain.
10. A method for decontaminating a material, comprising exposing the material to an amount of an antibacterial composition effective to decontaminate the material, wherein said composition comprises at least one bacteriophage having lytic activity to an Escherichia coli (E. coli) strain, said at least one bacteriophage being selected from the bacteriophages having a genome comprising a nucleotide sequence selected from any one of SEQ ID NOs: 1 to 15 or a sequence having at least 99% identity thereto, and said material is contaminated with the E. coli strain.
11. A method for preparing an antibacterial composition, comprising: a) producing at least one bacteriophage having lytic activity to an Escherichia coli (E. coli) strain, said at least one bacteriophage being selected from the bacteriophages having a genome comprising a nucleotide sequence selected from any one of SEQ ID NOs: 1 to 15 or a sequence having at least 99% identity thereto; and b) combining at least said bacteriophage with a pharmaceutically acceptable carrier or excipient, said pharmaceutically acceptable excipient or carrier comprising a preservative in an amount effective to preserve the activity of the bacteriophage.
12. A method for predicting or determining the efficacy of a bacteriophage therapy in a subject and treating said subject, wherein the method comprises: a) determining in vitro a lytic activity of a composition comprising at least one bacteriophage to an E. coli strain from a sample of said subject, said at least one bacteriophage having lytic activity to an Escherichia coli (E. coli) strain and being selected from the bacteriophages having a genome comprising a nucleotide sequence selected from any one of SEQ ID NOs: 1 to 15 or a sequence having at least 99% identity thereto; and b) treating the subject with the composition, when in step a) a lytic activity of said composition to at least one E. coli strain from said sample has been determined.
13. A method for selecting a subject or determining whether a subject is susceptible to benefit from a bacteriophage therapy and treating said subject, wherein the method comprises: a) determining a lytic activity of a composition comprising at least one bacteriophage to an E. coli strain from a sample of said subject, said at least one bacteriophage having lytic activity to an Escherichia coli (E. coli) strain and being selected from the bacteriophages having a genome comprising a nucleotide sequence selected from any one of SEQ ID NOs: 1 to 15 or a sequence having at least 99° A identity thereto; and b) treating the subject with the composition, when in step a) a lytic activity of said composition to at least one E. coli strain from said sample has been determined.
Therefore, patented invention anticipates the instant invention.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.-The specification shall contain a written description of the invention, and
of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and
process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-14 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a written description rejection.
The following quotation from section 2163 of the MPEP is a brief discussion of
what is required in a specification to satisfy the 35 U.S.C. 112 written description
requirement for a generic claim covering several distinct inventions:
The written description requirement for a claimed genus may be satisfied through
sufficient description of a representative number of species by actual reduction to practice (see i)(A), above), reduction to drawings (see i)(B), above), or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus (see i)(C), above). See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
A "representative number of species" means that the species which are adequately
described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus.
Thus, when a claim covers a genus of inventions, the specification must provide
written description support for the entire scope of the genus. Support for a genus is
generally found where the applicant has provided a number of examples sufficient so
that one in the art would recognize from the specification the scope of what is being
claimed or through disclosure of a functional characteristic of the claimed genus
coupled with a known or disclosed non-functional characteristic (structure) that
correlates to the function.
Claims 1 and 9-14 recite “having a genome comprising a nucleotide sequence of SEQ ID NO: 11 or 13…”. However, the recitation of “comprising a nucleotide sequence of SEQ ID NO: 11 or 13” includes bacteriophages with fragments of these sequences.
Claim 2 recites, “The composition of claim 1, further comprising at least one, two or three distinct bacteriophages having lytic activity to an E. coli strain, said distinct bacteriophages being selected from the bacteriophages having a genome comprising a nucleotide sequence selected from any one of SEQ ID NOs: 1 to 10, 12, 14-15 or a sequence having at least 90% identity thereto.”
Structurally, the claims are directed to a bacteriophages with genomes having fragments to SEQ ID NO:s 11 or 13 and a genus of differential bacteriophage genomes wherein such genomes may possess up to a 10% difference in the sequence compared to the sequences set forth by SEQ ID NO: 1-10, 12 and 14-15. Note that such difference(s) in sequence encompasses deletion(s), substitution(s) and/or addition(s) which may occur at any position(s) along the sequence of the entire genome.
Functionally, the claims require that the genus of bacteriophage and their genomes have lytic activity to an E. coli strain.
The specification fails to provide any structure to function correlations for any
structures having genomes with fragments of SEQ ID NO:s 11 or 13 and having up to a 10% difference compared to the sequence set forth by SEQ ID NO: 1-10, 12 and 14-15 and the required functional properties of the claims. Thus, it is not clear from the instant specification which sequence differences would be tolerated in maintaining the structural integrity of the bacteriophages so that the claimed functional properties would be maintained. Applicants have reduced to practice the bacteriophages with the genomes of SEQ ID NO:s 1-15 (see Table 1).
See prior art reference by Drulis-Kawa (2012-cited by the IDS) which describes
several steps which are crucial of lytic phages in its specific ability to kill bacteria,
including adsorption to a specific receptor, injection of genetic material, redirection of
host metabolism to phage DNA replication and phage protein synthesis, assembly and
packing of phage particles and bacterial cell lysis and phage progeny release; see p.
700, col. 2.
It has been well known that minor structural differences even among structurally
related compounds or compositions can result in substantially different biological or
pharmacological activities. It is known in the art that the substitution of some amino
acids within the protein sequence may cause the loss of function of the protein. Thus,
the large number of sequences encompassed by the current claims may or may not
lead to lytic activity to an E. coli strain. See the following publications that support this
unpredictability (Baker et al., Protein Structure Predication and Structural Genomics,
Science (2001) Vol. 294, No. 5540, pages 93- 96; Attwood, T. The Babel of
Bioinformatics, Science (2000) Vol. 290, no. 5491, pages 471-473); both references are
cited by the IDS. The skilled artisan cannot envision the detailed structure of a genus of
compounds that are contemplated in the invention. Conception is not achieved until
reduction to practice has occurred, regardless of the complexity or simplicity of the
structures disclosed in the as-filed specification. Thus, in view of the reasons set forth
above, one skilled in the art at the time the invention was made would not have
recognized that applicant was in possession of the claimed invention as presently
claimed.
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.
Claims 1-14 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 1 and 9-14 recite “having a genome comprising a nucleotide sequence of SEQ ID NO: 11 or 13…”. However, the recitation of “comprising a nucleotide sequence of SEQ ID NO: 11 or 13” is unclear since the claim includes fragments of the sequences, but the claim appears to try and limit the interpretation to SEQ ID NO: 11 or 13. It is suggested that applicants amend these claims to recite “having a genome comprising the nucleotide sequence of SEQ ID NO:s 11 or 13.” Claims 2-8 are also rejected because they depend from claim 1, but do not remedy this deficiency.
Claims 2 and 3 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of bacteriophages is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: each bacteriophage possesses a unique genome.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BENJAMIN P BLUMEL whose telephone number is (571)272-4960. The examiner can normally be reached M-F 8-5 EST.
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/BENJAMIN P BLUMEL/Primary Examiner, Art Unit 1671
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