DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 19 April 2026 (directing entry of the Amendment previously filed after final on 27 March 2026) has been entered.
Claims 15, 28, and 36 have been amended, and claims 15-19, 22, 24-25, 28, and 36-37 remain under consideration herein. Applicant’s amendments and arguments have been thoroughly considered, and have overcome the following objections/ rejections set forth in the prior Office action:
Several rejections under 35 USC 112(b) (indefiniteness), in view of Applicant’s clarifying amendments (although claim 15 and claims dependent therefrom remain indefinite for the reasons given below); and
The rejection of claim 15 and claims dependent therefrom under 35 USC 103, in view of the amendment of claim 15 to require that “said bacteriophage comprise at least one of” the group now recited in the claim (although it is noted that this amendment also necessitated new grounds of rejection as set forth below).
Claims 15-19, 22, 24-25, 28, and 36-37 remain rejected for the reasons given below. Any rejections and/or objections not reiterated in this action have been withdrawn. This action is non-final.
Claim Rejections - 35 USC § 112(b)/second paragraph
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 15-19, 22, 24-25, and 28 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 15-19, 22, 24-25, and 28 are indefinite over the recitation in independent claim 15 of the limitation “wherein said bacteriophage comprise at least one of: PΦ9 (VM75688), PΦ13 (350CIA), PΦ18 (258909), PΦ15 (278485-2), SΦ2 (E1392-75), SΦ9 (E7476), SΦ14 (VM75688), EΦ2 (278485-2), EΦ4 (VM75688), EΦ9 (e7476)”, because it is unclear what bacteriophage are being referenced by this language, and therefore further unclear what type of administering would/would not be embraced by the claims. First, the inclusion of parenthetic material is confusing and renders the boundaries of the claims unclear, as it is not clear how this language (which appears to refer to particular bacteria) further limits what is claimed, and whether these recitations are or are not even part of what is being claimed (e.g., are these descriptive, or a requirement that limits what is administered, etc.?). Second, the identities of the bacteriophage (viruses) being referenced are not clear, as these are not described in the specification (see the rejection under 35 USC 112(a) below), and as the prior art does not provide identifying information that would allow one of ordinary skill in the art to ascertain what particular phages/viruses are encompassed by the terminology employed. It is noted that searches of each recited bacteriophage using standard tools available to a practitioner (such as Google Scholar, STNext, and the ictvonline.org virus taxonomy database) did not provide adequate descriptive/identifying information regarding the bacteriophage names recited in the claims. Thus, neither the specification nor the prior art may be relied upon for guidance regarding the boundaries of what is being claimed, and the nature of what is being claimed is unclear. Accordingly, further clarification is required.
Claim Rejections - 35 USC § 112(a)/first paragraph
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 15-19, 22, 24-25, and 28 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 applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a written description rejection.
With regard to a complying written description of an invention, MPEP 2163.02 states:
Whenever the issue arises, the fundamental factual inquiry is whether the specification conveys with reasonable clarity to those skilled in the art that, as of the filing date sought, inventor was in possession of the invention as now claimed. See, e.g., Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Fed. Cir. 1991). An applicant shows that the inventor was in possession of the claimed invention by describing the claimed invention with all of its limitations using such descriptive means as words, structures, figures, diagrams, and formulas that fully set forth the claimed invention. Lockwood v. Am. Airlines, Inc., 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (Fed. Cir. 1997). Possession may be shown in a variety of ways including description of an actual reduction to practice, or by showing that the invention was "ready for patenting" such as by the disclosure of drawings or structural chemical formulas that show that the invention was complete, or by describing distinguishing identifying characteristics sufficient to show that the inventor was in possession of the claimed invention. See, e.g., Pfaff v. Wells Elecs., Inc., 525 U.S. 55, 68, 119 S.Ct. 304, 312, 48 USPQ2d 1641, 1647 (1998); Regents of the Univ. of Cal. v. Eli Lilly, 119 F.3d 1559, 1568, 43 USPQ2d 1398, 1406 (Fed. Cir. 1997); Amgen, Inc. v. Chugai Pharm., 927 F.2d 1200, 1206, 18 USPQ2d 1016, 1021 (Fed. Cir. 1991) (one must define a compound by “whatever characteristics sufficiently distinguish it”).
The limitation at issue is the new claim language (see independent claim 15, from which claims 16-19, 22, 24-25, and 28 depend) “wherein said bacteriophage comprise at least one of: PΦ9 (VM75688), PΦ13 (350CIA), PΦ18 (258909), PΦ15 (278485-2), SΦ2 (E1392-75), SΦ9 (E7476), SΦ14 (VM75688), EΦ2 (278485-2), EΦ4 (VM75688), EΦ9 (e7476)”. While the claim recites administering “an effective amount of bacteriophage that lyse E. coli expressing ecpR and/or kpsM, wherein said bacteriophage comprise” – such that the claims are not limited to administering only the specifically recited phage/viruses – given that the claims now require inclusion of one or more of the specifically recited phage/viruses noted above, a description of those phage adequate to identify them is required. Applicant’s disclosure does not include a reduction to practice of a method employing an “administering” as set forth in claim 15, and the specification includes only a single reference to the group of specific bacteriophage now recited in the claims, which employs essentially the same language of the claim (see page 12 of the substitute specification filed 13 Oct 2025). Thus, the specification provides only a single term for each phage/virus (it is noted that the parenthetic material in the claim and on page 12, while unclear/confusing, appears to refer to bacteria as opposed to phage/viruses); no additional descriptive information, synonyms, sequence information, drawings/figures, etc., that would aid in identifying the corresponding bacteriophage(s) is provided. As noted in the rejection under 35 USC 112(b) above, a search of the provided terminology using standard tools available to a practitioner (such as Google Scholar, STNext, and the ictvonline.org virus taxonomy database, using both “Φ” and “Phi” in queries) did not provide adequate descriptive/identifying information regarding the bacteriophage names recited in the claims. It is also noted that the prior art as exemplified by Krupovic et al (Arch Virol 161:1095 [2016]; cited herein) teaches that the use of “Φ”/“Phi” (as well as other Greek letters) for identification of bacterial viruses was being discouraged in the art by approximately 2016 (due to confusion, inconsistent use, lack of informational value, etc., as discussed by Krupovic et al), such that the terminology employed and relied upon by Applicant was known to be inadequately descriptive as of Applicant’s effective filing date. Accordingly, a sufficient written description to establish possession of the invention now set forth in amended independent claim 15 is lacking.
Claims 15-19, 22, 24-25, and 28 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
There are many factors to be considered when determining compliance with the enablement requirement of 35 USC 112(a), including, but not limited to: (A) the breadth of the claims; (B) the nature of the invention; (C) the state of the prior art; (D) the level of one of ordinary skill; (E) the level of predictability in the art; (F) the amount of direction provided by the inventor; (G) the existence of working examples; and (H) the quantity of experimentation needed to make or use the invention based on the content of the disclosure. In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988). All evidence related to each of these factors has been considered, and the conclusion that enablement is lacking, as set forth below, is based on the evidence as a whole. (MPEP 2164.01(a)).
Independent claim 15 (from which claims 16-19, 22, 24-25, and 28 depend) has been amended to recite an “administering” of bacteriophage “wherein said bacteriophage comprise at least one of: PΦ9 (VM75688), PΦ13 (350CIA), PΦ18 (258909), PΦ15 (278485-2), SΦ2 (E1392-75), SΦ9 (E7476), SΦ14 (VM75688), EΦ2 (278485-2), EΦ4 (VM75688), EΦ9 (e7476)”. While the claim recites administering “an effective amount of bacteriophage that lyse E. coli expressing ecpR and/or kpsM, wherein said bacteriophage comprise” – such that the claims are not limited to administering only the specifically recited phage/viruses – given that the claims now require inclusion of one or more of the specifically recited phage/viruses noted above, an ordinary artisan must be able to identify the recited phage/viruses in order to practice the method as claimed. As discussed above in the rejection of claims for lack of written description, an adequate description of the recited phage sufficient to identify them has not been provided. Again, Applicant’s disclosure does not include a reduction to practice of a method employing an “administering” as set forth in claim 15, and the specification includes only a single reference to the group of specific bacteriophage now recited in the claims, which employs essentially the same language of the claim (see page 12 of the substitute specification filed 13 Oct 2025). Thus, the specification provides only a single term for each phage/virus (it is noted that the parenthetic material in the claim and on page 12, while unclear/confusing, appears to refer to bacteria as opposed to phage/viruses); no additional descriptive information, synonyms, sequence information, drawings/figures, etc., that would aid in identifying the corresponding bacteriophage(s) is provided. Lacking sufficient guidance in the disclosure, one of skill in the art may look to the prior art for further enabling guidance regarding a claimed invention. However, as noted in the rejection under 35 USC 112(b) above, a search of the provided terminology using standard tools available to a practitioner (such as Google Scholar, STNext, and the ictvonline.org virus taxonomy database, using both “Φ” and “Phi” in queries) did not provide adequate descriptive/identifying information regarding the bacteriophage names recited in the claims. Further, it is reiterated that the prior art as exemplified by Krupovic et al (Arch Virol 161:1095 [2016]; cited herein) teaches that the use of “Φ”/“Phi” (as well as other Greek letters) for identification of bacterial viruses was being discouraged in the art by approximately 2016 (due to confusion, inconsistent use, lack of informational value, etc., as discussed by Krupovic et al), such that the terminology employed and relied upon by Applicant was known to be inadequately descriptive as of Applicant’s effective filing date. Accordingly, neither the specification nor the prior art provide sufficient enabling guidance regarding the specific types of bacteriophage that are required to use/practice Applicant’s invention as now claimed. Further, given the nature of what is lacking – identifying information regarding the types of phage that are sufficient to meet the requirements of the claims – no amount of experimentation would be sufficient to enable an ordinary artisan to make and use the claimed invention. Accordingly, enablement is lacking with regard to claim 15 and claims dependent therefrom (all of which require an “administering” meeting the requirements of independent claim 15).
Claim Rejections - 35 USC § 103
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.
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.
Claim(s) 36-37 remain rejected under 35 U.S.C. 103 as being unpatentable over Bert et al (Journal of Clinical Microbiology 48(8):2709-2714 [Aug 2010]; cited in IDS).
Bert et al teach that “infections caused by Escherichia coli organisms that translocate from the gut are a frequent and severe complication” experienced by patients with cirrhosis (see entire reference, particularly the Abstract) Bert et al disclose characterizing E. coli isolates obtained from blood and/or ascites of patients with cirrhosis via phylotyping and virulence genotyping, both of which detection methods are disclosed as employing PCR amplification of nucleic acid targets (see entire reference, particularly the Materials and Methods at page 2710, left column). Among the targets of detection by PCR amplification taught by Bert et al is the kpsM gene; see, e.g., page 2710, right column; Table 1 (first gene listed under “Miscellaneous”); page 2711, right column; Table 2 (each group B2 “Virulence gene profile”, with virulence genes taught as being “listed when they were present in ≥ 65% of isolates within the indicated group”). Further, Bert et al teach that kpsM was among the “most frequent VF genes” detected in their tested isolates (page 2710, right column; see also Tables 1 and 2), and was “common to all the group B2-associated clonal groups” (page 2711, right column; and Table 2); Bert et al thus also provide a determination/diagnosis of the clonal group and VF profiles of E. coli present in specific patients.
With regarding to the limitation in claim 36 “in a fecal sample of a human”, it is noted that Bert et al disclose the use in their methods of blood and ascitic fluid, not fecal samples. However, Bert et al state that “further studies are needed to compare the prevalence of these clonal groups in patients with invasive diseases and that in the fecal flora of cirrhotic patients” (page 2713, left column), providing an explicit suggestion and motivation to detect the genes of Bert et al (which include kpsM) in fecal samples of the same types of patient (or in fact the same patients). In view of Bert et al’s own teachings, it thus would have been prima facie obvious before the effective filing date of the claimed invention to have modified the methods of Bert et al so as to have included detecting kpsM in fecal samples; an ordinary artisan would have been so motivated because Bert et al state that such “further studies are needed”. With regard to the claim limitation “if E. coli expressing ecpR and/or kpsM are detected, or an increased amount of E. coli expressing ecpR and/or kpsM relative to a control sample is detected, administering an anti-hepatitis therapy or other chronic liver disease therapy to said human”, this action is clearly conditional/conditional in nature, given the statement that administering is performed “if” the recited condition(s) is/are present. Thus, Bert et al need only suggest the “detecting the present or amount” to meet the requirements of the claims. “The broadest reasonable interpretation of a method (or process) claim having contingent 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” (MPEP 2111.04(II)).
Additionally, to the extent that claims 36-37 may require the recited “administering” (to achieve the intended use “to treat a human….”), Bert et al also further teach that “Understanding the role of bacterial characteristics in the pathogenesis of BT has obvious implications for preventative measures in patients with cirrhosis, particularly those awaiting liver transplantation” (page 2713, right column), making clear that at least some cirrhotic patients (i.e., patients of the type subjected to their testing) are awaiting liver transplantation. Accordingly, it also 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 performed liver transplantation on any cirrhotic patient in which such transplantation was indicated, including those patients taught by Bert et al (either exhibiting or not exhibiting an “increased amount” of kpsM), simply for the benefit of appropriately treating such a patient. With further regard to claim 37, while the claim recites a further limitation of an activity not actually required by the present language of the claims, such a “treating” via liver transplantation (as taught by Bert et al) also meets the requirements of the claim.
The Reply traverses the prior rejection of claims 35 USC 103 on the grounds that Bert does not teach or suggest what is claimed and does not provide any motivation “to arrive at the method of treatment” recited in the claims (Reply page 6). Applicant further argues that the population studied by Bert including patients with viral hepatitis, a type of patient excluded from Applicant’s studies (Reply pages 6-7), and that the disclosure of Bert would not have led a person of ordinary skill in the art to have selected kpsM (Reply page 7).
These arguments have been thoroughly considered but are not persuasive. First, it is reiterated that the present claims do not require the recited treating/administering, as the claims plainly and clearly state that administering occurs “if” a certain type of result for kpsM testing is present. The teachings of Bert et al are clearly sufficient to suggest the “detecting” of the claims (i.e., that which the claims actually require), and while Applicant’s arguments focus on differences in patient populations (particularly with regard to alcoholic vs viral hepatitis, etc.), the claims under consideration simply recite “a human having hepatitis or other chronic liver disease”.
Thus, this feature upon which applicant’s arguments rely is not recited in the rejected claim(s). 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). Further, it is reiterated that Bert et al state that “Understanding the role of bacterial characteristics in the pathogenesis of BT has obvious implications for preventative measures in patients with cirrhosis, particularly those awaiting liver transplantation” (page 2713, right column), providing a suggestion and motivation to perform testing of the type they disclose (which includes testing of kpsM) on such patients (and which patients are already “awaiting liver transplantation”, such that this further step is also rendered obvious by Bert et al). Accordingly, Applicant’s arguments are non-persuasive given what is actually required by the claims presently under consideration.
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 36-37 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Independent claim 36 (from which claim 37 depends) recites “detecting the presence or amount of E. coli expressing ecpR and/or kpsM in a fecal sample of a human having hepatitis or other chronic liver disease”. The specification teaches that such presence or amount of E. coli expressing ecpR and/or kpsM “may be detected by any means, direct or indirect” (see paragraph 37); thus, the claim language encompasses not only direct detection of presence/amount of the bacteria in the sample, but “indirect” direction, which encompasses activities including, e.g., forming a conclusion regard presence/amount of bacteria based on other test results, i.e., activities that may be accomplished entirely in the human mind (a type of abstract idea).
This judicial exception is not integrated into a practical application because while the claims recite performing/administering a treatment “if” the recited “detecting” has a particular outcome, this outcome is clearly not required by the present claim language.
“The broadest reasonable interpretation of a method (or process) claim having contingent 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” (MPEP 2111.04(II)). Further, although the claims do encompass some embodiments requiring the “administering”, “A claim whose BRI covers both statutory and non-statutory embodiments embraces subject matter that is not eligible for patent protection and therefore is directed to non-statutory subject matter” (MPEP 2106.03(II)). The “detecting” of the claim (to the extent that it requires wet/physical steps of achieving detection) also sets forth nothing more than data gathering steps that do not add a meaningful limitation to the method as such steps are considered insignificant extra-solution activity. Thus, no practical application/ implementation is required by the present claim language. The claim(s) also do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the “detecting” of the claims is, based on the teachings of the disclosure, extremely broad and general (encompassing any of a variety of techniques sufficient to establish presence/amount of the bacteria in question). The claim thus encompasses the types of laboratory techniques/activities that the courts have recognized as well-understood, routine, and conventional activity in the life science arts when claimed a generic manner (as they are in the instant claims); see MPEP 2106.05(d)(II) (further, it is also noted that the prior art as exemplified by Bert et al [cited and discussed above] teaches detection of kpsM). With further regard to dependent claim 37, this claim recites a further limitation of the “administering”, which is not an activity required by the present claim language. Accordingly, neither claim 36 nor claim 37 is presently directed to patent eligible subject matter.
Conclusion
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.
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, 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.
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.
/DIANA B JOHANNSEN/Primary Examiner, Art Unit 1682
Prosecution Insights