FINAL ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
This action is responsive to the Amendments and Response filed 17 November 2025. Claims 1-5, 8-9, 11, 14, and 17 have been amended, claims 6-7 have been canceled, and claims 18-20 have been added. All prior rejections claims 6-7 are moot in view of the cancelation of those claims. Claims 15-17 and 20 remain/are withdrawn, and claims 1-5, 8-14, and 18-19 are now under consideration herein. Applicant’s amendments and arguments have been thoroughly reviewed, and have overcome the following objections/rejections set forth in the prior Office action:
The rejections of claims under 35 USC 112(b) in view of Applicant’s clarifying amendments; and
The rejection of claims under 35 USC 102(a)(1), in view of the amendment of claim 1 at III(e)(i) to require a ‘third cell population comprising a recombinantly engineered version of the microorganism, wherein the recombinantly engineered version of the microorganism comprises an expression library”.
Claims 1-5, 8-14, and 18-19 remain/are rejected for the reasons given below, which include new grounds of rejection necessitated by Applicant’s amendments. Any rejections and/or objections not reiterated in this action have been withdrawn. This action is FINAL.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Election/Restrictions
Applicant’s election without traverse of Group I in the reply filed on July 3, 2025 is acknowledged.
Claims 15-17 and claim 20 (which is a newly added claim dependent from withdrawn claims 16-17) remain/are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 July 3, 2025.
Claim Interpretation
With regard to claim 3 and its new dependent claim 18, it is noted that the recitation of the limitation “at least one said nucleic acid sequence determined in each of steps (b), (d), and (f) is determined by sequencing extra-genomic nucleic acids, wherein extra-genomic nucleic acids are naturally occurring in the microorganism or are not naturally occurring” it is interpreted as requiring that at least one of the three “determining a nucleic acid sequence” steps (as recited in claim 1) comprises sequencing extra-genomic nucleic acids in a microorganism of the corresponding cell population of that step (i.e., the recitation “the microorganism” in this context refers to a microorganism of the corresponding population). Furthermore, the recitation in claim 18 of the limitation “the extra-genomic nucleic acids are from an artificial plasmid transformed into the microorganism” is interpreted as referring to the same microorganism referenced in claim 3 (i.e., the microorganism with respect to which the sequencing of claim 3 is/was performed).
Claim Rejections - 35 USC § 103
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 INCLUDES NEW GROUNDS OF REJECTION NECESSITATED BY APPLICANT’S AMENDMENTS:
Claim(s) 1-5, 8-9, 11-14, 18, and 19 remain/are rejected under 35 U.S.C. 103 as being unpatentable over Westhoff et al (The ISME Journal 11;1168-1178 [Jan 2017]; cited in IDS) in view of Boolchandani et al (Antibiotics, Chapter 19, “Functional Metagenomics to Study Antibiotic Resistance” [2016]; cited in IDS).
Westhoff et al disclose the use of “experimental evolution” to study how the soil bacterium Streptomyces coelicolor responds to exposure to different levels of streptomycin, with a particular focus on low concentration exposures (see entire reference). Westhoff et al disclose that their methods comprise culturing two S. coelicolor strains – S. coelicolor A3(2) M145 (designated “WT”) and S. coelicolor A3(2) M145 Apra (designated “WTAPRA”), an isogenic strain carrying an integrated pSET152 plasmid conferring apramycin resistance” (see page 1169, right column under “Bacterial strains and culturing conditions”); it is noted that Westhoff et al teach that the MIC for both of these strains was determined to be 2 ug ml-1 of streptomycin (see page 1169, right column bridging to page 1170, left column). Westhoff et al teach culturing their microorganisms in the presence of both MIC and sub-MIC concentrations (and thus teach the culturing of multiple “first” and “second” populations of the same species of microorganism), followed by subsequent DNA extraction and sequencing, and sequence analysis relative to the known S. coelicolor A3 genome sequence (which constitutes a comparing to a “reference nucleic acid sequence” for the tested S. coelicolor, as recited in the amended “wherein” clause of claim 1) (see the Materials and Methods at page 1169, right column-page 1171, left column). It is noted that the sub-MIC levels of streptomycin as taught by Westhoff et al that allow for growth meet the requirement of “not substantially” inhibiting wild type growth (particularly as compared to the higher levels taught by Westhoff et al, which do inhibit wild-type growth). Westhoff et al disclose that their methods resulted in the identification of multiple nucleic acids encoding anti-microbial resistance markers, which markers constitute a type of “panel” that may function as an indicator of resistance (see, e.g., page 1173-page 1175, left column, including Table 2). Westhoff et al thus teach methods meeting the requirements of amended claim 1, other than the requirement for performing analogous testing with regard to a “third cell population comprising a recombinantly engineered version of the microorganism, wherein the recombinantly engineered version of the microorganism comprises an expression library”.
Boolchandani et al teach various methods employing functional metagenomics to study antibiotic resistance, stating that the “construction and screening of metagenomic expression libraries has great potential to identify novel genes and their functions” (see entire reference, particularly the Abstract). Boolchandani et al teach that such methods have advantages (of efficiency and power) as compared to traditional approaches for characterizing resistomes, stating that a transformant library of DNA cloned into an expression vector may be easily cultured and assayed for antibiotic resistance, followed by massively parallel sequencing of identified antibiotic resistance genes for further characterization (see overview at pages 307-308). In view of the teachings of Boolchandani et al, it 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 prepared a recombinantly engineered microorganism (including a recombinant S. coelicolor) comprising an expression library of potential antibiotic resistant genes, meeting the requirements of amended claim 1 (as well as dependent claim 8), for screening and identification additional markers of the type taught by Westhoff et al. An ordinary artisan would have been motivated to have made such a modification by the teachings of Boolchandani et al regarding the advantages of such a method in characterizing resistomes.
With regard to dependent claims 2-3 and 18, it is reiterated that Westhoff et al disclose the use of nucleic acid sequencing (see again page 1170, right column bridging to 1171, left column). With further regard to claims 3 and 18, implementation of the modification taught and suggested by Boolchandani et al employs cloning into an expression vector, i.e., extra-genomic nucleic acids that are “not naturally occurring” in the host bacteria, followed by transformation into those bacteria (such that performance of the suggested method with respect to the suggested “third population” meets the requirements of the claims) (see Boolchandani et al, including the protocols in particular at pages 310 and 314-317). Regarding claims 4-5, Westhoff et al teach further steps of culturing/plating of selected replicates (i.e., multiple such replicates) on media supplemented with 2 ug ml-1 of streptomycin, which meets the requirements of the claim (see, e.g., page 1170, left column). Regarding claims 9 and 19, it is reiterated that Streptomyces coelicolor is a bacterium, as noted above. Regarding claim 11, Westhoff et al teach the use of plates – a type of “solid surface” – in their culturing (see, e.g., page 1170). Regarding claim 12, streptomycin meets the requirement of being an antibiotic. Regarding claims 13-14, Westhoff et al further teach performing “fitness assays” in which spontaneous and evolved strains were tested for their ability to grow on various concentrations of streptomycin, which meets the requirements of the claims (see page 1170), thereby teaching and suggesting such further steps/activities.
It is noted that the Reply of 17 November 2025 provides a combined traversal of all rejections under 35 USC 103; these arguments are addressed below following all rejections.
Claim(s) 10 remains rejected under 35 U.S.C. 103 as being unpatentable over Westhoff et al in view of Boolchandani et al, as applied to claims 1-5, 8-9, 11-14, 18, and 19 above, and further in view of Baltz (Journal of General Microbiology 107:93-102 [1978]; previously cited).
The teachings of Westhoff et al and Boolchandani et al are set forth above. Neither Westhoff et al nor Boolchandani et al teach measuring the growth of microorganisms by cell doubling time, as required by claim 10. However, Baltz teaches that factors such as supplements added to growth media may alter Streptomyces cell doubling time, and further teaches and exemplifies the general use of cell doubling time as a standard measurement in tracking bacterial culture growth (see pages 94-95). In view of the teachings of Baltz, it 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 measured growth of any of the microorganisms taught and suggested by Westhoff et al and Boolchandani et al via tracking/measurement of cell doubling time, simply for the benefit of accurately tracking that growth in a standard manner (as exemplified by Baltz), while allowing for the detection of any problems or inconsistencies in bacterial growth that could adversely impact experimental results.
The Reply of 17 November 2025 traverses the prior rejections of claims under 35 USC 103 on the following grounds.
Applicant argues that the method of claim 1 would not have been obvious to a person of ordinary skill in the art (POSA) as no reason has been provided for a POSA to combine the “disparate teachings” of Westhoff and Boolchandani (Reply page 9). The Reply states that a POSA would not have combined the teachings of these references “because Boolchandani avoids the use of wild-type microorganisms” because a “large proportion….of bacteria are difficult to culture in the laboratory”, and further because Boochandani teaches that an advantage of their methods is that culturing is not required, with their methods also employing a “susceptible (and easily cultured) indicator strain” (Reply page 9 bridging to page 10). Applicant urges that – in contrast to Boolchandani - Westhoff employs wild-type strains “for studying evolution and persistence of resistant bacterial strains in nature”, and argues that the two references therefore conflict with one another (Reply page 10). (It is noted that a separate traversal of the rejection of claim 10 was not provided; therefore the traversal summarized above has been considered to the extent that it pertains to the rejections of all claims).
These arguments have been thoroughly considered but are not persuasive.
First, the claims are rejected as obvious over Westhoff in view of Boolchandani (not Boolchandani in view of Westhoff), i.e., the rejection relies on the teachings of Westhoff as the primary reference, with modifications as suggested by the teachings of Boolchandani. Given Westhoff’s teaching and successful culturing of S. coelicolor, the disadvantages discussed by Boolchandani as applying to wild-type microbes clearly do not apply to the type of bacteria employed by Westhoff (and this fact would have been readily apparent to a POSA). Further, both references pertain to the study of antibiotic resistance/ antibiotic resistance genes, with Boolchandani stating that “cultivation in the lab is the ‘gold standard’ for identifying bacteria with antibiotic resistance”; i.e., the references have common goals and relate to the same field of study, with Boolchandani acknowledging that the culture-based techniques employed by Westhoff are the “gold standard”. Further, Boolchandani employs steps of culturing to select resistant bacteria, i.e., steps analogous to those practiced by Westhoff (see, e.g., Figure 1, protocol at pages 311-312, 317). Thus, while the examiner agrees that Boolchandani teaches that their methods allow one to analyze microbes that are difficult to culture, the characterization of the two references as providing “disparate teachings” and being in conflict with one another is not supported by the actual content of the references. With regard to the alleged lack of reasons/motivation to modify Westhoff to employ further steps/activities as taught by Boolchandani, a POSA would have recognized that the further analysis of Boolchandani, providing the advantages taught by Boolchandani of efficiency and power, and “great potential to identify novel genes and their functions”, would complement the methods disclosed by Westhoff (as discussed in the rejection); any of these advantages constitutes a reasonably motivation to modify the methods of Westhoff in view of Boolchandani (and would have been recognized as such by a POSA). Thus, Applicant’s arguments are not persuasive with respect to nonobviousness of the rejected amended claims.
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.
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/DIANA B JOHANNSEN/Primary Examiner, Art Unit 1682