DETAILED ACTION
This action is in reply to papers filed 8/25/2025. Claims 30-42, 44-46 and 48-50 are pending and examined herein.
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 .
Examiner’s Note
All paragraph numbers throughout this office action, unless otherwise noted, are from the US PGPub of this application US20210024877A1, Published 1/28/2021.
Withdrawn Rejection(s)
The 103 (a) rejection of claims 48-50 as being unpatentable over O’Hara et al. (U.S. Patent 10876173, Filed 8/12/2015), Fischer et al. (PgPub US20160333339A1, Filed 5/12/2016) and Waters et al. (U.S. Patent US3854041A, Published 12/10/1974) is withdrawn in view of amendments made to claim 48.
The 103 (a) rejection of claims 30-32, 34-42 and 44-46 as being unpatentable over Hohnadel et al. (PgPub US20160257987A1, Published 9/8/2016), PubChem Compound Summary for CID 3423265, Sodium dodecyl sulfate (Accessed 5 February, 2024), Dryga et al. (PgPub US20170038374A1, Published 2/9/2017), Kubicek et al. (PgPub US20180142231A1, Filed 4/20/2015), O’Hara et al. (PgPub US20130196318A1, Published 8/1/2013) and Matheson et al. (PLoS One. 2014 Oct 31;9(10):e111437.) is withdrawn in view of amendments made to claim 30.
The 103 (a) rejection of claim 33 as being unpatentable over Hohnadel et al. (PgPub US20160257987A1, Published 9/8/2016), PubChem Compound Summary for CID 3423265, Sodium dodecyl sulfate (Accessed 5 February, 2024), Dryga et al. (PgPub US20170038374A1, Published 2/9/2017), Kubicek et al. (PgPub US20180142231A1, Filed 4/20/2015), O’Hara et al. (PgPub US20130196318A1, Published 8/1/2013) and Matheson et al. (PLoS One. 2014 Oct 31;9(10):e111437.) as applied to claims 30-32, 34-42 and 44-46 and further in view of O’Hara et al. (PgPub US20160083776A1, Published 3/24/2016), hereinafter referred to as O’Hara (b) is withdrawn in view of amendments made to claim 30
Rejection(s) Necessitated by Amendments
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.
Claim(s) 30-32, 34-42 and 44-46 rejected under 35 U.S.C. 103 as being unpatentable over Hohnadel et al. (PgPub US20160257987A1, Published 9/8/2016, previously cited), PubChem Compound Summary for CID 3423265, Sodium dodecyl sulfate (Accessed 5 February, 2024, previously cited), Dryga et al. (PgPub US20170038374A1, Published 2/9/2017, previously cited), Kubicek et al. (PgPub US20180142231A1, Filed 4/20/2015, previously cited), O’Hara et al. (PgPub US20130196318A1, Published 8/1/2013, previously cited) and Lowe et al. (PgPub US20130115590A1, Published 5/9/2013).
Hohnadel et al. teach a method for isolating and detecting microorganisms from a blood sample (as in claim 30b (in-part) and claim 45) (Pg. 1, para. 6; Pg. 1, para. 17) comprising mammalian cells (non-microorganism), comprising a) contacting the sample with a lysis buffer b) incubating the sample (as in claim 30a (in-part)) (Pg. 2, para. 42-43), c) lysing the mammalian cells (Pg. 2-3, para. 47), d) obtaining the microorganisms by removing the mammalian cells (as in claim 30b (in-part) and claim 36(in-part)), d) performing a universal lysis on the microorganisms (as in claim 32a (in-part)) and e) performing a specific or universal detection method for detecting the microorganisms (as in claim 31 (i), in-part)) (Pg. 1, para. 12). Hohnadel teaches the step of removing the mammalian cells may involve several washing (as in claim 35) and concentrating steps, including concentration methods such as magnetic trapping (Pg. 2, para. 43). Hohnadel teaches the lysis buffer that selectively lyses the mammalian cells is sodium dodecyl sulfate, a detergent (see PubMed Compound Summary) (as in claim 38) (Pg. 2, para. 28). Also of note, Hohnadel does not teach the detergent is conjugated to particles or beads (as in claim 39).
However, Hohnadel fails to teach incubating the sample with particles to form particle-microorganism complexes (as further in claim 30a).
Before the effective filing date of the claimed invention, Dryga et al. teach introducing magnetic particles to a biological sample (e.g., a tissue or body fluid sample). The sample is incubated to allow the particles to bind to pathogen in the sample (as in claim 30a and claim 44), and a magnetic field is applied to capture pathogen/magnetic particle complexes on a surface (as in claim 37 and claim 41). Dryga teaches a particular advantage of compositions of the invention is for capture and isolation of bacteria and fungi directly from blood samples (as in claim 45) at low concentrations that are present in many clinical samples (as low as 1 CFU/ml of bacteria or fungi in a body fluid (Pg. 1, para. 7). Continuing, Dryga et al. teach the magnetic particles include at least 70% superparamagnetic particles by weight (as optionally recited in claim 41) (Pg. 2, para. 17). In certain embodiments, the superparamagnetic particles are from about 100 nm (i.e. 0.1. μm) to about 250 nm in diameter (as in claim 40) (Pg. 2,para. 17). Dryga adds that the nanoparticles may be used that include a polymer coating material that incorporates magnetic material(s), such as nanometal material(s) (as in claim 42) (Pg. 3,para 24-27).
However, neither Hohnadel nor Dryga et al. teach the step of incubation is performed in the presence of sodium polyanethol sulfonate (as further in claim 30a).
Before the effective filing date of the claimed invention, Kubicek et al. teach a method for selectively depleting animal nucleic acids from non-animal nucleic acids in a sample, which comprises animal cells and at least one further type of cells, selected from microbial cells and plant cells or a combination thereof, to a lysis solution (Abstract). Kubicek teaches the lysis solution comprises sodium polyanethol sulfonate (as further in claim 30a) (Pg. 5, para. 63). Kubicek teaches the in particular for blood samples of blood cultures, it might be preferred to include such a polyanionic sulfonate, since said compound has a positive effect on the stability of microbial cells in such samples. Thus, said cells are maintained during the treatment to isolate them (Pg. 6, para. 69).
However, none of Hohnadel, Dryga et al. and Kubicek et al. teach the step of detecting an enzymatic activity of a nucleic acid molecule modifying enzyme associated with the microorganism (as in claim 31(i)).
Before the effective filing date of the claimed invention, O’Hara et al. teach detecting microorganisms, and more particularly to the detection of bacteria (Pg. 1, para. 2). Specifically, O’Hara teaches (a) contacting a lysed microorganism sample with a nucleic acid molecule which acts as a substrate for polymerase activity in the sample (as in claim 31(i)), (b) incubating the thus contacted sample under conditions suitable for polymerase activity (as in claim 32(b)); and (c) determining the presence (and/or the amount) of a nucleic acid molecule resulting from the action of the microorganism polymerase on the substrate nucleic acid molecule to indicate the presence of the microorganism (as in claim 32 (c)) (Pg. 2, para. 9). Regarding claim 34, O’Hara teaches the nucleic acid modifying enzyme comprises a DNA or RNA polymerase (Pg. 1-2, para. 8). O’Hara adds at para. 43 that their methods provide significant technical advantages, due in large part to the fact that a novel nucleic acid molecule is generated as part of the method and that the unreacted nucleic acid molecule will not contribute to the signal, and as a result no false positive signals should be produced when the methods are carried out (Pg. 3).
However, none of the aforementioned references teach the outer surface of the particles/beads capable of forming complexes with microorganisms comprises or is coated with carboxylic acid groups (as further in claim 30a (i)).
Before the effective filing date of the claimed invention, Lowe et al. taught materials and method for immobilizing, isolating and concentrating cells using carboxylated surfaces (Title) in blood (Pg. 3, para. 47). Lowe teaches the term “carboxylated surface” shall refer to a surface of a solid or quasi-solid, the surface comprising a free carboxylic acid group (Pg. 2,para. 30) (as in claim 30a(i)). Specifically, Lowe teaches a method of immobilizing a cell comprising contacting a carboxylated surface with a sample comprising the cell and a fixative agent, for a sufficient time to permit the cell to bind to the carboxylated surface (Abstract). Lowe teaches the carboxylated surface is provided by solid particles having an average size of 5 μm or less and optionally are magnetic (Pg. 4,para. 56). Notably, Lowe teaches the binding of the cell to the carboxylated surface is not mediated by a ligand-receptor interaction or an antibody-antigen interaction (Pg. 3, para. 46) . Neither does Lowe teach binding with a carbohydrate, a peptide derived from Apolipoprotein H protein or a Mannose Binding lectin protein ( as in claim 46). Lowe notes that the methods disclosed herein are particularly advantageous in that they can be fully automated. Using a surface comprising carboxylated moieties in particular in form of magnetic beads comprising carboxylated moieties allows cell isolation, lysis, and nucleic acid analysis to be performed without a centrifugation step, thereby permitting a high-throughput sample processing and analysis (Pg. 11, para. 128).
The combination of prior art cited above in all rejections under 35 U.S.C.103 satisfies the factual inquiries as set forth in Graham v. John Deere Co., 383 U.S. 1,148 USPQ 459 (1966). Once this has been accomplished the holdings in KSR can be applied (KSR International Co. v. Teleflex Inc. (KSR), 550 U.S. 389, 82 USPQ2d 1385 (2007): "Exemplary rationales that may support a conclusion of obviousness include: (A) Combining prior art elements according to known methods to yield predictable results; (B) Simple substitution of one known element for another to obtain predictable results; (C) Use of known technique to improve similar devices (methods, or products) in the same way; (D) Applying a known technique to a known device (method, or product) ready for improvement to yield predictable results; (E) "Obvious to try" - choosing from a finite number of identified, predictable solutions, with a reasonable expectation of success; (F) Known work in one field of endeavor may prompt variations of it for use in either the same field or a different one based on design incentives or other market forces if the variations are predictable to one of ordinary skill in the art; (G) Some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention."
In the present situation, rationales A and G are applicable. Before the effective filing date of the claimed invention, it would have been prima facie obvious to an artisan of ordinary skill to combine the teachings of Hohnadel et al., wherein Hohnadel teach a method for isolating and detecting microorganisms from a blood sample with the teachings of Dryga et al., wherein Dryga teach introducing magnetic particles to capture and isolate bacteria and fungi directly from blood samples, with the teachings of Kubicek et al., wherein Kubicek teach inclusion of a polyanionic sulfonate in a blood sample has a positive effect on the stability of microbial cells in such samples, with a reasonable expectation of arriving at the claimed invention. That is, one of ordinary skill in the art would have found it prima facie obvious to combine the methods of Hohnadel and Dryga et al. in order to detect microorganisms in a blood sample. Additionally, the skilled artisan would have found it prima facie obvious to include sodium polyanethol sulfonate in said blood sample as Kubicek teaches inclusion of such provides stability for the microbial cells in such samples. In view of the above, one of skill in the art would have further found it prima facie obvious to use the detailed method of O’Hara in order to detect an enzymatic activity of a nucleic acid molecule modifying enzyme associated with the microorganism as O’Hara specifically notes an advantage of their protocol is ability to produce no false positive signals. The skilled artisan would have found it prima facie obvious to use the antibody-free carboxylic coated magnetic particles of Lowe because Lowe teaches using a surface comprising carboxylated moieties in particular in form of magnetic beads comprising carboxylated moieties allows cell isolation, lysis, and nucleic acid analysis to be performed without a centrifugation step, thereby permitting a high-throughput sample processing and analysis.
Thus, the teachings of the cited prior art in the obviousness rejection above provide the requisite teachings and motivations with a clear, reasonable expectation. The cited prior art meets the criteria set forth in both Graham and KSR.
Therefore, the claimed invention, as a whole, was clearly prima facie obvious.
Prior Art Rejection 2
Claim 33 is rejected under 35 U.S.C. 103 as being unpatentable over Hohnadel et al. (PgPub US20160257987A1, Published 9/8/2016, previously cited), PubChem Compound Summary for CID 3423265, Sodium dodecyl sulfate (Accessed 5 February, 2024, previously cited), Dryga et al. (PgPub US20170038374A1, Published 2/9/2017, previously cited), Kubicek et al. (PgPub US20180142231A1, Filed 4/20/2015, previously cited), O’Hara et al. (PgPub US20130196318A1, Published 8/1/2013, previously cited) and Lowe et al. (PgPub US20130115590A1, Published 5/9/2013) as applied to claims 30-32, 34-42 and 44-46 above, and further in view of O’Hara et al. (PgPub US20160083776A1, Published 3/24/2016, previously cited), hereinafter referred to as O’Hara (b).
The teachings of Hohnadel et al., Dryga et al., Kubicek et al. , O’Hara et al. and Lowe et al. are relied upon as detailed above. And although O’Hara et al. teach microbes were beadmill-lysed and incubated with a DNA substrate in the presence of DNA polymerase buffer (Pg. 4, para. 56), none of the aforementioned references teach adding a lysis reagent containing the substrate nucleic acid molecule (as in claim 33).
Before the effective filing date of the claimed invention, O’Hara (b) teaches to test for the presence of detectable DNA polymerase extension activity, activity from crude bead mill lysates from viable human Platelet Concentrates (PC) collected via three different methodologies, Whole Blood Derived, Apheresis Non-Leukoreduced and Apheresis Leukoreduced was investigated (Pg. 6, para. 40). O’Hara (b) teaches the method comprises adding a cell lysis mix, comprising lysis reagents (as in claim 33), and a DNA polymerase and incubating the mixture (Pg. 6, para. 58-86).
When taken with the teachings of the Hohnadel et al., Dryga et al., Kubicek et al., O’Hara et al. and Lowe et al., wherein the combination teach a method of isolating, capturing and detecting microorganisms in a blood sample, one of ordinary skill in the art would have found it prima facie to substitute the mechanical lysis process of O’Hara for the chemical and mechanical lysis process of O’Hara (b). The skilled artisan would have found it prima facie obvious to do in order to increase the release of intracellular components.
Therefore, the claimed invention, as a whole, was clearly prima facie obvious.
Prior Art Rejection 3
Claims 48-50 are rejected under 35 U.S.C. 103 as being unpatentable over Lowe et al. (PgPub US20130115590A1, Published 5/9/2013), Witek et al. (Anal Chem. 2008 May 1;80(9):3483-91.) and O’Hara et al. (U.S. Patent 10876173, Filed 8/12/2015, previously cited).
Lowe et al. teach a kit (as in claim 48) for detecting a biomolecule, the kit comprising a solid support, such as a bead (as in claim 48a), having a carboxylated (carboxylic) surface (as in claim 48ai) adapted to bind a cell in blood (Pg. 3, para. 47), and optionally comprising a liquid composition for releasing the biomolecule from the cell (see claim 26 of Lowe). Lowe teaches if the biomolecule is an intracellular, it is released by lysing the cell. Lowe notes that any manner of lysing the cell can be used including use of chemical lysis, such as sodium dodecyl sulfate (as in claim 48 (c)) (Pg. 5, para. 62). Lowe teaches wherein binding of the cell to the carboxylated surface is not mediated by a ligand-receptor interaction or an antibody-antigen interaction (Pg. 3, para. 46). Lowe does not teach binding with a carbohydrate, a peptide derived from Apolipoprotein H protein or a Mannose Binding lectin protein (as in claim 50). Lowe teaches said kit comprises amplification means via PCR (Pg. 7, para. 79).
However, Lowe et al. fails to teach the kit comprises sodium polyanethol sulfonate (as further in claim 48b).
Before the effective filing date, Witek et al. report a simple and effective method for the high-throughput purification of a variety of nucleic acids (NAs) from whole cell lysates or whole blood using a photactivated polycarbonate solid-phase reversible immobilization (PPC-SPRI) microfluidic chip on the application of a high-throughput PPC-SPRI microchip for the purification of gDNA and TRNA of different origins (i.e., bacterial, mammalian) when found in complex matrices, including blood and blood containing high concentrations of sodium polyanetholesulfonate (SPS) (as in claim 48b), used as an anticoagulant (Pg. 3, last full paragraph).
However, neither Lowe et al nor Witek et al. the kit comprises a detection means for detecting the absence or presence of microorganisms in the bead microorganism complexes, wherein the detection means comprises a nucleic acid molecule (DNA) which acts as a substrate for nucleic acid modifying activity of the microorganisms, and wherein the nucleic acid molecule (DNA) is at least partially double stranded and comprises uracil residues in the complementary strand (as further in claim 49).
O’Hara et al. is drawn to the detection of enzymes such as polymerases as a useful indicator of the presence of a (viable) microorganism or microbe in a sample, in particular a sample that is unpurified blood or blood culture (paragraph bridging Col. 2 and Col. 3). Specifically, O’Hara et al. teach a sample comprising: (a) a DNA substrate consisting of a DNA sense strand and a uracil containing DNA antisense strand, wherein the two strands overlap to form a double stranded region and a single stranded portion of the antisense strand acts as a template with the sense strand of the double stranded region acting as a primer to create an extension product in the presence of polymerase activity; (b) a reverse primer having a sequence that is substantially identical to part of the sequence of the antisense strand; and (c) a forward primer having a sequence that is substantially identical to part of the sequence of the sense strand; wherein the forward primer and the reverse primer are separate molecules from the DNA substrate (as in claim 49) (see O’Hara at claim 7 and 8). O’Hara teaches the kit comprises reagents for lysing non-microorganism cells which do not lyse the cells of the microorganism to be detected (as in claim 48(c)) (Col. 10, line 39+).
The combination of prior art cited above in all rejections under 35 U.S.C.103 satisfies the factual inquiries as set forth in Graham v. John Deere Co., 383 U.S. 1,148 USPQ 459 (1966). Once this has been accomplished the holdings in KSR can be applied (KSR International Co. v. Teleflex Inc. (KSR), 550 U.S. 389, 82 USPQ2d 1385 (2007): "Exemplary rationales that may support a conclusion of obviousness include: (A) Combining prior art elements according to known methods to yield predictable results; (B) Simple substitution of one known element for another to obtain predictable results; (C) Use of known technique to improve similar devices (methods, or products) in the same way; (D) Applying a known technique to a known device (method, or product) ready for improvement to yield predictable results; (E) "Obvious to try" - choosing from a finite number of identified, predictable solutions, with a reasonable expectation of success; (F) Known work in one field of endeavor may prompt variations of it for use in either the same field or a different one based on design incentives or other market forces if the variations are predictable to one of ordinary skill in the art; (G) Some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention."
In the present situation, rationales A, B and G are applicable. Before the effective filing date of the claimed invention, it would have been prima facie obvious to an artisan of ordinary skill to combine the kit of Lowe et al., wherein Lowe teaches a kit for detecting a biomolecule in blood, the kit comprising a solid support, such as a bead, having a carboxylated (carboxylic) surface adapted to bind a cell and a lysing agent such as sodium dodecyl sulfate. Moreover, it would have been prima facie obvious to include SPS as Witek teaches SPS serves as an anticoagulant in blood culture. Thus, in order to prevent clotting of the blood culture, it would have been prima facie obvious to include SPS. It would also have been prima facie obvious to modify the kit of Lowe such that the generic PCR assay of Lowe is substituted for the PCR detection assay of O’Hara because O’Hara teaches their PCR assay is highly sensitive and quantitative and can be used to enumerate prokaryotic cells when presenting a purified or selected cell type and that has the capability to reproducibly measure DNA polymerase extension activity from less than 10 cfu of bacteria via coupling to bead lysis (see Abstract of O’Hara).
Therefore, the claimed invention, as a whole, was clearly prima facie obvious.
Comments on Applicant’s Remarks
On pg. 10, Applicant argues As described in the Applicant-Initiated Interview Summary, the arguments above regarding the kit claims ( claims 48-50) were submitted in response to the previous Final Office Action in this application, dated July 19, 2024, but are not addressed in the pending Non-Final Office Action. Applicant notes that pursuant to MPEP § 707.07(±), to maintain a complete and clear record of prosecution, "an examiner must provide clear explanations of all actions taken," including "tak[ing] note of the applicant's argument and answer[ing] the substance of it.” Applicant further adds that should the Office remain unpersuaded, Applicant respectfully requests a direct response to these arguments and that the next Office Action be made non-final.
In response to Applicant’s argument, Examiner notes that MPEP 706.07 (a) stats that a second or any subsequent actions on the merits shall be final, except where the examiner introduces a new ground of rejection that is neither necessitated by applicant’s amendment of the claims, nor based on information submitted in an information disclosure statement filed during the period set forth in 37 CFR 1.97(c) with the fee set forth in 37 CFR 1.17(p).
In the claims filed 11/7/2024 (prior to the Non-Final) rejection, claim 48 read as follows:
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In the claims filed 11/7/2024 (prior to the Non-Final) rejection, claim 48 read as follows:
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Applicant’s amendment necessitated a new ground’s of rejection of claim 48. Accordingly, and in view of MPEP 706.07 (a), Applicant’s arguments regarding a second action being non-final is moot.
Authorization to Initiate Electronic Communications
The examiner may not initiate communications via electronic mail unless and until applicants authorize such communications in writing within the official record of the patent application. See M.P.E.P. § 502.03, part II. If not already provided, Applicants may wish to consider supplying such written authorization in response to this Office action, as negotiations toward allowability are more easily conducted via e-mail than by facsimile transmission (the PTO's default electronic-communication method). A sample authorization is available at § 502.03, part II.
Conclusion
No claim is allowed.
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 extension fee 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 date of this final action.
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/TITILAYO MOLOYE/Primary Examiner, Art Unit 1632