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 .
Response to Amendment
The amendment filed 10/16/2025 is acknowledged. Regarding the Office action mailed 07/16/2025:
The rejections of claims 57 and 66 under 35 USC 112(b) are withdrawn and/or moot in view of the amendment.
The rejection of claims 67 and 68 under 35 USC 102 over Wilson (2015) is withdrawn and/or moot in view of the amendment and Applicant’s arguments regarding Wilson’s lack of teaching of 16S and 23S rRNA. As correctly noted by Applicant, Wilson’s teachings were with regard to 18S and 28S rRNA.
The rejection of claims 14, 15, 17, 19, 20, 25, 29, 30, 56, 60 and 65 under 35 USC 103 over Wilson (2015) in view of Grun (US 2009/0086205) is maintained and reiterated below. Applicant’s arguments will be addressed following the rejections.
The rejection of claim 69 under 35 USC 103 over Wilson (2015) in view of Polansky (US 2004/0023207) is withdrawn in view of the amendment to claim 69.
New grounds of rejection are also set forth below. This Office action is NON-FINAL.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 63 and 72 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 63 recites “and is protein-free”. It is not clear if this applies to both the insect cell culture medium and the mammalian cell culture medium options, or only to the latter.
Claim 72 recites “wherein the porous hydrogel particle”. There is no antecedent basis for this limitation. The Examiner will presume claim 72 should depend from claim 71.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim 67 is rejected under 35 U.S.C. 102(a)(2) as being anticipated by Walter (US 2020/0248259).
Regarding claim 67, Walter disclosed:
A method of identifying a fastidious microorganism,
Paragraph [0016]: “…method of determining optimal duration of administration of a therapeutic treatment to a subject infected with multiple-drug-resistant M. tuberculosis…”. M. tuberculosis is a fastidious microorganism.
the method comprising: performing a nucleic acid amplification for nucleic acid sequences associated with a fastidious microorganism species or genus in a sample obtained from a subject suspected of being infected by the fastidious microorganism,
Paragraph [0016]: “…measuring the pre-rRNA/mature rRNA ratio in a biological sample from the subject…”.
Paragraph [0034]: “…the measuring of the pre-rRNA/mature rRNA ratio comprises at least one method selected from the group consisting of RNAseq, qRT-PCR, Nanostring, and droplet digital PCR…”.
wherein performing the nucleic acid amplification comprises distributing nucleic acids from the sample into a plurality of partitions;
Paragraph [0034]: “…the measuring of the pre-rRNA/mature rRNA ratio comprises at least one method selected from the group consisting of RNAseq, qRT-PCR, Nanostring, and droplet digital PCR…”. Droplet digital PCR necessarily involves distributing nucleic acids into a plurality of partitions (“droplets”).
and analyzing nucleic acid amplification products derived from the nucleic acid amplification generated by amplification with a primer directed to an internal transcribed spacer (ITS) between two rRNA genes of the fastidious microorganism, wherein the two rRNA genes comprise 16S and 23S rRNA gene.
Paragraph [0026]: “…the pre-rRNA/mature rRNA ratio is at least one selected from the group consisting of ETS1/16S rRNA, ETS1/23S rRNA, ITS1/16S rRNA, ITS1/23S rRNA, ITS2/16S rRNA, and ITS2/23S rRNA…”.
Paragraph [0108]: “The PCR primer/probe sets for M. tuberculosis ETS1, ITS1 and 23S were validated by testing DNA from M. gordonae, M. avium, M. xenopi, M. szulgai, M. lentiflavum, M. neoaurum, M. mageritense, M. chelonae, M. cosmeticum, M. abscessus and human.” Note that ITS1 is between the 16S and 23S rRNA genes (Fig. 1).
Claims 14, 15, 19, 20, 25, 29, 30, 65, 67 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Andini (US 2017/0321257).
Regarding claim 14, Andini disclosed:
A method of identifying a fastidious microorganism in a sample,
Paragraph [0006]: “In one aspect, the invention includes a method for identifying bacteria in a biological sample from a subject…”
the method comprising: enriching the fastidious microorganism in a sample obtained from a subject suspected of being infected by the fastidious microorganism;
Paragraph [0006]: “…the method comprising: a) providing a biological sample from the subject; b) isolating bacterial DNA from the biological sample; c) amplifying at least a portion of an internal transcribed spacer (ITS) region of the bacterial DNA using at least one set of primers capable of specifically hybridizing to the ITS region, whereby an amplicon is produced; d) performing high resolution melt (HRM) analysis of the amplicon; and e) identifying the species of the bacteria by comparing an HRM curve for the amplicon to a matching reference HRM curve for genomic ITS DNA from a known bacterial species. The method may further comprise culturing the bacteria from the biological sample prior to amplification of the bacterial nucleic acids.”
performing a nucleic acid amplification for nucleic acid sequences associated with the fastidious microorganism, wherein performing the nucleic acid amplification comprises distributing nucleic acids from the sample into a plurality of partitions, and performing the nucleic acid amplification on the plurality of partitions;
Paragraph [0010]: “Amplification may be performed using polymerase chain reaction (PCR) techniques, such as, but not limited to, real-time PCR, droplet digital PCR (ddPCR), hot-start PCR, solid phase PCR, and touchdown PCR.” ddPCR necessarily involves distributing nucleic acids into a plurality of partitions (in the case of ddPCR, “droplets”) and performing PCR on the partitions.
and analyzing nucleic acid amplification products derived from the nucleic acid amplification, wherein analysis of the nucleic acid amplification products identifies the fastidious microorganism infecting the subject.
Paragraph [0006]: “…d) performing high resolution melt (HRM) analysis of the amplicon; and e) identifying the species of the bacteria by comparing an HRM curve for the amplicon to a matching reference HRM curve for genomic ITS DNA from a known bacterial species.”
Regarding the term “fastidious”, Andini applied the method to Borrelia burgdorferi; see paragraph [0051] and figure 22.
Regarding claim 15, Andini disclosed extracting the nucleic acid; paragraphs [0030], [0156], [0208], [0216], [0216].
Regarding claim 19, Andini disclosed the use of fluorescently labeled probes in the detection; paragraph [0139].
Regarding claim 20, Andini applied the method to Borrelia burgdorferi; see paragraph [0051] and figure 22.
Regarding claim 25, Andini disclosed “mammals” as subjects; paragraph [0145].
Regarding claim 29, Andini disclosed (paragraph [0006]): “The method may further comprise culturing the bacteria from the biological sample prior to amplification of the bacterial nucleic acids.” Andini disclosed blood cultures as one example; figure 1, table 1, paragraph [0216].
Regarding claim 30, Andini disclosed samples including blood, plasma, serum, urine, cerebrospinal fluid, and lymph; paragraph [0143].
Regarding claim 65, Andini disclosed (paragraph [0148]): “The ability to rapidly identify bacterial pathogens by HRM analysis should enable early treatment with appropriate antibiotics and reduce patient morbidity and mortality.”
Regarding claim 67, Andini disclosed:
A method of identifying a fastidious microorganism, the method comprising:
Paragraph [0006]: “In one aspect, the invention includes a method for identifying bacteria in a biological sample from a subject…”
performing a nucleic acid amplification for nucleic acid sequences associated with a fastidious microorganism species or genus in a sample obtained from a subject suspected of being infected by the fastidious microorganism,
Paragraph [0006]: “…the method comprising: a) providing a biological sample from the subject; b) isolating bacterial DNA from the biological sample; c) amplifying at least a portion of an internal transcribed spacer (ITS) region of the bacterial DNA using at least one set of primers capable of specifically hybridizing to the ITS region, whereby an amplicon is produced; d) performing high resolution melt (HRM) analysis of the amplicon; and e) identifying the species of the bacteria by comparing an HRM curve for the amplicon to a matching reference HRM curve for genomic ITS DNA from a known bacterial species. The method may further comprise culturing the bacteria from the biological sample prior to amplification of the bacterial nucleic acids.”
wherein performing the nucleic acid amplification comprises distributing nucleic acids from the sample into a plurality of partitions;
Paragraph [0010]: “Amplification may be performed using polymerase chain reaction (PCR) techniques, such as, but not limited to, real-time PCR, droplet digital PCR (ddPCR), hot-start PCR, solid phase PCR, and touchdown PCR.” ddPCR necessarily involves distributing nucleic acids into a plurality of partitions (“droplets”).
and analyzing nucleic acid amplification products derived from the nucleic acid amplification generated by amplification with a primer directed to an internal transcribed spacer (ITS) between two rRNA genes of the fastidious microorganism, wherein the two rRNA genes comprise 16S and 23S rRNA gene.
Paragraph [0006]: “…c) amplifying at least a portion of an internal transcribed spacer (ITS) region of the bacterial DNA using at least one set of primers capable of specifically hybridizing to the ITS region, whereby an amplicon is produced; d) performing high resolution melt (HRM) analysis of the amplicon; and e) identifying the species of the bacteria by comparing an HRM curve for the amplicon to a matching reference HRM curve for genomic ITS DNA from a known bacterial species.” The ITS is between the 16S and 23S rRNA genes; paragraph [0189].
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 56, 57 and 70-76 are rejected under 35 U.S.C. 103 as being unpatentable over Andini (US 2017/0321257) in view of Luchini (US 2012/0164749, IDS reference).
The disclosure of Andini has been discussed. In addition, regarding claim 70, Andini disclosed:
A method of identifying a fastidious microorganism in a sample,
Paragraph [0006]: “In one aspect, the invention includes a method for identifying bacteria in a biological sample from a subject…”
the method comprising: enriching the fastidious microorganism in a sample obtained from a subject suspected of being infected by the fastidious microorganism;
Paragraph [0006]: “…the method comprising: a) providing a biological sample from the subject; b) isolating bacterial DNA from the biological sample; c) amplifying at least a portion of an internal transcribed spacer (ITS) region of the bacterial DNA using at least one set of primers capable of specifically hybridizing to the ITS region, whereby an amplicon is produced; d) performing high resolution melt (HRM) analysis of the amplicon; and e) identifying the species of the bacteria by comparing an HRM curve for the amplicon to a matching reference HRM curve for genomic ITS DNA from a known bacterial species. The method may further comprise culturing the bacteria from the biological sample prior to amplification of the bacterial nucleic acids.”
performing a nucleic acid amplification for the nucleic acid sequences associated with the fastidious microorganism, wherein performing the nucleic acid amplification comprises distributing nucleic acids from the sample into a plurality of partitions, and performing the nucleic acid amplification on the plurality of partitions;
Paragraph [0010]: “Amplification may be performed using polymerase chain reaction (PCR) techniques, such as, but not limited to, real-time PCR, droplet digital PCR (ddPCR), hot-start PCR, solid phase PCR, and touchdown PCR.” ddPCR necessarily involves distributing nucleic acids into a plurality of partitions (in the case of ddPCR, “droplets”) and performing PCR on the partitions.
and analyzing nucleic acid amplification products derived from the nucleic acid amplification, wherein analysis of the nucleic acid amplification products identifies the fastidious microorganism infecting the subject.
Paragraph [0006]: “…d) performing high resolution melt (HRM) analysis of the amplicon; and e) identifying the species of the bacteria by comparing an HRM curve for the amplicon to a matching reference HRM curve for genomic ITS DNA from a known bacterial species.”
Regarding the term “fastidious”, Andini applied the method to Borrelia burgdorferi; see paragraph [0051] and figure 22.
Andini did not disclose capturing a biomarker from the fastidious microorganism, wherein the biomarker comprises nucleic acid sequences associated with the fastidious microorganism as recited in claim 70, or capturing the nucleic acid sequences that are extracted prior to performing the nucleic acid amplification, as recited in claim 56 (though Andini did disclose (paragraph [0216]): “Bacterial DNA was extracted from 500 μl aliquots of blood culture sample using a previously described protocol based on the Roche MagNA Pure extraction instrument…”, which may have functioned to “capture” extracted nucleic acids).
Andini also did not disclose that the “capturing” was carried out using a “porous hydrogel particle” (as recited in claims 57, 71 and 74), or that the “porous hydrogel particle” comprised an affinity for the nucleic acid (as recited in claims 57, 72 and 75), or that the “porous hydrogel particle” was a nanoparticle or magnetic particle (as recited in claims 73 and 76).
Luchini disclosed capture particles for harvesting analytes from solution, the particles made up of a polymeric matrix having a pore size that allows for the analytes to enter the capture particles (abstract). Luchini disclosed the particles could be used to protect analytes from degradation and to concentrate analytes present in low abundance (id.). Luchini disclosed that analytes included nucleic acids (paragraphs [0006], [0076], [0094]). Luchini disclosed that the particles could comprise affinity ligands, including nucleic acids (paragraph [0109]), and that “[a]nalyte-specific chemical or protein or nucleic acid affinity baits can be incorporated” (paragraph [0182]). Luchini disclosed the particles could be magnetic (paragraph [0062]). Luchini disclosed the particles could be nanoparticles (i.e., of nanometer scale in size; paragraph [0044]).
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the application to modify the method of Andini by incorporating a step of capturing the extracted nucleic acids prior to amplification using the particles of Luchini in order to concentrate the nucleic acids, as this would have rendered the method more sensitive for detecting microorganisms present at low abundance.
Claims 61 and 62 are rejected under 35 U.S.C. 103 as being unpatentable over Andini (US 2017/0321257) in view of GenBank Accession GQ856636 [online] 14 March 2011 [retrieved on 23 Jan 2026] retrieved from https://www.ncbi.nlm.nih.gov/nuccore/GQ856636.1.
The disclosure of Andini has been discussed. Andini taught using primers and probes to detect bacteria, including Borrelia, and targeted the ITS region between the 16S and 23S rRNA genes as discussed above. Andini did not teach the particular sequences of primers and probes recited in claims 61 and 62.
GenBank GQ856636 disclosed the sequence of the Borrelia burgdorferi 16S-23S ITS. The sequences of at least SEQ ID NO:4 and 6 are found within this known sequence:
SEQ ID NO: 4
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274
1172
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Greyscale
SEQ ID NO: 6
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260
1162
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Greyscale
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the application to modify the method of Andini by selecting appropriate probes and primers from the known sequence of the ITS from Borrelia burgdorferi as disclosed by GenBank GQ856636, including the sequences of SEQ ID NOs 4 and 6, to use when applying Andini’s method for detecting this pathogen. It was within the skill of the ordinary worker in the field to select appropriate primer and probe sequences from a known sequence for detecting that sequence.
Claim 64 is rejected under 35 U.S.C. 103 as being unpatentable over Andini (US 2017/0321257) in view of Berger (J. Clin. Micro. 30:359-361 (1992)).
The disclosure of Andini has been discussed. While Andini disclosed that the bacteria in the sample could be cultured prior to amplification (paragraph [0006]), and disclosed applying the method for the detection of Borrelia burgdorferi (paragraph [0051]), Andini did not disclose a culture medium comprising one of the components in claim 64.
Berger taught that Borrelia could be cultured in BSK medium, which contained sodium bicarbonate; page 359, right column.
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the application to modify the method of Andini when detecting Borrelia to use BSK medium, containing sodium bicarbonate, for culturing, since Berger taught this was a standard medium used for the culture of Borrelia.
Claim 69 is rejected under 35 U.S.C. 103 as being unpatentable over Andini (US 2017/0321257) in view of Polansky (US 2004/0023207, previously cited).
The disclosure of Andini has been discussed, including the teaching to culture the bacteria prior to amplification with primers hybridizing to the ITS region (e.g. by blood culture; paragraph [0006], figure 1). Andini did not disclose putting the primers or the medium used for culturing into a “kit”.
Polansky taught (paragraph [0919]): “Well known advantages of commercial kits include convenience and reproducibility due to manufacturing standardization, quality control and validation procedures.”
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the application to put the primers, culture medium, and other materials for performing the method of Andini into a “kit” to obtain the advantages of kits taught by Polansky.
Claim(s) 14, 15, 17, 19, 20, 25, 29, 30, 60, 65 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wilson (Experimental Parasitology 149:24-31 (2015), IDS ref) in view of Grun (US 2009/0086205, previously cited).
Wilson obtained blood from hamsters infected with Babesia, extracted the DNA, performed droplet digital PCR (ddPCR) assays using fluorescently labeled probes to distinguish between B. microti and B. duncani in order to detect these pathogens in the hamsters. The target of the ddPCR amplification was the ITS sequence (which occurs between the 18S and 28S rRNA genes). See abstract, last paragraph of introduction, section 2.2, Table 1, section 2.5, Figure 1.
Wilson did not disclose enriching the organism in the sample as recited in claim 14.
Grun disclosed (para [0007]): “Other current identification technologies, such as PCR, require a pre-enrichment step--i.e., a step in which the organism to be identified is grown for hours or days to provide the large number of organisms required for the identification method to be effective.”
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the application to add an enrichment step to the method of Wilson, as this would have increased the number of organisms present, making it easier to detect them.
Regarding claim 65, as Wilson taught Babesia to be a pathogen, it would have been obvious to treat subjects that had been detected as having such pathogen.
Claim(s) 14, 15, 17, 19, 20, 25, 30, 56, 57, 60, 65 and 70-76 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wilson (Experimental Parasitology 149:24-31 (2015), IDS ref) in view of Luchini (US 2012/0164749, IDS reference).
Wilson obtained blood from hamsters infected with Babesia, extracted the DNA, performed droplet digital PCR (ddPCR) assays using fluorescently labeled probes to distinguish between B. microti and B. duncani in order to detect these pathogens in the hamsters. The target of the ddPCR amplification was the ITS sequence (which occurs between the 18S and 28S rRNA genes). See abstract, last paragraph of introduction, section 2.2, Table 1, section 2.5, Figure 1.
Wilson did not disclose enriching the organism in the sample as recited in claim 14 or capturing the extracted nucleic acid using porous hydrogel particles as recited in claims 56, 57 and 70-76.
Luchini disclosed capture particles for harvesting analytes from solution, the particles made up of a polymeric matrix having a pore size that allows for the analytes to enter the capture particles (abstract). Luchini disclosed the particles could be used to protect analytes from degradation and to concentrate analytes present in low abundance (id.). Luchini disclosed that analytes included nucleic acids (paragraphs [0006], [0076], [0094]). Luchini disclosed that the particles could comprise affinity ligands, including nucleic acids (paragraph [0109]), and that “[a]nalyte-specific chemical or protein or nucleic acid affinity baits can be incorporated” (paragraph [0182]). Luchini disclosed the particles could be magnetic (paragraph [0062]). Luchini disclosed the particles could be nanoparticles (i.e., of nanometer scale in size; paragraph [0044]).
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the application to modify the method of Wilson by incorporating a step of capturing the extracted nucleic acids prior to amplification using the particles of Luchini in order to concentrate the nucleic acids, as this would have rendered the method more sensitive for detecting microorganisms present at low abundance. Note that this would also fall within the meaning of “enriching”.
Regarding claim 65, as Wilson taught Babesia to be a pathogen, it would have been obvious to treat subjects that had been detected as having such pathogen.
Response to Arguments
Applicant's arguments filed 10/16/2025 regarding the rejection of claims 14, 15, 17, 19, 20, 25, 29, 30, 56, 60 and 65 under 35 USC 103 over Wilson in view of Grun have been fully considered but they are not persuasive. Applicant’s argument is that Grun is non-analogous art and therefore “a person of ordinary skill in the art would not have considered Grun’s Raman spectroscopy to modify assays described in Wilson”. This argument is based on the premise that “Grun is directed to a fundamentally different technology than Wilson”. This argument is not persuasive because, while Grun’s methods are directed to Raman spectroscopy rather than PCR, Grun nevertheless taught something of relevance to PCR, which is what was cited in the rejection: namely that PCR requires a pre-enrichment step. Therefore, that portion of Grun relied on in the rejection is germane to the methods of Wilson, since Wilson was using PCR.
Conclusion
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/SAMUEL C WOOLWINE/ Primary Examiner, Art Unit 1681