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 .
Claim status
Claims 1-3 are pending following the Reply filed 02/05/2026. Claims 1 and 3 are withdrawn. Claim 2 is presently considered.
Withdrawn
The objection of claim 2 is withdrawn in light of the amendments.
The rejection of claim 2 under 35 U.S.C. 103 is withdrawn in light of Applicant’s arguments. See Response to Arguments for further discussion.
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.
Claim 2 is rejected under 35 U.S.C. 101 because the claimed invention is directed to the observation of a natural phenomenon without significantly more.
Step 1: It must first be determined if the claim is to a statutory category and, if so, proceed to step 2A prong 1.
Claim 2 recites a screening method for antimicrobial agents and falls within the statutory category of a process.
Step 2A, prong 1: Prong 1 requires the Examiner to evaluate whether the claim recites a judicial exception and, if so, proceed to prong 2.
Independent claim 2 recites “A screening method for antimicrobial agents comprising: supplying a sample containing a candidate antimicrobial agent to pan-resistant K. pneumoniae which has chromosomal DNA comprising the nucleotide sequence of SEQ ID NO: 1 and plasmid DNA comprising the nucleotide sequence of SEQ ID NO: 2.”
The specification describes this bacterium as an isolate that the inventors obtained and then sequenced, rather than a non-naturally engineered organism. For example, in view of the specification: the inventors “obtained a novel PDR K. pneumoniae ST11 isolate” from a patient (see pg. 4, para. [0007]); the inventors conducted whole-genome analysis of K. pneumoniae isolated from patients and determined the chromosomal and plasmid sequences (see pg. 6, para. [0014]); the screening method is described as supplying a candidate antimicrobial agent to this pan-resistant K. pneumoniae (see pg. 7, para. [0023]); “The pan-resistant K. pneumoniae found by the inventors has chromosomal DNA consisting of the SEQ ID NO: 1 and plasmid DNA consisting of the SEQ ID NO: 2…” (see pg. 7, para. [0024]); isolate TK1401 was previously identified from patient samples (see pg. 8, para. [0029]); the complete genome sequence was determined from the same isolate described in paras. [0007] and [0029] (see pg. 8, para. [0032]); and the complete genome sequence of isolate TK1401 is shown in SEQ ID NOs: 1 and 2 (see pg. 11, para. [0038]).
Thus, the claim recites a naturally occurring microorganism and its naturally occurring genomic sequences, i.e., a natural phenomenon / product of nature. The additional step of “supplying a sample containing a candidate antimicrobial agent” to that naturally occurring bacterium merely places the natural organism in contact with a test substance in order to determine its effects. This is the observation of a natural correlation/phenomenon which exists in principle apart from any human action and represents a judicial exception.
Step 2A, prong 2: Prong 2 requires the Examiner to evaluate whether the claim recites additional elements that integrate the exception into a practical application of that exception and, if not, proceed to step 2B. In order to integrate the recited judicial exception into a practical application, the claim will apply, rely on, or use the judicial exception that imposes a meaningful limit such that the claim is more than a drafting effort to monopolize the judicial exception. Examiners evaluate integration by identifying additional elements in the claim beyond the judicial exception and evaluating those elements individually and in combination to determine whether they integrate the exception in to a practical application. Examples that have been found by the Courts in which the exception was not integrated into a practical application include:
- Mere instructions to implement an abstract idea on a computer
- Adding generic instructions that the judicial exception should be used ("apply it")
- Adding insignificant extrasolution activity to the exception ("mere data gathering")
- Generally linking the use of the exception to a particular technological environment or field of use
In this case, there are no elements at all after the judicial exception and thus there cannot be any practical application of the exception claimed. The only action recited beyond the natural bacterium itself is supplying a sample containing a candidate antimicrobial agent to the bacterium. This is a broad, result-oriented instruction to apply the natural bacterium in a screening context, without reciting any meaningful limitation on how the screening is performed, how any result is measured, or any treatment/manufacturing step that would impose a practical application beyond use of the natural organism itself.
The specification confirms this step is generic and conventional. In particular, the specification explains that candidate antimicrobial samples are simply “given to pan-resistant K. pneumoniae,” and if a decrease in surviving bacteria is confirmed, the agent “can be evaluated” as effective (see pg. 7, para. [0024]). The specification describes ordinary antimicrobial susceptibility testing using a MicroScan WalkAway apparatus, Etest, and broth microdilution method (see pg. 8, para. [0031]), and the use of “known methods” and “commercially available software”, reflecting reliance on routine techniques rather than any asserted technical improvement in screening methodology (see pg. 6, para. [0018] and [0020]).
Claim 2 does not recite a specific improved assay format, a particular unconventional detection technique, a transformation of the bacterium, a treatment of a patient, or any other meaningful limitation that would amount to more than use of a natural organism as a screening tool.
This is similar to the decision in Mayo (566 U.S. 66 (2012)) where the claims also ended after the observation and was considered no more than “informing the doctor that metabolite concentrations above or below these thresholds ‘indicate a need’ to decrease or increase (respectively) the drug dosage”. In this case, the “supplying” of the sample informs others, such as doctors, that the response of the bacterium correlates to the efficacy of the antimicrobial agent. As such, there are no elements which are deemed significantly more than the judicial exception itself. The claim amounts to instructions to observe a relevant, naturally occurring response to a test substance in a relevant sample to inform others regarding what that observation indicates. As such, the claim as a whole is deemed ineligible.
Step 2B: Where a claim does not integrate the exception, a claim may nevertheless be patent eligible, for example where additional elements are “significantly more” than the exception such that the additional elements were unconventional in combination. Considerations include whether or not the claim adds a specific limitation or combination of limitations that are not well-understood, routine, conventional activity in the field, which is indicative that an inventive concept may be present; or simply appends well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, which is indicative that an inventive concept may not be present.
In this case, there are no elements at all after the judicial exception to consider as amounting to significantly more than the judicial exception. The only action recited beyond the natural bacterium itself is supplying a sample containing a candidate antimicrobial agent to the bacterium, which is a well-understood, routine and conventional laboratory activity.
Support from the specification includes: paragraph [0024], which describes the screening concept at a high level: candidate antimicrobial samples are given to the bacterium and efficacy is evaluated based on decreased survival; paragraph [0030], which describes ordinary culture and growth of bacterial strains; paragraph [0031], which describes routine susceptibility testing methods and standard laboratory equipment; and paragraph [0032], which describes routine genome sequencing/analysis procedures.
These passages indicate that the claim uses ordinary microbiological testing techniques on a naturally occurring bacterial isolate. There is no additional element, or ordered combination of elements, that is unconventional or that transforms the nature of the claim into patent-eligible subject matter. Thus, there is simply no argument that any portion of claim 2 was not routine, well-known, or conventional.
In conclusion, when taken as a whole and following current guidance for patent eligibility, the claim fails to meet the standard for patent eligibility as the claim is directed to a judicial exception without significantly more.
Therefore, claim 2 is not patent eligible.
Response to Arguments
Regarding the rejection of claim 2 under 35 U.S.C. 103, Applicant argues that de Man et al. does not disclose TK1401, a PDR Klebsiella pneumoniae strain, nor does it provide any nucleotide sequences corresponding to SEQ ID NO: 1 or NO: 2.
Applicant’s arguments have been fully considered and they are persuasive.
The examiner agrees that the de Man and Deck references do not teach a Klebsiella pneumoniae strain comprising SEQ ID NOs 1 and 2. See the Pertinent Prior Art section below for further discussion. Hence, the rejection has been withdrawn.
Pertinent Prior Art
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Deck (US 20160281125 A1; previously cited) teaches methods of determining whether a target bacteria is susceptible to an antimicrobial compound, comprising providing a sample comprising the target bacteria and maintaining the sample in the presence of an antimicrobial compound to provide an antimicrobial compound-exposed target bacterial sample (see Abstract). Deck also discloses that: (1) the emergence and spread of antimicrobial-resistant bacteria is a serious global health threat; (2) this development is associated with extensive and increasing use of antimicrobial agents; (3) coupled with the limited development of new antimicrobial agents, this has drastically limited the treatment options for resistant pathogens; (4) infections with resistant pathogens are associated with higher mortality, morbidity, and health care costs; and (5) early targeted antimicrobial compound treatment is an important prognostic factor especially in seriously ill patients (see pg. 1 para. [0002]). Accordingly, there is a demand for methods that can determine antimicrobial compound susceptibility and enable early targeted therapy as early in a treatment as possible (see pg. 1, para. [0003]).
Deck teaches that the methods of the disclosure can be used to screen a candidate compound to identify a compound having antimicrobial activity against a target bacteria (see pg. 5, para. [0050]). Deck teaches that the target bacteria express at least one gene product that confers in whole or in part resistance to an antibiotic or class of antibiotics to the target bacteria (see pg. 12, para. [0124]). In Deck’s Examples, antimicrobial compound susceptibility testing was conducted using meropenem-sensitive and meropenem-resistant strains of Klebsiella pneumoniae in the presence of imipenem, ertapenem, and meropenem (see pgs. 8-9, paras. [0080]-[0081], [0084]-[0087], [0089]-[0090]; Figs. 1-2, 5-8, 10-11). Hence, Deck teaches a screening method for antimicrobial agents comprising supplying a sample containing a candidate antimicrobial agent to antibiotic-resistant strains of K. pneumoniae.
de Man, et al. (Genomic Analysis of a Pan-Resistant Isolate of Klebsiella pneumoniae, United States 2016. mBio. 2018 Apr 3;9(2): e00440-18; previously cited) teach that antimicrobial resistance is a threat to public health globally and leads to an estimated 23,000 deaths annually in the United States alone. de Man discloses the genomic characterization of a pan-resistant Klebsiella pneumoniae strain that is non-susceptible to all 26 antibiotics tested that was isolated from a U.S. patient. de Man discloses that this is one of the first K. pneumoniae isolates in the United States to have been reported to the Centers for Disease Control and Prevention (CDC) as non-susceptible to all drugs tested, including all beta-lactams, colistin, and tigecycline. See Title and Abstract.
de Man teaches that carbapenem-resistant Enterobacteriaceae (CRE) can possess a variety of antimicrobial resistance mechanisms, both intrinsic and acquired, that render antimicrobials ineffective, and among these mechanisms, acquired carbapenemases, such as Klebsiella pneumoniae carbapenemase (KPC), are of greatest public health concern because of the potential for rapid dissemination of genes encoding these enzymes via mobile genetic elements, including plasmids (see pg. 2, para. 1). de Man teaches that evaluation of multidrug-resistant organisms using advanced molecular detection, including whole-genome sequencing, is needed to better understand the origins, acquisition, and spectrum of antimicrobial resistance mechanisms and their combination within a bacterial host (see pg. 5, para. 7).
However, the prior art above do not teach a pan-resistant K. pneumoniae having chromosomal DNA comprising the nucleotide sequence of SEQ ID NO: 1 and plasmid DNA comprising the nucleotide sequence of SEQ ID NO: 2.
GenBank CP021833 (cited on Form 892), identified as “Klebsiella pneumoniae strain AR_0120, complete genome” appears to be the closest prior art sequence to SEQ ID NO: 1 based on a series of sequence alignments (see “Sequence Alignment of SEQ ID NO: 1” cited on Form 892).
However, no prior art sequence has been found comprising the nucleotide sequence of instant SEQ ID NO: 2 (see, e.g., “ABSS Search Summary” cited on Form 892).
Therefore, in the absence of any evidence to the contrary, a pan-resistant K. pneumoniae having a chromosomal DNA comprising the nucleotide sequence of SEQ ID NO: 1 and plasmid DNA comprising the nucleotide sequence of SEQ ID NO: 2 is free of the prior art of record.
Conclusion
No claims are allowed.
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/DENNIS IGNATIUS ARMATO JR/Examiner, Art Unit 1651
/MELENIE L GORDON/Supervisory Patent Examiner, Art Unit 1651
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