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 .
Continued Examination Under 37 CFR 1.114
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 November 28, 2025 has been entered.
DETAILED ACTION
Claims 1-12, 17, 22 and 24 are cancelled. Claim 23 is withdrawn.
Claims 13-16 and 18-21 are under examination herein.
The rejections of claims 17 and 22 are withdrawn in light of the cancellation of the claims.
Priority
This application is a 371 of PCT/EP2020/082771 filed on 11/19/2020, which claims benefit of application FRANCE FR1913060 filed on 11/21/2019. For the purposes of art, the effective filing date is November 19, 2020.
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 13-16 and 18-21 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (abstract ideas – mental steps) without significantly more.
The claims recite a method for guiding the treatment to a patient infected with a strain of Gram-negative bacteria of the Enterobacteriaceae family comprising measuring an amount of 2-hydroxymyristate and 3-hydroxymyristate present in lipopolysaccharide of the bacteria; comparing said amount of 2-hydroxymyristate with said amount of 3-hydroxymyristate; concluding that the strain is pathogenic if a ratio of 2-hydroxymyristate to 3-hydroxymyristate is greater than 0.01; and initiating anti-infection treatments before an invasive infection, septic shock and death of patient. Thus, the claims are directed to a process (Step 1: Yes).
The claims set forth judicial exceptions which are abstract ideas. In claim 13, the amount of 2-hydroxymyristate and 3-hydroxymyristate acid is measured and compared, and if the ratio of 2-hydroxymyristate to 3-hydroxymyristate is greater than 0.01, it is concluded that the strain is pathogenic, which is a mental step (Step 2A: Yes).
This judicial exception of mental steps is not integrated into a practical application. The only additional elements recited are measuring the amount of 2-hydroxymyristate and 3-hydroxymyristate present in lipopolysaccharide of the bacteria in claim 13, and isolating the bacteria from a sample in claim 21. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the limitations do not impose any meaningful limits on practicing the abstract idea. While the claims recite an active method step of measuring the amount of 2-hydroxymyristate and the amount of 3-hydroxymyristate present in lipopolysaccharide of bacteria, and isolating the bacteria from a sample, these steps are a well-understood, routine and conventional activity known in the art before the filing of the current invention. While claim 13 contains an additional step of initiating anti-infection treatments before an invasive infection, septic shock and death, this step is recited at such generality that it is still considered to be well-understood, routine and conventional.
Gosiewski et al. (“Comparison of Methods for Isolation of Bacterial and Fungal DNA from Human Blood”, Current Microbiology, 2014, Vol. 68, pp.149-155; previously cited) describes the isolation of DNA from blood to detect Escherichia coli, Staphylococcus aureus, Candida albicans, and Aspergillus fumigatus (abstract). Gosiewski identifies ready-to-use kits on the market including Septifast (Roche) and Septitest (Molzym) that detect microbes in the blood (p.149 2nd column last paragraph – p. 150, 1st column top paragraph).
Gibbons et al. (“An Inner Membrane Dioxygenase that Generates the 2-Hydroxymyristate Moiety of Salmonella Lipid A”, Biochemistry, 2008, Vol. 47, No. 9, pp.2814-2825; previously cited) describes the synthesis of 2-hydroxymyristate modified lipid A in the presence of O2 by E. coli (p.2821, 2nd column top paragraph). Gibbons further identifies GC/MS analysis of 3-hydroxymyristate and 2-hydroxymyristate standards as the TMS derivatives of their methyl esters (p.2823, 2nd column 3rd paragraph).
Weil et al. (“Circulating levels of 3-hydroxymyristate, a direct quantification of endotoxaemia in noninfected cirrhotic patients”, Cirrhosis and Liver Failure, 2019, Vol.39, Issue 1, pp.106-114) describes measuring 3-hydroxymyristate (3-HM), a lipid component of lipopolysaccharide (abstract). Weil states that bacterial endotoxin lipopolysaccharide (LPS) is the culprit component of the outer surface of gram-negative bacteria and has been considered as a marker of endotoxaemia (p.107, 1st column 1st paragraph). Weil further discusses that the lipid A structure of LPS is composed of primary esterified acyl chains, most frequently represented in the different bacterial strains by 3-hydroxymyristate (3-HM) (p.107, 1st column 1st paragraph).
The isolation of bacteria from a blood sample is well-understood, routine and conventional in the field of sepsis detection in blood, as taught by Gosiewski et al. The concept of comparing a measured value to a reference value is well-understood, routine and conventional as taught by Gibbons et al. The concept of measuring 2-hydroxymyristate and 3-hydroxymyrsistate from lipid A of bacteria is well-understood, routine and conventional as taught by Gibbons et al. and Weil et al.
Thus, claims 13-16 and 18-21 are rejected under 35 U.S.C. §101.
Response to Arguments
Applicant argues that amended claim 13 now recites “for guiding the treatment to a patient infected with a strain of Gram-negative bacteria of the Enterobacteriaceae family” and “initiating anti-infection treatments before an invasive infection, septic shock and death of the patient”, which impose meaningful limits into a practice (See Remarks dated 11/28/25, p.6). Applicant argues that it is essential to differentiate strains with a high risk of human pathogenicity from those responsible for asymptomatic carriage in order to initiate appropriate treatments as early as possible and to not unnecessarily treat non-pathogenic strains and generate unnecessary antibiotic selection pressure (See Remarks dated 11/28/25, p.6 last paragraph).
Applicant's arguments filed November 28, 2025 have been fully considered but they are not persuasive. Although applicant has amended the preamble and added a step of “initiating anti-infection treatment”, these actions still comprise a judicial exception as discussed in the rejection above. The steps of “comparing said amount of 2-hydroxymyristate to said amount of 3-hydroxymyristate” and “concluding that the strain is pathogenic if a ratio of 2-hydroxymyristate and 3-hydroxymyristate is greater than 0.01” are mental steps. The step of “measuring the amount of 2-hydroxymyristate and 3-hydroxymyristate present in lipopolysaccharide of the bacteria” is a routine, conventional and well-known step in the art as taught by Gibbons et al. and Weil et al. The use of gas chromatography, gas-liquid chromatography, HPLC or mass spectrometry to measure the amount of 2-hydroxymyristate is well-known, routine and conventional in the art, and does not constitute significantly more, nor constitute a practical application that overcomes the judicial exception. The intended use of the method to guide the treatment to a patient infected with a strain of gram-negative bacteria is also a mental step, and does not contribute significantly more to overcome the judicial exception.
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 13-16, 18 and 21 are rejected under 35 U.S.C. 103 as being unpatentable over Gibbons et al. (“Oxygen Requirement for the Biosynthesis of the S-2-Hydroxymyristate Moiety in Salmonella typhimurium Lipid A”, The Journal of Biological Chemistry, 2000, Vol. 275, No. 42, pp.32940-32949; previously cited) in view of Munford (“Sensing Gram-Negative Bacterial Lipopolysaccharides: a Human Disease Determinant?”, Infection and Immunity, 2008, Vol. 76, No. 2, pp.454-465; previously cited), Bartholomew et al. (“2-Hydroxylation of Acinetobacter baumannii Lipid A Contributes to Virulence”, Infection and Immunity, 25 March 2019, Vol. 87, No.4, article e00066-19, 17 pages; previously cited) and Weil et al (“Circulating levels of 3-hydroxymyristate, a direct quantification of endotoxaemia in noninfected cirrhotic patients”, Cirrhosis and Liver Failure, 2019, Vol.39, Issue 1, pp.106-114).
Regarding claim 13, Gibbons teaches that Lipid A molecules of certain Gram-negative bacteria, including Salmonella typhimurium and Pseudomonas aeruginosa may contain secondary S-2-hydroxyacyl chains (abstract). Gibbons teaches that Lipopolysaccharide is the principal constituent of the outer leaflet of the outer membranes of Gram-negative bacteria, and recognition of LPS by mammalian cells activates innate immune responses (p.32940, 2nd column 2nd full paragraph). Gibbons further teaches the purification of 2-hydroxymyristate-modified Lipid A from E. coli cells using chromatography and TLC plates (p.32942, 1st column – Purification of Unmodified and 2-hydroxymyristate-modirided Lipid A from E. coli Cells Expressing S. typhimurium lpxO). Gibbons teaches that two closely migrating lipid A species were resolved and could be seen transiently as distinct white zones; the more slowly migrating component containing the 2-hydroxymyristate substituent (p.32942, 1st column last paragraph). Gibbons teaches that stimulation of S-2-hydroxymyristate biosynthesis at low Mg2+ concentrations suggest a function for 2-hydroxylation in pathogenesis (p.32941, 1st column 2nd paragraph). Gibbons further teaches that mutants defective in PhoP/PhoQ do not make any of these substituents, and such strains are much less virulent than wild type and are susceptible to cationic anti-microbial peptides (p.32946, 2nd column last paragraph).
Gibbons is silent about comparing 2-hydroxymyristate to 3-hydroxymyristate, and concluding that the strain is pathogenic if a ratio of 2-hydroxymyristate to 3-hydroxymyristate is greater than 0.01.
However, Munford teaches that a prominent role for host-LPS interactions in the pathogenesis of gram-negative bacterial diseases is plausible because LPS is the gram-negative bacterial molecule that vertebrates seem to detect most sensitively (p.454, 1st column, 3rd paragraph). Munford further teaches that the lipid A moiety retains certain features in almost all gram-negative bacteria, and it is this semiconserved structure that animals can sense to detect the presence of many gram-negative bacteria in their tissues (p.454, 1st column, 3rd paragraph). Munford teaches that the hydroxyl groups of the hydroxymyristates at positions 2’ and 3’ are substituted by laurate and myristate respectively (p.455, FIG. 1).
Bartholomew teaches that 2-hydroxylation of Acinetobacter baumannii lipid A contributes to virulence (title). Bartholomew teaches that the lipid A structure can be modified by pathogens in response to different conditions, which may result in resistance to cationic antimicrobial peptides, reduced or increased activation of inflammatory responses (p.1, 1st paragraph). Bartholomew teaches that LpxO encodes the enzyme responsible for the 2-hydroxylation of lipid A (abstract). Bartholomew further teaches the importance of LpxO-dependent modification in immune evasion, as 2-hydroxylation of lipid A limits the activation of the mitogen-activated protein kinase Jun N-terminal protein kinase to attenuate inflammatory responses (abstract).
Weil teaches measuring 3-hydroxymyristate (3-HM), a lipid component of lipopolysaccharide (abstract). Weil teaches bacterial endotoxin lipopolysaccharide (LPS) is the culprit component of the outer surface of gram-negative bacteria and has been considered as a marker of endotoxaemia (p.107, 1st column 1st paragraph). Weil further teaches the lipid A structure of LPS is composed of primary esterified acyl chains, most frequently represented in the different bacterial strains by 3-hydroxymyristate (3-HM) (p.107, 1st column 1st paragraph). Weil teaches LPS concentration was determined at baseline by direct quantification of 3-hydroxymyristate (3-HM) by high-performance liquid chromatography coupled with mass spectrometry (HPLC-MS/MS assay) (p.107, 2nd column last paragraph).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to measure the amount of 2-hydroxymyristate and measure the amount of 3-hydroxymyristate, because Gibbons teaches the purification of 2-hydroxymyristate-modified Lipid A from E. coli cells and Weil teaches the lipid A structure of LPS is most frequently represented by 3-hydroxymyristate. One of ordinary skill in the art would have been motivated to use 2-hydroxymyristate as an identifying feature of pathogenicity because Bartholomew teaches that the lipid A structure can be modified by pathogens which may result in resistance to cationic antimicrobial peptides. One of ordinary skill in the art would have found it beneficial to detect 2-hydroxymyristate as a pathogenic marker because both Gibbons and Bartholomew teach that there is a role of 2-hydroxylation as a marker of pathogenicity, and Munford teaches that the lipid A moiety retains certain features in almost all gram-negative bacteria, and animals can sense this semiconserved structure to detect the presence of many gram-negative bacteria in their tissues.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to compare the amount of 2-hydroxymyristate and 3-hydroxymyristate present in the sample because Gibbons teaches comparing 2-hydroxymyristate to a reference value, and Weil teaches 3-hydroxymyristate values to a baseline. One of ordinary skill in the art would reasonably expect that comparing the amount of 2-hydroxymyristate to the amount of 3-hydroxymyristate would predictably result in a ratio of 2-hydroxymyristae to 3-hydroxymyristate, and it was known in the art at the time of invention that bacterial lipid A contains both 2-hydroxymyristate and 3-hydroxymyristate.
While the references do not explicitly teach a ratio of 2-hydroxymyristate to 3-hydroxymyristate of greater than 0.01, it would have been obvious to one of ordinary skill in the art to determine a ratio as discussed above and then conclude whether a strain is pathogenic based on the value, because Gibbons teaches measuring both 2-hydroxymyristate and 3-hydroxymyristate, and also teaches comparing 2-hydroxymyristate to a reference value. One of ordinary skill in the art would reasonably expect that selecting the amount of 3-hydroxymyristate as the reference value in the method of Gibbons would predictably result in the determination of a ratio of 2-hydroxymyristate to 3-hydroxymyristate that one of ordinary skill in the art could then determine to be greater than 0.01.
Regarding claims 14-16, Gibbons teaches the bacteria Escherichia coli strain K12 (abstract).
Bartholomew teaches the bacteria Acinetobacter baumannii (title).
Gibbons and Bartholomew do not teach wherein the bacterium belongs to the genus Enterobacter (claims 14 and 15) or the species Enterobacter cloacae complex (claim 16).
However, Munford teaches the LPSx (lipid As) produced by commensals such as Klebsiella pneumoniae, Enterobacter cloacae, and E. coli have closely similar structures, and they elicit the same inflammatory responses with similar potencies (p.456, 1st column top paragraph). Munford further teaches that LPS preparations obtained from clinical isolates of Acinetobacter baumannii were potently proinflammatory towards human cells (p.457, 1st column 2nd paragraph).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Gibbons to replace the E. coli strain taught by Gibbons with the Enterobacter cloacae strain taught by Munford, because Munford teaches that Enterobacter cloacae and E. coli have closely similar lipid As structures and elicit the same inflammatory response with similar potencies, and further that Acinetobacter baumannii also was proinflammatory towards human cells. Each of Gibbons, Munford and Bartholomew teach the detection of lipopolysaccharide lipid A from gram-negative bacteria. One of ordinary skill in the art would reasonably expect that replacing E. coli with Enterobacter cloacae would predictably result a method for predicting the pathogenicity of a gram-negative bacteria of the Enterobacteriaceae family, because each of E. coli, Acinetobacter baumannii and Enterobacter cloacae are gram-negative bacteria, and it would amount to a simple replacement of one gram-negative bacteria strain for another, and it was known in the art at the time of invention that Enterobacter cloacae, Acinetobacter baumannii and E. coli lipid As had closely similar structures.
Regarding claim 18, for the purposes of prior art, the limitation “a method for predicting the resistance of strains of Enterobacter cloacae to antibiotics” is interpreted as an intended result, as there are no additional method steps recited. Thus, the method of Gibbons in view of Bartholomew and Munford would render the ability to predict the resistance of Enterobacter cloacae to antibiotics because Gibbons teaches the active method steps of measuring the amount of 2-hydroxymyristate present in the lipopolysaccharide of the bacteria and comparing with a reference value, and both Gibbons and Bartholomew identify the lack of 2-hydroxylation as a measure of sensitivity to cationic antimicrobial peptides. The method is obvious for the reasons set forth above.
Regarding claim 21, Gibbons teaches that 200 mL of bacteria was harvested by centrifugation at 4C; the cell pellet was resuspended in 80mL of phosphate-buffered saline to which was added 100mL of chloroform and 200mL of methanol to extract glycerophospholipids (relevant to further comprising a prior step of isolating the bacteria from the sample) (p.32942, 1st column 2nd paragraph).
Claims 19-20 are rejected under 35 U.S.C. 103 as being unpatentable over Gibbons et al. (“Oxygen Requirement for the Biosynthesis of the S-2-Hydroxymyristate Moiety in Salmonella typhimurium Lipid A”, The Journal of Biological Chemistry, 2000, Vol. 275, No. 42, pp.32940-32949; previously cited) in view of Munford (“Sensing Gram-Negative Bacterial Lipopolysaccharides: a Human Disease Determinant?”, Infection and Immunity, 2008, Vol. 76, No. 2, pp.454-465; previously cited), Bartholomew et al. (“2-Hydroxylation of Acinetobacter baumannii Lipid A Contributes to Virulence”, Infection and Immunity, 25 March 2019, Vol. 87, No.4, article e00066-19, 17 pages; previously cited) and Weil et al. (“Circulating levels of 3-hydroxymyristate, a direct quantification of endotoxaemia in noninfected cirrhotic patients”, Cirrhosis and Liver Failure, 2019, Vol.39, Issue 1, pp.106-114) as applied to claim 13 above, and further in view of Jayol et al. (“Rapid Detection of Polymyxin-Resistant Enterobacteriaceae from Blood Cultures”, Journal of Clinical Microbiology, 2016, Vol. 54, Issue 9, pp.2273-2277; previously cited).
The teachings of Gibbons et al., Munford, Bartholomew and Weil et al. are discussed above.
Regarding claims 19-20, Gibbons, Munford, Bartholomew and Weil do not teach wherein bacteria are present in a biological sample (claim 19) or wherein the biological sample is from a mammal and is selected from blood (claim 20).
However, Jayol teaches the rapid detection of polymyxin-resistant Enterobacteriaceae from blood cultures (title, abstract). Jayol teaches clinical blood cultures recovered from nonduplicate patients that were detected as positive by the BacT/Alert 3D blood culture system and stained as gram-negative (relevant to wherein the biological sample originates from a mammal, and is selected from blood) (p.2275, 1st column – Clinical blood cultures). Jayol teaches that rapid identification and antimicrobial susceptibility testing are essential for guiding clinicians in the selection of the most appropriate treatment for patients with bloodstream infections (p.2273, 1st column 2nd paragraph). Jayol further teaches that mortality rates from sepsis in intensive care units ranges from 20 to 60% worldwide, and inappropriate initial therapy for septic shock occurs in about 20% of patients resulting in 5-fold reduction in survival (p.2273, 1st column, 2nd paragraph).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of Gibbons, Munford, Bartholomew and Weil to replace the bacterial culture sample taught by Gibbons and Munford with a clinical blood sample taught by Jayol. One of ordinary skill in the art would have been motivated to determine the presence of bacteria in a blood sample because Jayol teaches that doing so allows a clinician to rapidly determine the best way to treat a blood infection. One of ordinary skill in the art would have found it beneficial to have a rapid test to help improve the mortality rates due to sepsis in the hospital.
Response to Arguments
Applicant argues that none of the cited prior art teaches or suggests the feature recited in amended claim 13, and all cited prior art references are silent regarding the measurement of 3-hydroxymyristate concentration, which is a critical feature recited in claim 13 (See Remarks dated 11/28/25, p.8 1st paragraph).
Applicant argues that even if the combination of the cited prior art is assumed to be proper, the combination fails to teach every element of the claimed invention (See Remarks dated 11/28/25, p.8 2nd paragraph).
Applicant's arguments filed November 28, 2025 have been fully considered but they are not persuasive.
As discussed in the rejection above, Gibbons teaches that recognition of LPS by mammalian cells activates innate immune responses. Gibbons teaches purifying 2-hydroxymyristate-modified Lipid A from E. coli using chromatography and TLC. Munford teaches that the lipid A moiety retains certain features in almost all gram-negative bacteria, and it is this structure that animals can sense to detect the presence of many gram-negative bacteria in their tissues. Bartholomew teaches that 2-hydroxylation of Acinetobacter baumannii lipid A contributes to virulence. Weil teaches the lipid A structure of LPS is composed of primary esterified acyl chains, most frequently represented in the different bacterial strains by 3-hydroxymyristate (3-HM), and teaches LPS concentration was determined at baseline by direct quantification of 3-hydroxymyristate (3-HM) by high-performance liquid chromatography coupled with mass spectrometry (HPLC-MS/MS assay). One of ordinary skill in the art would have been motivated to use 2-hydroxymyristate as an identifying feature of pathogenicity because Bartholomew teaches that the lipid A structure can be modified by pathogens which may result in resistance to cationic antimicrobial peptides. One of ordinary skill in the art would have been motivated to measure 3-hydroxymyristate because Weil teaches that lipid A structure of LPS is most frequently represented in different bacterial strains by 3-hydroxymyristate. One of ordinary skill in the art would have found it beneficial to do so because both Gibbons and Bartholomew teach that there is a role of 2-hydroxylation as a parker of pathogenicity, and Munford teaches that the lipid A moiety retains certain features in almost all gram-negative bacteria that can be sensed by animals.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DEEPA MISHRA whose telephone number is (571) 272-6464. The examiner can normally be reached Monday - Friday 9:30am - 3:30pm 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, Louise W. Humphrey can be reached on (571) 272-5543. 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.
/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/DEEPA MISHRA/Examiner, Art Unit 1657