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US 12,742,212 B2Granted
Method for predicting and evaluating antimicrobial therapy when molecular PCR diagnostic testing results yield multi-organisms and multi-resistant bacteria from a single DNA sample
AssigneeAdvanced Therapeutic Assist
InventorRobin Prince
Life of this patent
Estimating the term…
Abstract
A method for predicting and evaluating antimicrobial therapy for patient specific molecular results when molecular testing yields multi-organism and multi-resistant bacterial. Essential in the fight against antimicrobial resistance is the effective use of antibiotics. An exemplary method provides healthcare providers a therapeutic guide for optimizing patient outcomes by significantly improving antibiotic stewardship by using resistant gene enzymes to guide antibiotic therapy most likely to succeed.
Claims24
A method for providing a targeted therapy specific to a patient having a urinary tract infection, the method comprising:
- obtaining a urine sample from the patient;
- obtaining one or more clinical assessment factors selected from patient age, patient gender, source of the urine sample, environmental setting of the patient, antibiotic allergies of the patient, clinical status of the patient, and an assigned international classification of disease (ICD-10) code of the patient;
- performing or having performed reverse transcription quantitative polymerase chain reaction (RT-qPCR) to detect and identify microbial organisms in the urine sample and detect and identify potential antibiotic resistance genes in the microbial organisms;
- identifying one or more microbial organisms in the urine sample using the RT-qPCR, and categorizing each of the identified one or more microbial organisms as Gram-positive bacteria, Gram-negative bacteria, or fungal;
- using a semi-quantitative value from the RT-qPCR associated with each identified one or more microbial organism to identify a probable cause of the infection, wherein:
- (i) the probable cause of the infection is a Gram-positive bacteria or a Gram-negative bacteria when the RT-qPCR sample contains at least 50,000 copies/ml of a Gram-positive bacteria or a Gram-negative bacteria, or
- (ii) the probable cause of the infection is fungal;
- identifying one or more potential antibiotic resistant genes in the identified one or more microbial organism by the RT-qPCR, the potential antibiotic resistance genes selected from the group consisting of CTX-M, TEM, SHV, PER, VEB, GES, IMP, NDM, VIM, OXA, KPC, SUL, DFR, ErmA, ErmB, ErmC, MefA, Aph, AAC, TetM, TetB, QnrA, QnrS, QnrB, Gyrase, MecA, MecC, VanA, VanB, Mcr, ACT, MIR, FOX, DHA, ACC, AmpC, and subtypes thereof;
- and
- when the probable cause of the infection is Gram-positive bacteria or Gram-negative bacteria, and
- when the identified potential antibiotic resistance genes comprises one or more of TEM, SHV, CTX-M, PER-1, VEB, GES-1, and OXA-1,
- applying to the patient a target therapy of one or more antibiotic based on:
- (a) eliminating antibiotics most likely to fail due to the identified potential antibiotic resistance genes TEM, SHV, CTX-M, PER-1, VEB, GES-1, and OXA-1, and providing one or more antibiotic to override the potential antibiotic resistance, and
- (b) accounting for the one or more clinical assessments factors of the patient,
- wherein the target therapy eliminates penicillins, monobactams, first generation and second generation cephalosporins, and monotherapy third generation cephalosporins as likely to fail, and provides a combination of beta-lactamase inhibitor with a third generation cephalosporin to override the potential antibiotic resistance.
12 more elements
A method for providing a targeted therapy specific to a patient having a urinary tract infection, the method comprising:
- obtaining a urine sample from the patient;
- obtaining one or more clinical assessment factors selected from patient age, patient gender, source of the urine sample, environmental setting of the patient, antibiotic allergies of the patient, clinical status of the patient, and an assigned international classification of disease (ICD-10) code of the patient;
- performing or having performed reverse transcription quantitative polymerase chain reaction (RT-qPCR) to detect and identify microbial organisms in the urine sample and detect and identify potential antibiotic resistance genes in the microbial organisms;
- identifying one or more microbial organisms in the urine sample using the RT-qPCR, and categorizing each of the identified one or more microbial organisms as Gram-positive bacteria, Gram-negative bacteria, or fungal;
- using a semi-quantitative value from the RT-qPCR associated with each identified one or more microbial organism to identify a probable cause of the infection, wherein:
- (i) the probable cause of the infection is a Gram-positive bacteria or a Gram-negative bacteria when the RT-qPCR sample contains at least 50,000 copies/ml of a Gram-positive bacteria or a Gram-negative bacteria, or
- (ii) the probable cause of the infection is a fungal;
- identifying one or more potential antibiotic resistance genes selected from the group consisting of CTX-M, TEM, SHV, PER, VEB, GES, IMP, NDM, VIM, OXA, KPC, SUL, DFR, ErmA, ErmB, ErmC, MefA, Aph, AAC, TetM, TetB, QnrA, QnrS, QnrB, Gyrase, MecA, MecC, VanA, VanB, Mcr, ACT, MIR, FOX, DHA, ACC, AmpC, and subtypes thereof;
- when the probable cause of the infection is Gram-positive negative or Gram-negative bacteria, and
- when the identified potential antibiotic resistance genes comprise one or more of NDM, IMP, and VIM, applying to the patient a target therapy of one or more antibiotic based on:
- (a) eliminating antibiotics most likely to fail due to the potential antibiotic resistance genes NDM, IMP, and VIM, and providing one or more antibiotic to override the potential antibiotic resistance, and
- (b) accounting for the one or more clinical assessment factor of the patient,
- wherein the target therapy eliminates penicillins, carbapenems, and first generation to fifth generation cephalosporins except for Avycaz (ceftazidime/avibactam) and Aztreonam (monobactam) as likely to fail, and provides one or more of Avycaz and Aztreonam to override the potential antibiotic resistance.
10 more elements
A method for providing a targeted therapy specific to a patient having a urinary tract infection, the method comprising:
- obtaining a urine sample from the patient;
- obtaining one or more clinical assessment factors selected from patient age, patient gender, source of the urine sample, environmental setting of the patient, antibiotic allergies of the patient, clinical status of the patient, and an assigned international classification of disease (ICD-10) code of the patient;
- performing or having performed reverse transcription quantitative polymerase chain reaction (RT-qPCR) to detect and identify microbial organisms in the urine sample and detect and identify potential antibiotic resistance genes in the microbial organisms;
- identifying one or more microbial organisms in the urine sample using the RT-qPCR, and categorizing each of the identified one or more microbial organisms as Gram-positive bacteria, Gram-negative bacteria, or fungal;
- using a semi-quantitative value from the RT-qPCR associated with each identified one or more microbial organism to identify a probable cause of the infection, wherein:
- (i) the probable cause of the infection is a Gram-positive bacteria or a Gram-negative bacteria when the RT-qPCR sample contains at least 50,000 copies/ml of a Gram-positive bacteria or a Gram-negative bacteria, or
- (ii) the probable cause of the infection is a fungal;
- identifying one or more potential antibiotic resistance genes selected from the group consisting of CTX-M, TEM, SHV, PER, VEB, GES, IMP, NDM, VIM, OXA, KPC, SUL, DER, ErmA, ErmB, ErmC, MefA, Aph, AAC, TetM, TetB, QnrA, QnrS, QnrB, Gyrase, MecA, MecC, VanA, VanB, Mcr, ACT, MIR, FOX, DHA, ACC, AmpC, and subtypes thereof;
- when the probable cause of the infection is Gram-positive negative or Gram-negative bacteria, and
- when the identified potential antibiotic resistance genes comprise one or more of OXA-48 and OXA-51,
- applying to the patient a target therapy of one or more antibiotic based on:
- (a) eliminating antibiotics most likely to fail due to the potential antibiotic resistance genes OXA-48 and OXA-51, and providing one or more antibiotic to override the potential antibiotic resistance and
- (b) accounting for the one or more clinical assessment factor of the patient,
- wherein the target therapy eliminates penicillins, monobactams, carbapenems, and first generation to fifth generation cephalosporins except for Avycaz (ceftazidime/avibactam) as likely to fail, and provides Avycaz to override the potential antibiotic resistance.
11 more elements
A method for providing a targeted therapy specific to a patient having a urinary tract infection, the method comprising:
- obtaining a urine sample from the patient;
- obtaining one or more clinical assessment factors selected from patient age, patient gender, source of the urine sample, environmental setting of the patient, medicinal allergies of the patient, clinical status of the patient, and an assigned international classification of disease (ICD-10) code of the patient;
- performing or having performed reverse transcription quantitative polymerase chain reaction (RT-qPCR) to detect and identify microbial organisms in the urine sample and detect and identify potential antibiotic resistance genes in the microbial organisms;
- identifying one or more microbial organisms in the urine sample using the RT-qPCR, and categorizing each of the identified one or more microbial organisms as Gram-positive bacteria, Gram-negative bacteria, or fungal;
- using a semi-quantitative value from the RT-qPCR associated with each identified organism to identify a probable cause of the infection, wherein:
- (i) the probable cause of the infection is a Gram-positive bacteria or a Gram-negative bacteria when the RT-qPCR sample contains at least 50,000 copies/ml of a Gram-positive bacteria or a Gram-negative bacteria, or
- (ii) the probable cause of the infection is fungal;
- identifying one or more potential antibiotic resistance genes selected from the group consisting of CTX-M, TEM, SHV, PER, VEB, GES, IMP, NDM, VIM, OXA, KPC, SUL, DFR, ErmA, ErmB, ErmC, MefA, Aph, AAC, TetM, TetB, QnrA, QnrS, QnrB, Gyrase, MecA, MecC, VanA, VanB, Mcr, ACT, MIR, FOX, DHA, ACC, AmpC, and subtypes thereof;
- when the probable cause of the infection is Gram-positive or Gram-negative bacteria, and
- when the identified potential antibiotic resistance genes are one or more of ACT, MIR, FOX, and DHA,
- applying to the patient a target therapy of one or more antibiotic based on:
- (a) eliminating antibiotics most likely to fail due to the potential antibiotic resistance genes ACT, FOX, MIR, and DHA, and providing one or more antibiotic to override the potential antibiotic resistance, and
- (b) accounting for the one or more clinical assessment factor of the patient,
- wherein the target therapy eliminates penicillins, monobactams, first generation, second generation, and monotherapy third generation cephalosporins as likely to fail, and provides a combination of beta-lactamase inhibitor with a third generation cephalosporin to override the potential antibiotic resistance.
11 more elements
A method for providing a targeted therapy specific to a patient having a urinary tract infection, the method comprising:
- obtaining a urine sample from the patient;
- obtaining one or more clinical assessment factors selected from patient age, patient gender, source of the urine sample, environmental setting of the patient, medicinal allergies of the patient, clinical status of the patient, and an assigned international classification of disease (ICD-10) code of the patient;
- performing or having performed reverse transcription quantitative polymerase chain reaction (RT-qPCR) to detect and identify microbial organisms in the urine sample and detect and identify potential antibiotic resistance genes in the microbial organisms;
- identifying one or more microbial organisms in the urine sample using the RT-qPCR, and categorizing each of the identified one or more microbial organisms as Gram-positive bacteria, Gram-negative bacteria, or fungal;
- using a semi-quantitative value from the RT-qPCR associated with each identified organism to identify a probable cause of the infection, wherein:
- (i) the probable cause of the infection is a Gram-positive bacteria or a Gram-negative bacteria when the RT-qPCR sample contains at least 50,000 copies/ml of a Gram-positive bacteria or a Gram-negative bacteria, or
- (ii) the probable cause of the infection is fungal;
- identifying one or more potential antibiotic resistance genes selected from the group consisting of CTX-M, TEM, SHV, PER, VEB, GES, IMP, NDM, VIM, OXA, KPC, SUL, DFR, ErmA, ErmB, ErmC, MefA, Aph, AAC, TetM, TetB, QnrA, QnrS, QnrB, Gyrase, MecA, MecC, VanA, VanB, Mcr, ACT, MIR, FOX, DHA, ACC, AmpC, and subtypes thereof;
- when the probable cause of the infection is Enterobacteriaceae and the identified potential antibiotic resistance genes comprises AmpC, or
- when the probable cause of the infection is Escherichia coli and the identified potential antibiotic resistance genes comprises ACC,
- applying to the patient a target therapy of one or more antibiotic based on:
- (a) eliminating antibiotics most likely to fail due to the potential antibiotic resistance genes AmpC or ACC, and providing one or more antibiotic to override the potential antibiotic resistance, and
- (b) accounting for the one or more clinical assessment factor of the patient,
- wherein the target therapy eliminates penicillins, monobactams, carbapenems, and first generation, second generation, and third generation cephalosporins, except for Cefepime, Avycaz (ceftazidime/avibactam), and Ceftaroline as likely to fail, and provides one or more of Cefepime, Avycaz, and Ceftaroline to override the potential antibiotic resistance.
11 more elements
A method for providing a targeted therapy specific to a patient having a urinary tract infection, the method comprising:
- obtaining a urine sample from the patient;
- obtaining one or more clinical assessment factors selected from patient age, patient gender, source of the urine sample, environmental setting of the patient, antibiotic allergies of the patient, clinical status of the patient, and an assigned international classification of disease (ICD-10) code of the patient;
- performing or having performed reverse transcription quantitative polymerase chain reaction (RT-qPCR) to detect and identify microbial organisms in the urine sample and detect and identify potential antibiotic resistance genes in the microbial organisms;
- identifying one or more microbial organisms in the urine sample using the RT-qPCR, and categorizing each of the identified one or more microbial organisms as Gram-positive bacteria, Gram-negative bacteria, or fungal;
- using a semi-quantitative value from the RT-qPCR associated with each identified one or more microbial organism to identify a probable cause of the infection, wherein:
- (i) the probable cause of the infection is a Gram-positive bacteria or a Gram-negative bacteria when the RT-qPCR sample contains at least 50,000 copies/ml of a Gram-positive bacteria or a Gram-negative bacteria, or
- (ii) the probable cause of the infection is a fungal;
- identifying one or more potential antibiotic resistance genes selected from the group consisting of CTX-M, TEM, SHV, PER, VEB, GES, IMP, NDM, VIM, OXA, KPC, SUL, DFR, ErmA, ErmB, ErmC, MefA, Aph, AAC, TetM, TetB, QnrA, QnrS, QnrB, Gyrase, MecA, MecC, VanA, VanB, Mcr, ACT, MIR, FOX, DHA, ACC, AmpC, and subtypes thereof;
- when the probable cause of the infection is Enterobacteriaceae and
- when the identified potential antibiotic resistance genes comprise one or more of OXA-23, OXA-24, OXA-40, OXA-58, and OXA-72,
- applying to the patient a target therapy of one or more antibiotic based on:
- (a) eliminating antibiotics most likely to fail due to the potential antibiotic resistance genes OXA-23, OXA-24, OXA-40, OXA-58, and OXA-72, and providing one or more antibiotic to override the potential antibiotic resistance, and
- (b) accounting for the one or more clinical assessment factor of the patient,
- wherein the target therapy eliminates penicillins, monobactams, carbapenem, and first generation to fifth generation cephalosporins except for Avycaz (ceftazidime/avibactam), as likely to fail, and provides Avycaz (ceftazidime/avibactam) to override the potential antibiotic resistance.
11 more elements
Dependencies are inferred from the claim text.