WO2021211746A1 - Procédés de traitement d'infections polymicrobiennes - Google Patents

Procédés de traitement d'infections polymicrobiennes Download PDF

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Publication number
WO2021211746A1
WO2021211746A1 PCT/US2021/027336 US2021027336W WO2021211746A1 WO 2021211746 A1 WO2021211746 A1 WO 2021211746A1 US 2021027336 W US2021027336 W US 2021027336W WO 2021211746 A1 WO2021211746 A1 WO 2021211746A1
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Prior art keywords
patient
coli
infection
faecalis
resistance
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PCT/US2021/027336
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English (en)
Inventor
David A. BAUNOCH
Miguel F.R. PENARANDA
Michael L. OPEL
Maher BADIR
Natalie Luke
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CAP Diagnostics, LLC, dba Pathnostics
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Priority claimed from US16/848,651 external-priority patent/US11053532B2/en
Priority claimed from US17/178,091 external-priority patent/US20210172000A1/en
Application filed by CAP Diagnostics, LLC, dba Pathnostics filed Critical CAP Diagnostics, LLC, dba Pathnostics
Priority to CA3176586A priority Critical patent/CA3176586A1/fr
Publication of WO2021211746A1 publication Critical patent/WO2021211746A1/fr
Priority to PCT/US2022/016816 priority patent/WO2022178142A1/fr
Priority to EP22756936.5A priority patent/EP4294521A1/fr
Priority to CA3175879A priority patent/CA3175879A1/fr
Priority to IL294577A priority patent/IL294577A/en
Priority to US18/451,748 priority patent/US20230392185A1/en

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    • C—CHEMISTRY; METALLURGY
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    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/02—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving viable microorganisms
    • C12Q1/04—Determining presence or kind of microorganism; Use of selective media for testing antibiotics or bacteriocides; Compositions containing a chemical indicator therefor
    • C12Q1/10—Enterobacteria
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/40—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with one nitrogen as the only ring hetero atom, e.g. sulpiride, succinimide, tolmetin, buflomedil
    • A61K31/407—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with one nitrogen as the only ring hetero atom, e.g. sulpiride, succinimide, tolmetin, buflomedil condensed with other heterocyclic ring systems, e.g. ketorolac, physostigmine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/41—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with two or more ring hetero atoms, at least one of which being nitrogen, e.g. tetrazole
    • A61K31/42—Oxazoles
    • A61K31/424—Oxazoles condensed with heterocyclic ring systems, e.g. clavulanic acid
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/41—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with two or more ring hetero atoms, at least one of which being nitrogen, e.g. tetrazole
    • A61K31/425—Thiazoles
    • A61K31/429—Thiazoles condensed with heterocyclic ring systems
    • A61K31/43—Compounds containing 4-thia-1-azabicyclo [3.2.0] heptane ring systems, i.e. compounds containing a ring system of the formula, e.g. penicillins, penems
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/496—Non-condensed piperazines containing further heterocyclic rings, e.g. rifampin, thiothixene or sparfloxacin
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/535—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one oxygen as the ring hetero atoms, e.g. 1,2-oxazines
    • A61K31/5375—1,4-Oxazines, e.g. morpholine
    • A61K31/5383—1,4-Oxazines, e.g. morpholine ortho- or peri-condensed with heterocyclic ring systems
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/54—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one sulfur as the ring hetero atoms, e.g. sulthiame
    • A61K31/542—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one sulfur as the ring hetero atoms, e.g. sulthiame ortho- or peri-condensed with heterocyclic ring systems
    • A61K31/545—Compounds containing 5-thia-1-azabicyclo [4.2.0] octane ring systems, i.e. compounds containing a ring system of the formula:, e.g. cephalosporins, cefaclor, or cephalexine
    • A61K31/546—Compounds containing 5-thia-1-azabicyclo [4.2.0] octane ring systems, i.e. compounds containing a ring system of the formula:, e.g. cephalosporins, cefaclor, or cephalexine containing further heterocyclic rings, e.g. cephalothin
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/65—Tetracyclines
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/04—Peptides having up to 20 amino acids in a fully defined sequence; Derivatives thereof
    • A61K38/14—Peptides containing saccharide radicals; Derivatives thereof, e.g. bleomycin, phleomycin, muramylpeptides or vancomycin
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/02—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving viable microorganisms
    • C12Q1/18—Testing for antimicrobial activity of a material
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Definitions

  • the present application is related to polymicrobial infections, more particularly to polymicrobial infections and therapeutic solutions for treatment of said polymicrobial infections.
  • infectious diseases can affect multiple organs systems and are responsible for significant morbidity, mortality, and economic impact. Infectious agents most often present as a complex polymicrobial infections rather than as a single pathogen infection. Within the body, the pathogens of the polymicrobial infections coexist with each other and through bacterial interactions change both the type of antibiotics the organisms are susceptible and the level of antibiotics required to treat the infection.
  • a mixed population of microbes e.g., bacteria
  • a mixed population of microbes e.g., bacteria
  • the present invention describes specific polymicrobial infections and methods of treating said infections by either killing the microbes or methods of inhibiting growth of one or more of the microbes in a polymicrobial infection (e.g., inducing a bacteriostatic state), wherein a particular antibiotic or a group of antibiotics are selected based on the particular organisms in the polymicrobial infections.
  • a polymicrobial infection e.g., inducing a bacteriostatic state
  • certain polymicrobial infections have a surprising increase or decrease in antibiotic resistance.
  • the present invention describes treating a polymicrobial infection with Klebsiella pneumoniae and coagulase-negative Staphylococcus (CoNS) with amoxicillin/clavulanate since it was surprisingly found that the a polymicrobial infection with both Klebsiella pneumoniae and coagulase-negative Staphylococcus (CoNS) has a reduced odds of resistance to amoxicillin/clavulanate.
  • CoNS coagulase-negative Staphylococcus
  • the present invention also features methods for guiding the treatment of particular polymicrobial infections, e.g., methods for helping a physician or other healthcare provider choose an appropriate antibiotic for treating a polymicrobial infection.
  • the methods feature providing a physician or healthcare professional information (e.g., a report) about a polymicrobial infection, wherein the report provided includes the odds of resistance the particular polymicrobial infection has to one or more antibiotics.
  • the information can help guide the physician in the decision-making process. Without this information, the physician or healthcare provider may choose an inappropriate antibiotic for the infection, e.g., an antibiotic that the polymicrobial infection has increased odds of resistance to.
  • the physician or healthcare may see that the polymicrobial infection has a decreased odds of resistance to a particular antibiotic that in the case of a monomicrobial infection would not be appropriate for use.
  • the physician may see that the polymicrobial infection is susceptible to a weaker antibiotic, whereas in the case of a monomicrobial infection he/she may have opted for a stronger antibiotic. This may provide the physician with a broader range of antibiotics from which to choose.
  • the methods described herein may feature administering an antimicrobial to the patient having or suspected of having a particular polymicrobial infection.
  • the methods herein also include the step of detecting the presence of a particular combination of microbes in the polymicrobial infection, e.g., from a source of the infection from the patient.
  • the present invention features a method of treating a polymicrobial infection comprising Klebsiella pneumoniae and coagulase-negative Staphylococcus (CoNS) (or a method of killing or inhibiting growth of K. pneumoniae and coagulase-negative Staphylococcus (CoNS)), wherein the method comprises introducing amoxicillin/clavulanate to the K. pneumoniae and CoNS polymicrobial infection (e.g., administering amoxicillin/clavulanate to the patient having or suspected of having a polymicrobial infection with K. pneumoniae and CoNS), wherein K. pneumoniae and CoNS together have a decreased odds of resistance to amoxicillin/clavulanate.
  • a polymicrobial infection comprising Klebsiella pneumoniae and coagulase-negative Staphylococcus (CoNS)
  • the method comprises introducing amoxicillin/clavulanate to the K. pneumoniae and CoNS polymicrobial infection (e.g., administering amoxicillin/clavulan
  • the present invention also features a method of treating a polymicrobial infection comprising K. pneumoniae and coagulase-negative Staphylococcus (CoNS) (or a method of killing or inhibiting growth of K. pneumoniae and coagulase-negative Staphylococcus (CoNS)), wherein the method comprises introducing ceftriaxone to the K. pneumoniae and CoNS polymicrobial infection (e.g., administering ceftriaxone to the patient having or suspected of having a polymicrobial infection with K. pneumoniae and CoNS), wherein K. pneumoniae and CoNS together have a decreased odds of resistance to ceftriaxone.
  • the present invention also features a method of treating a polymicrobial infection comprising K. pneumoniae and coagulase-negative Staphylococcus (CoNS) (or a method of killing or inhibiting growth of K. pneumoniae and coagulase-negative Staphylococcus (CoNS)), wherein the method comprises introducing ciprofloxacin to the K. pneumoniae and CoNS polymicrobial infection (e.g., administering ciprofloxacin to the patient having or suspected of having a polymicrobial infection with K. pneumoniae and CoNS), wherein K. pneumoniae and CoNS together have a decreased odds of resistance to ciprofloxacin.
  • CoNS coagulase-negative Staphylococcus
  • the present invention also features a method of treating a polymicrobial infection comprising K. pneumoniae and coagulase-negative Staphylococcus (CoNS) (or a method of killing or inhibiting growth of K. pneumoniae and coagulase-negative Staphylococcus (CoNS)), wherein the method comprises introducing levofloxacin to the K. pneumoniae and CoNS polymicrobial infection (e.g., administering levofloxacin to the patient having or suspected of having a polymicrobial infection with K. pneumoniae and CoNS), wherein K. pneumoniae and CoNS together have a decreased odds of resistance to levofloxacin.
  • levofloxacin e.g., administering levofloxacin to the patient having or suspected of having a polymicrobial infection with K. pneumoniae and CoNS
  • the present invention also features a method of treating a polymicrobial infection comprising K. pneumoniae and coagulase-negative Staphylococcus (CoNS) (or a method of killing or inhibiting growth of K. pneumoniae and coagulase-negative Staphylococcus (CoNS)), wherein the method comprises introducing gentamicin to the K. pneumoniae and CoNS polymicrobial infection (e.g., administering gentamicin to the patient having or suspected of having a polymicrobial infection with K. pneumoniae and CoNS), wherein K. pneumoniae and CoNS together have a decreased odds of resistance to gentamicin.
  • gentamicin e.g., administering gentamicin to the patient having or suspected of having a polymicrobial infection with K. pneumoniae and CoNS
  • K. pneumoniae and CoNS together have a decreased odds of resistance to gentamicin.
  • the present invention also features a method of treating a polymicrobial infection comprising K. pneumoniae and coagulase-negative Staphylococcus (CoNS) (or a method of killing or inhibiting growth of K. pneumoniae and coagulase-negative Staphylococcus (CoNS)), wherein the method comprises introducing TMP/sulfamethoxazole to the K. pneumoniae and CoNS polymicrobial infection (e.g., administering TMP/sulfamethoxazole to the patient having or suspected of having a polymicrobial infection with K. pneumoniae and CoNS), wherein K. pneumoniae and CoNS together have a decreased odds of resistance to TMP/sulfamethoxazole.
  • CoNS coagulase-negative Staphylococcus
  • the methods of the present invention also include treating a polymicrobial infection comprising K. pneumoniae and coagulase-negative Staphylococcus (CoNS) may comprise introducing (e.g., administering) one or more antimicrobials selected from: amoxicillin/clavulanate, ceftriaxone, ciprofloxacin, levofloxacin, gentamicin, or TMP/sulfamethoxazole.
  • the present invention also features a method of guiding treatment of a polymicrobial infection comprising Klebsiella pneumoniae and coagulase-negative Staphylococcus (CoNS).
  • the method may comprise detecting the polymicrobial infection with K. pneumoniae and CoNS and providing a report showing one or more antibiotics to which K. pneumoniae and CoNS have increased and/or decreases resistance to.
  • the report may help the physician choose an appropriate antibiotic to administer to the patient.
  • CoNS Coagulase-negative Staphylococcus
  • the present invention also features a method of treating a polymicrobial infection comprising S. agalactiae and coagulase-negative Staphylococcus (CoNS) (or a method of killing or inhibiting growth of S. agalactiae and coagulase-negative Staphylococcus (CoNS)), wherein the method comprises introducing ceftriaxone to the S. agalactiae and CoNS polymicrobial infection (e.g., administering ceftriaxone to the patient having or suspected of having a polymicrobial infection with S. agalactiae and CoNS), wherein S. agalactiae and CoNS together have a decreased odds of resistance to ceftriaxone.
  • CoNS coagulase-negative Staphylococcus
  • the present invention also features a method of treating a polymicrobial infection comprising S. agalactiae and coagulase-negative Staphylococcus (CoNS) (or a method of killing or inhibiting growth of S. agalactiae and coagulase-negative Staphylococcus (CoNS)), wherein the method comprises introducing ciprofloxacin to the S. agalactiae and CoNS polymicrobial infection (e.g., administering ciprofloxacin to the patient having or suspected of having a polymicrobial infection with S. agalactiae and CoNS), wherein S.
  • CoNS coagulase-negative Staphylococcus
  • the present invention also features a method of treating a polymicrobial infection comprising S. agalactiae and coagulase-negative Staphylococcus (CoNS) (or a method of killing or inhibiting growth of S. agalactiae and coagulase-negative Staphylococcus (CoNS)), wherein the method comprises introducing levofloxacin to the S. agalactiae and CoNS polymicrobial infection (e.g., administering levofloxacin to the patient having or suspected of having a polymicrobial infection with S. agalactiae and CoNS), wherein S. agalactiae and CoNS together have a decreased odds of resistance to levofloxacin.
  • CoNS coagulase-negative Staphylococcus
  • the present invention also features a method of treating a polymicrobial infection comprising S. agalactiae and coagulase-negative Staphylococcus (CoNS) (or a method of killing or inhibiting growth of S. agalactiae and coagulase-negative Staphylococcus (CoNS)), wherein the method comprises introducing gentamicin to the S. agalactiae and CoNS polymicrobial infection (e.g., administering gentamicin to the patient having or suspected of having a polymicrobial infection with S. agalactiae and CoNS), wherein S. agalactiae and CoNS together have a decreased odds of resistance to gentamicin.
  • gentamicin e.g., administering gentamicin to the patient having or suspected of having a polymicrobial infection with S. agalactiae and CoNS
  • S. agalactiae and CoNS together have a decreased odds of resistance
  • the present invention also features a method of treating a polymicrobial infection comprising S. agalactiae and coagulase-negative Staphylococcus (CoNS) (or a method of killing or inhibiting growth of S. agalactiae and coagulase-negative Staphylococcus (CoNS)), wherein the method comprises introducing tetracycline to the S. agalactiae and CoNS polymicrobial infection (e.g., administering tetracycline to the patient having or suspected of having a polymicrobial infection with S. agalactiae and CoNS), wherein S. agalactiae and CoNS together have a decreased odds of resistance to tetracycline.
  • CoNS coagulase-negative Staphylococcus
  • the present invention also features a method of treating a polymicrobial infection comprising S. agalactiae and coagulase-negative Staphylococcus (CoNS) (or a method of killing or inhibiting growth of S. agalactiae and coagulase-negative Staphylococcus (CoNS)), wherein the method comprises introducing TM P/sulfa methoxazole to the S. agalactiae and CoNS polymicrobial infection (e.g., administering TMP/sulfamethoxazole to the patient having or suspected of having a polymicrobial infection with S. agalactiae and CoNS), wherein S. agalactiae and CoNS together have a decreased odds of resistance to TMP/sulfamethoxazole.
  • TM P/sulfa methoxazole to the S. agalactiae and CoNS polymicrobial infection
  • the present invention also features a method of treating a polymicrobial infection comprising S. agalactiae and coagulase-negative Staphylococcus (CoNS) (or a method of killing or inhibiting growth of S. agalactiae and coagulase-negative Staphylococcus (CoNS)), wherein the method comprises introducing vancomycin to the S. agalactiae and CoNS polymicrobial infection (e.g., administering vancomycin to the patient having or suspected of having a polymicrobial infection with S. agalactiae and CoNS), wherein S. agalactiae and CoNS together have a decreased odds of resistance to vancomycin
  • the methods of the present invention also include treating a polymicrobia! infection comprising S. agalactiae and coagulase-negative Staphylococcus (CoNS) may comprise introducing (e.g., administering) one or more antimicrobials selected from: ceftriaxone, ciprofloxacin, levofloxacin, gentamicin, tetracycline, TMP/sulfamethoxazole, or vancomycin
  • the present invention also features a method of guiding treatment of a polymicrobial infection comprising S. agalactiae and coagulase-negative Staphylococcus (CoNS).
  • the method may comprise detecting the polymicrobial infection with S. agalactiae and CoNS and providing a report showing one or more antibiotics to which S. agalactiae and CoNS have increased and/or decreases resistance to.
  • the report may help the physician choose an appropriate antibiotic to administer to the patient.
  • CoNS Coagulase-negative Staphylococcus
  • E. faecalis Coagulase-negative Staphylococcus
  • the present invention also features a method of treating a polymicrobial infection comprising E. faecalis and coagulase-negative Staphylococcus (CoNS) (or a method of killing or inhibiting growth of E. faecalis and coagulase-negative Staphylococcus (CoNS)), wherein the method comprises introducing gentamicin to the E. faecalis and CoNS polymicrobial infection (e.g., administering gentamicin to the patient having or suspected of having a polymicrobial infection with E. faecalis and CoNS), wherein E. faecalis and CoNS together have a decreased odds of resistance to gentamicin.
  • gentamicin e.g., administering gentamicin to the patient having or suspected of having a polymicrobial infection with E. faecalis and CoNS
  • E. faecalis and CoNS together have a decreased odds of resistance to gentamicin.
  • the present invention also features a method of treating a polymicrobial infection comprising E. faecalis and coagulase-negative Staphylococcus (CoNS) (or a method of killing or inhibiting growth of E. faecalis and coagulase-negative Staphylococcus (CoNS)), wherein the method comprises introducing tetracycline to the E. faecalis and CoNS polymicrobial infection (e.g., administering tetracycline to the patient having or suspected of having a polymicrobial infection with E. faecalis and CoNS), wherein E. faecalis and CoNS together have a decreased odds of resistance to tetracycline.
  • a polymicrobial infection comprising E. faecalis and coagulase-negative Staphylococcus (CoNS)
  • the method comprises introducing tetracycline to the E. faecalis and CoNS polymicrobial infection (e.g.
  • the present invention also features a method of treating a polymicrobial infection comprising E. faecalis and coagulase-negative Staphylococcus (CoNS) (or a method of killing or inhibiting growth of E. faecalis and coagulase-negative Staphylococcus (CoNS)), wherein the method comprises introducing vancomycin to the E. faecalis and CoNS polymicrobial infection (e.g., administering vancomycin to the patient having or suspected of having a polymicrobial infection with E. faecalis and CoNS), wherein E. faecalis and CoNS together have a decreased odds of resistance to vancomycin.
  • a polymicrobial infection comprising E. faecalis and coagulase-negative Staphylococcus (CoNS)
  • the method comprises introducing vancomycin to the E. faecalis and CoNS polymicrobial infection (e.g., administering vancomycin to the patient having or suspected
  • the methods of the present invention also include treating a polymicrobial infection comprising E. faecalis and coagulase-negative Staphylococcus (CoNS) may comprise introducing (e.g., administering) one or more antimicrobials selected from: amoxicillin/clavulanate, gentamicin, tetracycline, or vancomycin.
  • a polymicrobial infection comprising E. faecalis and coagulase-negative Staphylococcus (CoNS) may comprise introducing (e.g., administering) one or more antimicrobials selected from: amoxicillin/clavulanate, gentamicin, tetracycline, or vancomycin.
  • the present invention also features a method of guiding treatment of a polymicrobial infection comprising E. faecalis and coagulase-negative Staphylococcus (CoNS).
  • the method may comprise detecting the polymicrobial infection with E. faecalis and CoNS and providing a report showing one or more antibiotics to which E. faecalis and CoNS have increased and/or decreases resistance to.
  • the report may help the physician choose an appropriate antibiotic to administer to the patient.
  • CoNS Coagulase-negative Staphylococcus
  • the present invention also features a method of treating a polymicrobial infection comprising Coagulase-negative Staphylococcus (CoNS) and E. coli (or a method of killing or inhibiting growth of CoNS and E. coli), wherein the method comprises introducing amoxicillin/clavulanate to the CoNS and E. coli polymicrobial infection (e.g., administering amoxicillin/clavulanate to the patient having or suspected of having a polymicrobial infection with CoNS and E. coli), wherein CoNS and E. coli together have a decreased odds of resistance to amoxicillin/clavulanate.
  • CoNS and E. coli together have a decreased odds of resistance to amoxicillin/clavulanate.
  • the present invention also features a method of treating a polymicrobial infection comprising Coagulase-negative Staphylococcus (CoNS) and E. coli (or a method of killing or inhibiting growth of CoNS and E. coli), wherein the method comprises introducing ceftriaxone to the CoNS and E. coli polymicrobial infection (e.g., administering ceftriaxone to the patient having or suspected of having a polymicrobial infection with CoNS and E. coli), wherein CoNS and E. coli together have a decreased odds of resistance to ceftriaxone
  • the present invention also features a method of treating a polymicrobial infection comprising Coaguiase-negative Staphylococcus (CoNS) and E. coli (or a method of killing or inhibiting growth of CoNS and E. coli), wherein the method comprises introducing tetracycline to the CoNS and E. coli polymicrobial infection (e.g., administering tetracycline to the patient having or suspected of having a polymicrobial infection with CoNS and E. coli), wherein CoNS and E. coli together have a decreased odds of resistance to tetracycline.
  • CoNS and E. coli together have a decreased odds of resistance to tetracycline.
  • the present invention also features a method of treating a polymicrobial infection comprising Coaguiase-negative Staphylococcus (CoNS) and E. coli (or a method of killing or inhibiting growth of CoNS and E. coli), wherein the method comprises introducing TMP/sulfamethoxazole to the CoNS and E. coli polymicrobial infection (e.g., administering TMP/sulfamethoxazole to the patient having or suspected of having a polymicrobial infection with CoNS and E. coli), wherein CoNS and E. coli together have a decreased odds of resistance to TMP/sulfamethoxazole.
  • CoNS and E. coli together have a decreased odds of resistance to TMP/sulfamethoxazole.
  • the methods of the present invention also include treating a polymicrobial infection comprising CoNS and E. coli may comprise introducing (e.g., administering) one or more antimicrobials selected from: amoxicillin/clavulanate, ceftriaxone, tetracycline, or TMP/sulfamethoxazole.
  • the present invention also features a method of guiding treatment of a polymicrobial infection comprising E. coli and coaguiase-negative Staphylococcus (CoNS).
  • the method may comprise detecting the polymicrobial infection with E. coli and CoNS and providing a report showing one or more antibiotics to which E. coli and CoNS have increased and/or decreases resistance to.
  • the report may help the physician choose an appropriate antibiotic to administer to the patient.
  • the present invention also features a method of treating a polymicrobial infection comprising E. faecalis and S. agalactiae (or a method of killing or inhibiting growth of E. faecalis and S. agalactiae), wherein the method comprises introducing ampicillin to the E. faecalis and S. agalactiae polymicrobial infection (e.g., administering ampicillin to the patient having or suspected of having a polymicrobial infection with E. faecalis and S. agalactiae), wherein E. faecalis and S. agalactiae together have a decreased odds of resistance to ampicillin.
  • the present invention also features a method of treating a polymicrobial infection comprising E. faecalis and S. agalactiae (or a method of killing or inhibiting growth of E. faecalis and S. agalactiae ), wherein the method comprises introducing vancomycin to the E. faecalis and S. agalactiae polymicrobial infection (e.g., administering vancomycin to the patient having or suspected of having a polymicrobial infection with E. faecalis and S. agalactiae), wherein E. faecalis and S. agalactiae together have a decreased odds of resistance to vancomycin.
  • the methods of the present invention also include treating a polymicrobial infection comprising E. faecalis and S. agalactiae may comprise introducing (e.g., administering) one or more antimicrobials selected from: ampicillin or vancomycin.
  • the present invention also features a method of guiding treatment of a polymicrobial infection comprising E faecalis and S. agalactiae.
  • the method may comprise detecting the polymicrobial infection with E. faecalis and S. agalactiae and providing a report showing one or more antibiotics to which E. faecalis and S. agalactiae have increased and/or decreases resistance to.
  • the report may help the physician choose an appropriate antibiotic to administer to the patient.
  • the present invention also features a method of treating a polymicrobial infection comprising E. faecalis and P. miribiiis (or a method of killing or inhibiting growth of E. faecalis and P miribiiis), wherein the method comprises introducing meropenem to the E. faecalis and P. miribiiis polymicrobial infection (e.g., administering meropenem to the patient having or suspected of having a polymicrobial infection with E. faecalis and P. miribiiis), wherein E. faecalis and P. miribiiis together have a decreased odds of resistance to meropenem.
  • the present invention also features a method of guiding treatment of a polymicrobial infection comprising E. faecalis and P miribiiis.
  • the method may comprise detecting the polymicrobial infection with E. faecalis and P. miribiiis and providing a report showing one or more antibiotics to which E. faecalis and P miribiiis have increased and/or decreases resistance to.
  • the report may help the physician choose an appropriate antibiotic to administer to the patient.
  • the present invention also features a method of treating a polymicrobial infection comprising E. faecalis and P. aeruginosa (or a method of killing or inhibiting growth of E faecalis and P aeruginosa), wherein the method comprises introducing meropenem to the E. faecalis and P. aeruginosa polymicrobial infection (e.g., administering meropenem to the patient having or suspected of having a polymicrobiai infection with E. faecalis and P. aeruginosa), wherein E. faecalis and P. aeruginosa together have a decreased odds of resistance to meropenem.
  • a polymicrobial infection comprising E. faecalis and P. aeruginosa
  • the method comprises introducing meropenem to the E. faecalis and P. aeruginosa polymicrobial infection (e.g., administering meropenem
  • the present invention also features a method of guiding treatment of a polymicrobial infection comprising E. faecalis and P. aeruginosa.
  • the method may comprise detecting the polymicrobial infection with E. faecalis and P. aeruginosa and providing a report showing one or more antibiotics to which E. faecalis and P. aeruginosa have increased and/or decreases resistance to.
  • the report may help the physician choose an appropriate antibiotic to administer to the patient.
  • the present invention also features a method of treating a polymicrobial infection comprising E. faecalis and K. pneumoniae (or a method of killing or inhibiting growth of E. faecalis and K. pneumoniae ), wherein the method comprises introducing meropenem to the E. faecalis and K. pneumoniae polymicrobial infection (e.g., administering meropenem to the patient having or suspected of having a polymicrobial infection with E. faecalis and K. pneumoniae), wherein E. faecalis and K. pneumoniae together have a decreased odds of resistance to meropenem.
  • the present invention also features a method of treating a polymicrobial infection comprising E. faecalis and K. pneumoniae (or a method of killing or inhibiting growth of E. faecalis and K. pneumoniae), wherein the method comprises introducing tetracycline to the E. faecalis and K. pneumoniae polymicrobial infection (e.g., administering tetracycline to the patient having or suspected of having a polymicrobial infection with E. faecalis and K. pneumoniae), wherein E. faecalis and K. pneumoniae together have a decreased odds of resistance to tetracycline.
  • the methods of the present invention also include treating a polymicrobial infection comprising E. faecalis and K. pneumoniae may comprise introducing (e.g., administering) one or more antimicrobials selected from: meropenem or tetracycline.
  • the present invention also features a method of guiding treatment of a polymicrobial infection comprising E. faecalis and K. pneumoniae.
  • the method may comprise detecting the polymicrobial infection with E. faecalis and K. pneumoniae and providing a report showing one or more antibiotics to which E. faecalis and K. pneumoniae have increased and/or decreases resistance to.
  • the report may help the physician choose an appropriate antibiotic to administer to the patient.
  • the present invention also features a method of treating a polymicrobial infection comprising E. faecalis and E. coli (or a method of killing or inhibiting growth of E. faecalis and E. coli), wherein the method comprises introducing ampicillin/clavulanate to the E. faecalis and E. coli polymicrobial infection (e.g., administering ampicillin/clavulanate to the patient having or suspected of having a polymicrobial infection with E. faecalis and E. coli), wherein E. faecalis and E. coli together have a decreased odds of resistance to ampicillin/clavulanate.
  • the present invention also features a method of treating a polymicrobial infection comprising E. faecalis and E. coli (or a method of killing or inhibiting growth of E. faecalis and E. coli), wherein the method comprises introducing ampicillin/sulbactam to the E. faecalis and E. coli polymicrobial infection (e.g., administering ampicillin/sulbactam to the patient having or suspected of having a polymicrobial infection with E. faecalis and E. coli), wherein E. faecalis and E. coli together have a decreased odds of resistance to ampicillin/sulbactam.
  • the present invention also features a method of treating a polymicrobial infection comprising E. faecalis and E. coli (or a method of killing or inhibiting growth of E. faecalis and E. coll), wherein the method comprises introducing levofloxacin to the E. faecalis and E. coli polymicrobial infection (e.g., administering levofloxacin to the patient having or suspected of having a polymicrobial infection with E. faecalis and E. coli), wherein E. faecalis and E. coli together have a decreased odds of resistance to levofloxacin.
  • the present invention also features a method of treating a polymicrobial infection comprising E. faecalis and E. coli (or a method of killing or inhibiting growth of E. faecalis and E. coli), wherein the method comprises introducing meropenem to the E. faecalis and E. coli polymicrobial infection (e.g., administering meropenem to the patient having or suspected of having a polymicrobial infection with E faecalis and E. coli), wherein E. faecalis and E. coli together have a decreased odds of resistance to meropenem.
  • the present invention also features a method of treating a polymicrobial infection comprising E. faecalis and E. coli (or a method of killing or inhibiting growth of E. faecalis and E. coli), wherein the method comprises introducing tetracycline to the E. faecalis and E. coli polymicrobial infection (e.g., administering tetracycline to the patient having or suspected of having a polymicrobial infection with E. faecalis and E. coli), wherein E. faecalis and E. coli together have a decreased odds of resistance to tetracycline.
  • the methods of the present invention also include treating a polymicrobial infection comprising E. faecalis and E. coli may comprise introducing (e.g., administering) one or more antimicrobials selected from: ampicillin/clavulanate, ampicillin/sulbactam, levofloxacin, meropenem, or tetracycline.
  • the present invention also features a method of guiding treatment of a polymicrobial infection comprising E. faecalis and E. coli.
  • the method may comprise detecting the polymicrobial infection with E. faecalis and E. coli and providing a report showing one or more antibiotics to which E. faecalis and E. coil have increased and/or decreases resistance to.
  • the report may help the physician choose an appropriate antibiotic to administer to the patient.
  • the present invention also features a method of treating a polymicrobial infection comprising E. coli and S. agalactiae (or a method of killing or inhibiting growth of E. coli and S. agalactiae ), wherein the method comprises introducing ampicillin to the E. coli and S. agalactiae polymicrobial infection (e.g., administering ampicillin to the patient having or suspected of having a polymicrobial infection with E. coli and S. agalactiae), wherein E. coli and S. agalactiae together have a decreased odds of resistance to ampicillin.
  • a polymicrobial infection comprising E. coli and S. agalactiae
  • the method comprises introducing ampicillin to the E. coli and S. agalactiae polymicrobial infection (e.g., administering ampicillin to the patient having or suspected of having a polymicrobial infection with E. coli and S. agalactiae), wherein E.
  • the present invention also features a method of treating a polymicrobial infection comprising E. coli and S. agalactiae (or a method of killing or inhibiting growth of E. coli and S. agalactiae), wherein the method comprises introducing cefepime to the E. coli and S. agalactiae polymicrobial infection (e.g., administering cefepime to the patient having or suspected of having a polymicrobial infection with E. coli and S. agalactiae), wherein E. coli and S. agalactiae together have a decreased odds of resistance to cefepime.
  • the present invention also features a method of treating a polymicrobial infection comprising E. coli and S. agalactiae (or a method of killing or inhibiting growth of E. coli and S. agalactiae), wherein the method comprises introducing ceftazidime to the E. coli and S. agalactiae polymicrobial infection (e.g., administering ceftazidime to the patient having or suspected of having a polymicrobial infection with E. coli and S. agalactiae), wherein E. coli and S. agalactiae together have a decreased odds of resistance to ceftazidime.
  • the present invention also features a method of treating a polymicrobial infection comprising E. coli and S. agalactiae (or a method of killing or inhibiting growth of E. coli and S. agalactiae), wherein the method comprises introducing ceftriaxone to the E. coli and S. agalactiae polymicrobial infection (e.g , administering ceftriaxone to the patient having or suspected of having a polymicrobial infection with E. coli and S. agalactiae), wherein E. coli and S. agalactiae together have a decreased odds of resistance to ceftriaxone.
  • the present invention also features a method of treating a polymicrobial infection comprising E. coli and S. agalactiae (or a method of killing or inhibiting growth of E. coli and S. agalactiae), wherein the method comprises introducing ciprofloxacin to the E. coli and S. agalactiae polymicrobial infection (e.g., administering ciprofloxacin to the patient having or suspected of having a polymicrobial infection with E. coli and S. agalactiae), wherein E. coli and S. agalactiae together have a decreased odds of resistance to ciprofloxacin.
  • the present invention also features a method of treating a polymicrobial infection comprising E. co!i and S. agalactiae (or a method of killing or inhibiting growth of E. coli and S. agalactiae), wherein the method comprises introducing levofloxacin to the E. coli and S. agalactiae polymicrobial infection (e.g., administering levofloxacin to the patient having or suspected of having a polymicrobial infection with E. coli and S. agalactiae), wherein E. coli and S. agalactiae together have a decreased odds of resistance to levofloxacin.
  • the present invention also features a method of treating a polymicrobial infection comprising E. coli and S. agalactiae (or a method of killing or inhibiting growth of E. coli and S. agalactiae), wherein the method comprises introducing tetracycline to the E coli and S. agalactiae polymicrobial infection (e.g., administering tetracycline to the patient having or suspected of having a polymicrobial infection with E. coli and S. agalactiae), wherein E. coli and S. agalactiae together have a decreased odds of resistance to tetracycline.
  • the present invention also features a method of treating a polymicrobial infection comprising E. coli and S. agalactiae (or a method of killing or inhibiting growth of E. coli and S. agalactiae), wherein the method comprises introducing TMP/sulfamethoxazole to the E. coli and S. agalactiae polymicrobial infection (e.g., administering TMP/sulfamethoxazole to the patient having or suspected of having a polymicrobial infection with E. coli and S. agalactiae), wherein E. coli and S. agalactiae together have a decreased odds of resistance to TMP/sulfamethoxazole.
  • the present invention also features a method of treating a polymicrobial infection comprising E. coli and P. mirabilis (or a method of killing or inhibiting growth of E. coli and P. mirabilis), wherein the method comprises introducing cefaclor to the E. coli and P. mirabilis polymicrobial infection (e.g., administering cefaclor to the patient having or suspected of having a polymicrobial infection with E. coli and P mirabilis), wherein E. coli and P. mirabilis together have a decreased odds of resistance to cefaclor.
  • the present invention also features a method of treating a polymicrobial infection comprising E. coli and P. mirabilis (or a method of killing or inhibiting growth of E. coli and P. mirabilis), wherein the method comprises introducing cefazolin to the E. coli and P. mirabilis polymicrobial infection (e.g., administering cefazolin to the patient having or suspected of having a polymicrobial infection with E. coli and P. mirabilis), wherein E. coli and P. mirabilis together have a decreased odds of resistance to cefazolin.
  • the present invention also features a method of treating a polymicrobial infection comprising E. coli and P. mirabilis (or a method of killing or inhibiting growth of E. coli and P. mirabilis), wherein the method comprises introducing cefoxitin to the E. coli and P. mirabilis polymicrobial infection (e.g., administering cefoxitin to the patient having or suspected of having a polymicrobial infection with E. coli and P mirabilis), wherein E. coli and P. mirabilis together have a decreased odds of resistance to cefoxitin.
  • the present invention also features a method of treating a polymicrobial infection comprising E. coli and P. mirabilis (or a method of killing or inhibiting growth of E. coli and P mirabilis), wherein the method comprises introducing ceftazidime to the E. coli and P. mirabilis polymicrobial infection (e.g., administering ceftazidime to the patient having or suspected of having a polymicrobial infection with E. coli and P mirabilis), wherein E. coli and P. mirabilis together have a decreased odds of resistance to ceftazidime.
  • the present invention also features a method of treating a polymicrobial infection comprising E. coli and P. mirabilis (or a method of killing or inhibiting growth of E. coli and P. mirabilis), wherein the method comprises introducing ceftriaxone to the E. coli and P. mirabilis polymicrobial infection (e.g , administering ceftriaxone to the patient having or suspected of having a polymicrobial infection with E. coli and P. mirabilis), wherein E. coli and P mirabilis together have a decreased odds of resistance to ceftriaxone.
  • the methods of the present invention also include treating a polymicrobial infection comprising E. coli and P mirabilis may comprise introducing (e.g., administering) one or more antimicrobials selected from: cefaclor, cefazolin, cefoxitin, ceftazidime, or ceftriaxone.
  • the present invention also features a method of guiding treatment of a polymicrobial infection comprising E. coli and P mirabilis.
  • the method may comprise detecting the polymicrobial infection with E. coli and P mirabilis and providing a report showing one or more antibiotics to which E. coli and P. mirabilis have increased and/or decreases resistance to.
  • the report may help the physician choose an appropriate antibiotic to administer to the patient.
  • the present invention also features a method of treating a polymicrobial infection comprising E. coli and K. pneumoniae (or a method of killing or inhibiting growth of E. coli and K. pneumoniae), wherein the method comprises introducing levofloxacin to the E. coli and K. pneumoniae polymicrobial infection (e.g., administering levofloxacin to the patient having or suspected of having a polymicrobial infection with E. coli and K. pneumoniae), wherein E. coli and K. pneumoniae together have a decreased odds of resistance to levofloxacin.
  • the present invention also features a method of treating a polymicrobial infection comprising E. coli and K. pneumoniae (or a method of killing or inhibiting growth of E. coli and K. pneumoniae), wherein the method comprises introducing tetracycline to the E. coli and K. pneumoniae polymicrobial infection (e.g., administering tetracycline to the patient having or suspected of having a polymicrobial infection with E. coli and K. pneumoniae), wherein E. coli and K. pneumoniae together have a decreased odds of resistance to tetracycline.
  • the methods of the present invention also include treating a polymicrobial infection comprising E. coli and K. pneumoniae may comprise introducing (e.g., administering) one or more antimicrobials selected from: levofloxacin or tetracycline.
  • the present invention also features a method of treating a polymicrobial infection comprising E. coli and K. oxytoca (or a method of killing or inhibiting growth of E. coli and K. oxytoca), wherein the method comprises introducing cefepime to the E. coli and K. oxytoca polymicrobial infection (e.g., administering cefepime to the patient having or suspected of having a polymicrobial infection with E. coli and K. oxytoca), wherein E. coli and K. oxytoca together have a decreased odds of resistance to cefepime.
  • the present invention also features a method of treating a polymicrobial infection comprising E. coli and K. oxytoca (or a method of killing or inhibiting growth of E. coli and K. oxytoca), wherein the method comprises introducing tetracycline to the E. coli and K. oxytoca polymicrobial infection (e.g., administering tetracycline to the patient having or suspected of having a polymicrobial infection with E. coli and K. oxytoca), wherein E. coli and K. oxytoca together have a decreased odds of resistance to tetracycline.
  • the methods of the present invention also include treating a polymicrobial infection comprising E. coli and K. oxytoca may comprise introducing (e.g., administering) one or more antimicrobials selected from: cefepime, ciprofloxacin, or tetracycline.
  • the present invention also features a method of guiding treatment of a polymicrobial infection comprising E. coli and K. oxytoca.
  • the method may comprise detecting the polymicrobial infection with E. coli and K. oxytoca and providing a report showing one or more antibiotics to which E. coli and K. oxytoca have increased and/or decreases resistance to. The report may help the physician choose an appropriate antibiotic to administer to the patient.
  • the present invention also features methods for treating a patient having or suspected of having a polymicrobial infection comprising a combination of E. coli and K. Pneumoniae. In certain embodiments, the method comprising: detecting the presence of both E. coli and K.
  • Pneumoniae in a source of the infection obtained from the patient and administering to the patient an antibiotic other than ampicillin/sulbactam or cefaclor, wherein E. coli and K. Pneumoniae together have an increased odds of resistance to ampicillin/sulbactam and cefaclor.
  • the present invention also features methods for treating a patient having or suspected of having a polymicrobial infection comprising a combination of E. faecalis and K. Pneumoniae.
  • the method comprises detecting the presence of both E. faecalis and K. Pneumoniae in a source of the infection obtained from the patient; and administering to the patient an antibiotic other than amoxicillin/clavulanate or ampicillin/sulbactam, wherein E. faecalis and K. Pneumoniae together have an increased odds of resistance to amoxicillin/clavulanate and ampicillin/sulbactam.
  • the present invention also features methods for treating a patient having or suspected of having a polymicrobial infection comprising a combination of E. faecalis and S. agalactiae.
  • the method comprises detecting the presence of both E. faecalis and S. agalactiae in a source of the infection obtained from the patient; and administering to the patient an antibiotic other than tetracycline wherein E. faecalis and S. agalactiae together have an increased odds of resistance to tetracycline.
  • the present invention also features methods for treating a patient having or suspected of having a polymicrobial infection comprising a combination of E. coli and CoNS.
  • the method comprises detecting the presence of both E. coli and CoNS in a source of the infection obtained from the patient; and administering to the patient an antibiotic other than levofloxacin, wherein E. coli and CoNS together have an increased odds of resistance to levofloxacin.
  • the present invention is not limited to the aforementioned polymicrobial infections and administered antibiotics.
  • FIG. 3 depicts examples of polymicrobial infections that experience decreases or increases in antibiotic sensitivity, relative to monomicrobial infections.
  • FIG. 5 depicts various odds ratios of resistance, comparing polymicrobial infections with monomicrobial infections.
  • FIG. 6 depicts examples of polymicrobial infections that experience decreases or increases in antibiotic sensitivity, relative to monomicrobial infections.
  • FIG. 8 is a continuation of FIG. 6 and FIG. 7, depicting examples of polymicrobial infections that experience decreases or increases in antibiotic sensitivity, relative to monomicrobial infections.
  • FIG. 9 shows correlations between organisms found in polymicrobial infections, particularly polymicrobial infections with 2, 3, 4, 5, 6, or 7 organisms.
  • FIG. 10 shows correlations between organisms found in polymicrobial infections, excluding E. coli.
  • the strength of correlation is represented by the width of the edge connecting the genes. Only correlations greater than 0.1 are shown
  • FIG. 11 depicts an exemplary Antibiotic Source Plate with well contents and antibiotic concentration (pg/mL).
  • Nitro nitrofurantoin
  • Cipro ciprofloxacin
  • Mero meropenem
  • Ceftiaxone ceftriaxone
  • TMP/SMX trimethoprim + sulfamethoxazole
  • Pip/Tazo piperacillin + tazobactam
  • Levo levofloxacin
  • Cefoxitin cefoxitin
  • Tetra tetracycline
  • Amp/Sulb ampicillin + sulbactam
  • Amp ampicillin
  • Vanco vancomycin.
  • the term “Highest Single Agent Interaction Principle'’ refers to a statistical model wherein the resistance of the polymicrobial infection is predicted to be the resistance of the bacteria with the highest resistance. For example, if species A is resistant with a probability 20%, and species B is resistant with a probability 50%, then the probability of resistance of the pool is 50%.
  • the term “Union Principle” refers to a statistical model wherein the polymicrobial infection of species A and B is made up of one colony (or one genetic variant) of species A and one colony (or one genetic variant) of species B, and the polymicrobial infection is resistant if either the colony of species A is resistant, or if the colony of species B is resistant.
  • an antibiotic is applied to the polymicrobial infection, it may kill off species A, but if species B survives, the polymicrobial infection is called resistant.
  • the term “Logistic Additive Model” refers to a statistical model wherein the effects of species A and species B on the resistance of the polymicrobial infection is estimated in a logistic model.
  • the effect of species A is the odds ratio of resistance when species A is present relative to when it is not present; similarly, the effect of species B is the odds ratio of resistance when species B is present relative to when it is not.
  • the additive model predicts the effect of both species as the sum of the log odds-ratio; or the product of the two individual odds-ratios. For example, if the background resistance rate is 50%, the expected polymicrobial infection (species A and B) resistance with no interactions is 20%; if the background resistance rate is 20%, the expected polymicrobial infection resistance is 50%.
  • Antibiotics include, but are not limited to, penicillins, tetracyclines, cephalosporins, quninolones, lincomycins, macrolides, sulronamides, glycopeptide antibiotics, aminoglycosides, carbapenems, ansamycins, lipopeptides, monobactams, nitrofurans, oxaxolidinones, and polypeptides.
  • Cephalosporin antibiotics include, but are not limited to, cefadroxil, cephradine, cefazolin, cephalexin, cefepime, ceftaroline, loracarbef, cefotetan, cefuroxime, cefprozil, cefoxitin, cefaclor, ceftibuten, cetriaxone, cefotaxime, cefpodoxime, cefdinir, cefixime, cefditoren, ceftizoxime, cefoperazone, cefalotin, cefamanadole, ceftaroline fosamil, cetobiprole, and ceftazidime.
  • Cephalosporin antibiotics are often used in combination with beta-lactamase inhibitors to provide broader spectrum activity; these combination antibiotics include, but are not limited to, avibactam/ceftazidime and ceftolozane/tazobactam.
  • Quinolone antibiotics include, but are not limited to, lomefloxacin, ofloxacin, norfloxacin, gatifloxacin, ciprofloxacin, moxifloxacin, levofloxacin, gemifloxacin, cinoxacin, nalidixic acid, trovaloxacin, enoxacin, grepafloxacin, temafloxacin, and sparfloxacin.
  • Locomycin antibiotics include, but are not limited to, clindamycin and lincomycin.
  • Macrolide antibiotics include, but are not limited to, azithromycin, clarithromycin, erythromycin, telithromycin, dirithromycin, roxithromycin, troleandomycin, spiramycin, and fidazomycin.
  • Sulfonamide antibiotics include, but are not limited to, sulfamethoxazole, sulfasalazine, mafenide, sulfacetamide, sulfadiazine, silver sufadiazine, sulfadimethoxine, sulfanilimide, sulfisoxazole, sulfonamidochrysoidine, and sulfisoxazole. Sulfonamide antibiotics are often used in combination with trimethoprim to improve bactericidal activity.
  • Glycopeptide antibiotics include, but are not limited to, dalbavancin, oritavancin, telavancin, teicoplanin, and vancomycin.
  • Amikacin kanamycin
  • neomycin netilmicin
  • streptomycin and spectinomycin.
  • Carbapenem antibiotics include, but are not limited to, imipenem, meropenem, doripenem, ertapenem, and imipenem /cilastatin.
  • Ansamycin antibiotics include, but are not limited to, geldanamycin, herbimycin, and rifaximin.
  • Lipopeptide antibiotics include, but are not limited to, daptomycin.
  • [00119JMonobactam antibiotics include, but are not limited to, aztreonam.
  • Nitrofuran antibiotics include, but are not limited to furazolidone and nitrofurantoin.
  • Oxaxolidinone antibiotics include, but are not limited to, linezolid, posizolid, radezolid, and torezolid.
  • Polypeptide antibiotics include, but are not limited to, bacitracin, colistin, and polymyxin B.
  • antibiotics which are not part of any of the above-mentioned groups include, but are not limited to, clofazimine, dapsone, capreomycin, cycloserine, ethambutol, ethionamide, isoniazid, pyrazinamide, rifampicin, rifabutin, rifapentine, streptomycin, arsphenamide, chloramphenicol, fosfomycin, fusidic acid, metronidazole, mupirocin, platensimycin, quinupristin/dalfopristin, thiamphenicol, tigecycline, tinidazole, and trimethoprim.
  • the scope of the presently disclosed methods encompasses the inclusion of antibiotics not yet known, or not yet approved by regulatory authorities.
  • the presently claimed assay can be performed with any anti-bacterial agent and is not limited to the antibiotics disclosed herein.
  • Disclosed herein are methods for detecting polymicrobial infections as well as treating polymicrobial infections, wherein a mixed population of microbes (e.g., bacteria) are present in a patient sample and the microbes are not first isolated from the sample.
  • a mixed population of microbes e.g., bacteria
  • the present invention describes specific polymicrobial infections and methods of treating said infections, wherein a particular antibiotic or a group of antibiotics are selected based on the composition of the polymicrobial infections.
  • certain polymicrobial infections show a surprising reduction in antibiotic resistance relative to what might be expected.
  • Klebsiella has a relatively high resistance rate to ampicillin.
  • CNS or CoNS coagulase-negative Staphylococcus
  • FIG. 1 shows a detailed example of the combinations of E. coli and K. pneumoniae and the effects on resistance to ampicillin/sulbactam, cefaclor, and tetracycline.
  • E. coli and K. pneumoniae When combined, E. coli and K. pneumoniae have a higher resistance to ampicillin/sulbactam and cefaclor relative to what would be expected (e.g., based on the union principle or single highest agent principle). However, E. coli and K. pneumoniae together have a reduced resistance to tetracycline relative to what would be expected (e.g., based on the union principle or single highest agent principle).
  • FIG. 2 shows the effects of organism interactions on antibiotic resistance for a variety of microbes and antibiotics.
  • An upward arrow indicates an increase in resistance (e.g., a decrease in susceptibility).
  • a downward arrow indicates a decrease in resistance (e.g., an increase in susceptibility).
  • Examples of organism interactions that result in a decrease in resistance includes but is not limited to:
  • E. coli and S. agalactiae, or E. faecalis and S. agalactiae show a decrease in resistance to ampicillin.
  • E. faecalis and E. coli show a decrease in resistance to ampicillin/sulbactam.
  • mirabiiis show a decrease in resistance to cefaclor or cefazolin.
  • E. coli and K. oxytoca, or E. coli and S. agalactiae show a decrease in resistance to cefepime.
  • E. coli and P. mirabiiis show a decrease in resistance to cefoxitin.
  • E. coli and P. mirabiiis, or E. coli and S. agalactiae show a decrease in resistance to ceftazidime.
  • CoNS Coagulase-negative Staphylococcus
  • E. coli E. coli
  • Coagulase-negative Staphylococcus (CoNS) and K. pneumoniae, or Coagulase-negative Staphylococcus (CoNS) and S. agalactiae, or E. coli and K. oxytoca, or E. coli and S. agalactiae show a decrease in resistance to ciprofloxacin
  • Coagulase-negative Staphylococcus (CoNS) and E. faecalis show a decrease in resistance to gentamicin.
  • Coagulase-negative Staphylococcus (CoNS) and E. faecalis show a decrease in resistance to gentamicin.
  • E. faecalis and E. coli show a decrease in resistance to meropenem.
  • Coagulase-negative Staphylococcus (CoNS) and E. coli or Coagulase-negative Staphylococcus (CoNS) and E. faecalis, or Coagulase-negative Staphylococcus (CoNS) and S. agalactiae, or E. coli and K. oxytoca, or E. coli and K. pneumoniae, or E. coli and S.
  • Coagulase-negative Staphylococcus (CoNS) and E. coli, or Coagulase-negative Staphylococcus (CoNS) and K. pneumoniae, or Coagulase-negative Staphylococcus (CoNS) and S. agalactiae, or E. faecalis and E. coli show a decrease in resistance to TMP/sulfamethoxazole.
  • CoNS Coagulase-negative Staphylococcus
  • S. agalactiae or E. faecalis and S. agalactiae show a decrease in resistance to vancomycin.
  • FIG. 3, FIG. 4, FIG. 5, FIG. 6, FIG. 7, and FIG. 8 also show effects of organism interactions on antibiotic resistance.
  • FIG. 9 and FIG. 10 show correlations between the presence of particular organisms found in polymicrobial infections.
  • the present invention describes methods of treating polymicrobial infections, such as the aforementioned polymicrobial infections, with appropriate antibiotics, such as the antibiotics to which the polymicrobial infections have decreased resistance.
  • the methods herein may comprise the detection of the presence of the combination of the bacteria (e.g., the two or more bacteria in a polymicrobial infection) in a source of the infection obtained from the patient.
  • the detection process may not necessarily involve first isolating each bacterium from the source of infection.
  • the present invention features methods of treating a patient having or suspected of having a polymicrobial infection comprising a combination of E. faecalis and E. coli.
  • the method comprises administering one or a combination of amoxicillin/clavulanate, ampicillin/sulbactam, levofloxacin, meropenem, or tetracycline.
  • the present invention also features methods for treating a patient having or suspected of having a polymicrobial infection comprising a combination of E. faecalis and K. pneumoniae.
  • the method comprises administering one or a combination of meropenem or tetracycline.
  • the present invention also features methods for treating a patient having or suspected of having a polymicrobial infection comprising a combination of E. faecalis and P. aeruginosa.
  • the method comprises administering meropenem to the patient.
  • the present invention also features methods for treating a patient having or suspected of having a polymicrobial infection comprising a combination of E. faecalis and P. miribiiis.
  • the method comprises administering meropenem to the patient.
  • the present invention also features methods for treating a patient having or suspected of having a polymicrobial infection comprising a combination of E. faecalis and S. agalactiae.
  • the method comprises administering one or a combination of ampicillin or vancomycin.
  • ABR Antibiotic Resistance
  • samples may be collected from subjects according to standard collection protocols in sterile containers and are transported to the testing facility.
  • An example of the preparation of the antibiotic resistance (ABR) testing plates involves two steps. First is preparation of antibiotic solutions and the second is preparation of the bacterial growth medium plate.
  • the antibiotics to be tested for any given sample include antibiotics known to be useful for treating the tissue having the suspected infection, or any antibiotics requested by a medical or laboratory professional having knowledge of the particular patient sample. It is anticipated that most assays will be performed with a standard panel of antibiotics based on the type and location of infection suspected by a medical professional.
  • the standard panel of antibiotics comprises nitrofurantoin, ciprofloxacin, meropenem, ceftriaxone, trimethoprim/sulfamethoxazole, piperacillin/tazobactam, levofloxacin, cefoxitin, tetracycline, ampicillin/sulbactam, ampicillin, and vancomycin.
  • patients with known antibiotic allergies or sensitivities, or with a history of antibiotic resistance may require customized panels of antibiotics.
  • the assay can be performed simultaneous with an unlimited number of antibiotics.
  • Antibiotic stock solutions are prepared using solvents suitable for each antibiotic and then 10x solutions are prepared and stored in multi-well plates to allow efficient transfer to testing plates. Each antibiotic is tested at a minimum of concentrations.
  • concentrations, four concentrations, five concentrations, six concentrations, seven concentrations, eight concentrations, nine concentrations, or ten concentrations of an antibiotic, or antibiotic combination are included in the assay.
  • serial dilutions of the antibiotics are prepared wherein each dilution represents half the concentration of the higher concentration.
  • the 10x antibiotic solutions are stored in the multi-well plate according to a plate plan established for the antibiotic panel chosen for the assay. Exemplary plate plans are depicted in the Antibiotic Source Plates in FIG. 11 and FIG. 12. Antibiotic stocks and 10x solutions are stored at 2-8°C until needed.
  • the ABR testing plates may be multi-well plates (e.g., 6-well, 12-well, 24-well, 48-well, 96-well, 384-well plates, or any multi-well plate suitable for this purpose) capable of containing bacterial growth medium and culturing bacteria.
  • the plates are 96-well plates.
  • sterile agar-bacterial growth medium is dispensed into each well of the plate.
  • Exemplary agar-bacterial growth medium include, but are not limited to Mueller-Hinton agar, blood agar, trypticase soy agar, etc.
  • Samples for the disclosed antibiotic resistance testing may be optionally diluted in sterile aqueous solution or mixed with bacterial growth medium.
  • a volume of sample for the disclosed antibiotic resistance testing are first mixed with a growth medium and incubated for 0-24 hours at an incubation temperature of 35 ⁇ 4°C.
  • the samples are then diluted with saline and then mixed with growth medium and added to room temperature ABR testing plates at 9/10 volume of each well in the multi-well plate.
  • samples are added to room temperature ABR plates at 1/20 volume of bacterial growth medium present in the well.
  • a single patient specimen is used for each ABR plate. If multiple patient specimens are to be tested, each specimen is assayed in its own plate. Once inoculated, the plates are covered and incubated to encourage bacterial growth.
  • Embodiments where a single sample is assayed using more than one plate are also within the scope of the present method.
  • the plates can be used to culture either anaerobic or aerobic bacteria.
  • the plates are incubated at a temperature and in a reduced-oxygen environment to encourage growth of anaerobic bacteria.
  • the plates are incubated at a temperature and in an oxygen-containing environment to encourage growth of aerobic bacteria.
  • the incubation temperature can vary depending on the expected types of bacteria but will most likely be in a range of 35-40°C.
  • the plates containing samples are incubated for 12-48 hours, 12-24 hours, 24-28 hours, 12-36 hours, 14-30 hours, 16-24 hours, 16-20 hours, or 16-18 hours, or any range bounded by these numbers.
  • bacteria present in each well are recovered by resuspension in an aqueous liquid.
  • suitable liquids include, but are not limited to, water, saline, culture medium, etc.
  • the aqueous liquid should be sterile, or at least free from bacterial growth.
  • a volume of liquid equal to 100% of the volume of bacterial growth medium is carefully added to the wells of the ABR plate and allowed to sit for at least 30 minutes. In some embodiments, the plates are allowed to sit for 35 minutes, 40 minutes, 45 minutes, 50 minutes, or 60 minutes. The resulting suspension is then carefully removed from each well into individual wells of a clean multi-well plate according to the predetermined plate plan.
  • the plates are optionally agitated to cause mixing of the bacteria with the liquid prior to removal of the suspension.
  • the multi-well plate will be applied to OD 600 measurement immediately after incubation.
  • the multi-well plate containing the bacteria-containing suspension is then read in a spectrophotometer.
  • the optical density of the recovered liquid is measured at OD 600 multiple times to correct for uneven distribution of bacteria particles in the suspension.
  • the plates are read one time, two times, three times, four times, five times, six times, seven times, or eight times. The multiple plate reads occur in sequence without allowing the suspension to settle in the wells.
  • each well contains a blend of antibiotics (AB-blend).
  • this no-growth well contains sodium azide (Na-Azide).
  • the blanked value is representative of the ability of bacteria to grow in the presence of the particular antibiotic in the well.
  • the blanked results are then converted into a “resistance” (R) or “sensitive” (S) score based on a threshold value.
  • R resistance
  • S sensitive
  • the threshold value is for an agar-containing medium.
  • a threshold value has been determined at 0.010 to 1.000, 0.010-0.090, 0.015 to 0.035, or 0.020 to 0.030 based on correlations to a standard reference method.
  • the threshold value as been determined at about 0.010, about 0.015, about 0.020, about 0.025, about 0.030, about 0.035, about 0.040, about 0.045, about 0.050, about 0.055, about 0.060, about 0.065, about 0.070, about 0.075, about 0.080, about 0.085, or about 0.090 based on correlations to a standard reference method.
  • a threshold value has been determined at 0.025 based on correlations to a standard reference method.
  • the threshold value is for a liquid medium. In some embodiments, a threshold value has been determined at 0.010-1.000, 0.020-0.090, 0.050-0.080, 0.055 to 0.075, or 0.060 to 0.070 based on correlation to a consensus score between two standard reference methods.
  • the threshold value as been determined at about 0.010, about 0.015, about 0.020, about 0.025, about 0.030, about 0.035, about 0.040, about 0.045, about 0.050, about 0.055, about 0.060, about 0.065, about 0.070, about 0.075, about 0.080, about 0.085, about 0.090, or about 0.095 based on correlation to a consensus score between two standard reference methods.
  • a threshold value has been determined at 0.065 based on correlation to a consensus score between two standard reference methods.
  • any adjusted OD 600 measurement greater than blank OD 600 measurement can be determined as indicative of bacterial growth and applied as a threshold value by correlation to a standard reference method or combination of reference methods.
  • Results of the antibiotic resistance assay disclosed herein are transmitted to the appropriate medical professional who then has the option of prescribing an antibiotic, or antibiotics, shown to be active against the patient’s infection, changing the antibiotic to a more effective antibiotic, or ordering additional testing.
  • Example 1 Bacterial Organism Interactions as Detected by Pooled Antibiotic Susceptibility testing ( P-AST ) in Polymicrobial Urine Specimens
  • AST antibiotic susceptibility testing
  • P-AST Pooled Antibiotic Susceptibly Testing
  • the present invention describes Pooled Antibiotic Susceptibility Testing (P-AST), which involves simultaneously growing all detected bacteria together in the presence of antibiotics and then measuring susceptibility.
  • P-AST considers interactions between cohabiting bacterial species.
  • Urine specimens were obtained from patients presenting with UTI-like symptoms to 37 urology clinics. The odds of resistance were estimated for 18 antibiotics relative to increasing numbers of bacterial species in a specimen. It was found that antimicrobial susceptibility patterns in polymicrobial specimens differed from those observed in monomicrobial specimens. Since standard of care relies on assessment of antibiotic susceptibility in monomicrobial infections, these findings show that P-AST could serve as a more accurate predictor of antibiotic susceptibility.
  • Inclusion criteria included: symptoms of acute cystitis, complicated UTI, persistent UTI, recurrent UTI, prostatitis, pyelonephritis, interstitial cystitis (at any age), symptoms of other conditions at >60 years of age, specimen volumes sufficient to permit urine culture and Multiplex Polymerase Chain Reaction (M-PCR) combined with Pooled Antibiotic Sensitivity Testing (P-AST), patient informed consented, documented times at which the specimens were collected and stabilized with boric acid in grey-top tubes.
  • Exclusion criteria included prior participation in this study, antibiotics taken for any reason other than UTI at the time of enrollment, chronic (>10 days) indwelling catheters, self-catheterization, and urinary diversion. Antibiotic susceptibility data were available for 1 ,352 of the 3,124 patients (43.3%).
  • DNA extraction was performed using the KingFisher/MagMAXTM Automated DNA Extraction instrument and the MagMAXTM DNA Multi-Sample Ultra Kit (ThermoFisher, Carlsbad, CA). 1 mL of urine were transferred to 96-well deep-well plates, sealed, and centrifuged to concentrate the samples, and then the supernatant was removed. Enzyme Lysis Mix (200 ⁇ L/well) was added to the samples, which were then incubated for 20 min at 65°C. Proteinase K Mix (PK Mix) was added (50 ⁇ L/well) and incubated for 30 min at 65°C.
  • PK Mix Proteinase K Mix
  • Lysis buffer 125 ⁇ L/well
  • DNA Binding Bead Mix 40 ⁇ L/well
  • the samples were vortexed for a minimum of 5 min.
  • Each 96-well plate was loaded into the KingFisher/MagMAX Automated DNA Extraction instrument, which was operated in accordance with standard operating procedures.
  • DNA analysis was conducted using the Guidance ® UTI Test (Pathnostics, Irvine, CA), which consists of both M-PCR and P-AST. Samples were mixed with universal PCR master mix and amplified using TaqMan technology on the Life Technologies 12K Flex OpenArray SystemTM (Life Technologies, Carlsbad, CA). DNA samples were spotted in duplicate on 112-format OpenArray chips. Plasmids unique to each bacterial species being tested were used as positive controls. Any appropriate target may be usable as an inhibition control, e.g., Candida tropicalis, B. atrophaeus, etc. A data analysis tool developed by Pathnostics was used to sort data, assess the quality of data, summarize control sample data, identify positive assays, calculate concentrations, and generate draft reports.
  • Probes and primers were used to detect the following pathogenic bacteria: Acinetobacter baumannii, Actinotignum schaalii, Aerococcus urinae, Alloscardovia omnicolens, Citrobacter freundii, Citrobacter koseri, Corynebacterium riegelii, Enterobacter aerogenes, Enterococcus faecalis, Escherichia coli, Klebsiella oxytoca, Klebsiella pneumoniae, Morganella morganii, Mycobacterium tuberculosis, Mycoplasma genitalium, Mycoplasma hominis, Pantoea agglomerans, Proteus mirabilis, Providencia stuartii, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Streptococcus agalactiae, and Ureaplasma urealyticum.
  • CoNS Coagulase negative staphylococci
  • VNS Viridans group streptococci
  • the Pooled Antibiotic Sensitivity Test is permitting the organisms identified to grow in the presence of antibiotics and measuring the minimum concentration of antibiotic to inhibit growth.
  • Antibiotic susceptibility testing is performed when at least a single organism within a pool of organisms reaches a certain threshold, (e.g., at least 3,000 cells/ml, at least 5,000 cells/ml, at least 10,000 cells/ml, etc.) and can grow in the presence of the antibiotic in the assay within the time of testing. (Note: 10,000 cells/ml is equivalent to 10,000 CFU/ml.)
  • the present invention is not limited to a 10,000 cells/mL threshold.
  • P-AST was performed by aliquoting 1 mL of patient urine specimen into a 1.7 mL microcentrifuge tube. After centrifugation, the supernatant was aspirated and discarded, leaving approximately 100 or 50 ⁇ L (minimum volume left above pellet created from centrifugation) of patient sample in the microcentrifuge tube.
  • One mL of Mueller Hinton Growth Media was then aliquoted into the patient sample in the microcentrifuge tube and the tubes were incubated at 35°C in a non-C0 2 incubator for 6 hours. Non-inoculated liquid MH-media is incubated as the negative control to confirm the media used is not contaminated.
  • Those samples that reached a minimum threshold of 10,000 cells/mL were then diluted by aliquoting 0.5 mL of sample into a 50 mL conical tube containing Mueller Hinton Growth Media (in this example, the dilution was 1:60, e.g., 500 pL was added to 29.5 mL).
  • 96-well plates pre-loaded with antibiotics were then inoculated with diluted samples and incubated along with control plates for 12-16 hours at 35°C in a single layer.
  • Optical density of samples was then read on a DensiCHEK plate reader.
  • the turbid samples were diluted/normalized to the same concentration and then added to a volume of liquid, e.g., 29.5 mL of liquid MH-media.
  • a spectrophotometer plate reader
  • the present invention is not limited to a concentration of 10,000 cells/mL.
  • Logistic regression was used to compare resistance rates in monomicrobial and polymicrobial infections. Specifically, 18 different logistic regression models were fit to the data: the response variable was an indicator of whether the specimen was resistant to the specific antibiotic or not and the predictor variable was an indicator of whether the infection was monomicrobial or polymicrobial. Specimens were classified as monomicrobial if a single bacterial species was detected above the 10000 cells/mL threshold; they were classified as polymicrobial if two or more distinct bacteria species were detected above that threshold. Similar logistic regression models also were run, using the number of distinct bacterial species as the predictor variable. The present invention is not limited to a concentration of 10,000 cells/mL.
  • HSAP Highest Single Agent Principle
  • UP Union Principle
  • the UP assumes a pair of bacteria (species A and B) is made up of one genetic variant of species A and one genetic variant of species B, and that the pool is resistant if either species A is resistant or if species B is resistant. If species A is resistant with probability P(A), and species B is resistant with probability P(B), then the probability of resistance of the pool is:
  • Odds ratios of antibiotic resistance in polymicrobial versus monomicrobial specimens are shown in Table 1 , along with the odds ratio of resistance for each increase in the number of bacterial species in polymicrobial specimens.
  • the resistance rates of polymicrobial samples were generally higher than the rates of monomicrobial samples; 10 of 18 antibiotics had statistically higher resistance rates for polymicrobial samples.
  • the odds of resistance for each additional species identified in a polymicrobial specimen increased for ampicillin, amoxicillin/clavulanate, five of the six of the cephalosporins tested, vancomycin, and tetracycline.
  • FIG. 2 shows the effect of specific species interactions on the probability of increased or decreased resistance to each antibiotic tested. No interactions were detected for nitrofurantoin and piperacillin/tazobactam. Whereas the odds of resistance to ampicillin, amoxicillin/clavulanate, 6 different cephalosporins, vancomycin, and tetracycline increased with increasing number of detected species (FIG. 2), there were 19 instances for which 11 of the 13 bacterial pairs resulted in reduced susceptibility to the same antibiotics,
  • the UP model identified 49 statistically significant interactions, all of which showed decreased probability of resistance to the antibiotics tested.
  • FIG. 1 shows the predicted probabilities of resistance to ampicillin/sulbactam, cefaclor, and tetracycline by monomicrobial positive cultures for E. coli and K. pneumoniae and a polymicrobial culture positive for both E. coli and K. pneumoniae.
  • the pairing of E. coli and K. pneumoniae resulted in either a significant increase or significant decrease in the probability of resistance depending on the antibiotic tested.
  • the resistance rate was higher than either E. coli or K. pneumoniae alone.
  • the resistance rate to tetracycline of same combination of species, E. coli and K. pneumoniae was intermediate between the resistance rates to each species alone.
  • pneumoniae resulted in increased resistance to amoxicillin/clavulanate and ampicillin/sulbactam, but decreased resistance to levofloxacin, meropenem, and tetracycline.
  • E. faecalis combined with S. agalactiae produced an increase in resistance to tetracycline, but decreased resistance to ampicillin and vancomycin.
  • the combination of CoNS and E. coli produced an increased probability in resistance to levofloxacin, but the same combination produced a decreased probability in resistance to amoxicillin/clavulanate, ceftriaxone, tetracycline, and trimethoprim/sulfamethoxazole.
  • the observed effects on antibiotic resistance in polymicrobial infections may be due to cooperative and/or competitive interactions between bacteria.
  • Resistant bacteria can cooperatively protect susceptible bacteria by degrading antibiotics, as occurs when secreted beta-lactamase degrades beta-lactam antibiotics.
  • Antibiotic resistance can be conferred by one bacterium on another bacterium by means of horizontal gene transfer (HGT) of antibiotic resistance genes.
  • HGT horizontal gene transfer
  • Bacterial interactions with host macrophages can promote HGT.
  • P. aeruginosa when present in biofilms, produces extracellular DNA that induces neutrophils to produce pro-inflammatory cytokines (IL-8 and IL-1 beta). The ensuing inflammation can promote HGT involving E. coli.
  • antibiotics can also promote HGT: antibiotics that cause bacterial lysis release DNA and proteins that can be taken up by other bacteria.
  • one bacterium can stimulate gene expression in another bacterium, resulting in upregulation of efflux pumps leading to increased antibiotic resistance.
  • Bacterial community spatial structuring within a polymicrobial biofilm may also affect the efficacy of antibiotics.
  • Type VI secretion systems secrete proteases that digest IgA, surface receptors that bind the constant region of IgG, and virulence factor/adhesin proteins that promote colonization.
  • Type VI secretion systems allow Gram-negative bacteria to secrete antibacterial toxins directly into other bacteria.
  • Type VI systems mediate DNA acquisition via HGT; an example is the capacity for A. baumannii to rapidly acquire resistance genes from E. coli by means of Type VI transfer systems.
  • Urine samples suitable for processing with this assay are collected, transported, and stored using BD Vacutainer (gray top) tubes or other suitable leak-proof sterile container. Urine samples may be held at room temperature for 48 hours before test results are compromised.
  • Antibiotics not received in ready-made solutions were dissolved in appropriate solvent and according to their individual solubility at 10x the concentration desired in the assay as antibiotic stocks. Antibiotic stocks are stored at 2-8°C and protected from direct sunlight. Prepared antibiotic stock solutions were aliquoted into a 96-deep well plate (Thermo Fisher Scientific) to form an Antibiotic Source Plate, as shown in FIG. 11 and identified by antibiotic name and concentration ( ⁇ g/mL; 10x final concentration).
  • Antibiotics include in this assay were nitrofurantoin, ciprofloxacin, meropenem, ceftriaxone, trimethoprim, sulfamethoxazole, piperacillin, tazobactam, levofloxacin, cefoxitin, tetracycline, ampicillin, sulbactam, and vancomycin, either singly or in combination.
  • One well was designated AB-blend which contained a combination of antibiotics to ensure there was no bacterial growth.
  • the antibiotics (10 ⁇ L) at various concentrations were then aliquoted into desired wells from the Antibiotic Source Plate. After the antibiotics were introduced to the agar medium, the ABR microplates were allowed to sit for at least 1 hr before use. If long-term storage is required, ABR microplates containing antibiotic-infuse agar are stored at 2-8°C in the dark.
  • Controls include: No-antibiotic control, Negative control plate, and AB-Blend.
  • No antibiotic control Any well containing medium that is not infused with antibiotics to ensure viability of bacterial cells present in patient urine samples and included in each plate. If the no-antibiotic control for any given patient does not yield growth, a secondary test is performed using the same patient sample without dilution.
  • Negative control plate Microplate containing antibiotic-infused agar medium without addition of patient sample or cultured bacterial organisms to ensure non-contamination of reagents.
  • AB-Blend One or more wells containing a combination of antibiotics to ensure there is no bacterial growth.
  • Table 2 [00198] Each well position corresponds to a particular antibiotic at a certain concentration according to the plate plan. Addition of the antibiotic legend is depicted in Table 3.
  • the sample contains bacteria sensitive to nitrofurantoin, ciprofloxacin, meropenem, ceftriaxone, piperacillin/tazobactam, and cefoxitin.
  • the results for levo are equivocal.
  • the MIC for each drug can then be provided.
  • the minimum inhibitory concentration (MIC) is the minimum test antibiotic concentration to which the sample is sensitive.
  • An exemplary MIC determination for meropenem based on the results above is depicted in Table 7.
  • Inter-assay precision was evaluated by testing three samples from the "Accuracy” sample set over three days. Intra-assay precision was evaluated by testing each of these samples in triplicate in one batch. Precision for each sample was assessed by determining the consensus result of all 5 replicates and then counting the number of replicates that match the consensus. This number was then divided by the sum of all measurements (sum of measurements for all drugs) to determine the % precision. The overall precision was calculated by dividing the sum of all correct matches by the total number of measurements from all samples. The assay demonstrated very good precision (Table 9).
  • Analytic sensitivity or the limit of detection (LOD) was assessed by determined the lowest bacterial concentration that yielded accurate results. In certain cases, bacterial concentrations lower than 10,000 cells/mL are not considered positive for UTI and therefore the lowest concentration tested was 10,000 cells/mL. Consistent results (>98%) correlation to the consensus results were obtained at the lowest bacterial concentrations tested. The LOD of this assay was 10,000 cells/mL, Note, the present invention is not limited to a concentration of 10,000 cells/mL.
  • the analytic specificity of this assay was assessed by testing samples at bacterial concentrations of 100,000,000 cells/mL. Such concentrations are not typically observed in routine UTI patient samples but were achieved in saturated overnight bacterial cultures. Assessment of analytic measurement range (AMR) was then performed by testing three samples from the “Accuracy” sample set each diluted as follows: 100,000,000 cells/mL, 1,000,000 cells/mL, 100,000 cells/mL and 10,000 cells/mL Consistent results (>94%) correlation to the consensus results were obtained at all bacterial concentrations tested.
  • the assay is specific at bacterial concentration up to 100,000,000 cells/mL
  • the present invention is not limited to a concentration of 10,000 cells/mL
  • Urine samples suitable for processing with this assay are collected, transported, and stored using BD Vacutainer tubes or other suitable leak-proof sterile containers. Urine samples may be held at room temperature for 48 hours before test results are compromised.
  • Antibiotics not received in ready-made solutions were dissolved in appropriate solvents and according to their individual solubility to 5Gx the concentration desired in the assay and stored as antibiotic stocks. Antibiotic stocks are stored at 2-8°C and protected from direct sunlight. Prepared antibiotic stock solutions were aliquoted into a 96-deep well plate (ThermoFisher Scientific) to form a 50x Antibiotic Source Plate and then diluted 1:5 to form a 10x Antibiotic Source Plate, as shown in FIG. 12 where each well is identified by antibiotic name and concentration (pg/mL; 10x final concentration).
  • Antibiotics included in this assay were amoxicillin, clavulanate, ampicillin, sulbactam, cefaclor, cefazolin, cefepime, cefoxitin, ceftazidime, ceftriaxone, ciprofloxacin, gentamicin, levofloxacin, meropenem, nitrofurantoin, piperacillin, tazobactam, tetracycline, trimethoprim, sulfamethoxazole, and vancomycin, either singly or in combination.
  • One well was assigned sodium azide to ensure no bacterial growth would be observed in that well.
  • the plate was removed from the incubator and carefully uncovered and the OD600 was determined for each appropriate well by spectrophotometer. Five separate measurements were taken of each well on a plate and the mean OD600 measurement calculated for each well.
  • the MIC for each drug can then be provided.
  • the minimum inhibitory concentration (MIC) is the minimum test antibiotic concentration to which the sample is sensitive.
  • An exemplary MIC determination for meropenem based on the results above is depicted in Table 16.
  • Inter-Assay precision was evaluated by testing five samples over three different days. Intra-Assay precision was evaluated by testing the same five samples in triplicate in a single day. Percent concordance was calculated to measure the precision of results obtained by this assay. The assay demonstrated very good precision (Table 18).
  • Analytic sensitivity was evaluated by creating a dilution series of E. coli and E. faecalis with the lowest bacterial concentration at less than 100 ce!ls/mL for each organism. Each dilution level for each isolate was tested to show reproducibility of results down to the lowest concentration. 98% correlation was observed across all dilution levels for both isolates, indicating the limit of detection (LOD) of this assay is less than 100 cells/ml.
  • LOD limit of detection
  • This assay utilizes a pre-culture step prior to introducing samples to antibiotics.
  • the duration of this pre-culture incubation was tested at 6 and 16 hours for 2 isolates (E. coli and E. faecalis). Good accuracy for each isolate was observed after both 6 and 16 hour pre-culture incubations, indicating a pre-culture window of 6 to 16 hours for this assay. Results displayed below in Table 19.
  • samples are introduced to antibiotics, they are incubated for 12 to 16 hours. This incubation length was determined by obtaining OD measurements for Precision samples after 12 and 16 hours of incubation. Good percent concordance was observed for all samples across within a 12 to 16 hour incubation window (Table 20).

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Abstract

L'invention concerne des procédés de détection et de traitement d'infections polymicrobiennes, une population mixte de microbes (par exemple, des bactéries) étant présente dans un échantillon de patient et les microbes n'étant pas tout d'abord isolés de l'échantillon. Par exemple, la présente invention concerne des infections polymicrobiennes spécifiques et des procédés de traitement desdites infections, un antibiotique particulier ou un groupe d'antibiotiques étant choisi sur la base de la composition des infections polymicrobiennes.
PCT/US2021/027336 2017-04-19 2021-04-14 Procédés de traitement d'infections polymicrobiennes WO2021211746A1 (fr)

Priority Applications (6)

Application Number Priority Date Filing Date Title
CA3176586A CA3176586A1 (fr) 2020-04-14 2021-04-14 Procedes de traitement d'infections polymicrobiennes
PCT/US2022/016816 WO2022178142A1 (fr) 2021-02-17 2022-02-17 Procédés et systèmes de détermination de l'adéquation de compositions pour inhiber la croissance d'échantillons polymicrobiens
EP22756936.5A EP4294521A1 (fr) 2021-02-17 2022-02-17 Procédés et systèmes de détermination de l'adéquation de compositions pour inhiber la croissance d'échantillons polymicrobiens
CA3175879A CA3175879A1 (fr) 2021-02-17 2022-02-17 Procedes et systemes de determination de l'adequation de compositions pour inhiber la croissance d'echantillons polymicrobiens
IL294577A IL294577A (en) 2021-02-17 2022-07-07 Systems and methods for determining the suitability of preparations to prevent the growth of multi-bacterial samples
US18/451,748 US20230392185A1 (en) 2017-04-19 2023-08-17 Methods and systems for determining suitability of compositions for inhibiting growth of polymicrobial samples

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US202063063093P 2020-08-07 2020-08-07
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