[go: up one dir, main page]

WO2014165274A2 - Procédés de diagnostic, de prévention et de traitement d'infections pathogéniques résistantes aux médicaments au moyen de séquences de réplikine - Google Patents

Procédés de diagnostic, de prévention et de traitement d'infections pathogéniques résistantes aux médicaments au moyen de séquences de réplikine Download PDF

Info

Publication number
WO2014165274A2
WO2014165274A2 PCT/US2014/025053 US2014025053W WO2014165274A2 WO 2014165274 A2 WO2014165274 A2 WO 2014165274A2 US 2014025053 W US2014025053 W US 2014025053W WO 2014165274 A2 WO2014165274 A2 WO 2014165274A2
Authority
WO
WIPO (PCT)
Prior art keywords
replikin
pathogen
peptide
seq
drug
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/US2014/025053
Other languages
English (en)
Other versions
WO2014165274A3 (fr
Inventor
Samuel Bogoch
Elenore S. BOROCH
Samuel Winston Bogoch
Anne-Elenore Bogoch Borsanyi
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Individual
Original Assignee
Individual
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Individual filed Critical Individual
Publication of WO2014165274A2 publication Critical patent/WO2014165274A2/fr
Publication of WO2014165274A3 publication Critical patent/WO2014165274A3/fr
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

Links

Classifications

    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/02—Bacterial antigens
    • A61K39/04—Mycobacterium, e.g. Mycobacterium tuberculosis
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/02—Bacterial antigens
    • A61K39/025—Enterobacteriales, e.g. Enterobacter
    • A61K39/0266—Klebsiella
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/02—Bacterial antigens
    • A61K39/08—Clostridium, e.g. Clostridium tetani
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/02—Bacterial antigens
    • A61K39/09—Lactobacillales, e.g. aerococcus, enterococcus, lactobacillus, lactococcus, streptococcus
    • A61K39/092—Streptococcus

Definitions

  • Antimicrobial agents have been in use in modern medicine for eight decades against pathogenic infections and have greatly reduced morbidity and mortality from infectious diseases. Nevertheless, because of their wide-spread use and effectiveness over time (both in animals and humans), certain pathogenic microorganisms have developed resistance, rendering some antimicrobial therapies less effective or even ineffective against pathogens previously susceptible to the drugs. Resistance to antimicrobials has been identified in fungi, viruses, parasites, and bacteria. Certain pathogens have developed resistance to one antimicrobial therapy while other pathogens have developed resistance to more than one therapy including more than one class of antibiotic therapy. In certain instances, resistance has evolved such that no known antimicrobial agent against a specific pathogen is available for effective treatment. Drug-resistance in these pathogens is tragic and expensive with more death, longer hospitalization, and more suffering. Additionally, drugs that are used to replace ineffective therapies may be less effective, more expensive, and/or more toxic.
  • Resistance to antibiotic treatment is a particularly- relevant form of drug resistance wherein sub-populations of a pathogen survive exposure to one or more antibiotic therapies resulting in a sub-population that is not treatable with previously-effective antibiotic therapies or previously-effective doses of antibiotic therapies.
  • Development of resistance in certain sub-populations is a significant threat in public health including a significant threat in nosocomial diseases.
  • Certain nosocomial pathogens have developed resistance to multiple antibiotic families. These populations are considered multidrug resistant pathogens.
  • Drug-resistant pathogens include, for example, Extensively Drug-resistant Tuberculosis, Gonococcus, Klebsiella, Clostridium, Streptococcus, Methicillin-resistant Staphylococcus, and drug-resistant E. coli. Resistance has also been noted in some fungi, including in patients with weakened immune systems. Fungi with populations demonstrating antimicrobial resistance include Candida albicans, Candida glabrata, and Aspergillus spp. Antimicrobial resistance in malaria has been a continuing problem for many years.
  • Antimicrobial resistance has likewise been observed in a wide-range of other parasites.
  • Tuberculosis remains a major infectious disease, accounting for approximately 3 million deaths per year worldwide.
  • a series of effective drugs were developed over several decades that have recently been challenged by two new circumstances.
  • the first challenging circumstance is the mutation of the tuberculosis genome to more lethal drug resistant forms.
  • the second challenging circumstance is the association of tuberculosis with AIDS, both resulting in high mortality cases in such areas as KwaZulu-Natal in South Africa and in Europe and Asia.
  • Tuberculosis has previously been defined as tuberculosis that demonstrates resistance to at least isoniazid and rifampin, resistance to any member of the fluoroquinolone family, and resistance to at least one second-line drug, which would include, for example, kanamycin, amikacin, and capreomycin.
  • Klebsiella populations expressing carbapenase enzyme have likewise been identified with resistance to the class of carbapenem antibiotic therapies. Multi-drug resistant populations have additionally been identified.
  • a strain of Clostridium difficile has also now been identified that is resistant to flouroquinolone antibiotics. This strain is highly-toxic and is resistant to antibiotics such as ciprofloxacin and levofloxacin. Since 2005, the strain has been reported to cause
  • MRSA methicillin-resistant staphylococcus aureus
  • Streptococcus species are another family of bacteria observed to be resistant to common drug therapies such as penicillin.
  • Vaccines against these drug-resistant pathogens have been considered. No satisfactory vaccine has yet to be produced. In some circumstance, vaccine development has been hindered by limited acquired immunity to infection.
  • the present invention provides surprising therapies and vaccines for drug-resistant pathogens.
  • the inventors have previously identified a family of conserved, small protein sequences that relate to rapid replication in influenza and other viruses.
  • the family of protein sequences is known as Replikins. Rapid replication is characteristic of virulence in viruses where Replikin sequences are identified or where concentrations of Replikin sequences are present. Rapid replication has been associated with the presence of Replikin sequence structures in protein sequences. Replikin sequences have been further associated with viral outbreaks, epidemics and increased rates of host mortality.
  • the present invention provides methods of determining if a population of pathogen is drug sensitive or drug resistant and compounds and compositions for prevention and treatment of infections of drug resistant pathogens.
  • a first non- limiting aspect of the present invention provides a method of determining if a pathogen or population of pathogen is drug sensitive or drug resistant.
  • a non- limiting embodiment of the first aspect of the present invention provides a method of diagnosing the drug sensitivity or drug resistance of a pathogen comprising determining a Replikin concentration of said pathogen and diagnosing the pathogen as drug resistant if the Replikin concentration is greater than 4.0 per 100 amino acid residues and drug sensitive if the Replikin concentration is 4.0 or less.
  • the pathogen is a bacterial pathogen.
  • the bacterial pathogen is a
  • the pathogen is Neisseria gonorrhoeae, Mycobacterium tuberculosis, Klebsiella pneumoniae, Clostridium difficile, or Streptococcus pneumoniae.
  • the pathogen is a fungus.
  • the pathogen is Candida albicans, Candida glabrata, or Aspergillus.
  • the pathogen is malaria or other parasitic pathogen.
  • a non- limiting embodiment of the first aspect of the invention provides a method of diagnosing if a population of pathogens is increasing in drug resistance comprising (1) determining a Replikin concentration of a plurality of specimens of an initial population of pathogen at a given time or in a given location and determining the percentage of said specimens having a Replikin concentration of greater than 4.0 Replikin sequences per 100 amino acid residues, (2) determining a Replikin concentration of a plurality of specimens of a different population of the pathogen at a different time or different location and determining the percentage of said specimens having a Replikin concentration of greater than 4.0 Replikin sequences per 100 amino acid residues, and (3) if the percentage of specimens having a Replikin concentration of greater than 4.0 Replikin sequences per 100 amino acid residues in the initial population of pathogens is greater than the percentage of specimens having a
  • the population of pathogens is a population of bacterial pathogen.
  • the bacterial pathogen is a
  • the pathogen is Neisseria gonorrhoeae, Mycobacterium tuberculosis, Klebsiella pneumoniae, Clostridium difficile, or Streptococcus pneumoniae.
  • the pathogen is a fungus.
  • the pathogen is Candida albicans, Candida glabrata, or Aspergillus.
  • the pathogen is malaria or other parasitic pathogen.
  • a non- limiting embodiment of the first aspect of the invention provides a method of determining an increase in drug-resistance in a population of a pathogen, comprising determining the percent of isolates of the pathogen from a population at a first and a second time period having a Replikin concentration of greater than 4.0 and if the percent of isolates having a Replikin concentration of greater than 4.0 increases between the first and second time period, determining that the pathogenic population is increasing in drug resistance from the first to the second time period.
  • a further non- limiting embodiment of the first aspect of the invention provides a computer readable medium having stored thereon instructions, which when executed, cause a processor to perform a method of determining if a pathogen or population of pathogen is drug sensitive or drug resistant.
  • the processor reports a prediction to a display, user, researcher, or other machine or person.
  • the processor identifies to a display, user, researcher, or other machine or person, a portion of a pathogen predicted to be drug-resistant, wherein said portion may be employed as a therapeutic or diagnostic compound.
  • Said portion may be a Replikin peptide sequence or plurality of Replikin peptide sequences or any other structure or portion of said genome of said pathogen including a Replikin Peak Gene.
  • a non- limiting computer readable medium may be non- transitory. Software comprising methods of the invention and related data may be carried on a signal.
  • a second non- limiting aspect of the present invention provides an isolated or synthesized protein fragment or peptide comprising at least one peptide sequence that is at least 50% homologous with at least one Replikin peptide sequence identified in a pathogen identified in a population of pathogens having a higher percentage of specimens with a Replikin concentration of greater than 4.0 Replikin sequences per 100 amino acid residues than specimens of another population of the same pathogen.
  • the at least one peptide sequence may be at least 80% homologous with at least one Replikin peptide sequence so identified.
  • the at least one peptide sequence may be at least 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, or 99% or more homologous with at least one Replikin peptide so identified.
  • the at least one peptide sequence may be at least 53%, 57%, 64%, 67%, 70%, 76%, 80%, 82%, 87%, 91%, or 93% or more homologous with at least one Replikin peptide so identified.
  • the population of pathogen is a bacterial pathogen, fungal pathogen, or parasitic pathogen.
  • the bacterial pathogen is a Gonococcus pathogen, Tuberculosis pathogen, Klebsiella pathogen, Clostridium pathogen, Streptococcus pathogen, Staphylococcus pathogen, or E. coli pathogen.
  • the bacterial pathogen is Neisseria gonorrhoeae, Mycobacterium tuberculosis, Klebsiella pneumoniae, Clostridium difficile, or Streptococcus pneumoniae.
  • the pathogen is a fungus.
  • the fungus may include, but is not limited to, Candida albicans, Candida glabrata, and
  • the pathogen may also be a malarial pathogen or other parasitic pathogen.
  • the isolated or synthesized protein fragment or peptide may comprise at least one Replikin peptide sequence or at least one homologue of the at least one Replikin sequence.
  • the isolated or synthesized protein fragment or peptide may consist essentially of at least one Replikin peptide or at least one homologue of said at least one Replikin peptide sequence.
  • the isolated or synthesized protein fragment or peptide may consist of at least one Replikin peptide sequence or at least one homologue of said at least one Replikin peptide sequence.
  • Another non- limiting embodiment provides an isolated or synthesized peptide sequence comprising at least one functional fragment of a Replikin sequence identified in a population of pathogens having a higher percentage of specimens with a Replikin concentration of greater than 4.0 Replikin sequences per 100 amino acid residues than specimens of another population of the same pathogen.
  • the isolated or synthesized protein fragment or peptide may comprise at least one Replikin peptide sequence of SEQ ID NO(s): 1-21, 22-56, or 57-119 or at least one homologue of SEQ ID NO(s): 1-21, 22-56, or 57-119.
  • the isolated or synthesized protein fragment or peptide may consists essentially of at least one Replikin peptide sequence of SEQ ID NO(s): 1-21, 22-56, or 57- 119 or at least one homologue of SEQ ID NO(s): 1-21, 22-56, or 57-119.
  • the isolated or synthesized protein fragment or peptide may consist of at least one Replikin peptide sequence of SEQ ID NO(s): 1-21, 22-56, or 57-119 or at least one homologue of SEQ ID NO(s): 1-21 , 22-56, or 57-119.
  • Another non-limiting embodiment provides an isolated or synthesized peptide sequence comprising at least one functional fragment of at least one Replikin peptide sequence of SEQ ID NO(s): 1-21, 22-56, or 57-119.
  • a homologue and a functional fragment of a Replikin sequence includes and is not limited to SEQ ID NO(s): 120-122 and homologues and functional fragments likewise understood by the ordinary skilled artisan upon reviewing the teachings of this specification.
  • a non- limiting embodiment of the second aspect of the invention provides an isolated or synthesized protein, protein fragment, polypeptide, or peptide comprising at least one Replikin peptide of a drug-resistant pathogen.
  • the drug- resistant pathogen is a drug-resistant bacterial pathogen.
  • a further embodiment of the second aspect of the invention provides an isolated or synthesized protein, protein fragment, polypeptide, or peptide comprising at least one peptide sequence that is at least 30%, 40%, 50%, 60%, 70%, 80%, 90% 95%, or 100%, homologous with at least one Replikin peptide sequence identified in a drug-resistant pathogen.
  • the at least one sequence is one of SEQ ID NO(s): 1-21, 22-56, or 57-119.
  • an isolated or synthesized protein fragment or peptide may consist of 50, 60, 70, 80, 90, 100, 150, or up to 200 amino acid residues.
  • the isolated or synthesized protein fragment or peptide comprises at least one Replikin peptide sequence, at least one homologue of at least one Replikin sequence, or at least one functional fragment of at least one Replikin sequence.
  • the isolated or synthesized protein, protein fragment, polypeptide, or peptide consists of 7 to about 50 amino acids comprising at least one peptide that is at least 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or 100%, homologous with at least one Replikin peptide sequence identified in a drug-resistant pathogen or a drug-resistant bacterial pathogen.
  • said at least one Replikin peptide sequence is at least one peptide sequence of SEQ ID NO(s): 1-21, 22-56, or 57-119.
  • a homologue and a functional fragment of at least one Replikin peptide sequence includes SEQ ID NO(s): 120-122.
  • the isolated or synthesized protein, protein fragment, polypeptide, or peptide consists essentially of a Replikin peptide identified in a drug-resistant pathogen or drug- resistant bacterial pathogen.
  • the Replikin peptide sequence is at least one peptide sequence of SEQ ID NO(s): 1-21, 22-56, or 57-119.
  • a further non- limiting embodiment provides a peptide consisting of any one of SEQ ID NO(s): 1-21, 22-56, or 57-119.
  • Another non-limiting embodiment of the second aspect of the invention provides a biosynthetic composition comprising the protein, protein fragment, polypeptide, or peptide of an aspect of the invention.
  • the biosynthetic composition consists essentially of a Replikin peptide of a drug-resistant pathogen or drug- resistant bacterial pathogen or consists of a Replikin peptide of a drug-resistant pathogen or drug-resistant bacterial pathogen.
  • an isolated protein, protein fragment, polypeptide, or peptide is chemically synthesized by solid phase methods.
  • a third non- limiting aspect of the present invention provides an immunogenic and/or blocking composition comprising at least one protein, protein fragment, polypeptide, or peptide of any one of the above-listed proteins, protein fragments, polypeptides, or peptides including and not limited to comprising at least one Replikin peptide sequence identified in a drug-resistant pathogen or drug-resistant bacterial pathogen or at least one homologue of said at least one Replikin peptide identified in a drug-resistant pathogen or drug-resistant bacterial pathogen or at least one functional fragment of at least one Replikin peptide sequence identified in a drug-resistant pathogen or drug-resistant bacterial pathogen.
  • the immunogenic and/or blocking compound comprises at least one peptide sequence of SEQ ID NO(s): 1-21, 22-56, or 57-119.
  • the immunogenic and/or blocking composition comprises at least one peptide consisting essentially of any one of SEQ ID NO(s): 1-21, 22-56, or 57-119.
  • the immunogenic and/or blocking composition comprises at least one peptide consisting of any one of SEQ ID NO(s): 1-21, 22-56, or 57-119 or at least one functional fragment of any one of SEQ ID NO(s): 1-21, 22-56, or 57-119.
  • the at least one peptide consists of 50, 60, 70, 80, 90, 100, 150, or up to 200 amino acid residues.
  • the at least one peptide comprises at least one Replikin peptide sequence, at least one homologue of at least one Replikin sequence, or at least one functional fragment of at least one Replikin sequence.
  • a fourth non- limiting aspect of the present invention provides a vaccine comprising at least one protein, protein fragment, polypeptide, or peptide of any one of the above-listed proteins, protein fragments, polypeptides, or peptides.
  • the vaccine comprises at least one peptide sequence of any one of SEQ ID NO(s): 1-21, 22-56, or 57-119, comprises at least one peptide sequence consisting essentially of any one of SEQ ID NO(s): 1-21 , 22-56, or 57-119, and/or comprises at least one peptide sequence consisting of any one of SEQ ID NO(s): 1-21, 22-56, or 57-119, at least one homologue of any one of SEQ ID NO(s): 1-21, 22-56, or 57- 119, or at least one functional fragment of any one of SEQ ID NO(s): 1-21, 22-56, or 57-119 or at least one Replikin peptide sequence identified in a drug-resistant pathogen or drug- resistant bacterial pathogen or at least one homologue or functional fragment of a Replikin peptide sequence identified in a drug-resistant pathogen or drug-resistant bacterial pathogen.
  • the vaccine comprises a mixture of a plurality of peptide sequences of any of SEQ ID NO(s): 1-21, a mixture of a plurality of sequence of any of SEQ ID NO(s): 22-56, or a mixture of plurality of peptide sequences of any of SEQ ID NO(s): 57-119, and/or a mixture of a plurality of homologues of peptide sequences of any of SEQ ID NO(s): 1-21, 22-56, or 57- 119.
  • Such mixture may include homologues or functional fragments such as SEQ ID NO(s): 120-122.
  • the vaccine comprises a mixture of a plurality of peptide sequences of any of SEQ ID NO(s): 1-119. In a further non-limiting embodiment, the vaccine comprises a mixture of a plurality of peptide sequences consisting essentially of any one or more of SEQ ID NO(s): 1-21, 22-56, or 57-119. In a further non- limiting embodiment, the vaccine comprises a mixture of a plurality of peptide sequences consisting of any one or more of SEQ ID NO(s): 1-21, 22-56, or 57-119.
  • the vaccine comprises a mixture of a plurality of peptide sequences consisting of each of SEQ ID NO(s): 1-21, or each of SEQ ID NO(s): 22-56, or each of SEQ ID NO(s): 57-119, or each of SEQ ID NO(s): 1-119.
  • the vaccine comprises a mixture of Replikin peptides.
  • the vaccine comprises an approximately equal molar mixture of the isolated or synthesized peptides of
  • the vaccine comprises approximately equal weight of the isolated or synthesized peptides of SEQ ID NO(s): 1-21, 22-56, or 57-119.
  • the vaccine comprises a
  • the vaccine is for the treatment or prevention of a drug-resistant pathogen.
  • the vaccine is directed against Clostridium spp., Streptococcus spp., or Klebsiella spp. In a further non-limiting embodiment, the vaccine is directed again
  • the vaccine is directed against a bacterial pathogen such as a
  • the pathogen is Neisseria gonorrhoeae or
  • the pathogen is a fungus.
  • the pathogen is Candida albicans, Candida glabrata, or Aspergillus.
  • the pathogen is malaria or other parasitic pathogen.
  • a fifth non- limiting aspect of the invention provides an antibody, antibody fragment, or binding agent that preferentially binds to at least a portion of an amino acid sequence of at least one protein, protein fragment, polypeptide, or peptide comprising a peptide sequence that is at least 30%, 40%, 50%, 53%, 57%, 60%, 64%, 67%, 70%, 76%, 80%, 82%, 87%, 90%, 91%, 93%, or 95% or more homologous with at least one Replikin peptide sequence identified in a drug-resistant pathogen or a drug-resistant bacterial pathogen.
  • the at least one Replikin peptide sequence is at least one peptide sequence of SEQ ID NO(s): 1-21, 22-56, or 57-119.
  • the antibody, antibody fragment, or binding agent preferentially binds at least one Replikin peptide sequence identified in a drug-resistant pathogen or a drug-resistant bacterial pathogen.
  • the antibody, antibody fragment, or binding agent preferentially binds within at least one Replikin peptide sequence.
  • the antibody, antibody fragment, or binding agent preferentially binds solely within at least one Replikin peptide sequence, homologue, or functional fragment thereof.
  • the antibody, antibody fragment, or binding agent preferentially binds an isolated or synthesized Replikin peptide. In a further non-limiting embodiment, the antibody, antibody fragment, or binding agent preferentially binds a homologue or functional fragment or a Replikin peptide sequence.
  • a sixth non- limiting aspect of the present invention provides a method of making a vaccine comprising: selecting at least one isolated or synthesized protein, protein fragment, polypeptide, or peptide comprising at least one peptide sequence that is at least 30%, 40%, 50%, 53%, 57%, 60%, 64%, 67%, 70%, 76%, 80%, 82%, 87%, 90%, 91%, 93%, 95%, or 100% homologous with at least one Replikin peptide sequence identified in drug-resistant pathogen or drug-resistant bacterial pathogen as a component of a vaccine; and making said vaccine.
  • the method of making a vaccine comprises selecting at least one isolated or synthesized peptide of SEQ ID NO(s): 1-21, 22-56, or 57-119, as at least one component and making said vaccine with the at least one component.
  • the vaccine may comprise at least one of SEQ ID NO(s): 120-122.
  • the method of making a vaccine comprises selecting at least two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, twenty, or twenty-one or more isolated or synthesized Replikin peptide sequences identified in a drug-resistant pathogen or drug-resistant bacterial pathogen (or homologues thereof) and/or isolated or synthesized functional fragments of Replikin peptide sequences identified in a drug-resistant pathogen or drug-resistant bacterial pathogen.
  • the isolated or synthesized Replikin peptide sequences or functional fragments of Replikin peptide sequences comprise at least one peptide sequence of SEQ ID NO(s): 1-21, 22-56, or 57-119, at least one functional fragment of at least one peptide sequence of SEQ ID NO(s): 1-21, 22-56, or 57- 119, or at least one functional fragment of at least one Replikin peptide sequence identified in a drug-resistant pathogen or drug-resistant bacterial pathogen.
  • the at least one isolated or synthesized protein, protein fragment, polypeptide, or peptide has the same amino acid sequence as at least one protein, protein fragment, polypeptide or peptide identified in a drug-resistant pathogen or drug-resistant bacterial pathogen up to seven days, one month, six months, one year, two years, or three years prior to making said vaccine.
  • a seventh non- limiting aspect of the present invention provides a method for preventing or treating drug-resistant pathogenic infection comprising administering at least one isolated or synthesized protein, protein fragment, polypeptide, or peptide comprising at least one peptide sequence to a subject, where the peptide sequence is at least 30%, 40%, 50%, 53%, 57%, 60%, 64%, 67%, 70%, 76%, 80%, 82%, 87%, 90%, 91%, 93%, 95%, or
  • the Replikin peptide sequence is at least one peptide sequence of SEQ ID NO(s): 1-21, 22-56, or 57-119 or at least one homologue or functional fragment thereof.
  • the at least one isolated or synthesized protein fragment, polypeptide, or peptide consists of at least one peptide sequence that is at least 30%, 40%, 50%, 53%, 57%, 60%, 64%, 67%, 70%, 76%, 80%, 82%, 87%, 90%, 91%, 93%, 95%, or more homologous with at least one of the peptide sequences of SEQ ID NO(s): 1-21 , 22-56, or 57-119.
  • the at least one isolated or synthesized peptide of SEQ ID NO(s): 1-21 , 22-56, or 57-119 is administered to a human or other animal.
  • the at least one Replikin peptide sequence is at least one peptide sequence of SEQ ID NO(s): 1-21, 22- 56, or 57-119.
  • a non- limiting embodiment provides use of at least one peptide sequence that is at least 30%, 40%, 50%, 53%, 57%, 60%, 64%, 67%, 70%, 76%, 80%, 82%, 87%, 90%, 91 %, 93%, 95%, or 100% homologous with at least one Replikin peptide identified in a drug- resistant pathogen or a drug-resistant bacterial pathogen in the manufacture of a medicament for preventing or treating drug-resistant pathogenic infection.
  • An eighth non- limiting aspect of the present invention provides nucleic acid sequences and compositions comprising nucleic acid sequences that encode for a Replikin peptide sequence isolated from or identified in a drug-resistant pathogen.
  • the nucleic acid sequence encodes for at least one of SEQ ID NO(s): 1-119.
  • the nucleic acid sequence is antisense to a fragment or to all of a sequence that encodes for a Replikin peptide sequence or is antisense to a sequence that encodes for any one or more of SEQ ID NO(s): 1-119 or a fragment thereof.
  • a nucleic acid sequence may encode more than a Replikin peptide sequence or fragment thereof.
  • Nucleic acid sequences may be comprised in a blocking agent or vaccine.
  • Figure 1 illustrates percentage of specimens of Gonococcus ⁇ Neisseria gonorrhoeae) available at the PubMed website of the National Center for Biotechnology Information (http://www.ncbi. nlm.nih.gov/) identified as having a Replikin concentration of greater than 4.0 per 100 amino acid residues for specimens identified as drug sensitive, specimens identified as resistant to the Cefixime antibiotic, specimens identified as resistant to Rifampicin antibiotic, specimens identified as resistant to Quinoline antibiotic, and specimens identified as resistant to Tetracycline antibiotic.
  • the percentage of specimens with Replikin concentrations of greater than 4.0 and the percentage of bacteria resistant to a particular antibiotic are observed to be proportional to the time in use of the particular antibiotic.
  • Figure 2 illustrates percentage of genomic sequences of Mycobacterium tuberculosis of five specific strains available at the PubMed website of the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/) identified as having a Replikin concentration of greater than 4.0 per 100 amino acid residues. Percentage of sequences having a concentration of greater than 4.0 are individually illustrated for each of strains KZN 4207, KZN 1435, KZN R506, H37Ra, H37Rv, and KZN 605.
  • Strain KZN 4207 is identified as fully drug sensitive
  • strain KZN 1435 is identified as drug resistant
  • strain KZN R506 is identified as drug resistant
  • strain KZN 605 is identified as extremely drug resistant.
  • Strains H37Ra and H37Rv are identified as attenuated virulence and virulent, respectively. Number of sequences analyzed for each of strains KZN 4207, KZN 1435, KZN R506, H37Ra, H37Rv, and KZN 605 were 3,883, 2,610, 1,278, 3,350, 1 ,217, and 2,592, respectively.
  • Figure 3 illustrates percentage of specimens of carbapenem-resistant Klebsiella pneumoniae available at the PubMed website of the National Center for Biotechnology Information (http://www.ncbi.nim.nih.gov/) identified as having a Replikin concentration of greater than 4.0 per 100 amino acid residues for specimens isolated in years 2007 through 2012.
  • An outbreak of carbapenem-resistant Klebsiella pneumoniae struck the U.S. National Institutes of Health Clinical Center in 2011 affecting 18 patients. Eleven of the 18 patients died of the infection.
  • Figure 4 illustrates percentage of specimens of drug-resistant Clostridium difficile available at the PubMed website of the National Center for Biotechnology
  • a "Replikin sequence” is an amino acid sequence of 7 to about 50 amino acids comprising (1) a first lysine residue located six to ten residues from a second lysine residue, (2) at least one histidine residue; and (3) at least 6% lysine residues.
  • a Replikin sequence may have a lysine residue on one end of the sequence and a lysine residue or histidine residue on the other end of the sequence.
  • a Replikin sequence is the shortest amino acid sequence of 7 to 50 amino acid residues comprising (1) a first lysine residue located six to ten residues from a second lysine residue, (2) at least one histidine residue; and (3) at least 6% lysine residues.
  • the Replikin sequence may comprise any number of lysine residues and any number of histidine residues so long as any two lysine residues and any one histidine residue reflect the requirements of the Replikin sequence.
  • a Replikin sequence counted as part of the Replikin concentration of a sequence of amino acid residues may comprise overlapping Replikin sequences.
  • Replikin sequence can also refer to a nucleic acid sequence encoding an amino acid sequence having 7 to about 50 amino acids comprising:
  • amino acid sequence may have a lysine residue on one end of the sequence and a lysine residue or histidine residue on the other end of the sequence or may be the shortest amino acid sequence having any two lysine residues and any one histidine residue reflecting the requirements of the Replikin sequence.
  • Replikin CountTM or “Replikin Concentration” refers to the number of Replikin sequences per 100 amino acids in a protein, protein fragment, virus, or organism. A higher Replikin concentration in a first strain of a virus or organism has been found to correlate with more rapid replication of the first virus or organism as compared to a second, earlier-arising or later-arising strain of the virus or organism having a lower Replikin concentration. Replikin concentration is determined by counting the number of Replikin sequences in a given amino acid sequence or in a nucleic acid that encodes at least one Replikin peptide sequence.
  • One aspect of the current invention provides a method of diagnosing the drug sensitivity or drug resistance of a pathogen comprising determining if a Replikin concentration is greater than 4.0 per 100 amino acid residues.
  • a Replikin concentration of greater than 4.0 per 100 amino acid residues denotes drug resistance and a concentration or 4.0 or less per 100 amino acid residues denotes drug sensitivity.
  • "drug-resistant" pathogens reflect populations of a pathogen that does not respond to treatment with an antimicrobial therapy at the same therapeutic level as other populations of the same pathogen at previous times or in different geographical areas.
  • peptide or "protein” refers to a compound of two or more amino acids in which the carboxyl group of one amino acid is attached to an amino group of another amino acid via a peptide bond.
  • isolated or “synthesized” peptide or biologically-active portion thereof refers to a peptide that is, after purification, substantially free of cellular material or other contaminating proteins or peptides from the cell or tissue source from which the peptide is derived, or substantially free from chemical precursors or other chemicals when chemically synthesized by any method, or substantially free from contaminating peptides when synthesized by recombinant gene techniques.
  • a protein or peptide may be isolated in silico from nucleic acid or amino acid sequences that are available through public or private databases or sequence collections.
  • An "encoded” or “expressed” protein, protein sequence, protein fragment sequence, or peptide sequence is a sequence encoded by a nucleic acid sequence that encodes the amino acids of the protein or peptide sequence with any codon known to one of skill in the art now or hereafter. It should be noted that it is well-known in the art that, due to redundancy in the genetic code, individual nucleotides can be readily exchanged in a codon and still result in an identical amino acid sequence.
  • a method of identifying a Replikin amino acid sequence also encompasses a method of identifying a nucleic acid sequence that encodes a Replikin amino acid sequence wherein the Replikin amino acid sequence is encoded by the identified nucleic acid sequence.
  • a nucleic acid sequence that encodes a Replikin peptide sequence or a homologue or fragment thereof encodes only the Replikin peptide sequence or a homologue or fragment thereof and not more than the Replikin peptide sequence or a homologue or fragment thereof.
  • an "isolate” is any organism isolated from a natural source wherein a natural source includes, but is not limited to, a reservoir of an organism or virus, a vector of an organism or virus, or a host of an organism or virus.
  • Obtaining,” “isolating,” or “identifying” an isolate is any action by which an amino acid or nucleic acid sequence within an isolate is obtained including, but not limited to, isolating an isolate and sequencing any portion of the genome or protein sequences of the isolate, obtaining any nucleic acid sequence or amino acid sequence of an isolate, wherein the nucleic acid sequence or amino acid sequence may be analyzed for Replikin concentration, or any other means of obtaining the Replikin concentration of a virus isolated from a natural source at a time point or within a time period.
  • Isolated or related words may also mean: identified within such a Replikin sequence identified within a larger polypeptide.
  • Replikin sequences described herein are fragments, variants, analogs, or chemical derivatives of Replikin sequences that retain at least a portion of the immunological cross reactivity with an antibody specific for the Replikin sequence.
  • a fragment of the Replikin peptide refers to any subset of the molecule.
  • “functional fragment" of the Replikin peptide or a Replikin Peak Gene is any subset of the molecule that retains at least a portion of immunological cross reactivity with an antibody specific for the Replikin peptide or Replikin Peak Gene.
  • Variant peptides may be made by direct chemical synthesis, for example, using methods well known in the art.
  • An analog of a Replikin peptide sequence to a non-natural protein substantially similar to either the entire protein or a fragment thereof.
  • Chemical derivatives of a Replikin peptide sequence contain additional chemical moieties not normally a part of the peptide or peptide fragment.
  • homologue or “homologous” or “homology” or “sequence identity” are used to indicate that an amino acid sequence or nucleic acid sequence exhibits substantial structural or functional equivalence with another sequence. Any structural or functional differences between sequences having sequence identity or homology will be de minimus; that is, they will not affect the ability of the sequence to function as indicated in the desired application. Structural differences are considered de minimus if there is a significant amount of sequence overlap or similarity between two or more different sequences or if the different sequences exhibit similar physical characteristics even if the sequences differ in length or structure. Such characteristics include, for example, the ability to hybridize under defined conditions, or in the case of proteins and peptides, immunological cross-reactivity, similar enzymatic activity, etc. The ordinary skilled practitioner can readily determine each of these characteristics by art-known methods.
  • the sequences are aligned for optimal comparison purposes ⁇ e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes).
  • gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes).
  • at least 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 99% or more of the length of a reference sequence is aligned for comparison purposes.
  • the amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared.
  • amino acid or nucleic acid “identity” is equivalent to amino acid or nucleic acid "homology”
  • the percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences as compared to the total length of the sequence identified as a reference sequence.
  • a "Replikin Peak Gene” means a segment of a genome, protein, segment of protein, or protein fragment in which an expressed gene or gene segment has a highest concentration of continuous, non-interrupted and overlapping Replikin sequences (number of Replikin sequences per 100 amino acids) when compared to other segments or named genes of the genome.
  • Replikin Peak Gene a whole protein or gene or gene segment that contains the amino acid portion having the highest concentration of continuous Replikin sequences is also referred to as the Replikin Peak Gene. More than one RPG may be identified within a gene, gene segment, protein, or protein fragment.
  • An RPG may have a terminal lysine or a terminal histidine, two terminal lysines, or a terminal lysine and a terminal histidine.
  • an RPG may have a terminal lysine or a terminal histidine, two terminal lysines, or a terminal lysine and a terminal histidine or may likewise have neither a terminal lysine nor a terminal histidine so long as the terminal portion of the RPG contains a Replikin sequence or Replikin sequences defined by the definition of a Replikin sequence, namely, an amino acid sequence having 7 to about 50 amino acids comprising: (1) at least one lysine residue located six to ten amino acid residues from a second lysine residue;
  • an RPG may include the protein or protein fragment that contains an identified RPG.
  • a Replikin concentration in the RPG may be used to track changes in virulence and lethality.
  • the RPG may be used as an immunogenic compound or as a vaccine.
  • Whole proteins or protein fragments containing RPGs are likewise useful for diagnostic, therapeutic and preventive purposes, such as, for example, to be included in immunogenic compounds, vaccines and for production of therapeutic or diagnostic antibodies.
  • continuous Replikin sequences means a series of two or more Replikin sequences that are overlapped and/or are directly covalently linked.
  • an increase or decrease in "virulence” includes an increase or decrease in virulence, morbidity, lethality, host mortality, rate of replication, rate of distribution, and/or expansion of a drug-resistant pathogen.
  • geographic region is an area differentiated from another area by space. For example, China is a geographic region that may be differentiated from the geographic region of India. Likewise a geographic region may be a hospital, a clinic, a town, or city, or continent or any area differentiable from another area. A geographic region may encompass the entire earth if an isolate or plurality of isolates from a given time period is compared to isolates from another time period over the entire earth and no geographic differentiation is undertaken for the comparison.
  • binding molecule such as, for example, an antibody
  • structure to which it binds antigen
  • binding molecule preferentially recognizes the structure to which it binds even when present among other molecules (such as in a mixture of molecules).
  • binding affinity may be determined by one of ordinary skill in the art using, for example, BIACORE, enzyme-linked
  • a binding molecule may cross-react with related antigens and preferably does not cross-react with affinity to unrelated antigens.
  • Binding between a binding molecule and the structure to which it binds may be mediated by covalent or non-covalent attachment, or both.
  • One aspect of the present invention provides therapies, including vaccines, against drug-resistant pathogens.
  • One non- limiting embodiment of the one aspect is a vaccine against a drug-resistant bacteria, fungus, or parasite.
  • drug-resistant pathogens include, and are not limited to, Tuberculosis, Gonococcus, Klebsiella, Clostridium,
  • Streptococcus Staphylococcus
  • E. coli E. coli
  • Candida Aspergillus
  • malaria malaria
  • a vaccine may comprise at least one protein, protein fragment, polypeptide, or peptide comprising at least one Replikin sequence identified in a drug-resistant pathogen or at least one sequence that is at least 30%, 40%, 50%, 53%, 57%, 60%, 64%, 67%, 70%, 76%, 80%, 82%, 87%, 90%, 91%, 93%, 95% or more homologous with at least one Replikin sequence identified in a drug-resistant pathogen.
  • the vaccine may further comprise a mixture of proteins, protein fragments, polypeptides, or peptides comprising at least one Replikin sequence identified in a drug-resistant pathogen or at least one homologue of the at least one Replikin sequence.
  • the vaccine may comprise a peptide that consist essentially of a Replikin sequence identified in a drug-resistant pathogen or homologue or functional fragment thereof or may comprise a peptide that consists of a Replikin sequence identified in a drug-resistant pathogen or homologue or functional fragment thereof.
  • a vaccine comprising any one or more peptide sequences of SEQ ID NO(s): 1- 21 is provided herein against Clostridium species, including Clostridium difficile.
  • SEQ ID NO: 120 is provided as an example of a homologue and functional fragment of SEQ ID NO:
  • a vaccine comprising any one or more peptide sequences of SEQ ID NO(s): 22-56 is provided herein against Streptococcus species including Streptococcus pneumoniae.
  • SEQ ID NO: 121 is provided as an example of a homologue and functional fragment of SEQ ID NO(s): 40 and 41 and may be comprised in a vaccine against Streptococcus species.
  • a vaccine comprising any one or more peptide sequences of SEQ ID NO(s): 57-119 is provided herein against
  • SEQ ID NO: 122 is provided as an example of a homologue and functional fragment of SEQ ID NO(s): 105 and 106 and may be comprised in a vaccine against Klebsiella species.
  • These vaccines are designed to generate an immune or blocking response in the subject that antagonizes infectivity, replication, and shedding of these drug-resistant bacteria. Any bacteria that are not blocked at entry into the subject will be blocked from replication within the subject or in association with tissue of the subject.
  • a non- limiting embodiment of the present invention provides a method a making a vaccine comprising identifying a population having an increasing number of specimens with Replikin concentrations above 4.0, identifying at least one Replikin sequence in at least one specimen with a Replikin concentration above 4.0, and manufacturing a vaccine comprising the at least one Replikin sequence or a homologue or functional fragment thereof.
  • a peptide vaccine of the invention may include a single Replikin peptide sequence identified in a pathogen or pathogen population (or homologue or functional fragment thereof) or may include a plurality of Replikin sequences observed in particular strains (or homologues or functional fragments thereof).
  • a peptide vaccine may comprise a Replikin peptide sequence or plurality of Replikin peptide sequences, it may consist essentially of a Replikin peptide sequence or a plurality of Replikin peptide sequences, or may consist of a Replikin peptide sequence or plurality of Replikin peptide sequences.
  • a vaccine may include one or more conserved Replikin peptide sequences in combination with one or more new Replikin peptide sequences or may be based on new Replikin peptide sequences in a population increasing in drug-resistance.
  • a vaccine may comprise a protein or protein fragment comprising a Replikin peptide sequence or may comprise a peptide comprising a Replikin peptide sequence or may comprise a peptide consisting essentially of a Replikin peptide sequence or may be a Replikin sequence.
  • a protein or protein fragment for inclusion in a vaccine may be identified by identifying a Replikin peptide sequence within a protein or protein fragment or a homologue of a Replikin peptide sequence within a protein or protein fragment.
  • a vaccine may comprise a pharmaceutically acceptable carrier and/or adjuvant and/or excipient.
  • Polypeptides, protein fragments, or peptides comprising a Replikin peptide sequence, consisting essentially of a Replikin peptide sequence, or consisting of a Replikin peptide sequence can be synthesized by any method, including chemical synthesis, biosynthetic synthesis, solid-phase synthesis, or recombinant gene technology, and may include non-Replikin sequences.
  • Vaccine composition may comprise a pharmaceutically acceptable carrier and/or adjuvant and/or excipient.
  • the Replikin peptide sequences for use as immunogenic or blocking targets in a bacterial or pathogenic vaccine are those Replikin sequences observed to "re- emerge" after an absence from the amino acid sequence for one or more years.
  • the vaccines of one aspect of the present invention can be administered alone or in combination with antimicrobial drugs, such as gancyclovir; interferon; interleukin; M2 inhibitors, such as, amantadine, rimantadine; neuraminidase inhibitors, such as zanamivir and oseltamivir; and the like, as well as with combinations of antimicrobial drugs.
  • antimicrobial drugs such as gancyclovir; interferon; interleukin; M2 inhibitors, such as, amantadine, rimantadine; neuraminidase inhibitors, such as zanamivir and oseltamivir; and the like, as well as with combinations of antimicrobial drugs.
  • One vaccine of one aspect of the present invention may be administered to any animal capable of producing antibodies in an immune response or capable of mounting an antimicrobial response such as an innate immune response or a mucosal immune response.
  • a vaccine may be administered to a mouse, a rabbit, a chicken, a shrimp, a pig, or a human.
  • a vaccine of the invention may be directed at a range of strains of a drug-resistant pathogen or a particular strain of pathogen.
  • the pathogen may be a bacterium, a fungus, a parasite, or any other infectious pathogen.
  • the Replikin peptide sequences reflecting one aspect of the invention alone or in various combinations reflect immunogenic or blocking targets that may be administered to a subject, in a non-limited embodiment, by i.v. intramuscular injection, by mouth, or by spray inhalation, intranasal administration, or intraocular administration (or any other route known to one of skill in the art).
  • the peptides or polypeptides comprising the peptide sequences are administered in order to stimulate the immune system of the subject to produce antibodies to the peptide and/or in order to produce a blocking action.
  • the dosage of peptides or protein fragments is in the range of from about 0.01 ⁇ g to about 500 mg, about 0.05 ⁇ g to about 200 mg, or about 0.075 ⁇ g to about 30 mg, from about 0.09 ⁇ g to about 20 mg, from about 0.1 ⁇ g to about 10 mg, from 10 ⁇ g to about 1 mg, and from about 50 ⁇ g to about 500 ⁇ g.
  • the skilled practitioner can readily determine the dosage and number of dosages needed to produce an effective immune response.
  • nucleic acid sequences and compositions comprising nucleic acid sequences that encode for the above-discussed proteins, protein fragment, polypeptides, and peptides including, for example, nucleic acid sequences that encode for a Replikin peptide sequence identified in a drug-resistant pathogen.
  • nucleic acid sequence may encode for any one or more of SEQ ID NO(s): 1- 119 or a fragment thereof. These sequences may be comprised in a blocking agent or vaccine.
  • isolated or synthesized proteins, protein fragment, polypeptides, or peptides comprising Replikin peptide sequences may be used to generate antibodies, which may be used, for example to provide passive immunity in an individual or for diagnostic purposes. See, e.g. WO 2006/088962 and WO 2008/143717 (each incorporated herein by reference in their entirety).
  • Homologues of Replikin sequences may be comprised in vaccine against replication of drug-resistant pathogens.
  • a vaccine may comprise a peptide that is 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 99% or more homologous with a Replikin sequence identified in a drug-resistant pathogen.
  • KGGGQWEHK (SEQ ID NO: 18) is 67% homologous with HYHRSNKGGGQWEHK (SEQ ID NO: 16) since SEQ ID NO: 18 shares 10 exact residues with the C-terminal end of SEQ ID NO: 16 and SEQ ID NO: 16 is fifteen residues long.
  • SEQ ID NO: 18 is available as a peptide in a vaccine as a homologue of SEQ ID NO: 16.
  • HRSNKGGGQWEHKK (SEQ ID NO: 17) is 87% homologous with SEQ ID NO: 16 since SEQ ID NO: 17 shares thirteen exact residues with SEQ ID NO: 16, which is 15 residues long.
  • KTHRGAAK (SEQ ID NO: 2) is 80% homologous with SEQ ID NO: 1.
  • homology examples include SNKGGGQW (SEQ ID NO: 120), which is 53% homologous with SEQ ID NO: 16 and 57% homologous with SEQ ID NO: 17.
  • Any functional homologue of a Replikin sequence may be used as a target for controlling replication in a drug-resistant pathogen.
  • a functional homologue allows the immune system to target the structure and function of a Replikin sequence in the drug-resistant pathogen.
  • HLGLTKADMLYPRK (SEQ ID NO: 41) is 82% homologous with HNGHLGLTKADMLYPRK (SEQ ID NO: 40).
  • HLGLTKADMLYPR (SEQ ID NO: 121) is 93% homologous with SEQ ID NO: 41 and 76% homologous with SEQ ID NO: 40.
  • Any functional homologue of a Replikin sequence in streptococcus may be used as a target for controlling drug-resistant replication.
  • a functional homologue allows the immune system to target the structure and function of a Replikin sequence in the drug-resistant pathogen.
  • KGYDVKATHK (SEQ ID NO: 106) is 91 % homologous with KMKGYDVKATH (SEQ ID NO: 105).
  • GYDVKAT (SEQ ID NO: 122) is 70% homologous with SEQ ID NO: 106 and 64% homologous with SEQ ID NO: 105.
  • Any functional homologue of a Replikin sequence in Klebsiella may be used as a target for controlling drug-resistant replication.
  • a functional homologue allows the immune system to target the structure and function of a Replikin sequence in the drug-resistant pathogen.
  • a vaccine may be formulated with a pharmaceutically acceptable excipient, carrier, or adjuvant.
  • a pharmaceutically acceptable carrier or excipient is water.
  • Excipients, carriers, or adjuvants may include, but are not limited to, excipients, carriers and adjuvants known to those of skill in the art now or hereafter.
  • compositions of an aspect of the invention may be formulated for delivery by any available route including, but not limited to parenteral (e.g., intravenous), intradermal, subcutaneous, oral, nasal, bronchial, ophthalmic, transdermal (topical), transmucosal or any other routes.
  • parenteral e.g., intravenous
  • intradermal subcutaneous, oral, nasal, bronchial
  • ophthalmic e.g., transdermal (topical), transmucosal or any other routes.
  • pharmaceutically acceptable carrier includes solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration.
  • Supplementary active compounds can also be incorporated into the compositions.
  • a pharmaceutical composition is formulated to be compatible with its intended route of administration.
  • Solutions or suspensions used for intranasal, intraocular, spray inhalation, parenteral (e.g., intravenous), intramuscular, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water (for dermal, nasal, or ocular application, spraying, or injection), saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide.
  • Preparations may be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
  • compositions suitable for injectable use typically include sterile aqueous solutions (water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion.
  • suitable carriers include physiological saline, bacteriostatic water, Cremophor ELTM (BASF,
  • PBS phosphate buffered saline
  • the relevant carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyetheylene glycol, and the like), and suitable mixtures thereof.
  • Synthetic peptides may be carried in sterile water with no additional materials.
  • Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
  • dispersions are prepared by incorporating the active compound into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above.
  • Administration of the vaccine via any method may produce an immune or blocking response in the animal or human, it may further produce an antibody response in the animal or human.
  • the vaccine may produce a protective effect in the animal or human.
  • the vaccine of the present invention may be administered to a rabbit, a chicken, a shrimp, a pig, a ferret, a human, or any animal capable of an immune or blocking response. Because of the universal nature of Replikin sequences, a vaccine of the invention may be directed at a range of strains of drug-resistant pathogens, including drug-resistant bacterial pathogens.
  • One aspect of the present invention is a method of stimulating the immune system of a subject with at least one compound comprising at least one Replikin sequence identified in a drug-resistant bacterium or other pathogen or at least one isolated or synthesized homologue of at least one Replikin sequence identified in a drug-resistant bacterium or other pathogen.
  • the at least one Replikin sequence of the compound reflects an immunogenic target against which the immune system of the subject responds. Because at least a functional portion of the immunogenic structure of the target is maintained in a functional fragment of the at least one Replikin sequence, a functional fragment of the Replikin sequence is likewise a target against which the immune system of the subject responds.
  • the compound may comprise a protein comprising the at least one Replikin sequence or functional fragment thereof, a protein fragment, a polypeptide, or a peptide comprising the at least one Replikin sequence or homologue or functional fragment thereof.
  • the compound may comprise more than one protein, protein fragment, polypeptide or peptide.
  • the compound may further be a composition of a plurality of synthesized or isolated Replikin sequences.
  • Another non-limiting aspect of the present invention provides an isolated or synthesized peptide that is an immunogenic fragment of a Replikin sequence of a drug- resistant pathogen. Such fragments are functional fragments. Immunogenic fragments of a Replikin sequence are fragments that provide at least a portion of cross-reactivity with an antibody or antibody fragment against the Replikin sequence.
  • One embodiment of an aspect of the present invention provides an isolated or synthesized immunogenic (or functional) fragment of at least one Replikin sequence of a drug-resistant pathogen as a target for control of replication of the pathogen.
  • One embodiment provides the isolated or synthesized immunogenic fragment as an antigen for stimulating the immune system of a subject, including but not limited to a human, to produce antibodies against the fragment.
  • Another embodiment of an aspect of the invention provides the isolated or synthesized immunogenic fragment as a vaccine or as a component of a vaccine in combination with an acceptable pharmaceutical carrier or in combination with other proteins, peptides, immunogenic substances, and/or adjuvant(s).
  • the virus may have been blocked in its intracellular transport to the RNA or in synthesis of virus on RNA or in transport from the RNA to excretion. Wherever the block occurs, the fact is that the examination of the excreta of the chicken showed complete absence of virus.
  • the vaccine additionally provided a protective effect against replication of the virus in the chickens' system (no virus was excreted in the feces or saliva of the chickens).
  • mucosal immunity in addition to other immunities, is an important aspect of the immunity imparted by Replikin-based vaccines.
  • Replikin peptides in general are seen to be conserved across strains of drug- resistant bacteria.
  • Example 7 herein provides an illustration of this conservation.
  • the key amino acid residues that provide for the Replikin sequence structure are the lysine and histidine residues, wherein a Replikin sequence has at least one lysine on one terminus and at least one lysine or one histidine on the other terminus, at least one lysine that is six to ten residues from at least one other lysine, at least one histidine, and at least six percent lysine residues in total between the terminal lysine and the terminal lysine or histidine.
  • a homologue of SEQ ID NO: 1 is any sequence with a lysine at position one, a histidine at position five, and a lysine at position ten.
  • a homologue of SEQ ID NO: 22 is any sequence with a lysine at position one, a lysine at position eleven and a histidine at position fourteen.
  • a homologue of SEQ ID NO: 57 is any sequence with a lysine at position one, a lysine at position eight, and a histidine at position sixteen. These are provided as examples and one of ordinary skill can determine similar homologues of any identified Replikin sequence, including any of SEQ ID NO(s): 1-119. Any of these homologues provides excellent targets for controlling replication of drug- resistant pathogens.
  • Neisseria gonorrhoeae Mycobacterium tuberculosis, Klebsiella pneumoniae, Clostridium difficile, or Streptococcus pneumonia and including carbapenem-resistant Klebsiella.
  • One aspect of the present invention provides a method of diagnosing and/or determining the drug sensitivity or drug resistance of a pathogen. Diagnostics may be undertaken by isolating genomic and/or proteomic sequences of a pathogen and determining a Replikin concentration of the pathogen. A single specimen with a Replikin concentration greater than 4.0 returns a warning signal that the specimen is from a population of drug- resistant pathogens and more specimens should be analyzed from the population since many populations of bacteria have no Replikin concentrations of 4.0 or greater and all populations of resistant bacteria examined show specimens having Replikin concentrations greater than 4.0.
  • the drug-resistance of a pathogen is diagnosed where a non-response in a patient suffering from an infection follows administration of an antimicrobial.
  • the drug-resistance of a pathogen is diagnosed where a practitioner observes any reason to believe an antimicrobial treatment is not effective. The method provides a practitioner with evidence of drug-resistance where a Replikin concentration is greater than 4.0 Replikin sequences per 100 amino acid residue and evidence of drug sensitivity where a Replikin concentration is 4.0 or less.
  • a non- limiting embodiment of the aspect of the invention provides a method of diagnosing the drug sensitivity or drug resistance of a pathogen comprising (1) determining a Replikin concentration of a plurality of specimens of an initial population of pathogen at a given time or in a given location and determining the percentage of said specimens having a Replikin concentration of greater than 4.0 Replikin sequences per 100 amino acid residues, (2) determining a Replikin concentration of a plurality of specimens of a different population of the pathogen at a different time or different location and determining the percentage of said specimens having a Replikin concentration of greater than 4.0 Replikin sequences per 100 amino acid residues, and (3) if the percentage of specimens having a Replikin concentration of greater than 4.0 Replikin sequences per 100 amino acid residues in the initial population of pathogens is greater than the percentage of specimens having a Replikin concentration of greater than 4.0 Replikin sequences per 100 amino acid residues in the different population, diagnosing the initial population of path
  • a population may be considered a drug- resistant population if the percentage of specimens having a Replikin concentration of greater than 4.0 Replikin sequences per 100 amino acid residues is 5% or more (see Figure 2), is 10% or more (see Figure 2), is 15% or more (see Figure 3), is 20% or more (see Figures 3 and 4), is 30% or more, is 40% or more, or is 50% or more (see Figure 4).
  • the diagnostic method may be practiced on any pathogen including any fungal pathogen, any parasitic pathogen, or any bacterial pathogen.
  • the diagnostic method may be practiced on a malarial pathogen, a Gonococcus pathogen, a Tuberculosis pathogen, a Klebsiella pathogen, a Clostridium pathogen, a Streptococcus pathogen, a Staphylococcus pathogen, or an E. Coli pathogen.
  • the bacterial pathogen is Neisseria gonorrhoeae, Mycobacterium tuberculosis, Klebsiella pneumoniae, Clostridium difficile, Streptococcus pneumoniae, or Staphylococcus aureus.
  • An increase in percentage of specimens having a Replikin concentration of greater than 4.0 indicates an increase in drug-resistance.
  • Statistical analysis provides levels of certainty concerning differentiation of Replikin concentrations among different populations. P values indicate degree of statistical certainty with reference to the relationship between differences in Replikin concentration and drug-resistance.
  • a p value of less than 0.10 reflects less statistical certainty than a p value of less than 0.05, which reflects less statistical certainty than a p value of less than 0.01, which reflects less statistical certainty than a p value of less than 0.001.
  • Differentiation of Replikin concentrations may be made at p values of less than 0.1, 0.05, 0.01, and 0.001 or whatever statistical device is applied by those of skill in the art. See, e.g., WO 2009/132209, Figures 3 and 4 and description thereof.
  • Another non-limiting aspect provides a method of diagnosing drug-resistant pathogens comprising identifying a Replikin sequence of a drug-resistant pathogen or Replikin Peak Gene sequence of a drug-resistant pathogen in an animal, including human, infected by a drug-resistant pathogen identified by the methods described herein.
  • the blood or tissue of human or other animal may be screened for a Replikin sequence or a Replikin Peak Gene sequence of a drug-resistant pathogen.
  • an antibody or other binding agent may be used to screen for a Replikin sequence or Replikin Peak Gene sequence.
  • the blood or tissue of human or other animal may be screened for DNA or RNA that includes a sequence encoding for a Replikin sequence or a Replikin Peak Gene sequence.
  • nucleic acid sequences encoding for (or antisense to) Replikin sequences or Replikin Peak Gene sequences may be used in hybridization assays of biopsied tissue or blood, e.g., Southern or Northern analysis, including in situ hybridization assays, to diagnose the presence of a drug-resistant pathogen in a tissue sample or an environmental sample.
  • binding agents that bind at least to a functional fragment of a Replikin sequence identified in a drug-resistant pathogen.
  • Binding agents are provided including an antibody, antibody fragment, or binding agent that binds to at least a portion of an amino acid sequence of at least one protein, protein fragment, polypeptide, or peptide comprising at least one peptide A, where peptide A is at least 30%, 40%, 50%, 60%, 70%, 80%, 90% or 95%, or 100%, homologous with at least one Replikin peptide identified in a drug-resistant pathogen, which may include, for example, at least one Replikin peptide sequence of SEQ ID NO(s): 1-119.
  • the amino acid sequence of a protein fragment, polypeptide, or peptide may partially match the amino acid sequence of an expressed whole protein where at least one, five, ten, twenty, thirty, forty, fifty, one hundred, two hundred, three hundred, four hundred, five hundred or more amino acid residues of the amino acid sequence of the expressed whole protein are not present in the protein fragment, polypeptide, or peptide.
  • the amino acid sequence of the protein fragment, polypeptide, or peptide may also partially match the amino acid sequence of an expressed whole protein where at least one, ten, twenty, thirty, forty, fifty, sixty, seventy, eighty, ninety, one hundred, one hundred fifty, two hundred, two hundred fifty, three hundred, three hundred fifty, four hundred, four hundred fifty, five hundred, five hundred fifty or more amino acid residues of the amino acid sequence of at least one terminus of the expressed whole protein are not present at least one terminus of said protein fragment, polypeptide, or peptide.
  • Binding agents are also provided including an antibody, antibody fragment, or binding agent that binds to at least a portion of an amino acid sequence that is 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 95% or more homologous with at least one Replikin peptide of a drug-resistant bacterium.
  • the length of a polypeptide comprising the Replikin peptide sequence or homologue may be one, five, ten, twenty, thirty, forty, fifty or more amino acid residues longer than the identified Replikin sequence with which it is homologous.
  • Binding agents are also provided that bind to at least a portion of an amino acid sequence of at least one of SEQ ID NO(s): 1-119.
  • Binding agents may specifically or preferentially bind to the target protein, protein fragment, polypeptide, or peptide. Binding agents may specifically or preferentially bind to a homologue of at least one of SEQ ID NO(s): 1-119. Binding agents may likewise specifically or preferentially bind to a peptide consisting of any one of SEQ ID NO(s): 1-119.
  • Binding agents may also specifically or preferentially bind to a portion of a peptide consisting of any one of SEQ ID NO(s): 1-119 including a single amino acid within a homologue of SEQ ID NO(s): 1-119, two amino acids, three amino acids, four amino acids, five amino acids, or any number of amino acids spread within or outside a homologue.
  • the isolated Replikin peptide sequences may be used to generate antibodies, which may be used, for example for diagnostic purposes, to identify protein or protein fragments of interest for development of vaccines and other therapies, or, for example, to provide passive immunity in an subject.
  • antibodies include but are not limited to polyclonal, monoclonal, chimeric, humanized, single chain, Fab fragments and fragments produced by a Fab expression library.
  • Antibodies that are linked to a cytotoxic agent may also be generated.
  • Antibodies may also be administered in combination with an antiviral agent.
  • combinations of antibodies to different Replikins may be administered as an antibody cocktail.
  • An antibody or other binding agent of an aspect of the invention may bind to a Replikin peptide or a Replikin Peak Gene. It may bind to a protein or protein fragment comprising a Replikin peptide or a Replikin Peak Gene. It may also bind to a portion of a Replikin peptide or a portion of a Replikin Peak Gene or a portion of a protein, protein fragment, polypeptide, or peptide comprising a Replikin peptide or Replikin Peak Gene.
  • An antibody or other binding agent that specifically binds to a portion of a Replikin peptide or a portion of a Replikin Peak Gene generally binds to an epitope on the Replikin peptide or an epitope that is at least partially on the Replikin peptide or to an epitope on the Replikin Peak Gene or an epitope that is at least partially on the Replikin Peak Gene when the antibody or fragment of the antibody binds to the epitope more readily than it would bind to a random, unrelated epitope.
  • Monoclonal antibodies to Replikin sequences may be prepared by using any technique that provides for the production of antibody molecules. These include but are not limited to the hybridoma technique originally described by Kohler and Milstein, ⁇ Nature, 1975, 256:495-497), the human B-cell hybridoma technique (Kosbor et al., 1983,
  • Antibodies or other binding agents to any peptides observed to be present in a drug-resistant pathogen and combinations of such antibodies are useful in the treatment and/or prevention of pathogenic infection, including Replikin peptide sequences and functional fragments thereof, Replikin Peak Gene peptide sequences, and Replikin sequences isolated within Replikin Peak Gene peptide sequences.
  • Antibody fragments that contain binding sites for a Replikin sequence may be generated by known techniques.
  • fragments include but are not limited to F(ab')2 fragments which can be produced by pepsin digestion of the antibody molecules and the Fab fragments that can be generated by reducing the disulfide bridges of the F(ab')2 fragments.
  • Fab expression libraries can be generated (Huse et al., 1989, Science, 246:1275-1281) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity.
  • immune serum containing antibodies to one or more Replikin sequences obtained from an individual exposed to one or more Replikin sequences may be used to induce passive immunity in another individual or animal.
  • Immune serum may be administered via i.v. to a subject in need of treatment.
  • Passive immunity also can be achieved by injecting a recipient with preformed antibodies to one or more Replikin sequences or functional fragments thereof.
  • Passive immunization may be used to provide immediate protection to individuals who have been exposed to a drug-resistant infectious pathogen.
  • Administration of immune serum or preformed antibodies is routine and the skilled practitioner can readily ascertain the amount of serum or antibodies needed to achieve the desired effect.
  • the invention further provides a nucleic acid sequence that is antisense to a nucleic acid that encodes for any Replikin peptide present in or identified in a drug-resistant bacterial isolate.
  • This may include one of SEQ ID NO(s): 1-119 or a small interfering nucleic acid sequence that interferes with a nucleic acid sequence that is 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 95% or more homologous with a nucleic acid that encodes any Replikin peptide sequence of a drug-resistant pathogen including, for example, any one of SEQ ID NO(s): 1-119 or is 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more homologous with a nucleic acid that is antisense to a nucleic acid that encodes for any one of SEQ ID NO(s): 1-119.
  • Antisense and siRNA sequences are short and directed specifically against the sequence that encodes a Replikin sequence or a fragment thereof.
  • the nucleotide sequence of the invention may be used in hybridization assays of biopsied tissue or blood, e.g., Southern or Northern analysis, including in situ hybridization assays, to diagnose the presence of a particular drug-resistant bacterial strain in a tissue sample or an environmental sample, for example.
  • the present invention also provides kits containing antibodies or binding agents specific for particular Replikin sequences or functional fragments thereof that are present in a particular isolate, or containing nucleic acid molecules (sense or antisense) that hybridize specifically to a particular Replikin sequence or fragment thereof, and optionally, various buffers and/or reagents needed for diagnosis.
  • oligoribonucleotide sequences that include antisense RNA and DNA molecules and ribozymes that function to inhibit the translation of Replikin-containing mRNA.
  • Both antisense RNA and DNA molecules and ribozymes may be prepared by any method known in the art.
  • the antisense molecules can be incorporated into a wide variety of vectors for delivery to a subject. The skilled practitioner can readily determine the best route of delivery, although generally intravenous or intramuscular delivery is routine. The dosage amount is also readily ascertainable.
  • An aspect of the invention further provides antisense nucleic acid molecules that are complementary to a nucleic acid of the invention, wherein the antisense nucleic acid molecule is complementary to a nucleotide sequence encoding a peptide of the invention.
  • the nucleic acid sequence may be anti-sense to a nucleic acid sequence that has been demonstrated to be conserved over a period of six months to one or more years and/or which are present in a strain of drug-resistant bacteria shown to have an increase in concentration of Replikin sequences.
  • compositions comprising RNAi- inducing entities used to inhibit or reduce bacterial infection or replication including small interfering RNA, which is a class of about 10 to about 50 and often about 20 to about 25 nucleotide-long double- stranded RNA molecules. siRNA is involved in the RNA
  • siRNAs also act in RNAi-related pathways, e.g., as an antimicrobial mechanism.
  • compositions of the invention may comprise a single siRNA species targeted to a target transcript or may comprise a plurality of different siRNA species targeting one or more target transcripts.
  • the invention provides a small interfering nucleic acid sequence that is about 10 to about 50 nucleic acids in length and is 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 95% or more homologous with a nucleic acid that encodes for any portion of a bacterial Replikin peptide including, for example, any portion of SEQ ID NO(s): 1-119 or is 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 95% or more homologous with a nucleic acid that is antisense to a nucleic acid that encodes for any portion of a Replikin peptide, including, for example, a portion of one of SEQ ID NO(s): 1-119.
  • the nucleic acid sequence is about 15 to about 30 nucleic acids. In a further non- limiting embodiment, the nucleic acid sequence is about 20 to about 25 nucleic acids. In a further non-limiting embodiment, the nucleic acid sequence is about 21 nucleic acids.
  • a determination of a drug-resistant pathogen or population of pathogens may be performed by a processor. A determination may be output to a user or display. Likewise, a particular Replikin peptide or Replikin Peak Gene within an isolate or population of isolates of one or more drug-resistant pathogens or pathogens identified as increasing in drug- resistance may be identified and output to a user or display.
  • a machine-readable storage medium may contain executable instructions that, when executed by a processor, cause the processor to provide sufficient data to a user, a printout, or a display such that the user or a user of the printout or display may identify drug resistance in a pathogen or population of pathogen.
  • a non-limiting computer readable medium may be non-transitory. Software comprising methods of the invention and related data may be carried on a signal.
  • a computer system may include a processor coupled to a network, and a memory coupled to a processor, wherein the memory contains a plurality of instruction to perform the methods of determining drug-resistance described herein.
  • a user of outputted data from a processor, storage medium, machine-readable medium, or computer system may include any person or any machine that records or analyzes the outputted data.
  • a display or printout may include any mechanism by which data is outputted so that any person or any machine may record or analyze the outputted data, including a printed document, a visual impulse, an aural impulse, or any other perceivable impulse, a computer monitor, a set of numbers, or any other display or printout of data including a digital recording medium.
  • Biotechnology Information http ://www.ncbi. nlm. nih. go v/) for reported sequences from Gonococcus ⁇ Neisseria gonorrhoeae specimens reported as generally sensitive to antibiotics or as resistant to specific antibiotics (Cefixime, Rifampicin, Quinoline, and Tetracycline). Replikin concentration was determined for specimens identified as drug sensitive, specimens identified as resistant to the Cefixime antibiotic, specimens identified as resistant to
  • Rifampicin antibiotic specimens identified as resistant to Quinoline antibiotic, and specimens identified as resistant to Tetracycline antibiotic. Percentage of specimens in a particular group having a Replikin concentration of greater than 4.0 was recorded. The percentage of specimens with Replikin concentrations of greater than 4.0 and the percentage of bacteria resistant to a particular antibiotic were observed to be proportional to the time in use of the particular antibiotic.
  • Table 1 provides the percentage of specimens of Gonococcus in a given drug- sensitive or drug-resistant population having a Replikin concentration of greater than 4.0 Replikin sequences per 100 amino acid residues.
  • the data reflect analysis of 5,110 genomic sequences of Gonococcus. The data are illustrated in Figure 1.
  • Strain KZN 4207 was identified as fully drug sensitive
  • strain KZN 1435 was identified as drug resistant
  • strain KZN R506 was identified as drug resistant
  • strain KZN 605 was identified as extremely drug resistant.
  • Strains H37Ra and H37Rv were identified as attenuated virulence and virulent, respectively.
  • Genomic Replikin concentration in influenza virus has previously been shown to range from 0.1 to 4.0 for viruses not rapidly replicating and not producing outbreaks to over 4.0 to 10.0 or more for outbreaks. Minorities of viruses occasionally are observed to have Replikin concentrations of 20 to 30.
  • Table 2 provides the percentage of specimens of specific strains of tuberculosis with particular drug sensitivities or virulence having a Replikin concentration of greater than 4.0. The data are illustrated in Figure 2. TABLE 2
  • a vaccine is provided herein against drug-resistant, highly- lethal tuberculosis strains.
  • the information also now provides up to two years of time to thoroughly test and distribute vaccines to high risk individuals in the countries identified; thus for the first time, a quantitative genomic Replikins method to both predict initial outbreaks and to prevent spread.
  • the vaccine comprises Replikin sequences identified in drug-resistant strains of tuberculosis.
  • One vaccine comprises Replikin sequences identified in the extremely drug- resistant KZN 605 strain.
  • Tuberculosis remains a major infectious disease, which accounts for approximately 3 million deaths per year worldwide.
  • a series of effective drugs have been developed over several decades which have been recently challenged by two new
  • Table 3 provides the percentage of specimens of carbapenem-resistant
  • the data are illustrated in Figure 3.
  • concern about outbreaks of carbapenem- resistant Klebsiella has recently been expressed by the CDC (in, for example, the New York Times and elsewhere) but neither current clinical nor current sequence data has yet been published. Nevertheless, the data concerning percentage of specimens of Klebsiella having Replikin concentrations of greater than 4.0 suggest the 2011 outbreak of Klebsiella is not yet over.
  • Klebsiella pneumoniae is reported as a significant cause of nosocomial infections. Infections are particularly reported in patients with compromised immunities. An outbreak of carbapenem-resistant Klebsiella pneumoniae struck the U.S. National Institutes of Health Clinical Center in 2011 affecting 18 patients. Eleven of the 18 patients died of the infection.
  • FIG. 3 illustrates that an increase in percentage of specimens of carbapenem-resistant Klebsiella pneumoniae with Replikin concentration greater than 4.0 rose to 22% in the year before the outbreak and maintained a level of 20% at the time of the outbreak.
  • Replikin sequences for manufacture of a vaccine again an outbreak of carbapenem-resistant Klebsiella pneumoniae are provided in Example 7.
  • Biotechnology Information http://www.ncbi.n1m.nih. gov/) for reported sequences from specimens of drug-resistant Clostridium difficile. Specimens were available for years 1998 through 2011. Applicants analyzed the sequences and identified the percentage of sequences having a Replikin concentration of greater than 4.0 per 100 amino acid residues for specimens isolated in years 1998 through 2011.
  • Table 4 provides the percentage of specimens of drug-resistant Clostridium difficile reported as isolated in years 1998 through 2011 and having a Replikin concentration of greater than 4.0 Replikin sequences per 100 amino acid residues.
  • the data reflect analysis of 86,581 genomic sequences of Clostridium difficile. The data are illustrated in Figure 4. TABLE 4
  • a vaccine against drug-resistant Clostridium dijjicile was developed.
  • the vaccine comprises any one or more of the following sequences:
  • KRAKAFKKH (SEQ ID NO: 4)
  • KKHILTK (SEQ ID NO: 5)
  • KHILTKK (SEQ ID NO: 6)
  • HILTKKSAKTK (SEQ ID NO: 7)
  • KYKRAKHMK (SEQ ID NO: 9)
  • KRAKHMK (SEQ ID NO: 10)
  • HMKDNWKTK (SEQ ID NO: 12)
  • HVDAAKGMVNWAK (SEQ ID NO: 21).
  • the vaccine targets replication of drug-resistant Clostridium difficile by targeting the structure and function of Replikin sequences.
  • the immunogenic nature of Replikin sequences allows for an immune response.
  • a blocking response is also provided.
  • the vaccine comprises any one or more of the following sequences:
  • HNEVKRGTTLQQVRK (SEQ ID NO: 36)
  • HNGHLGLTKADMLYPRK (SEQ ID NO: 40)
  • HNRLIRRWLPKGTKKTTPK SEQ ID NO: 42
  • HIVRTIYCKECGKELIQK SEQ ID NO: 44
  • the vaccine targets replication of drug-resistant Streptococcus species by targeting the structure and function of Replikin sequences.
  • the immunogenic nature of Replikin sequences allows for an immune response.
  • a blocking response is also provided.
  • HCSSREGKESTEMK (SEQ ID NO: 60)
  • HLRKTLKDDLASK (SEQ ID NO: 61)
  • HLRKTLKDDLASK (SEQ ID NO: 62)
  • HLMNNKDCFFCK (SEQ ID NO: 63)
  • HCEIKALLDRAK (SEQ ID NO: 66)
  • HGIKARLPEK (SEQ ID NO: 74)
  • HWEKPATLNTDK (SEQ ID NO: 77)
  • HGKLKILIK (SEQ ID NO: 78)
  • HLKDGAEAK (SEQ ID NO: 86)
  • HDRILVKLFSGAK (SEQ ID NO: 87)
  • KGEAHHALK (SEQ ID NO: 96)
  • KRHLLALK (SEQ ID NO: 98)
  • HARKERIMTK (SEQ ID NO: 119)
  • a vaccine against carbapenem-resistant Klebsiella pneumoniae was developed.
  • the vaccine comprises any one or more of SEQ ID NO(s): 57-119.
  • SEQ ID NO(s): 57-119 Each of these peptides is conserved in carbapenem-resistant pathogen and may be comprised in a vaccine that targets carbapenem-resistant Klebsiella pneumoniae or Klebsiella pneumoniae generally. Any combination of two or more of the sequences may be comprised in such a vaccine.
  • the vaccine may comprise any one of SEQ ID NO(s): 57-119 with the addition of at least one other different sequence from SEQ ID NO(s): 57-119.
  • the vaccine may comprise any combination of two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, twenty, or any number up to all 63 of the peptides of SEQ ID NO(s): 57-119.
  • the vaccine targets replication of drug-resistant Klebsiella species by targeting the structure and function of Replikin sequences.
  • the immunogenic nature of Replikin sequences allows for an immune response.
  • a blocking response is also provided.

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Immunology (AREA)
  • Medicinal Chemistry (AREA)
  • Microbiology (AREA)
  • Mycology (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Epidemiology (AREA)
  • Animal Behavior & Ethology (AREA)
  • General Health & Medical Sciences (AREA)
  • Public Health (AREA)
  • Veterinary Medicine (AREA)
  • Communicable Diseases (AREA)
  • Pulmonology (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Medicines Containing Antibodies Or Antigens For Use As Internal Diagnostic Agents (AREA)
  • Peptides Or Proteins (AREA)

Abstract

La présente invention concerne des procédés pour déterminer si un pathogène ou une population de pathogènes est sensible à un médicament ou résistante à un médicament et des composés et des compositions pour la prévention et le traitement d'infections par des pathogènes résistants aux médicaments.
PCT/US2014/025053 2013-03-13 2014-03-12 Procédés de diagnostic, de prévention et de traitement d'infections pathogéniques résistantes aux médicaments au moyen de séquences de réplikine Ceased WO2014165274A2 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201361779324P 2013-03-13 2013-03-13
US61/779,324 2013-03-13

Publications (2)

Publication Number Publication Date
WO2014165274A2 true WO2014165274A2 (fr) 2014-10-09
WO2014165274A3 WO2014165274A3 (fr) 2014-12-11

Family

ID=51659328

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2014/025053 Ceased WO2014165274A2 (fr) 2013-03-13 2014-03-12 Procédés de diagnostic, de prévention et de traitement d'infections pathogéniques résistantes aux médicaments au moyen de séquences de réplikine

Country Status (1)

Country Link
WO (1) WO2014165274A2 (fr)

Family Cites Families (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2008143717A2 (fr) * 2007-01-18 2008-11-27 Samuel Bogoch Procédés permettant de déterminer la létalité d'agents pathogènes et de malignités impliquant des replikin de pointe
WO2010123519A1 (fr) * 2009-04-23 2010-10-28 Samuel Bogoch Séquences de réplikine pour la prévention/le traitement de la grippe et la détermination de l'infectiosité/la létalité

Also Published As

Publication number Publication date
WO2014165274A3 (fr) 2014-12-11

Similar Documents

Publication Publication Date Title
Nie et al. Outer membrane protein A (OmpA) as a potential therapeutic target for Acinetobacter baumannii infection
Yang et al. A vaccine targeting the RBD of the S protein of SARS-CoV-2 induces protective immunity
AU2012273123C1 (en) Methods of treating and preventing Staphylococcus aureus infections and associated conditions
Liu et al. Fob1 and Fob2 proteins are virulence determinants of Rhizopus oryzae via facilitating iron uptake from ferrioxamine
JP6142077B2 (ja) 呼吸器ウイルス感染の阻害活性を有するペプチド、その使用、およびその製造方法
Kamle et al. Chitinase 3-like-1 is a therapeutic target that mediates the effects of aging in COVID-19
JP2025107346A (ja) 敗血症の処置のためのチモシンαの使用
Shu et al. Streptococcus pneumoniae PepO promotes host anti-infection defense via autophagy in a Toll-like receptor 2/4 dependent manner
US20190071706A1 (en) Compositions and methods for preventing and treating disease
US20240218059A1 (en) TGF-Beta 1 INHIBITORS FOR PREVENTING AND TREATING SARS-COV-2
EP2547361A1 (fr) Composants de vaccin bactérien provenant du staphylocoque doré et leurs utilisations
Hamaoka et al. Efficacy comparison of adjuvants in PcrV vaccine against Pseudomonas aeruginosa pneumonia
CA3206461A1 (fr) Composition(s) antigenique(s) et methodes(s) d'utilisation contre porphyromonas gingivalis pour la prevention et/ou le traitement d'une infection et/ou de maladies
WO2015057966A2 (fr) Thérapies, vaccins, et procédés prédictifs pour les virus du syndrome respiratoire du moyen-orient (mers-cov)
CN105037561B (zh) 一种融合蛋白cmfo及其应用
WO2018192083A1 (fr) Inhibiteurs de protéase du virus zika et leurs méthodes d'utilisation
WO2014165274A2 (fr) Procédés de diagnostic, de prévention et de traitement d'infections pathogéniques résistantes aux médicaments au moyen de séquences de réplikine
EP2421546A1 (fr) Séquences de réplikine pour la prévention/le traitement de la grippe et la détermination de l'infectiosité/la létalité
KR20110005710A (ko) 변형된 Ｃｐｎ10 및 ＰＲＲ 시그널링
WO2013166183A2 (fr) Séquences de réplikine et leurs anticorps pour des produits de diagnostic, des produits thérapeutiques et des vaccins contre un prion et les maladies neurodégénératives comprenant la maladie d'alzheimer
JP2008514196A (ja) Ａ群連鎖球菌ＣｒｇＥタンパク質
US20090162379A1 (en) Inhibitors of S. aureus SdrD protein attachment to cells and uses therefor
US20240226156A1 (en) Anti-fibrotic tissue resident memory t cells and uses thereof
WO2014074927A1 (fr) Procédés d'identification, de prévention et de traitement d'un virus de maladie aléoutienne du vison virulent à l'aide de séquences de réplikine
Sze et al. Characterisation of Staphylococcus aureus virulence factor EsxA and structure-based screening of EsxA inhibitors for combating methicillin-resistant S aureus: abridged secondary publication

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 14778780

Country of ref document: EP

Kind code of ref document: A2

122 Ep: pct app. not ent. europ. phase

Ref document number: 14778780

Country of ref document: EP

Kind code of ref document: A2