Methods and systems for determining suitability of compositions for inhibiting growth of polymicrobial samples

A method for treating a polymicrobial infection in a patient in need thereof, wherein the patient either has a polymicrobial infection or is suspected of having polymicrobial infection, said method comprises:

• a) obtaining or having obtained a sample from a source of the polymicrobial infection or suspected polymicrobial infection in the patient;
• b) subjecting or having subjected a first portion of the sample to genetic identification testing, wherein genetic identification testing detects and identifies one or more organisms in the sample;
• wherein if genetic identification testing detects one or more organisms in the sample then the patient has a polymicrobial infection;
• c) subjecting or having subjected a second portion of the sample to genetic resistance marker testing, wherein genetic resistance marker testing is effective for detecting and identifying one or more resistance genes that confers resistance to one or more therapeutic agents;
• d) subjecting or having subjected a third portion of the sample to pooled phenotypic antibiotic resistance testing, wherein pooled phenotypic antibiotic resistance testing either or both:
• (i) identifies one or more therapeutic agents to which the polymicrobial infection is resistant, and or (ii) identifies one or more therapeutic agents to which the polymicrobial infection is susceptible, wherein organisms in the polymicrobial infection in the third portion of the sample are not first isolated before the pooled phenotypic antibiotic resistance testing;
• e) applying results from (b), (c), and (d) to a predetermined set of thresholds in a database that indicates therapeutic agents that are effective for treating polymicrobial infections, wherein applying results from (b), (c), and (d) identifies at least one therapeutic agent that is effective for treating the polymicrobial infection in the patient;
• and
• f) administering at least one therapeutic agent identified in (e) to the patient, wherein the at least one therapeutic agent is effective for treating the polymicrobial infection.