Systems, apparatus, and methods for generating and analyzing resistome profiles

A method, comprising:

• receiving a first sample including an organism at an assay device, the first sample associated with a geographic location;
• processing, by the assay device, the first sample to extract genetic information associated with the organism;
• generating, based on the genetic information, first data representative of at least one measure of antibiotic resistance of the organism;
• identifying the organism based on at least the first data;
• determining at least one of an antibiotic susceptibility phenotype, an identity of an antibiotic resistance gene, and an antibiotic to which the organism is non-susceptible based on at least the first data;
• generating a first pattern associated with the first sample, the first pattern comprising:
• an organism identification code indicating the organism identified based on the first data;
• and
• at least one of:
• a phenotype code indicating the antibiotic susceptibility phenotype determined from the first data;
• a genotype code indicating the identity of the antibiotic resistance gene determined from the first data;
• and
• a susceptibility code indicating the antibiotic to which the organism is non-susceptible determined from the first data;
• comparing the first pattern to at least one known pattern;
• calculating a degree of similarity between the first pattern and the at least one known pattern;
• generating a first resistome profile based on at least the first pattern;
• and
• automatically generating a real-time alert when the degree of similarity is above threshold, the real-time alert and indicating the presence of an antibiotic-resistant organism at the geographic location such that at least one of the geographic location or a patient associated with the geographic location can be at least one of treated, disinfected, or isolated.