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

Abstract

Systems, apparatus, and methods are disclosed for generating a resistome profile for a subject, monitoring an infection state of one or more subjects, and/or identifying a potential infection outbreak at a facility, for example, by obtaining first data representative of at least one measure of antibiotic resistance of an organism from a first sample, identifying the organism, 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, generating and comparing a first pattern to at least one known pattern to determine and generate a profile uniqueness identifier indicating a degree of similarity above a threshold between the first pattern and the at least one known pattern.

1 . A system, comprising:
 at least one communication interface;   at least one memory for storing processor executable instructions; and   at least one processor, communicatively coupled to the at least one communication interface and the at least one memory, wherein upon execution of the processor-executable instructions, the at least one processor:
 generates a first resistome profile for a first subject based on first data representative of at least one measure of antibiotic resistance of an organism from a first sample; 
 generates a second resistome profile for the first subject based on second data representative of at least one measure of antibiotic resistance of an organism from a second sample; 
 compares the first resistome profile to the second resistome profile; 
 determines a degree of difference between the first resistome profile and the second resistome profile; and 
 automatically generates, via the communication interface, a real-time alert when the degree of difference is above the threshold, indicating a change in the infection state of the first subject. 
   
     
     
         2 . The system of  claim 1 , wherein upon execution of the processor-executable instructions, the at least one processor further at least one of determines or modifies a course of treatment for the first subject based on at least the change in the infection state of the first subject. 
     
     
         3 . A system, comprising:
 at least one communication interface;   at least one memory for storing processor executable instructions; and   at least one processor, communicatively coupled to the at least one communication interface and the at least one memory, wherein upon execution of the processor-executable instructions, the at least one processor:
 generates a first resistome profile for a first subject based on first data representative of at least one measure of antibiotic resistance of an organism from a first sample; 
 assign a first infection state to the first subject based on the first resistome profile; 
 generates a second resistome profile for a second subject based on second data representative of at least one measure of antibiotic resistance of an organism from a second sample; 
 compares the first resistome profile to the second resistome profile; 
 assigns a second infection state to the second subject based at least in part on the comparison of the first resistome profile to the second resistome profile; and 
 automatically sends an alert via the communication system based on the second infection state. 
   
     
     
         4 . A system, comprising:
 at least one communication interface;   at least one memory for storing processor executable instructions; and   at least one processor, communicatively coupled to the at least one communication interface and the at least one memory, wherein upon execution of the processor-executable instructions, the at least one processor:
 generates a first resistome profile for a first subject based on first data representative of at least one measure of antibiotic resistance of an organism from a first sample; 
 compares the first resistome profile to a plurality of candidate resistome profiles, each candidate resistome profile from the plurality of candidate resistome profiles being associated with an infection outbreak potential; and 
 if a degree of similarity between the first resistome profile and a candidate resistome profile from the plurality of candidate resistome profiles is above a first threshold and an infection outbreak potential associated with that candidate resistome profile is above a second threshold, automatically generate an alert that a facility associated with the first resistome profile is at risk of an infection outbreak. 
   
     
     
         5 . The system of  claim 4 , wherein the plurality of candidate resistome profiles is stored in a computer database. 
     
     
         6 . The system of  claim 4 , wherein a candidate resistome profile comprising a phenotype code indicating a carbapenem-resistant Enterobacteriaceae is ranked above the second threshold according to a high potential basis for indicating an infection outbreak. 
     
     
         7 . The system of  claim 4 , further comprising a graphical display communicatively coupled to the at least one processor, wherein upon execution of the processor-executable instructions, the at least one processor further displays an indication of the classification using a graphical representation, the graphical representation comprising at least one of:
 a quick response (QR) code;   a tube graph; or   an epidemiology star chart.   
     
     
         8 . The system of  claim 4 , wherein the first resistome profile includes:
 an organism identification code associated with the organism;   a phenotype code indicating an antibiotic susceptibility phenotype of the organism;   a genotype code indicating an identity of the antibiotic resistance gene associated with the antibiotic susceptibility phenotype; and   a susceptibility code indicating an antibiotic to which the organism is non-susceptible.   
     
     
         9 . The system of  claim 8 , wherein the genotype code is from a plurality of genotype codes, each genotype code from the plurality of genotype codes indicating an identity of a different antibiotic resistant gene. 
     
     
         10 . The system of  claim 4 , wherein at least one candidate resistome profile from the plurality of candidate resistome profiles is associated with a second subject at the facility associated with the first resistome profile. 
     
     
         11 . The system of  claim 4 , wherein at least one candidate resistome profile from the plurality of candidate resistome profiles is associated with an infected patient who has at least one of a central line blood infection, ventilator associated pneumonia, a urinary tract infection, or a surgical site infection. 
     
     
         12 . The system of  claim 4 , wherein at least one candidate resistome profile from the plurality of candidate resistome profiles is derived from in silico data from a reference organism involved in an outbreak. 
     
     
         13 . The system of  claim 4 , wherein the first resistome profile and at least one candidate resistome profile from the plurality of candidate resistome profiles includes metadata associated with a location, the alert being associated with a spread of an infection to and/or from a location associated with the first subject. 
     
     
         14 . The system of  claim 4 , wherein the first resistome profile and at least one candidate resistome profile from the plurality of candidate resistome profiles includes metadata associated with a location, the alert being associated a quantity of samples associated with the location associated with the first subject and that have resistome profiles with a degree of similarity to the first resistome profile that is above the first threshold. 
     
     
         15 . The system of  claim 1 , wherein the first resistome profile includes:
 an organism identification code associated with an organism;   a phenotype code indicating an antibiotic susceptibility phenotype of the organism;   a genotype code indicating an identity of the antibiotic resistance gene associated with the antibiotic susceptibility phenotype; and   a susceptibility code indicating an antibiotic to which the organism is non-susceptible.   
     
     
         16 . The system of  claim 3 , wherein the first resistome profile includes:
 an organism identification code associated with the organism;   a phenotype code indicating an antibiotic susceptibility phenotype of the organism;   a genotype code indicating an identity of the antibiotic resistance gene associated with the antibiotic susceptibility phenotype; and   a susceptibility code indicating an antibiotic to which the organism is non-susceptible.   
     
     
         17 . The system of  claim 3 , wherein the second infection state is assigned to the second subject based at least in part on a degree of similarity between the first resistome profile and the second resistome profile being above a threshold. 
     
     
         18 . The system of  claim 3 , wherein:
 the second infection state is the same as the first infection state; and   the alert indicates a transmission between the first patient and the second patient.   
     
     
         19 . The system of  claim 3 , wherein
 the first sample is associated with a first geographic location;   the second sample is associated with a second geographic location; and   the alert indicates a transmission between the first geographic location and the second geographic location.   
     
     
         20 . The system of  claim 3 , wherein the first resistome profile is from a plurality of candidate resistome profiles, upon execution of the processor-executable instructions, the at least one processor further:
 compares the first resistome profile to each resistome profile from the plurality of candidate resistome profiles; and   calculates a repetition index indicating a number of resistome profiles from the plurality of candidate resistome profiles which the second resistome profile matches with a degree of similarity above a threshold,   the alert indicating an increase in a number of patients infected with the organism and indicating an outbreak potential.