Devices and methods for antibiotic susceptibility testing

A detection module of a molecular diagnostic device configured to detect the presence of a target organism and the presence of at least one of a first target allele within the target organism associated with resistance to a treatment or a second target allele within the target organism associated with susceptibility to the treatment, the detection module comprising:

• a flow member defining a detection channel configured to receive an output solution from an amplification module, the output solution containing a first amplicon comprising a first genetic locus in a polynucleotide associated with the target organism and a second amplicon comprising a second genetic locus in a polynucleotide associated with a single nucleotide polymorphism (SNP) locus in the polynucleotide;
• a first detection surface within the detection channel, a first probe being adhered to the first detection surface, the first probe designed to bind to the first genetic locus in a polynucleotide associated with the target organism and facilitate production of a first signal indicating the presence of the target organism;
• a second detection surface within the detection channel, a second probe being adhered to the second detection surface, the second probe designed to bind to the second genetic locus if the second genetic locus comprises the first target allele and facilitate production of a second signal indicating the presence of the first target allele within the target organism associated with resistance to the treatment;
• and
• a third detection surface within the detection channel, a third probe being adhered to the third detection surface, the third probe designed to bind to the second genetic locus if the second genetic locus comprises the second target allele and facilitate production of a third signal indicating the presence of the second target allele within the target organism associated with susceptibility to the treatment.

A probe set for detecting presence and susceptibility of a target organism to a drug, comprising:

• a first oligonucleotide probe substantially complementary to a non-polymorphic locus in a polynucleotide of the target organism;
• a second oligonucleotide probe substantially complementary to a polymorphic locus in a polynucleotide of the target organism, the second probe comprising a nucleotide sequence matched to an allele of the polymorphic locus associated with resistance to the drug;
• and
• a third oligonucleotide probe substantially complementary to the polymorphic locus, the third probe comprising a nucleotide sequence matched to an allele of the polymorphic locus associated with susceptibility to the drug, wherein
• the second oligonucleotide probe has a second probe melting temperature for hybridization to the polymorphic locus comprising the allele of the polymorphic locus associated with resistance to the drug,
• the third oligonucleotide probe has a third probe melting temperature for hybridization to the polymorphic locus comprising the allele of the polymorphic locus associated with susceptibility to the drug, and
• the second oligonucleotide probe melting temperature is different from the third oligonucleotide probe melting temperature.