COMPOSITIONS AND METHODS FOR DETECTING ANTIBIOTIC RESPONSIVE mRNA EXPRESSION SIGNATURES AND USES THEREOF

A composition comprising:

• a set of nucleic acid probes corresponding to the probes listed in Table 3 and Table 4;
• a set of nucleic acid probes corresponding to the probes listed in Table 5 and Table 6;
• a set of nucleic acid probes that includes a first probe comprising a sequence selected from the group consisting of SEQ ID NOs:
• 1877-2762 and a second probe comprising a sequence selected from the group consisting of SEQ ID NOs:
• 2763-3648, optionally wherein the first probe comprises a sequence of SED ID NO:
• (1877+n) and the second probe comprises a sequence of SEQ ID NO:
• (2763+n), wherein n=an integer ranging from 0 to 885, optionally wherein one or both of the first and second probes further comprises a tag sequence;
• a kit comprising a set of nucleic acid probes corresponding to the probes listed in Table 3 and Table 4, and instructions for its use;
• a kit comprising a set of nucleic acid probes corresponding to the probes listed in Table 5 and Table 6, and instructions for its use;
• or
• a kit comprising a set of nucleic acid probes that includes a first probe comprising a sequence selected from the group consisting of SEQ ID NOs:
• 1877-2762 and a second probe comprising a sequence selected from the group consisting of SEQ ID NOs:
• 2763-3648, and instructions for its use, optionally wherein the first probe comprises a sequence of SED ID NO:
• (1877+n) and the second probe comprises a sequence of SEQ ID NO:
• (2763+n), wherein n=an integer ranging from 0 to 885, optionally wherein one or both of the first and second probes further comprises a tag sequence.

A method of treating a patient, comprising:

• obtaining a sample including one or more bacterial cells, wherein the sample is obtained from a patient or an environmental source;
• processing the sample to enrich the one or more bacterial cells;
• contacting the sample with one or more antibiotic compounds;
• lysing the sample to release messenger ribonucleic acid (mRNA) from the one or more bacterial cells;
• hybridizing the released mRNA to at least one set of two nucleic acid probes, wherein each nucleic acid probe includes a unique barcode or tag;
• detecting the hybridized nucleic acid probes;
• identifying one or more genetic resistance determinants;
• determining the identity of the one or more bacterial cells and the antibiotic susceptibility of each of the identified one or more bacterial cells;
• and
• administering to the patient an appropriate antibiotic based on the determination of the identity and the antibiotic susceptibility of the one or more bacterial cells.