Direct-from-specimen microbial growth inhibition spectrums under antibiotic exposure and comparison to conventional antimicrobial susceptibility testing

Increasing global travel and changes in the environment may increase the frequency of contact with a natural host carrying an infection, and therefore increase our chances of encountering microorganisms previously unknown to humans. During an emergency (man-made, natural disaster, or pandemic), the etiology of infection might be unknown at the time of patient treatment. The existing local or global Antimicrobial Stewardship Programs might not be fully prepared for emerging/re-emerging infectious disease outbreaks, especially if they are caused by an unknown organism, engineered bioterrorist attack, or rapidly evolving superbug. We demonstrate an antimicrobial efficacy profiling method that can be performed in hours directly from clinical urine specimens. The antimicrobial potency is determined by the microbial growth inhibition and compared to conventional antimicrobial susceptibility testing (AST) results. The oligonucleotide probe pairs on the sensor were designed to target gram-negative bacteria, specifically Enterobacterales and Pseudomonas aeruginosa. A total of 10 remnant clinical specimens from the CLIA labs of New York-Presbyterian Queens were tested, resulting in 100% categorical agreement with reference AST methods (Vitek and broth microdilution method). The combined categorical susceptibility reporting of 12 contrived urine specimens was 100% for ciprofloxacin, gentamicin, and meropenem over a range of microbial loads from 105 to 108 CFU/mL.