Adaptive Patterns of Antibiotic Sensitivity in Uncharacterized Pathogenic Strains X and Y

Abstract

Accelerating rates of antibiotic resistance necessitate the identification of hitherto uncharacterized pathogenic strains as the foundation for therapeutic guidance. We here investigate the phenotypic as well as genotypic adaptation of two hitherto uncharacterized clinical isolates, hereafter referred to as Strain X as well as Strain Y, to a panel of clinically significant antibiotics. Employing standardised antimicrobial susceptibility testing (broth microdilition) as well as time-kill assays as part of whole-genome sequencing, we established divergent adaptation profiles. Strain X demonstrated a classical inducible resistance phenotype to β-lactams (e.g., a 32-fold increase in MIC of ceftazidime after pre-exposure), coupled together with the over-expression of a candidate AmpC β-lactamase as well as efflux pump gene sets. Strain Y, however, demonstrated a tolerant phenotype defined as inhibition of rapid killing after exposure to high doses of ciprofloxacin as well as gentamicin, without an equivalent MIC increase. This tolerant phenotype was associated with the upregulation of toxin-antitoxin modules as well as stress response gene sets. We determined biofilm assays that Strain X upregulated biofilm output after sub-inhibitory doses of antibiotics, whereas Strain Y biofilm output was constitutive as well as unaltered. These findings delineate an important dichotomy within survival adaptation strategies: Strain X employs inducible high-level resistance, whereas Strain Y employs a tolerance-persistence strategy. This distinction possesses important ramifications vis-à-vis duration of therapy as well as antibiotic selection, wherein diagnostic methodologies that identify resistance as well as tolerance are needed.