Identifying drivers of β-lactam/β-lactamase inhibitor resistance emergence and spread before their clinical deployment

Understanding the landscape of resistance to antibiotics before their clinical deployment could inform strategies to slow the development of resistance upon their introduction. We evaluated the associations between bacterial genotypes, patient clinical characteristics, and medical exposures with resistance to two recently approved {beta}-lactam/{beta}-lactamase inhibitor combinations in carbapenem-resistant Klebsiella pneumoniae collected before their clinical deployment. Whole-genome sequencing revealed that even within the clonal sequence type 258, genetic background influenced baseline resistance levels and the propensity for resistance to emerge and spread. Resistance in ST258 clade II was mediated by convergent mutation at a small number of loci, which rarely spread amongst patients. In contrast, resistance in clade I was influenced by a lineage-defining insertion in the OmpK36 porin, which made resistance accessible via the blaKPC transposon moving to a higher copy number plasmid, and was in turn associated with transmissible resistance. Distinguishing patients based on whether resistance was acquired via plasmid-mediated versus mutational resistance revealed that while exposure to carbapenems and cephalosporins were associated with mutational resistance, plasmid-associated resistance in clade I was not associated with antibiotic exposures. These findings underscore how pre-clinical surveillance in clinically relevant populations can identify potential drivers of resistance that could inform molecular surveillance and antibiotic stewardship interventions to prolong the efficacy of novel antibiotics.