The evolutionary mechanism of non-carbapenemase carbapenem-resistant phenotypes in Klebsiella spp
Natalia C. Rosas, Jonathan J. Wilksch, Jake Barber, Jiahui Li, Yanan Wang, Zhewei Sun, Andrea Rocker, Chaille T. Webb, Laura Perlaza-Jiménez, Christopher J. Stubenrauch, Dhanasekaran Vijaykrishna, Jiangning Song, George Taiaroa, Mark R. Davies, Richard A. Strugnell, Qiyu Bao, Tieli Zhou, Michael J. McDonald, Trevor Lithgow
Abstract
Antibiotic resistance is driven by selection, but the degree to which a bacterial strain’s evolutionary history shapes the mechanism and strength of resistance remains an open question. Here, we reconstruct the genetic and evolutionary mechanisms of carbapenem resistance in a clinical isolate of Klebsiella quasipneumoniae . A combination of short- and long-read sequencing, machine learning, and genetic and enzymatic analyses established that this carbapenem-resistant strain carries no carbapenemase-encoding genes. Genetic reconstruction of the resistance phenotype confirmed that two distinct genetic loci are necessary in order for the strain to acquire carbapenem resistance. Experimental evolution of the carbapenem-resistant strains in growth conditions without the antibiotic revealed that both loci confer a significant cost and are readily lost by de novo mutations resulting in the rapid evolution of a carbapenem-sensitive phenotype. To explain how carbapenem resistance evolves via multiple, low-fitness single-locus intermediates, we hypothesised that one of these loci had previously conferred adaptation to another antibiotic. Fitness assays in a range of drug concentrations show how selection in the antibiotic ceftazidime can select for one gene ( bla DHA-1 ) potentiating the evolution of carbapenem resistance by a single mutation in a second gene ( ompK36 ). These results show how a patient’s treatment history might shape the evolution of antibiotic resistance and could explain the genetic basis of carbapenem-resistance found in many enteric-pathogens.