Centre to Impact AMR, Monash University, Clayton, Australia.
Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia.
Elife. 2023 Jul 6;12:e83107. doi: 10.7554/eLife.83107.
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 . 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 () potentiating the evolution of carbapenem resistance by a single mutation in a second gene (). 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.
抗生素耐药性是由选择驱动的，但细菌菌株的进化史在多大程度上塑造了耐药机制和强度，仍然是一个悬而未决的问题。在这里，我们重建了临床分离株 对碳青霉烯类药物耐药性的遗传和进化机制。短读和长读测序、机器学习以及遗传和酶分析的结合，确定了这种耐碳青霉烯类药物的菌株不携带碳青霉烯酶编码基因。耐药表型的遗传重建证实，为了使该菌株获得碳青霉烯类药物耐药性，两个不同的遗传基因座是必需的。在没有抗生素的生长条件下对碳青霉烯类耐药菌株进行实验进化表明，两个基因座都赋予了显著的代价，并且容易通过新产生的突变丢失，导致碳青霉烯类敏感表型的快速进化。为了解释碳青霉烯类耐药性如何通过多个低适应度的单基因座中间产物进化，我们假设其中一个基因座以前曾赋予了对另一种抗生素的适应性。在一系列药物浓度的适应性测定中，头孢他啶抗生素的选择如何能够选择一个基因 ()，通过第二个基因 ()中的单个突变促进碳青霉烯类耐药性的进化，这说明了患者的治疗史如何影响抗生素耐药性的进化，并解释了许多肠道病原体中发现的碳青霉烯类耐药性的遗传基础。
