Gaszek Ilona Kamila, Yildiz Muhammed Sadik, Meng Devin, de la Paz Jose Alberto, Alvarez Sophia Maria, Morcos Faruck, Lin Milo, Toprak Erdal
Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
bioRxiv. 2025 Jul 11:2025.07.08.663783. doi: 10.1101/2025.07.08.663783.
The rapid evolution of extended-spectrum β-lactamases (ESBLs) represents a global health threat, undermining the efficacy of β-lactams, the most extensively used antibiotic class. To elucidate the evolutionary dynamics underlying β-lactam resistance, we constructed a comprehensive combinatorial mutant library comprising all 55,296 possible TEM-1 β-lactamase variants integrating 18 clinically observed mutations across 13 key residues. Over eight million empirical fitness measurements were obtained under selection pressure with both a native antibiotic substrate (ampicillin) and a novel antibiotic (aztreonam), establishing the largest experimentally determined fitness landscape for antibiotic resistance to date. Through graph-theoretic and epistatic analyses, we discovered that selection with ampicillin resulted in weak epistasis, with mutants rarely surpassing the fitness of the wild-type enzyme. Conversely, aztreonam selection elicited extensive higher-order epistasis, generating a rugged fitness landscape characterized by increased phenotypic unpredictability. Interpretable machine-learning analyses identified context-dependent epistatic interactions necessary for achieving high-level aztreonam resistance. Further evolutionary statistical analyses, including direct coupling analysis and latent generative landscapes, showed that top-performing TEM-1 variants consistently adhered to conserved epistatic patterns found in naturally occurring β-lactamases. Our findings demonstrate that higher-order epistasis critically shapes fitness landscape ruggedness when enzymes adapt to novel substrates, whereas adaptations to native substrates exhibit predictably smoother landscapes. This integrated experimental and computational framework provides a foundation for predictive evolutionary pharmacology, enabling assessments of newly developed β-lactams or emerging β-lactamase variants for their potential contribution to ESBL evolution. Importantly, incorporating graph-theoretically informed evolutionary constraints can strategically disrupt evolutionary pathways, presenting a viable approach to mitigate the rise of antibiotic resistance.
超广谱β-内酰胺酶(ESBLs)的快速进化构成了全球健康威胁,削弱了β-内酰胺类药物(使用最广泛的抗生素类别)的疗效。为了阐明β-内酰胺耐药性背后的进化动态,我们构建了一个全面的组合突变体文库,其中包含整合了13个关键残基上18个临床观察到的突变的所有55296种可能的TEM-1β-内酰胺酶变体。在天然抗生素底物(氨苄青霉素)和新型抗生素(氨曲南)的选择压力下,我们获得了超过八百万次的经验性适应性测量,建立了迄今为止最大的抗生素耐药性实验确定适应性景观。通过图论和上位性分析,我们发现用氨苄青霉素进行选择会导致较弱的上位性,突变体很少超过野生型酶的适应性。相反,氨曲南选择引发了广泛的高阶上位性,产生了一个崎岖的适应性景观,其特征是表型不可预测性增加。可解释的机器学习分析确定了实现高水平氨曲南耐药性所需的上下文依赖性上位性相互作用。进一步的进化统计分析,包括直接耦合分析和潜在生成景观分析,表明表现最佳的TEM-1变体始终遵循天然存在的β-内酰胺酶中发现的保守上位性模式。我们的研究结果表明,当酶适应新底物时,高阶上位性对适应性景观的崎岖程度起着关键作用,而对天然底物的适应则表现出可预测的更平滑景观。这种综合的实验和计算框架为预测进化药理学提供了基础,能够评估新开发的β-内酰胺类药物或新兴的β-内酰胺酶变体对ESBL进化的潜在贡献。重要的是,纳入图论指导的进化约束可以从战略上破坏进化途径,提供一种减轻抗生素耐药性上升的可行方法。