Data from: Bypass of genetic constraints during mutator evolution to antibiotic resistance

Genetic constraints can block many mutational pathways to optimal genotypes in real fitness landscapes, yet the extent to which this can limit evolution remains to be determined. Interestingly, mutator bacteria elevate only specific types of mutations, and therefore could be very sensitive to genetic constraints. Testing this possibility is not only clinically relevant, but can also inform about the general impact of genetic constraints in adaptation. Here, we evolved 576 populations of two mutator and one wild-type Escherichia coli to doubling concentrations of the antibiotic cefotaxime. All strains carried TEM-1, a β-lactamase enzyme well known by its low availability of mutational pathways. Crucially, one of the mutators does not elevate any of the relevant first-step mutations known to improve cefatoximase activity. Despite this, both mutators displayed a similar ability to evolve more than 1000-fold resistance. Initial adaptation proceeded in parallel through general multi-drug resistance mechanisms. High-level resistance, in contrast, was achieved through divergent paths; with the a priori inferior mutator exploiting alternative mutational pathways in PBP3, the target of the antibiotic. These results have implications for mutator management in clinical infections and, more generally, illustrate that limits to natural selection in real organisms are alleviated by the existence of multiple loci contributing to fitness.在真实的适合度景观（fitness landscape）中，遗传约束（genetic constraints）会阻断诸多通往最优基因型的突变通路，然而这类约束对演化过程的限制程度仍有待确定。值得关注的是，增变菌株（mutator bacteria）仅会提升特定类型的突变频率，因此对遗传约束可能极为敏感。验证这一可能性不仅具有临床相关性，还能帮助我们理解遗传约束对适应性演化的普遍影响。 本研究中，我们针对2株增变大肠杆菌（Escherichia coli）与1株野生型大肠杆菌，共演化得到576个种群，所用抗生素为头孢噻肟（cefotaxime），浓度采用两倍梯度递增。所有菌株均携带TEM-1型β-内酰胺酶（β-lactamase），该酶的已知可及突变通路数量极少。关键之处在于，其中1株增变菌株不会提升任何已知可增强头孢噻肟酶活性的相关一阶突变。即便如此，两类增变菌株均展现出类似的演化能力，可获得超过1000倍的耐药性。初始适应过程普遍通过多药耐药（multi-drug resistance）机制并行发生。与之形成对比的是，高水平耐药的获得则依赖于分化各异的通路：事先被认为适应性较差的那株增变菌株，通过靶向该抗生素的青霉素结合蛋白3（PBP3）利用了其他突变通路。 本研究结果对临床感染中的增变菌株管理具有指导意义，且更广泛地表明：当存在多个可贡献适合度（fitness）的基因座时，真实生物中自然选择（natural selection）所受的限制会得到缓解。