Identification of Evolutionary Trajectories Associated with Antimicrobial Resistance Using Microfluidics

In vitro experimental evolution of pathogens to antibiotics is commonly used for the identification of clinical biomarkers associated with antibiotic resistance. Microdroplet emulsions allow exquisite control of spatial structure, species complexity, and selection microenvironments for such studies. We investigated the use of monodisperse microdroplets in experimental evolution. Using Escherichia coli adaptation to doxycycline, we examined how changes in environmental conditions such as droplet size, starting lambda value, selection strength, and incubation method affected evolutionary outcomes. We also examined the extent to which emulsions could reveal potentially new evolutionary trajectories and dynamics associated with antimicrobial resistance. Interestingly, we identified both expected and unexpected evolutionary trajectories including large-scale chromosomal rearrangements and amplification that were not observed in suspension culture methods. As microdroplet emulsions are well-suited for automation and provide exceptional control of conditions, they can provide a high-throughput approach for biomarker identification as well as preclinical evaluation of lead compounds.

病原体针对抗生素的体外实验进化研究，通常用于鉴定与抗生素耐药性相关的临床生物标志物。微滴乳液（microdroplet emulsions）可为这类研究提供对空间结构、物种复杂度以及选择微环境的精细调控能力。本研究针对单分散微滴（monodisperse microdroplets）在实验进化中的应用展开探究：以大肠杆菌（Escherichia coli）对多西环素（doxycycline）的适应性进化为模型，考察了液滴尺寸、初始λ值、选择强度以及培养方式等环境条件变化对进化结果的影响；同时分析了微滴乳液能够揭示与抗菌耐药性相关的潜在新型进化轨迹及动力学特征的程度。值得注意的是，本研究既观测到了预期内的进化轨迹，也发现了悬浮培养法中未曾记录的意外进化事件——其中包括大规模染色体重排与基因扩增现象，此类事件在悬浮培养体系中从未被观测到。由于微滴乳液适配自动化操作且可实现优异的条件调控能力，其可为生物标志物鉴定以及先导化合物的临床前评价提供一种高通量研究方案。