Evolution of Microbes and Mobile Genetic Elements

santosA 2023


Alfonso Santos

Junior Leader La Caixa



We apply fundamental evolutionary experiments and bioinformatic analysis on human and animal pathogens to understand the evolution of microbes in real-life scenarios.



Santos-Lopez A, Fritz Melissa, Lombardo J, Burr A, Heinrich V, Marshall CW, Cooper VS. Evolved resistance to a novel cationic peptide antibiotic requires high mutation supply. Evolution, Medicine and Public Health, 2022, 10, 1, 266-276

delaFuente J, Toribio-Celestino L, Santos-Lopez A, Leon-Sampedro R, Alonso-del Valle A, Costas C, Hernandez-Garcia M, Cui L, Rodriguez-Beltran J, Bikard D, Canton R, San Millan A. Within-patient evolution of plasmid-mediated antmicrobial resistance. Nature Ecology and Evolution 2022. 6, 1980–1991

Santos-Lopez A, Rodriguez-Beltran J, San Millan A. The bacterial capsule is a gatekeeper for mobile DNA. PLoS Biology 2022. 19(7): e3001308

Santos-Lopez A, Marshall CW, Haas A, Turner C, Rasero J, Cooper VS. The roles of history, chance and natural selection in the evolution of antibiotic resistance. eLife 2021; 10:e70676

Santos-Lopez A, Marshall CW, Scribner MR, Snyder D, Cooper VS. Evolutionary pathways to antibiotic resistance are dependent upon environmental structure and bacterial lifestyle. eLife 2019; 8:e47612

More publications



Can we predict evolution? Can we experimentally anticipate the evolutionary dynamics of pathogens that impact human and animal health? Specifically, can we foresee how pathogens will develop resistance to antibiotics?

At the Evolution of Microbes and Mobile Genetic Elements laboratory, we conduct experimental evolution assays, followed by whole-genome-sequencing and innovative bioinformatic analysis, in an effort to predict the emergence and spread of resistance in clinical settings. Antibiotic resistance can arise through both vertical transmission (via point mutations) and horizontal transmission (involving mobile genetic elements). It is influenced by environmental conditions, bacterial lifestyle, and genetic background. Hence, my research aims to analyse the evolution of bacteria by examining both vertical and horizontal adaptation, using a diverse range of pathogens and bacterial lifestyles.

Currently, our main focus is to enhance our understanding of two crucial aspects: 1) the role of mobile genetic elements in bacterial adaptation, and 2) how external conditions, bacterial lifestyle, and evolutionary history shape the evolution of antibiotic resistance.

Ultimately, the goal of my research is to predict the evolutionary trajectories of pathogens in clinical scenarios and use evolutionary biology to develop and optimize new antibiotic treatments for both animal and human pathogens.

Santos Lopez 2022


grupo ASantos 2023 Laboratory Members



Alfonso Santos-lópez Junior Leader "La Caixa"
Pedro Herrador Technician
Jorge Sastre-Dominguez Predoctoral Researcher

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