Computational models identifying within-host evolution of pathogens using high-throughput DNA sequencing

抗微生物药物耐药性（AMR）是对动物的全球性威胁。然而，对于感染重要动物（如肉牛和奶牛）的病原体，人们对其发生和传播知之甚少。每次感染都代表了对抗菌素具有不同敏感性的多种病原体的种群。当宿主群体在药物治疗的选择性压力下结合免疫反应进化时，通常会发生抗菌素耐药性。下一代DNA测序（NGS）技术的巨大飞跃使我们能够在不需要在实验室中培养病原体的情况下对宿主种群进行测序(即，

Antimicrobial resistance (AMR) is a global threat to animals. However, its occurrence and transmission are poorly understood for pathogens infecting important animals, e.g. beef and dairy cattle. Each infection represents a population of multiple strains of a pathogen with different sensitivities to antimicrobials. Often AMR occurs when this within-host population evolves under the selective pressure of drug treatments in conjunction with immune responses. Huge leaps in next-generation DNA sequencing (NGS) technology allow us to sequence within-host populations of a pathogen without the need to grow them in the laboratory (i.e.,