Personalised genomic investigation reveals strain heterogeneity during chronic infection with E. coli ST131: The complete genome of E. coli ST131 Str. U14A

Recurrent urinary tract infections (rUTI) are extremely common, with ~25% of all women who suffer an initial UTI experiencing a recurrence within one year of the original infection. rUTI often occurs when bacteria from the initial infection persist after treatment. Escherichia coli ST131 is a major contributor to hospital and community acquired UTI and is strongly associated with limited treatment options and high rates of recurrence. Here, using a combination of both short and long read sequencing technologies we examined the dynamics of an E. coli ST131 population isolated over a 5-year period (2012-2016) from the urine and feces of a single individual. This longitudinal study provides the first comprehensive, in vivo, genomic analysis of a clonal lineage within a single individual and serves as a valuable resource for understanding how plasmid dynamics contribute to pathogen evolution in a chronic long-term infection.

复发性尿路感染（recurrent urinary tract infections, rUTI）极为常见，约25%首次罹患尿路感染（urinary tract infection, UTI）的女性会在初次感染后一年内出现复发。复发性尿路感染通常是由于初次感染的细菌在治疗后仍持续存在所引发。大肠杆菌ST131（Escherichia coli ST131）是医院获得性与社区获得性尿路感染的主要致病菌之一，且与有限的治疗选择及高复发率密切相关。本研究结合短读长与长读长测序技术，对一名受试者在2012至2016年的5年间从其尿液与粪便中分离得到的大肠杆菌ST131菌群动态变化进行了分析。这项纵向研究首次对单一个体内的克隆谱系开展了全面的体内基因组分析，可为解析质粒动态如何促进慢性长期感染中病原体的进化提供宝贵的研究资源。