Table_5_Within-Host Microevolution of Pseudomonas aeruginosa Urinary Isolates: A Seven-Patient Longitudinal Genomic and Phenotypic Study.XLSX

BackgroundPseudomonas aeruginosa is responsible for up to 10% of healthcare associated urinary tract infections (UTI), which can be difficult to treat and can lead to bacterial persistence. While numerous whole genome sequencing (WGS) analyses have explored within-host genomic adaptation and microevolution of P. aeruginosa during cystic fibrosis (CF) infections, little is known about P. aeruginosa adaptation to the urinary tract.
ResultsWhole genome sequencing was performed on 108 P. aeruginosa urinary isolates, representing up to five isolates collected from 2 to 5 successive urine samples from seven patients hospitalized in a French hospital over 48–488 days. Clone type single nucleotide polymorphisms (ctSNPs) analysis revealed that each patient was colonized by a single clone type (<6000 SNPs between two isolates) at a given time and over time. However, 0–126 SNPs/genome/year were detected over time. Furthermore, large genomic deletions (1–5% of the genome) were identified in late isolates from three patients. For 2 of them, a convergent deletion of 70 genes was observed. Genomic adaptation (SNPs and deletion) occurred preferentially in genes encoding transcriptional regulators, two-component systems, and carbon compound catabolism. This genomic adaptation was significantly associated with a reduced fitness, particularly in artificial urine medium, but no strict correlation was identified between genomic adaptation and biofilm formation.
ConclusionThis study provides the first insight into P. aeruginosa within-host evolution in the urinary tract. It was driven by mutational mechanisms and genomic deletions and could lead to phenotypic changes in terms of fitness and biofilm production. Further metabolomic and phenotypic analyses are needed to describe in-depth genotype-phenotype associations in this complex and dynamic host-environment.

背景 铜绿假单胞菌（Pseudomonas aeruginosa）可导致高达10%的医疗相关性尿路感染（urinary tract infections, UTI），此类感染往往难以治愈，且可能引发细菌持续定植。尽管已有诸多全基因组测序（whole genome sequencing, WGS）分析探索了囊性纤维化（cystic fibrosis, CF）感染过程中铜绿假单胞菌的宿主内基因组适应与微进化，但学界对该菌在尿路中的适应机制仍知之甚少。
结果 本研究对108株铜绿假单胞菌尿路分离株开展全基因组测序，这些分离株采自法国某医院7名住院患者的2至5份连续尿液样本，采集间隔为48至488天，每名患者最多可获取5株分离株。克隆型单核苷酸多态性（clone type single nucleotide polymorphisms, ctSNPs）分析显示，在任意时间点及随访周期内，每名患者均仅被单一克隆型定植（两株分离株间单核苷酸多态性数量少于6000）。然而，随时间推移，每基因组每年可检测到0至126个单核苷酸变异。此外，在3名患者的晚期分离株中鉴定出大片段基因组缺失（覆盖基因组的1%至5%），其中2株分离株存在70个基因的趋同缺失。基因组适应（单核苷酸变异与缺失）优先发生于编码转录调控因子、双组分系统以及碳化合物分解代谢的基因中。此类基因组适应显著与适应性降低相关，尤其在人工尿液培养基中，但未发现基因组适应与生物膜形成之间存在严格的相关性。
结论 本研究首次揭示了铜绿假单胞菌在尿路内的宿主内进化过程，该过程由突变机制与基因组缺失所驱动，并可引发适应性与生物膜生成能力方面的表型改变。后续需开展更深入的代谢组学与表型分析，以全面阐明这一复杂且动态的宿主-环境互作系统中基因型与表型之间的关联。