Genetic and functional enrichments associated with Enterococcus faecalis isolated from the urinary tract.
Genetic and functional enrichments associated with Enterococcus faecalis isolated from the urinary tract.
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粪肠球菌是与尿路感染 (UTI) 相关的主要革兰氏阳性细菌。粪肠球菌是一种机会性病原体，是人类胃肠道 (GIT) 的共生菌，它在 GIT 中的存在是尿路感染的诱发因素。人们对粪肠球菌如何在尿路 (UT) 中定植和生存知之甚少，尤其是在无并发症或复发性尿路感染中。 UT 与 GIT 不同，其特点是营养景观稀疏和独特的环境压力源。在这项研究中，我们从绝经后妇女的尿液中分离出 37 种临床粪肠球菌菌株并进行了测序。我们生成了 33 个闭合基因组组件和 4 个高度连续的草图组件，并进行了比较基因组学分析研究，以确定尿液粪肠球菌与从人类胃肠道和血液中分离的粪肠球菌富含的遗传特征。系统发育分析显示，尿液菌株之间存在高度多样性，尿液和肠道菌株之间的相关性比血液菌株之间的相关性更密切。质粒复制子 (rep) 分型进一步强调了可能的 UT-GIT 互连，确定了尿液和肠道粪肠球菌之间的九种共享重复类型。对尿粪肠球菌抗菌药物耐药性的基因型和表型分析均显示，对一线尿路感染抗生素呋喃妥因和氟喹诺酮类药物很少有耐药性，并且没有万古霉素耐药性。最后，通过比较泌尿系和肠道菌株中基因的存在和缺失，我们确定了泌尿系菌株中富集的 19 个候选基因。这些基因参与糖转运、钴胺素输入、葡萄糖代谢和基因表达转录后调控的核心过程。尿路感染（UTI）是一个全球性健康问题，给医疗保健系统带来沉重负担。女性受尿路感染的影响尤为严重，超过 60% 的女性一生中至少经历过一次尿路感染。尿路感染可能会复发，特别是在绝经后女性中，导致生活质量下降和可能危及生命的并发症。了解病原体如何在泌尿道中定殖和生存对于确定由于抗菌素耐药率上升而迫切需要的新治疗靶点是必要的。粪肠球菌（一种通常与尿路感染相关的细菌）如何适应尿路仍有待研究。在这里，我们生成了从绝经后妇女的尿液中分离出的临床尿液粪肠球菌的高质量封闭基因组集合，我们将其与详细的临床元数据一起使用，对可能与泌尿道中粪肠球菌存活有关的遗传因素进行了强有力的比较基因组研究。
Enterococcus faecalis is the leading Gram-positive bacterial species implicated in urinary tract infection (UTI). An opportunistic pathogen, E. faecalis is a commensal of the human gastrointestinal tract (GIT), and its presence in the GIT is a predisposing factor for UTI. How E. faecalis colonizes and survives in the urinary tract (UT) is poorly understood, especially in uncomplicated or recurrent UTI. The UT is distinct from the GIT and is characterized by a sparse nutrient landscape and unique environmental stressors. In this study, we isolated and sequenced a collection of 37 clinical E. faecalis strains from the urine of primarily postmenopausal women. We generated 33 closed genome assemblies and 4 highly contiguous draft assemblies and conducted a comparative genomics analysis study to identify genetic features enriched in urinary E. faecalis with respect to E. faecalis isolated from the human GIT and blood. Phylogenetic analysis revealed high diversity among urinary strains and a closer relatedness between urine and gut isolates than blood isolates. Plasmid replicon (rep) typing further underscored possible UT-GIT interconnection, identifying nine shared rep types between urine and gut E. faecalis. Both genotypic and phenotypic analyses of antimicrobial resistance among urinary E. faecalis revealed infrequent resistance to the front-line UTI antibiotics nitrofurantoin and fluoroquinolones and no vancomycin resistance. Finally, comparing gene presence and absence among urinary and gut strains, we identified 19 candidate genes enriched among urinary strains. These genes are involved in the core processes of sugar transport, cobalamin import, glucose metabolism, and post-transcriptional regulation of gene expression. Urinary tract infection (UTI) is a global health issue that imposes a substantial burden on healthcare systems. Women are disproportionately affected by UTI, with >60% of women experiencing at least one UTI in their lifetime. UTIs can recur, particularly in postmenopausal women, leading to diminished quality of life and potentially life-threatening complications. Understanding how pathogens colonize and survive in the urinary tract is necessary to identify new therapeutic targets that are urgently needed due to rising rates of antimicrobial resistance. How Enterococcus faecalis, a bacterium commonly associated with UTI, adapts to the urinary tract remains understudied. Here, we generated a collection of high-quality closed genome assemblies of clinical urinary E. faecalis isolated from the urine of postmenopausal women that we used alongside detailed clinical metadata to perform a robust comparative genomic investigation of genetic factors that may be involved in E. faecalis survival in the urinary tract.
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DOI：
10.1038/nrmicro3432
发表时间：
2015-05
期刊：
Nature reviews. Microbiology
影响因子：
--
作者：
Flores-Mireles AL;Walker JN;Caparon M;Hultgren SJ
通讯作者：
Hultgren SJ
影响因子：
10.7
作者：
Hoang DT;Chernomor O;von Haeseler A;Minh BQ;Vinh LS
通讯作者：
Vinh LS
影响因子：
12.3
作者：
Brynildsrud O;Bohlin J;Scheffer L;Eldholm V
通讯作者：
Eldholm V
影响因子：
5.2
作者：
通讯作者：
--
DOI：
10.1093/jac/dkaa345
发表时间：
2020-12-01
期刊：
The Journal of antimicrobial chemotherapy
影响因子：
--
作者：
Bortolaia V;Kaas RS;Ruppe E;Roberts MC;Schwarz S;Cattoir V;Philippon A;Allesoe RL;Rebelo AR;Florensa AF;Fagelhauer L;Chakraborty T;Neumann B;Werner G;Bender JK;Stingl K;Nguyen M;Coppens J;Xavier BB;Malhotra-Kumar S;Westh H;Pinholt M;Anjum MF;Duggett NA;Kempf I;Nykäsenoja S;Olkkola S;Wieczorek K;Amaro A;Clemente L;Mossong J;Losch S;Ragimbeau C;Lund O;Aarestrup FM
通讯作者：
Aarestrup FM