Comparative genomic analysis of clinical Enterococcus faecalis distinguishes strains isolated from the bladder.
Comparative genomic analysis of clinical Enterococcus faecalis distinguishes strains isolated from the bladder.
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DOI：
10.1186/s12864-023-09818-z
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发表时间：
2023-12-07
期刊：
影响因子：
4.4
通讯作者：
中科院分区：
文献类型：
--
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粪肠球菌是临床感染中最常见的分离肠球菌。这种细菌因其在物种内外共享遗传内容的能力而臭名昭著。随着水平基因转移能力的提高，这个物种内巨大的基因组多样性已经被确定。许多研究人员假设粪肠球菌表现出生态位适应性，以建立感染或在人体的各个部位定植。在这里，我们假设从人类膀胱中分离的粪肠杆菌菌株与从其他来源分离的临床菌株相比，将携带独特的基因组内容。该分析包括从膀胱、泌尿生殖器、血液和粪便样本中分离的111个粪肠球菌基因组的比较。系统基因组比较显示分离源和谱系之间没有关联；然而，辅助基因组比较区分了血液和膀胱基因组。进一步的基因富集分析确定了与泌尿生殖系统、血液和粪便基因组相比，膀胱基因组中富集或罕见的基因功能、毒力因子、抗生素耐药基因和质粒相关基因。使用这些发现作为训练数据和682个公开可用的基因组作为测试数据，机器学习分类器成功地以高精度区分了膀胱和非膀胱菌株。对这种分化具有重要意义的基因通常与转座因子和噬菌体有关，包括几乎只存在于膀胱和泌尿生殖系统基因组中的3种前噬菌体。与从身体其他部位分离的菌株相比，从膀胱分离的粪肠球菌菌株含有独特的基因组内容。这种基因组多样性很可能是由于水平基因转移，正如系统基因组聚类的缺乏和转座因子和噬菌体的富集所证明的那样。对这些富集基因如何影响宿主-微生物相互作用的研究可能会阐明成功的膀胱定植和疾病建立所需的基因功能。在线版本包含补充材料，可在10.1186/s12864-023-09818-z获得。
Enterococcus faecalis is the most commonly isolated enterococcal species in clinical infection. This bacterium is notorious for its ability to share genetic content within and outside of its species. With this increased proficiency for horizontal gene transfer, tremendous genomic diversity within this species has been identified. Many researchers have hypothesized E. faecalis exhibits niche adaptation to establish infections or colonize various parts of the human body. Here, we hypothesize that E. faecalis strains isolated from the human bladder will carry unique genomic content compared to clinical strains isolated from other sources. This analysis includes comparison of 111 E. faecalis genomes isolated from bladder, urogenital, blood, and fecal samples. Phylogenomic comparison shows no association between isolation source and lineage; however, accessory genome comparison differentiates blood and bladder genomes. Further gene enrichment analysis identifies gene functions, virulence factors, antibiotic resistance genes, and plasmid-associated genes that are enriched or rare in bladder genomes compared to urogenital, blood, and fecal genomes. Using these findings as training data and 682 publicly available genomes as test data, machine learning classifiers successfully distinguished between bladder and non-bladder strains with high accuracy. Genes identified as important for this differentiation were often related to transposable elements and phage, including 3 prophage species found almost exclusively in bladder and urogenital genomes. E. faecalis strains isolated from the bladder contain unique genomic content when compared to strains isolated from other body sites. This genomic diversity is most likely due to horizontal gene transfer, as evidenced by lack of phylogenomic clustering and enrichment of transposable elements and prophages. Investigation into how these enriched genes influence host-microbe interactions may elucidate gene functions required for successful bladder colonization and disease establishment. The online version contains supplementary material available at 10.1186/s12864-023-09818-z.
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影响因子：
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