基于基因组的肠球菌属特征分析：一种从人类肠道中分离出的新兴病原体。

Genomic-based characterization of Enterococcus spp.: an emerging pathogen isolated from human gut.

机构信息

Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan.

Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, MN, 55108, USA.

出版信息

Mol Biol Rep. 2021 Jun;48(6):5371-5376. doi: 10.1007/s11033-021-06540-5. Epub 2021 Jul 7.

DOI:10.1007/s11033-021-06540-5

PMID:34232463

Abstract

BACKGROUND

Enterococci are ubiquitous microorganisms having diverse ecological niches but most prominently in gastrointestinal tract of humans and animals. Production of enterocins makes them a good probiotic candidate. However, their role as probiotics has become ambiguous in the last few years because of the presence of virulence factors and antibiotic resistance genes. These virulence traits are known to be transferred genetically, which makes them opportunistic pathogens in the gastrointestinal tract leading to serious concerns about their being used as probiotics. In the present study, Enterococcusspp. isolated from the human gut were subjected to Whole-Genome Sequencing (WGS) to determine the presence of resistance and virulence genes.

METHODS AND RESULTS

Four human origins Enterococcus spp. including Enterococcus faecalis, Enterococcus casseliflavus, and two Enterococcus gallinarum were isolated from human fecal samples and further cultured on blood agar. Sanger sequencing was done using Applied Biosystems 3730xl DNA Analyzer. These strains were further subjected to WGS using oxford nanopore technology MinION. Raw data were analyzed using the free online tool epi2me. The Comprehensive Antibiotic Resistance Database (CARD) and RAST (Rapid Annotation using Subsystem Technology) software were used to look for the presence of antibiotic resistance genes in these strains. Resistance determinants for clinically important antibiotics (vancomycin) and functional virulence factor genes were detected. G-view server was used for comparative genomics of all strains.

CONCLUSION

The genomic sequencing of Enterococcus suggested that E. faecalis, E. casseliflavus, and E. gallinarum strains are opportunistic pathogens, having antibiotic resistance genes. All isolates had vancomycin resistance genes, which were expressed phenotypically. Genes related to bacteriocin resistance were also present in E. casseliflavus and E. gallinarum.

摘要

背景

肠球菌是一种无处不在的微生物，具有多种生态位，但最常见于人类和动物的胃肠道。肠球菌产生肠球菌素，使它们成为一种很好的益生菌候选物。然而，由于存在毒力因子和抗生素耐药基因，它们作为益生菌的作用在最近几年变得模糊不清。这些毒力特征已知是通过遗传方式转移的，这使它们成为胃肠道中的机会性病原体，引起了人们对将其用作益生菌的严重关注。在本研究中，从人类肠道中分离出的肠球菌属被进行全基因组测序（WGS），以确定耐药性和毒力基因的存在。

方法和结果

从人类粪便样本中分离出 4 株来自人类的肠球菌属，包括粪肠球菌、黄色肠球菌和 2 株鸡肠球菌，并进一步在血琼脂上培养。使用 Applied Biosystems 3730xl DNA Analyzer 进行 Sanger 测序。这些菌株进一步使用牛津纳米孔技术 MinION 进行 WGS。使用免费的在线工具 epi2me 对原始数据进行分析。使用综合抗生素耐药数据库（CARD）和 RAST（使用子系统技术快速注释）软件来寻找这些菌株中抗生素耐药基因的存在。检测到了对临床重要抗生素（万古霉素）和功能毒力因子基因的耐药决定因素。使用 G-view 服务器对所有菌株进行比较基因组学分析。