Genome insights of Enterococcus raffinosus CX012922, isolated from the feces of a Crohn’s disease patient

Gut Pathogens

Xunchao Cai¹  Long Xu¹  Yao Peng²  Hailan Zhao³  Yuqiang Nie⁴  Youlian Zhou⁴  Yongjian Zhou⁴  Hongli Huang⁴ 

[1] Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, 518071, Shenzhen, Guangdong, People’s Republic of China;Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People’s Hospital, 510180, Guangzhou, Guangdong, People’s Republic of China;Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, 518071, Shenzhen, Guangdong, People’s Republic of China;Department of Gastroenterology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, 510006, Guangzhou, Guangdong, People’s Republic of China;Department of Gastroenterology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, 510006, Guangzhou, Guangdong, People’s Republic of China;Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People’s Hospital, 510180, Guangzhou, Guangdong, People’s Republic of China;

关键词: Enterococcus;    Megaplasmid;    Antibiotic resistance genes;    Virulence factor;    Toxin-antitoxin system;   

DOI  :  10.1186/s13099-021-00468-8

来源: Springer

【 摘 要 】

BackgroundEnterococcus raffinosus is one of the Enterococcus species that often cause nosocomial infections. To date, only one E. raffinosus genome has been completely assembled, and the genomic features have not been characterized. Here, we report the complete genome sequence of the strain CX012922, isolated from the feces of a Crohn’s disease patient, and perform a comparative genome analysis to the relevant Enterococcus spp. strains in silico.ResultsDe novo assembly of the sequencing reads of the strain CX012922 generated a circular genome of 2.83 Mb and a circular megaplasmid of 0.98 Mb. Phylogenomic analysis revealed that the strain CX012922 belonged to the E. raffinosus species. By comparative genome analysis, we found that some strains previously identified as E. raffinosus or E. gilvus should be reclassified as novel species. Genome islands (GIs), virulence factors, and antibiotic genes were found in both the genome and the megaplasmid, although pathogenic genes were mainly encoded in the genome. A large proportion of the genes encoded in the megaplasmid were involved in substrate utilization, such as raffinose metabolism. Giant megaplasmids (~1 Mb) equipped with toxin-antitoxin (TA) systems generally formed symbiosis relationships with the genome of E. raffinosus strains.ConclusionsEnterococcus spp. have a higher species-level diversity than is currently appreciated. The pathogenicity of E. raffinosus is mainly determined by the genome-encoded virulence factors, while the megaplasmid broadens the gene function pool. The symbiosis between the genome and the megaplasmids endows E. raffinosus with large genomic sizes as well as versatile gene functions, especially for their colonization, adaptation, virulence, and pathogenesis in the human gut.

【 授权许可】

CC BY