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

Abstract

Background Enterococcus 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. Results De 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. Conclusions Enterococcus 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.

Inter-species diversity and functional genomic analyses of closed genome assemblies of clinically isolated, megaplasmid-containing Enterococcus raffinosus Er676 and ATCC49464

“…Of note, COG category J genes relating to translation, ribosomal structure and biogenesis comprised only 0.516 % of the megaplasmid pangenome (eight genes) compared to 4.516 % of the chromosome pangenome (184 genes, P =0.0301) (). Previous reports indicated that the megaplasmid of CX012922 lacked an identifiable encoded replication initiation protein, which we also observed in Er676 and ATCC49464 (Table 1) [12]. Together, the observed enrichment of DNA replication genes within the chromosome and the lack of an encoded replication initiation protein in the megaplasmid suggest that he megaplasmid may rely on chromosomally encoded genes for its replication.…”

“…Indeed, the recent publication of two E. raffinosus complete genomes, F162_2 and CX012922, each containing a similar megaplasmid confirmed this observation [12, 13].…”

“…Indeed, large inter-species diversity has been reported for other enterococci and E. raffinosus [12, 73]. Much of the chromosomal diversity is due to prophage integration and transposable elements, indicating unique genes are attributed to horizontal gene transfer.…”

“… E. raffinosus has been reported to encode raffinose metabolism genes on its megaplasmid, suggesting that the megaplasmid plays an important role in the metabolic plasticity of the species [12]. Interestingly, the closest relative to E.…”

“… E. raffinosus has been reported to possess a megaplasmid, a genetic feature uncommon within the genus Enterococcus , that encodes diverse accessory genes particularly involved in carbohydrate metabolism and other vital cellular functions [12]. These observations were based on the complete genome assemblies of CX012922 and F162_2 strains that were isolated from a human faecal sample and Swiss water stream environment, respectively, and were published in 2021 [12, 13].…”