Dataset Information

Complete genome sequences of two Enterococcus faecium strains and comparative genomic analysis.

ABSTRACT: Enterococci are used for improvement of the intestinal environment and have clinical benefits. Enterococcus faecalis and Enterococcus faecium have similar morphologies, leading to confusion between the two species. In order to identify the National Institute for Food and Drug Control (strain 140623) and Shin Biofermin S (strain SBS-1, one of the cocci), which are widely used clinically, the present study sequenced and analyzed these two strains. The biochemical characteristics, gas chromatography and mass spectrometry results of 140623 and SBS-1 revealed that the two strains were more similar to E. faecium than E. faecalis. The genomes of 140623 and SBS-1 contained 2,812,926 bp and 2,797,745 bp, respectively, based on Illumina HiSeq 2000 sequencing. Phylogenetic analysis demonstrated that 140623 and SBS-1 belonged to the phylogenetic group of E. faecium. The Gene Ontology, Kyoto Encyclopedia of Genes and Genomes and Clusters of Orthologous Groups classifications of the two sequenced genomes were highly conserved with reference to E. faecium strains. A total of 6 putative virulence-associated genes, 15 antibiotic resistance genes and 31 genes associated with bacterial toxins were identified from 140623 and SBS-1, representing their resistance mechanisms in natural environments and their potential for clinical use in food and drug safety.

SUBMITTER: Gan YQ

PROVIDER: S-EPMC7027042 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Complete genome sequences of two Enterococcus faecium strains and comparative genomic analysis.

Gan Yong-Qi YQ Zhang Tao T Gan Yong-Qiang YQ Zhao Zhuang Z Zhu Bin B

Experimental and therapeutic medicine 20200114 3

Enterococci are used for improvement of the intestinal environment and have clinical benefits. Enterococcus faecalis and Enterococcus faecium have similar morphologies, leading to confusion between the two species. In order to identify the National Institute for Food and Drug Control (strain 140623) and Shin Biofermin S (strain SBS-1, one of the cocci), which are widely used clinically, the present study sequenced and analyzed these two strains. The biochemical characteristics, gas ...[more]

PMID: 32104261

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Project description:Enterococci are among the leading causes of hospital-acquired infections in the United States and Europe, with Enterococcus faecalis and Enterococcus faecium being the two most common species isolated from enterococcal infections. In the last decade, the proportion of enterococcal infections caused by E. faecium has steadily increased compared to other Enterococcus species. Although the underlying mechanism for the gradual replacement of E. faecalis by E. faecium in the hospital environment is not yet understood, many studies using genotyping and phylogenetic analysis have shown the emergence of a globally dispersed polyclonal subcluster of E. faecium strains in clinical environments. Systematic study of the molecular epidemiology and pathogenesis of E. faecium has been hindered by the lack of closed, complete E. faecium genomes that can be used as references.In this study, we report the complete genome sequence of the E. faecium strain TX16, also known as DO, which belongs to multilocus sequence type (ST) 18, and was the first E. faecium strain ever sequenced. Whole genome comparison of the TX16 genome with 21 E. faecium draft genomes confirmed that most clinical, outbreak, and hospital-associated (HA) strains (including STs 16, 17, 18, and 78), in addition to strains of non-hospital origin, group in the same clade (referred to as the HA clade) and are evolutionally considerably more closely related to each other by phylogenetic and gene content similarity analyses than to isolates in the community-associated (CA) clade with approximately a 3-4% average nucleotide sequence difference between the two clades at the core genome level. Our study also revealed that many genomic loci in the TX16 genome are unique to the HA clade. 380 ORFs in TX16 are HA-clade specific and antibiotic resistance genes are enriched in HA-clade strains. Mobile elements such as IS16 and transposons were also found almost exclusively in HA strains, as previously reported.Our findings along with other studies show that HA clonal lineages harbor specific genetic elements as well as sequence differences in the core genome which may confer selection advantages over the more heterogeneous CA E. faecium isolates. Which of these differences are important for the success of specific E. faecium lineages in the hospital environment remain(s) to be determined.

Dataset Information

Complete genome sequences of two Enterococcus faecium strains and comparative genomic analysis.

Publications

Complete genome sequences of two <i>Enterococcus faecium</i> strains and comparative genomic analysis.

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