Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes

Department of Medicine, Division of Infectious Disease, Houston, TX, USA. .
BMC Microbiology (Impact Factor: 2.73). 07/2012; 12(1):135. DOI: 10.1186/1471-2180-12-135
Source: PubMed


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.

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Available from: Jessica Galloway-Peña, Oct 09, 2015
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    • "E. faecium T-110 which is a non-pathogenic probiotic strain possessed a single plasmid of 44,086 bp, which was named as pEFT-110. Similarly, the other non-pathogenic strain E. faecium NRRL B-2354 also contained a single plasmid, while the pathogenic strains possessed multiple plasmids (Qin et al., 2012; Lam et al., 2012; Lam et al., 2013; Kopit et al., 2014). The plasmid from E. faecium T-110 showed the highest identity to the plasmid from the non-pathogenic strain NRRL B-2354 (98% identity and 93% query coverage) and the lowest similarity to the pathogenic strain Aus0004 (97% identity and 81% query coverage) (Lam et al., 2012; Kopit et al., 2014). "
    Journal of Genetics and Genomics 08/2014; 42(1). DOI:10.1016/j.jgg.2014.07.002 · 3.59 Impact Factor
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    • "In addition, complete genome sequences of five Enterococcus spp. with (E. casseliflavus EC2018: NC_021023; E. faecalis V58319: NC_004668, NC_004669, NC_004670, and NC_004671; E. faecium Aus000420: NC_017022, NC_017023, NC_017024, and NC_017032; E. faecium DO21: NC_017960, NC_017961, NC_017962, and NC_017963; E. hirae ATCC 979022: NC_015845 and NC_018081) were obtained from the NCBI website for genome comparisons. GenomeMatcher23 and In Silico Molecular Cloning Genomics Edition (IMC-GE) software (In Silico Biology, Japan) were also used for intra- and inter-QU 25 genome comparisons. "
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    ABSTRACT: Enterococcus mundtii QU 25, a non-dairy bacterial strain of ovine faecal origin, can ferment both cellobiose and xylose to produce l-lactic acid. The use of this strain is highly desirable for economical l-lactate production from renewable biomass substrates. Genome sequence determination is necessary for the genetic improvement of this strain. We report the complete genome sequence of strain QU 25, primarily determined using Pacific Biosciences sequencing technology. The E. mundtii QU 25 genome comprises a 3 022 186-bp single circular chromosome (GC content, 38.6%) and five circular plasmids: pQY182, pQY082, pQY039, pQY024, and pQY003. In all, 2900 protein-coding sequences, 63 tRNA genes, and 6 rRNA operons were predicted in the QU 25 chromosome. Plasmid pQY024 harbours genes for mundticin production. We found that strain QU 25 produces a bacteriocin, suggesting that mundticin-encoded genes on plasmid pQY024 were functional. For lactic acid fermentation, two gene clusters were identified—one involved in the initial metabolism of xylose and uptake of pentose and the second containing genes for the pentose phosphate pathway and uptake of related sugars. This is the first complete genome sequence of an E. mundtii strain. The data provide insights into lactate production in this bacterium and its evolution among enterococci.
    DNA Research 02/2014; 21(4). DOI:10.1093/dnares/dsu003 · 5.48 Impact Factor
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    • "In this current study, genome and phenotype comparisons were performed to explore in more detail the differences between 13 ST17 and 15 ST203 E. faecium isolates to help explain the emergence of ST203 and its success as an opportunistic hospital pathogen. We fully assembled and annotated the genome of E. faecium ST203 Aus0085, the first complete ST203 reference sequence, and compared it with the recently fully assembled and annotated genomes of ST17 Aus0004 and ST18 isolate TX16 [22,23]. Growth rates and biofilm formation were also measured for a collection of ST17 and ST203 isolates, and virulence was assessed in the Greater Wax Moth (Galleria mellonella) invertebrate model. "
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    ABSTRACT: In this report we have explored the genomic and microbiological basis for a sustained increase in bloodstream infections at a major Australian hospital caused by Enterococcus faecium multi-locus sequence type (ST) 203, an outbreak strain that has largely replaced a predecessor ST17 sequence type. To establish a ST203 reference sequence we fully assembled and annotated the genome of Aus0085, a 2009 vancomycin-resistant Enterococcus faecium (VREfm) bloodstream isolate, and the first example of a completed ST203 genome. Aus0085 has a 3.2 Mb genome, comprising a 2.9 Mb circular chromosome and six circular plasmids (2 kb¿130 kb). Twelve percent of the 3222 coding sequences (CDS) in Aus0085 are not present in ST17 E. faecium Aus0004 and ST18 E. faecium TX16. Extending this comparison to an additional 12 ST17 and 14 ST203 E. faecium hospital isolate genomes revealed only six genomic regions spanning 41 kb that were present in all ST203 and absent from all ST17 genomes. The 40 CDS have predicted functions that include ion transport, riboflavin metabolism and two phosphotransferase systems. Comparison of the vancomycin resistance-conferring Tn1549 transposon between Aus0004 and Aus0085 revealed differences in transposon length and insertion site, and van locus sequence variation that correlated with a higher vancomycin MIC in Aus0085. Additional phenotype comparisons between ST17 and ST203 isolates showed that while there were no differences in biofilm-formation and killing of Galleria mellonella, ST203 isolates grew significantly faster and out-competed ST17 isolates in growth assays. Here we have fully assembled and annotated the first ST203 genome, and then characterized the genomic differences between ST17 and ST203 E. faecium. We also show that ST203 E. faecium are faster growing and can out-compete ST17 E. faecium. While a causal genetic basis for these phenotype differences is not provided here, this study revealed conserved genetic differences between the two clones, differences that can now be tested to explain the molecular basis for the success and emergence of ST203 E. faecium.
    BMC Genomics 09/2013; 14(1):595. DOI:10.1186/1471-2164-14-595 · 3.99 Impact Factor
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