%0 Journal Article %J BMC Microbiol %D 2012 %T Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. %A Qin, Xiang %A Galloway-Peña, Jessica R %A Sillanpaa, Jouko %A Roh, Jung Hyeob %A Nallapareddy, Sreedhar R %A Chowdhury, Shahreen %A Bourgogne, Agathe %A Choudhury, Tina %A Muzny, Donna M %A Buhay, Christian J %A Ding, Yan %A Dugan-Rocha, Shannon %A Liu, Wen %A Kovar, Christie %A Sodergren, Erica %A Highlander, Sarah %A Petrosino, Joseph F %A Worley, Kim C %A Gibbs, Richard A %A Weinstock, George M %A Murray, Barbara E %K DNA, Bacterial %K Enterococcus faecium %K Genome, Bacterial %K Humans %K Molecular Sequence Data %K Sequence Analysis, DNA %X

BACKGROUND: 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.

RESULTS: 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.

CONCLUSIONS: 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.

%B BMC Microbiol %V 12 %P 135 %8 2012 Jul 07 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/22769602?dopt=Abstract %R 10.1186/1471-2180-12-135 %0 Journal Article %J J Bacteriol %D 2009 %T A collagen-binding adhesin, Acb, and ten other putative MSCRAMM and pilus family proteins of Streptococcus gallolyticus subsp. gallolyticus (Streptococcus bovis Group, biotype I). %A Sillanpaa, Jouko %A Nallapareddy, Sreedhar R %A Qin, Xiang %A Singh, Kavindra V %A Muzny, Donna M %A Kovar, Christie L %A Nazareth, Lynne V %A Gibbs, Richard A %A Ferraro, Mary J %A Steckelberg, James M %A Weinstock, George M %A Murray, Barbara E %K Adhesins, Bacterial %K Fimbriae, Bacterial %K Gene Expression Profiling %K Gene Expression Regulation, Bacterial %K Genome, Bacterial %K Multigene Family %K Streptococcus %X

Members of the Streptococcus bovis group are important causes of endocarditis. However, factors associated with their pathogenicity, such as adhesins, remain uncharacterized. We recently demonstrated that endocarditis-derived Streptococcus gallolyticus subsp. gallolyticus isolates frequently adhere to extracellular matrix (ECM) proteins. Here, we generated a draft genome sequence of an ECM protein-adherent S. gallolyticus subsp. gallolyticus strain and found, by genome-wide analyses, 11 predicted LPXTG-type cell wall-anchored proteins with characteristics of MSCRAMMs, including a modular architecture of domains predicted to adopt immunoglobulin (Ig)-like folding. A recombinant segment of one of these, Acb, showed high-affinity binding to immobilized collagen, and cell surface expression of Acb correlated with the presence of acb and collagen adherence of isolates. Three of the 11 proteins have similarities to major pilus subunits and are organized in separate clusters, each including a second Ig-fold-containing MSCRAMM and a class C sortase, suggesting that the sequenced strain encodes three distinct types of pili. Reverse transcription-PCR demonstrated that all three genes of one cluster, acb-sbs7-srtC1, are cotranscribed, consistent with pilus operons of other gram-positive bacteria. Further analysis detected expression of all 11 genes in cells grown to mid to late exponential growth phases. Wide distribution of 9 of the 11 genes was observed among S. gallolyticus subsp. gallolyticus isolates with fewer genes present in other S. bovis group species/subspecies. The high prevalence of genes encoding putative MSCRAMMs and pili, including a collagen-binding MSCRAMM, among S. gallolyticus subsp. gallolyticus isolates may play an important role in the predominance of this subspecies in S. bovis endocarditis.

%B J Bacteriol %V 191 %P 6643-53 %8 2009 Nov %G eng %N 21 %1 https://www.ncbi.nlm.nih.gov/pubmed/19717590?dopt=Abstract %R 10.1128/JB.00909-09 %0 Journal Article %J Microbiology (Reading) %D 2008 %T Identification and phenotypic characterization of a second collagen adhesin, Scm, and genome-based identification and analysis of 13 other predicted MSCRAMMs, including four distinct pilus loci, in Enterococcus faecium. %A Sillanpaa, Jouko %A Nallapareddy, Sreedhar R %A Prakash, Vittal P %A Qin, Xiang %A Höök, Magnus %A Weinstock, George M %A Murray, Barbara E %K Adhesins, Bacterial %K Bacterial Adhesion %K Circular Dichroism %K Collagen %K DNA, Bacterial %K Enterococcus faecium %K Enzyme-Linked Immunosorbent Assay %K Fimbriae, Bacterial %K Flow Cytometry %K Genes, Bacterial %K Genome, Bacterial %K Multigene Family %K Phenotype %K Protein Binding %K Protein Conformation %K Recombinant Proteins %K Reverse Transcriptase Polymerase Chain Reaction %K RNA, Bacterial %K Substrate Specificity %X

Attention has recently been drawn to Enterococcus faecium because of an increasing number of nosocomial infections caused by this species and its resistance to multiple antibacterial agents. However, relatively little is known about the pathogenic determinants of this organism. We have previously identified a cell-wall-anchored collagen adhesin, Acm, produced by some isolates of E. faecium, and a secreted antigen, SagA, exhibiting broad-spectrum binding to extracellular matrix proteins. Here, we analysed the draft genome of strain TX0016 for potential microbial surface components recognizing adhesive matrix molecules (MSCRAMMs). Genome-based bioinformatics identified 22 predicted cell-wall-anchored E. faecium surface proteins (Fms), of which 15 (including Acm) had characteristics typical of MSCRAMMs, including predicted folding into a modular architecture with multiple immunoglobulin-like domains. Functional characterization of one [Fms10; redesignated second collagen adhesin of E. faecium (Scm)] revealed that recombinant Scm(65) (A- and B-domains) and Scm(36) (A-domain) bound to collagen type V efficiently in a concentration-dependent manner, bound considerably less to collagen type I and fibrinogen, and differed from Acm in their binding specificities to collagen types IV and V. Results from far-UV circular dichroism measurements of recombinant Scm(36) and of Acm(37) indicated that these proteins were rich in beta-sheets, supporting our folding predictions. Whole-cell ELISA and FACS analyses unambiguously demonstrated surface expression of Scm in most E. faecium isolates. Strikingly, 11 of the 15 predicted MSCRAMMs clustered in four loci, each with a class C sortase gene; nine of these showed similarity to Enterococcus faecalis Ebp pilus subunits and also contained motifs essential for pilus assembly. Antibodies against one of the predicted major pilus proteins, Fms9 (redesignated EbpC(fm)), detected a 'ladder' pattern of high-molecular-mass protein bands in a Western blot analysis of cell surface extracts from E. faecium, suggesting that EbpC(fm) is polymerized into a pilus structure. Further analysis of the transcripts of the corresponding gene cluster indicated that fms1 (ebpA(fm)), fms5 (ebpB(fm)) and ebpC(fm) are co-transcribed, a result consistent with those for pilus-encoding gene clusters of other Gram-positive bacteria. All 15 genes occurred frequently in 30 clinically derived diverse E. faecium isolates tested. The common occurrence of MSCRAMM- and pilus-encoding genes and the presence of a second collagen-binding protein may have important implications for our understanding of this emerging pathogen.

%B Microbiology (Reading) %V 154 %P 3199-3211 %8 2008 Oct %G eng %N Pt 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/18832325?dopt=Abstract %R 10.1099/mic.0.2008/017319-0 %0 Journal Article %J Genome Biol %D 2008 %T Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF. %A Bourgogne, Agathe %A Garsin, Danielle A %A Qin, Xiang %A Singh, Kavindra V %A Sillanpaa, Jouko %A Yerrapragada, Shailaja %A Ding, Yan %A Dugan-Rocha, Shannon %A Buhay, Christian %A Shen, Hua %A Chen, Guan %A Williams, Gabrielle %A Muzny, Donna %A Maadani, Arash %A Fox, Kristina A %A Gioia, Jason %A Chen, Lei %A Shang, Yue %A Arias, Cesar A %A Nallapareddy, Sreedhar R %A Zhao, Meng %A Prakash, Vittal P %A Chowdhury, Shahreen %A Jiang, Huaiyang %A Gibbs, Richard A %A Murray, Barbara E %A Highlander, Sarah K %A Weinstock, George M %K Animals %K Anti-Bacterial Agents %K Bacterial Proteins %K Biofilms %K DNA, Bacterial %K Drug Resistance, Bacterial %K Enterococcus faecalis %K Fusidic Acid %K Genetic Variation %K Genome, Bacterial %K Genomics %K Interspersed Repetitive Sequences %K Membrane Proteins %K Mice %K Operon %K Repetitive Sequences, Nucleic Acid %K Rifampin %K Sequence Homology, Nucleic Acid %X

BACKGROUND: Enterococcus faecalis has emerged as a major hospital pathogen. To explore its diversity, we sequenced E. faecalis strain OG1RF, which is commonly used for molecular manipulation and virulence studies.

RESULTS: The 2,739,625 base pair chromosome of OG1RF was found to contain approximately 232 kilobases unique to this strain compared to V583, the only publicly available sequenced strain. Almost no mobile genetic elements were found in OG1RF. The 64 areas of divergence were classified into three categories. First, OG1RF carries 39 unique regions, including 2 CRISPR loci and a new WxL locus. Second, we found nine replacements where a sequence specific to V583 was substituted by a sequence specific to OG1RF. For example, the iol operon of OG1RF replaces a possible prophage and the vanB transposon in V583. Finally, we found 16 regions that were present in V583 but missing from OG1RF, including the proposed pathogenicity island, several probable prophages, and the cpsCDEFGHIJK capsular polysaccharide operon. OG1RF was more rapidly but less frequently lethal than V583 in the mouse peritonitis model and considerably outcompeted V583 in a murine model of urinary tract infections.

CONCLUSION: E. faecalis OG1RF carries a number of unique loci compared to V583, but the almost complete lack of mobile genetic elements demonstrates that this is not a defining feature of the species. Additionally, OG1RF's effects in experimental models suggest that mediators of virulence may be diverse between different E. faecalis strains and that virulence is not dependent on the presence of mobile genetic elements.

%B Genome Biol %V 9 %P R110 %8 2008 %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/18611278?dopt=Abstract %R 10.1186/gb-2008-9-7-r110