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

Qin, Xiang; Galloway-Peña, Jessica; Sillanpää, Jouko; Roh, Jung Hyeob; Nallapareddy, Sreedhar R.; Chowdhury, Shahreen; Bourgogne, Agathe; Choudhury, Tina; Buhay, Christian; Ding, Yan; Dugan-Rocha, Shannon; Lin, Wen; Kovar, Christie; Sodergren, Erica; Highlander, Sarah K.; Petrosino, Joseph F.; Worley, Kim C.; Gibbs, Richard A.; Weinstock, George M.; Murray, Barbara E.

doi:10.1186/1471-2180-12-135

Cited by 132 publications

(116 citation statements)

References 112 publications

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“…We selected these 37 strains to represent the E. faecium phylogeny. Together with three additional strains (DO [TX16], NRRL B-2354 [33,35], and E1293 [GenBank accession no. NZ_AHWU00000000]), the set of 40 strains used for building the cgMLST scheme included clade A1 (9 isolates), clade A2 (18 isolates), clade B (12 isolates), and one strain that appears to be a hybrid of clades A and B.…”

Section: Resultsmentioning

confidence: 99%

“…An E. faecium cgMLST scheme was set up using SeqSphereϩ version 2.3 (Ridom GmbH, Münster, Germany [http://www.ridom.de /seqsphere/]) using 40 E. faecium whole-genome sequences publicly available in GenBank (ftp://ftp.ncbi.nih.gov/genomes/) as of August 2014 (see Table S1 in the supplemental material) (17,(32)(33)(34)(35). This set included three completed genome sequences, of which E. faecium strain Aus0004 (36) (GenBank accession no.…”

Section: Methodsmentioning

confidence: 99%

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Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium

et al. 2015

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Enterococcus faecium, a common inhabitant of the human gut, has emerged in the last 2 decades as an important multidrugresistant nosocomial pathogen. Since the start of the 21st century, multilocus sequence typing (MLST) has been used to study the molecular epidemiology of E. faecium. However, due to the use of a small number of genes, the resolution of MLST is limited. Whole-genome sequencing (WGS) now allows for high-resolution tracing of outbreaks, but current WGS-based approaches lack standardization, rendering them less suitable for interlaboratory prospective surveillance. To overcome this limitation, we developed a core genome MLST (cgMLST) scheme for E. faecium. cgMLST transfers genome-wide single nucleotide polymorphism (SNP) diversity into a standardized and portable allele numbering system that is far less computationally intensive than SNPbased analysis of WGS data. The E. faecium cgMLST scheme was built using 40 genome sequences that represented the diversity of the species. The scheme consists of 1,423 cgMLST target genes. To test the performance of the scheme, we performed WGS analysis of 103 outbreak isolates from five different hospitals in the Netherlands, Denmark, and Germany. The cgMLST scheme performed well in distinguishing between epidemiologically related and unrelated isolates, even between those that had the same sequence type (ST), which denotes the higher discriminatory power of this cgMLST scheme over that of conventional MLST. We also show that in terms of resolution, the performance of the E. faecium cgMLST scheme is equivalent to that of an SNP-based approach. In conclusion, the cgMLST scheme developed in this study facilitates rapid, standardized, and high-resolution tracing of E. faecium outbreaks. In the last 2 decades, Enterococcus faecium has emerged as an important multidrug-resistant nosocomial pathogen causing an increasing number of bloodstream infections, mainly in debilitated patients (1-3). Currently, Ͼ90% of the E. faecium strains causing infections have acquired ampicillin resistance, and an increasing number of health care-associated infections and outbreaks are caused by E. faecium strains that are resistant to both ampicillin and vancomycin (4). The global emergence of ampicillin-and vancomycin-resistant E. faecium (VRE) as nosocomial pathogens started in the United States in the late 1980s/early 1990s and occurred in other parts in the world 1 or 2 decades later. In Europe, more particularly in France, Germany, Denmark, and the Netherlands, VRE first spread among livestock due to the use of the vancomycin analog avoparcin as a growth promoter, and it only relatively recently became an important nosocomial pathogen (5, 6). Different molecular typing methods have been used to study the epidemiology of E. faecium, ranging from fingerprint-based methods, like pulsed-field gel electrophoresis (PFGE) (7), ribotyping (8), and amplified fragment length polymorphism (9), to PCR-based methods, like multilocus variable-number tandemrepeat analysis (10) and the sequenced-bas...

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium

et al. 2015

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“…The genome of E. faecium TX16 (DO) contains four pilus-encoding gene clusters predicted to form four distinct pilus-like structures (10,(14)(15)(16). Indeed, the conditional expression of two distinct types of pili was demonstrated in an E. faecium hospital-acquired bloodstream isolate (15).…”

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confidence: 99%

Role of the Emp Pilus Subunits of Enterococcus faecium in Biofilm Formation, Adherence to Host Extracellular Matrix Components, and Experimental Infection

et al. 2016

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cEnterococcus faecium is an important cause of hospital-associated infections, including urinary tract infections (UTIs), bacteremia, and infective endocarditis. Pili have been shown to play a role in the pathogenesis of Gram-positive bacteria, including E. faecium. We previously demonstrated that a nonpiliated ⌬empABC::cat derivative of E. faecium TX82 was attenuated in biofilm formation and in a UTI model. Here, we studied the contributions of the individual pilus subunits EmpA, EmpB, and EmpC to pilus architecture, biofilm formation, adherence to extracellular matrix (ECM) proteins, and infection. We identified EmpA as the tip of the pili and found that deletion of empA reduced biofilm formation to the same level as deletion of the empABC operon, a phenotype that was restored by reconstituting in situ the empA gene. Deletion of empB also caused a reduction in biofilm, while EmpC was found to be dispensable. Significant reductions in adherence to fibrinogen and collagen type I were observed with deletion of empA and empB, while deletion of empC had no adherence defect. Furthermore, we showed that each deletion mutant was significantly attenuated in comparison to the isogenic parental strain, TX82, in a mixed-inoculum UTI model (P < 0.001 to 0.048), that reconstitution of empA restored virulence in the UTI model, and that deletion of empA also resulted in attenuation in an infective endocarditis model (P ‫؍‬ 0.0088). Our results indicate that EmpA and EmpB, but not EmpC, contribute to biofilm and adherence to ECM proteins; however, all the Emp pilins are important for E. faecium to cause infection in the urinary tract.

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“…S1 and Table S3 in the supplemental material). The GC content of the NRRL B-2354 chromosome (38.03%) is similar to that of other E. faecium strains, including TX16 (also known as DO) (38.15%) (20) and Aus0004 (38.36%) (21). The GC content of the plasmid is lower (35.98%) than that of the chromosome but similar to that of the megaplasmids of other E. faecium strains (see Table S3 in the supplemental material).…”

Section: Resultsmentioning

confidence: 54%

“…There are currently over 200 publicly available E. faecium draft genomes. The best-characterized genomes are for strain TX16 (also referred to as DO), isolated from an individual with endocarditis (20), and strain Aus0004, isolated from the bloodstream of a hospitalized patient (21). Several draft genomes of community-associated strains are also currently available in public databases, but none have been characterized in depth.…”

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confidence: 99%

Safety of the Surrogate Microorganism Enterococcus faecium NRRL B-2354 for Use in Thermal Process Validation

Kopit

Kim

Siezen

et al. 2014

Appl Environ Microbiol

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dEnterococcus faecium NRRL B-2354 is a surrogate microorganism used in place of pathogens for validation of thermal processing technologies and systems. We evaluated the safety of strain NRRL B-2354 based on its genomic and functional characteristics. The genome of E. faecium NRRL B-2354 was sequenced and found to comprise a 2,635,572-bp chromosome and a 214,319-bp megaplasmid. A total of 2,639 coding sequences were identified, including 45 genes unique to this strain. Hierarchical clustering of the NRRL B-2354 genome with 126 other E. faecium genomes as well as pbp5 locus comparisons and multilocus sequence typing (MLST) showed that the genotype of this strain is most similar to commensal, or community-associated, strains of this species. E. faecium NRRL B-2354 lacks antibiotic resistance genes, and both NRRL B-2354 and its clonal relative ATCC 8459 are sensitive to clinically relevant antibiotics. This organism also lacks, or contains nonfunctional copies of, enterococcal virulence genes including acm, cyl, the ebp operon, esp, gelE, hyl, IS16, and associated phenotypes. It does contain scm, sagA, efaA, and pilA, although either these genes were not expressed or their roles in enterococcal virulence are not well understood. Compared with the clinical strains TX0082 and 1,231,502, E. faecium NRRL B-2354 was more resistant to acidic conditions (pH 2.4) and high temperatures (60°C) and was able to grow in 8% ethanol. These findings support the continued use of E. faecium NRRL B-2354 in thermal process validation of food products.

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

Cited by 132 publications

References 112 publications

Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium

Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium

Role of the Emp Pilus Subunits of Enterococcus faecium in Biofilm Formation, Adherence to Host Extracellular Matrix Components, and Experimental Infection

Safety of the Surrogate Microorganism Enterococcus faecium NRRL B-2354 for Use in Thermal Process Validation

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