Genomic and SNP Analyses Demonstrate a Distant Separation of the Hospital and Community-Associated Clades of Enterococcus faecium

Galloway-Peña, Jessica; Roh, Jung Hyeob; Latorre, Mauricio; Qin, Xiang; Murray, Barbara E.

doi:10.1371/journal.pone.0030187

Cited by 127 publications

(148 citation statements)

References 34 publications

(101 reference statements)

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“…As introduced above, we recently reported the existence of two subpopulations of E. faecium, one containing primarily community-associated strains (CA clade; also called clade B) and one containing mostly hospital-associated strains (HA clade; also called clade A) (12,15). These two clades differ by ϳ3.5 to 4.2% of their nucleotides at the core genome level.…”

Section: Resultsmentioning

confidence: 93%

“…The locus tags for the WxL locus C of TX16 (DO) are HMPREF0351_10114 to HMPREF0351_10119, where SwpC is HMPREF0351_10114 and LwpC is HMPREF0351_10115. NCBI BLAST then was used to find the WxL loci in TX1330 (a community-associated [CA] commensal isolate of clade B) and TX82 (a hospital-associated [HA] clinical isolate of clade A that we have used extensively in experimental models) using the sequences obtained from TX16 (12)(13)(14)(15)(16)(17). Confirmatory sequencing of the TX1330 and TX82 WxL loci were performed using the primers in Table S2 in the supplemental material.…”

Section: Methodsmentioning

confidence: 99%

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The Identification and Functional Characterization of WxL Proteins from Enterococcus faecium Reveal Surface Proteins Involved in Extracellular Matrix Interactions

Galloway-Peña

Liang²,

Singh

et al. 2015

J Bacteriol

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fThe WxL domain recently has been identified as a novel cell wall binding domain found in numerous predicted proteins within multiple Gram-positive bacterial species. However, little is known about the function of proteins containing this novel domain. Here, we identify and characterize 6 Enterococcus faecium proteins containing the WxL domain which, by reverse transcription-PCR (RT-PCR) and genomic analyses, are located in three similarly organized operons, deemed WxL loci A, B, and C. Western blotting, electron microscopy, and enzyme-linked immunosorbent assays (ELISAs) determined that genes of WxL loci A and C encode antigenic, cell surface proteins exposed at higher levels in clinical isolates than in commensal isolates. Secondary structural analyses of locus A recombinant WxL domain-containing proteins found they are rich in ␤-sheet structure and disordered segments. Using Biacore analyses, we discovered that recombinant WxL proteins from locus A bind human extracellular matrix proteins, specifically type I collagen and fibronectin. Proteins encoded by locus A also were found to bind to each other, suggesting a novel cell surface complex. Furthermore, bile salt survival assays and animal models using a mutant from which all three WxL loci were deleted revealed the involvement of WxL operons in bile salt stress and endocarditis pathogenesis. In summary, these studies extend our understanding of proteins containing the WxL domain and their potential impact on colonization and virulence in E. faecium and possibly other Gram-positive bacterial species. Enterococcus faecium is one of the "no ESKAPE" pathogens responsible for a considerable percentage of nosocomial infections; its ability to cause life-threatening infections and resistance to antibiotics cause considerable difficulties for patients and physicians (1). To date, many of the potential virulence determinants that have been described in E. faecium are MSCRAMMs (microbial surface components recognizing adhesive matrix molecules); these include adhesins or pili anchored to the cell surface by an LPxTG-like motif and contain IgG-like folds (2). Our group previously performed a bioinformatic search for novel surface proteins that might be virulence factors in the E. faecium endocarditis strain TX16 (also known as DO) (3). During this search, we identified a locus which included predicted proteins possessing the previously described WxL domain colocated with a predicted LPxTG-like protein (Fms6) (3, 4).The WxL domain is comprised of several conserved residues along with a highly conserved YXXX(L/I/V)TWXLXXXP motif and a second WxL proximal motif in the last ϳ120 to 190 C-terminal residues of a protein (4,5). Genes encoding proteins with the WxL domain were first described in Lactobacillus plantarum as part of a novel gene cluster found in a subset of low-GϩC-content Gram-positive bacterial species, one of which is E. faecium (6, 7). Bioinformatics and transcriptome data in L. plantarum predicted these loci form cell surface protein complexes involved in ca...

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Section: Resultsmentioning

confidence: 93%

Section: Methodsmentioning

confidence: 99%

The Identification and Functional Characterization of WxL Proteins from Enterococcus faecium Reveal Surface Proteins Involved in Extracellular Matrix Interactions

Galloway-Peña

Liang²,

Singh

et al. 2015

J Bacteriol

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“…Potential sSNP sites were determined using the parsimonious assumption that each codon has only one potential sSNP site. Generations per year were estimated at a range from 100 to 300 to allow for a broad estimation (37)(38)(39)(40). The experimentally determined synonymous mutation rate of 1.4 ϫ 10 Ϫ10 (41) was used.…”

Section: Methodsmentioning

confidence: 99%

Chemoreceptor Gene Loss and Acquisition via Horizontal Gene Transfer in Escherichia coli

2013

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Ridge, Tennessee, USA b Chemotaxis allows bacteria to more efficiently colonize optimal microhabitats within their larger environment. Chemotaxis in Escherichia coli is the best-studied model system, and a large number of E. coli strains have been sequenced. The Escherichia/ Shigella genus encompasses a great variety of commensal and pathogenic strains, but the role of chemotaxis in their association with the host remains poorly understood. Here we show that the core chemotaxis genes are lost in many, but not all, nonmotile strains but are well preserved in all motile strains. The genes encoding the Tar, Tsr, and Aer chemoreceptors, which mediate chemotaxis to a broad spectrum of chemical and physical cues, are also nearly uniformly conserved in motile strains. In contrast, the clade of extraintestinal pathogenic E. coli strains apparently underwent an ancestral loss of Trg and Tap chemoreceptors, which sense sugars, dipeptides, and pyrimidines. The broad range of time estimated for the loss of these genes (1 to 3 million years ago) corresponds to the appearance of the genus Homo. Escherichia coli strains are ubiquitous colonizers of the intestines of mammals and birds (1). There are several highly adapted E. coli clones that have acquired virulence traits and cause a broad spectrum of disease, including enteric/diarrheal disease, urinary tract infections (UTIs), and sepsis/meningitis (2). Depending on the site of infection, pathogenic strains are classified as intestinal E. coli (IPEC) or extraintestinal pathogenic E. coli (ExPEC), and distinct pathotypes (based on clinical manifestation) are recognized within both categories. The most common ExPEC pathotypes include uropathogenic E. coli (UPEC), meningitis-associated E. coli (MNEC), and avian-pathogenic E. coli (APEC) (2, 3). Motility was shown to be important for the colonization of both commensal and pathogenic E. coli strains, as well as for the pathogenesis of the latter (4, 5): however, the exact role of motility and the underlying chemotaxis system in these processes remain poorly understood. The molecular machinery that controls chemotaxis in E. coli has been the subject of intensive investigation (6, 7). Its components include chemoreceptors, also known as methyl-accepting chemotaxis proteins (MCPs), a histidine kinase (CheA), an adaptor protein (CheW), a methyltransferase (CheR), and a methylesterase (CheB), as well as a response regulator (CheY) and its phosphatase (CheZ). E. coli has five chemoreceptors. Tsr mediates attractant responses to serine and quorum autoinducer AI-2 (8, 9), as well as responses to oxygen, redox, and oxidizable substrates (10, 11). It was also recently shown to mediate taxis to 3,4-dihydroxymandelic acid, a metabolite of norepinephrine that is produced by human cells (Mike Manson, personal communication). Tar mediates attractant responses to aspartate and maltose (9, 12) and negative responses to metal ions (13). Trg mediates attractant responses to ribose and galactose (14), and Tap mediates attractant responses to di...

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“…The infections caused by E. faecium, which include urinary tract infections (UTIs), bloodstream infections, and endocarditis, among others, represent a major therapeutic challenge due to the typical resistance of this species to multiple antibiotics (2). Several lines of evidence, including molecular epidemiological studies based on multilocus sequence typing (MLST) (3)(4)(5) and comparative whole-genome analyses (6,7), indicate that E. faecium strains that cause outbreaks and infections in hospitalized patients (HA clade or subclade A1) are considerably different from those forming part of the normal microbiota of healthy individuals (community-associated [CA] clade or clade B). Indeed, HA clade strains, compared to CA clade strains, are associated with increased presence, differential expression, and/or carriage of functional forms of genes encoding putative or confirmed virulence determinants that can participate in the adhesion of E. faecium to host tissues, including Acm (adhesin of collagen from E. faecium) (8), Esp (enterococcal surface protein) (9), other MSCRAMMs (microbial surface component recognizing adhesive matrix molecules) (10,11), and proteinaceous surface structures known as pili (10).…”

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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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Genomic and SNP Analyses Demonstrate a Distant Separation of the Hospital and Community-Associated Clades of Enterococcus faecium

Cited by 127 publications

References 34 publications

The Identification and Functional Characterization of WxL Proteins from Enterococcus faecium Reveal Surface Proteins Involved in Extracellular Matrix Interactions

The Identification and Functional Characterization of WxL Proteins from Enterococcus faecium Reveal Surface Proteins Involved in Extracellular Matrix Interactions

Chemoreceptor Gene Loss and Acquisition via Horizontal Gene Transfer in Escherichia coli

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

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