Novel Bacteriophages in Enterococcus spp.

Fard, Ramin Mazaheri Nezhad; Barton, Mary; Heuzenroeder, Michael W.

doi:10.1007/s00284-009-9555-z

Cited by 33 publications

(24 citation statements)

References 55 publications

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“…Phage found in enterococci usually belong to the Podoviridae , Siphoviridae or Myoviridae , but others including Inoviridae , Leviviridae , Guttaviridae and Fuselloviridae have also been reported [108, 109]. …”

Section: Resultsmentioning

confidence: 99%

Comparative genomics of Enterococcus spp. isolated from bovine feces

et al. 2017

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Background Enterococcus is ubiquitous in nature and is a commensal of both the bovine and human gastrointestinal (GI) tract. It is also associated with clinical infections in humans. Subtherapeutic administration of antibiotics to cattle selects for antibiotic resistant enterococci in the bovine GI tract. Antibiotic resistance genes (ARGs) may be present in enterococci following antibiotic use in cattle. If located on mobile genetic elements (MGEs) their dissemination between Enterococcus species and to pathogenic bacteria may be promoted, reducing the efficacy of antibiotics.ResultsWe present a comparative genomic analysis of twenty-one Enterococcus spp. isolated from bovine feces including Enterococcus hirae (n = 10), Enterococcus faecium (n = 3), Enterococcus villorum (n = 2), Enterococcus casseliflavus (n = 2), Enterococcus faecalis (n = 1), Enterococcus durans (n = 1), Enterococcus gallinarum (n = 1) and Enterococcus thailandicus (n = 1). The analysis revealed E. faecium and E. faecalis from bovine feces share features with human clinical isolates, including virulence factors. The Tn917 transposon conferring macrolide-lincosamide-streptogramin B resistance was identified in both E. faecium and E. hirae, suggesting dissemination of ARGs on MGEs may occur in the bovine GI tract. An E. faecium isolate was also identified with two integrative conjugative elements (ICEs) belonging to the Tn916 family of ICE, Tn916 and Tn5801, both conferring tetracycline resistance.ConclusionsThis study confirms the presence of enterococci in the bovine GI tract possessing ARGs on MGEs, but the predominant species in cattle, E. hirae is not commonly associated with infections in humans. Analysis using additional complete genomes of E. faecium from the NCBI database demonstrated differential clustering of commensal and clinical isolates, suggesting that these strains may be specifically adapted to their respective environments.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-017-0962-1) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Comparative genomics of Enterococcus spp. isolated from bovine feces

et al. 2017

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“…Bacteriophage-mediated transduction can transfer antibiotic resistance between enterococci [44,45] and many bacteriophages have also been identified in E. faecium [44]. To identify phage genes on the TX16 genome, Prophinder and Prophage Finder were used to search for prophage loci [46,47].…”

Section: Resultsmentioning

confidence: 99%

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

Qin

Galloway-Peña²,

Sillanpää³

et al. 2012

BMC Microbiol

130

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BackgroundEnterococci 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.ResultsIn 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.ConclusionsOur 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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“…E. faecalis genomes, in particular, have retained a number of integrated prophages, although the E. faecalis genome is rapidly evolving (8,9). With many new E. faecalis phages being identified and the fact that many of the sequenced E. faecalis isolates contain one or more prophages (8,9,19), it is likely that these elements are integrally important to E. faecalis physiology.…”

Section: Discussionmentioning

confidence: 99%

A composite bacteriophage alters colonization by an intestinal commensal bacterium

Duerkop¹,

Clements

Rollins

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

206

187

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The mammalian intestine is home to a dense community of bacteria and its associated bacteriophage (phage). Virtually nothing is known about how phages impact the establishment and maintenance of resident bacterial communities in the intestine. Here, we examine the phages harbored by Enterococcus faecalis, a commensal of the human intestine. We show that E. faecalis strain V583 produces a composite phage (ϕV1/7) derived from two distinct chromosomally encoded prophage elements. One prophage, prophage 1 (ϕV1), encodes the structural genes necessary for phage particle production. Another prophage, prophage 7 (ϕV7), is required for phage infection of susceptible host bacteria. Production of ϕV1/7 is controlled, in part, by nutrient availability, because ϕV1/7 particle numbers are elevated by free amino acids in culture and during growth in the mouse intestine. ϕV1/7 confers an advantage to E. faecalis V583 during competition with other E. faecalis strains in vitro and in vivo. Thus, we propose that E. faecalis V583 uses phage particles to establish and maintain dominance of its intestinal niche in the presence of closely related competing strains. Our findings indicate that bacteriophages can impact the dynamics of bacterial colonization in the mammalian intestinal ecosystem.T he human gastrointestinal tract is colonized with a highly diverse population of bacteria (1). Many of these bacteria produce bacteriophage (phage), further increasing the complexity of this ecosystem. Recent studies of human intestinal viromes have shown that these viromes are dominated by lysogenic prophages that are integrated into the chromosomes of their bacterial hosts (2). In numerous other ecological systems, phages profoundly influence ecological networks by serving as reservoirs of genetic diversity (3, 4) and acting as predators of susceptible bacterial strains (5). However, little is known about how resident phages may influence the assembly and maintenance of bacterial communities in the mammalian intestine.Enterococcus faecalis is an abundant member of the human intestinal microflora, and by adulthood, it can constitute as much as 0.5-0.9% of the total bacterial content of the intestinal tract (Table S1) (6). A Gram-positive facultative anaerobe, E. faecalis is a leading cause of antibiotic-resistant nosocomial bacteremia and endocarditis (7). Genomic sequencing has revealed a high degree of variation among E. faecalis genomes (8). Some of this variation can be attributed to an array of integrated prophage elements that encode components required for the production of phage particles.The first E. faecalis genome to be sequenced was strain V583, a clinical blood isolate that is vancomycin-resistant (9). The V583 chromosome harbors seven putative prophages designated prophages 1-7 (Fig. 1). At least two of these prophage elements seem to encode cryptic or satellite phage genomes (10) that, by themselves, do not produce functional phage particles but may encode accessory components that aid in the lytic cycle of other integrated pro...

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Novel Bacteriophages in Enterococcus spp.

Cited by 33 publications

References 55 publications

Comparative genomics of Enterococcus spp. isolated from bovine feces

Comparative genomics of Enterococcus spp. isolated from bovine feces

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

A composite bacteriophage alters colonization by an intestinal commensal bacterium

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