Guidance on the safety assessment of<i>Enterococcus faecium</i>in animal nutrition

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doi:10.2903/j.efsa.2012.2682

Cited by 70 publications

(26 citation statements)

References 37 publications

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“…CLenriched genes included IS16 (ortholog_6478), a sequence that has been extensively used to screen for CL E. faecium (36)(37)(38)(39). However, according to the genome comparisons performed here, two other ME (ortholog_2867 and ortholog_5905) were more highly associated with CL strains and might be more useful predictors of CL genotypes among E. faecium strains.…”

Section: Discussionmentioning

confidence: 97%

Nonclinical and Clinical Enterococcus faecium Strains, but Not Enterococcus faecalis Strains, Have Distinct Structural and Functional Genomic Features

Kim

Marco

2014

Appl Environ Microbiol

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Certain strains of Enterococcus faecium and Enterococcus faecalis contribute beneficially to animal health and food production, while others are associated with nosocomial infections. To determine whether there are structural and functional genomic features that are distinct between nonclinical (NC) and clinical (CL) strains of those species, we analyzed the genomes of 31 E. faecium and 38 E. faecalis strains. Hierarchical clustering of 7,017 orthologs found in the E. faecium pangenome revealed that NC strains clustered into two clades and are distinct from CL strains. NC E. faecium genomes are significantly smaller than CL genomes, and this difference was partly explained by significantly fewer mobile genetic elements (ME), virulence factors (VF), and antibiotic resistance (AR) genes. E. faecium ortholog comparisons identified 68 and 153 genes that are enriched for NC and CL strains, respectively. Proximity analysis showed that CL-enriched loci, and not NC-enriched loci, are more frequently colocalized on the genome with ME. In CL genomes, AR genes are also colocalized with ME, and VF are more frequently associated with CLenriched loci. Genes in 23 functional groups are also differentially enriched between NC and CL E. faecium genomes. In contrast, differences were not observed between NC and CL E. faecalis genomes despite their having larger genomes than E. faecium. Our findings show that unlike E. faecalis, NC and CL E. faecium strains are equipped with distinct structural and functional genomic features indicative of adaptation to different environments. Enterococcus faecium and Enterococcus faecalis are Gram-positive bacteria in the Firmicutes phylum and are found on plants, in foods, and in the gastrointestinal tracts (GIT) of animals (1). These species are members of the polyphyletic group of bacteria known as lactic acid bacteria and have important roles in food and beverage fermentations. Certain strains of E. faecium confer beneficial or probiotic effects on animal and human health (2). Conversely, strains of E. faecium and E. faecalis are also associated with nosocomial infections resulting in endocarditis and bacteremia and represent a significant reservoir of antibiotic resistance genes (2).The genetic features of E. faecium and E. faecalis were investigated previously to identify lineages specific to community and clinical environments (3-7). Virulence factors (VF), antibiotic resistance (AR) genes, mobile genetic elements (ME), and multilocus sequence typing (MLST) patterns are associated with the potential of E. faecium and E. faecalis to cause disease in humans (8, 9). Despite such studies, the structural and functional features of enterococcal genomes are not fully understood. We hypothesized that the lineage-specific differences observed previously were only a fraction of the greater, more significant distinctions between nonclinical (NC) and clinical (CL) strains, and the opposing environmental and health-specific associations are the result of broader niche-specific adaptations that can be o...

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Section: Discussionmentioning

confidence: 97%

Nonclinical and Clinical Enterococcus faecium Strains, but Not Enterococcus faecalis Strains, Have Distinct Structural and Functional Genomic Features

Kim

Marco

2014

Appl Environ Microbiol

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“…E. durans KLDS6.0930 lacks the established markers associated with the clinical strains, including esp, hyl , and IS16 , which were specified by the EFSA as targets for the safety evaluation of E. faecium strains intended as additives for animal feed (EFSA, 2012b). On the other hand, enterococci that contain a type II-A CRISPR system are reported to be non-pathogenic (Palmer and Gilmore, 2010).…”

Section: Discussionmentioning

confidence: 99%

Evaluating the Safety of Potential Probiotic Enterococcus durans KLDS6.0930 Using Whole Genome Sequencing and Oral Toxicity Study

Zhan

Evivie

et al. 2018

Front. Microbiol.

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Enterococcus durans KLDS6.0930 has previously been shown to have probiotic potential. However, being a potential clinical pathogen, it becomes necessary to evaluate its safety status for novel potential probiotic use. The purpose of this study is to systematically evaluate the safety of E. durans KLDS6.0930 based on its genomics, phenotypic characteristics and oral toxicity. The complete genome of E. durans KLDS6.0930 was sequenced and analyzed for safety-related genes. Antibiotic susceptibility and the production of harmful metabolites were tested. A 28-day repeated oral dose toxicity test was implemented in rats. In vitro, E. durans KLDS6.0930 was resistant to five antibiotics, with intrinsic resistances to four antibiotics and no identified genes for the last. E. durans KLDS6.0930 was not hemolytic and virulence factors were non-functional in its genome. E. durans KLDS6.0930 produced a small amount of tyramine and phenethylamine; genes encoding tyramine decarboxylase were identified. In addition, genotype and phenotype analyses showed that the strain did not have the ability to generate D-lactic acid, indole, or nitroreductase. In vivo, E. durans KLDS6.0930 did not induce adverse effects on the organs, hematological and serum biochemical parameters, or cecal bacterial populations in the oral toxicity test. These results indicate that E. durans KLDS6.0930 can be safely used as a potential probiotic for human consumption and animal feed.

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“…Those loci were specified by the European Food Safety Authority (EFSA) as targets for the safety evaluation of E. faecium strains intended as additives for animal feed (73). EFSA recommends examining for the presence of esp, hyl, and IS16 as well as sensitivity to ampicillin as exclusion criteria (73). E. faecium NRRL B-2354 lacks these genes and, as discussed above, is sensitive to ampicillin.…”

Section: Discussionmentioning

confidence: 99%

“…This includes esp, hyl, and IS16 commonly found in clinical isolates (56,72). Those loci were specified by the European Food Safety Authority (EFSA) as targets for the safety evaluation of E. faecium strains intended as additives for animal feed (73). EFSA recommends examining for the presence of esp, hyl, and IS16 as well as sensitivity to ampicillin as exclusion criteria (73).…”

Section: Discussionmentioning

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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Guidance on the safety assessment ofEnterococcus faeciumin animal nutrition

Cited by 70 publications

References 37 publications

Nonclinical and Clinical Enterococcus faecium Strains, but Not Enterococcus faecalis Strains, Have Distinct Structural and Functional Genomic Features

Nonclinical and Clinical Enterococcus faecium Strains, but Not Enterococcus faecalis Strains, Have Distinct Structural and Functional Genomic Features

Evaluating the Safety of Potential Probiotic Enterococcus durans KLDS6.0930 Using Whole Genome Sequencing and Oral Toxicity Study

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

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