Nonclinical and clinical Enterococcus faecium strains, but not Enterococcus faecalis strains, have distinct structural and functional genomic features.

Abstract:

: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 CL-enriched 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.

journal_name

Appl Environ Microbiol

authors

Kim EB,Marco ML

doi

10.1128/AEM.03108-13

subject

Has Abstract

pub_date

2014-01-01 00:00:00

pages

154-65

issue

1

eissn

0099-2240

issn

1098-5336

pii

AEM.03108-13

journal_volume

80

pub_type

杂志文章
  • Isolation of Vibrio cholerae serotype O1 from the eastern oyster, Crassostrea virginica.

    abstract::Two strains of Vibrio cholerae serotype O1 Inaba were isolated from eastern oysters, Crassostrea virginica, collected from estuarine waters in Florida during April 1980. The oyster meats and waters from which the oysters were collected had low fecal coliform counts, and the area had no prior evidence of sewage contami...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.41.2.559-560.1981

    authors: Hood MA,Ness GE,Rodrick GE

    更新日期:1981-02-01 00:00:00

  • Polyphenolic extract from maple syrup potentiates antibiotic susceptibility and reduces biofilm formation of pathogenic bacteria.

    abstract::Phenolic compounds are believed to be promising candidates as complementary therapeutics. Maple syrup, prepared by concentrating the sap from the North American maple tree, is a rich source of natural and process-derived phenolic compounds. In this work, we report the antimicrobial activity of a phenolic-rich maple sy...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.00239-15

    authors: Maisuria VB,Hosseinidoust Z,Tufenkji N

    更新日期:2015-06-01 00:00:00

  • Feral Swine in the United States Have Been Exposed to both Avian and Swine Influenza A Viruses.

    abstract::Influenza A viruses (IAVs) in swine can cause sporadic infections and pandemic outbreaks among humans, but how avian IAV emerges in swine is still unclear. Unlike domestic swine, feral swine are free ranging and have many opportunities for IAV exposure through contacts with various habitats and animals, including migr...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.01346-17

    authors: Martin BE,Sun H,Carrel M,Cunningham FL,Baroch JA,Hanson-Dorr KC,Young SG,Schmit B,Nolting JM,Yoon KJ,Lutman MW,Pedersen K,Lager K,Bowman AS,Slemons RD,Smith DR,DeLiberto T,Wan XF

    更新日期:2017-09-15 00:00:00

  • Urease-encoding genes in ammonia-oxidizing bacteria.

    abstract::Many but not all ammonia-oxidizing bacteria (AOB) produce urease (urea amidohydrolase, EC 3.5.1.5) and are capable of using urea for chemolithotrophic growth. We sequenced the urease operons from two AOB, the beta-proteobacterium Nitrosospira sp. strain NpAV and the gamma-proteobacterium Nitrosococcus oceani. In both ...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/aem.70.4.2342-2348.2004

    authors: Koper TE,El-Sheikh AF,Norton JM,Klotz MG

    更新日期:2004-04-01 00:00:00

  • Purification and characterization of a pyruvated-mannose-specific xanthan lyase from heat-stable, salt-tolerant bacteria.

    abstract::A xanthanase complex secreted by a consortium of heat-stable, salt-tolerant bacteria includes a lyase that specifically removes terminal pyruvated beta-d-mannose residues from the side chains of xanthan gum. The enzyme was purified to homogeneity from the culture broth following ion-exchange chromatography and gel per...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.57.9.2523-2528.1991

    authors: Ahlgren JA

    更新日期:1991-09-01 00:00:00

  • Mechanism for oxidation of high-molecular-weight substrates by a fungal versatile peroxidase, MnP2.

    abstract::Unlike general peroxidases, Pleurotus ostreatus MnP2 was reported to have a unique property of direct oxidization of high-molecular-weight compounds, such as Poly R-478 and RNase A. To elucidate the mechanism for oxidation of polymeric substrates by MnP2, a series of mutant enzymes were produced by using a homologous ...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.02080-07

    authors: Tsukihara T,Honda Y,Sakai R,Watanabe T,Watanabe T

    更新日期:2008-05-01 00:00:00

  • Effects of cultivation conditions on folate production by lactic acid bacteria.

    abstract::A variety of lactic acid bacteria were screened for their ability to produce folate intracellularly and/or extracellularly. Lactococcus lactis, Streptococcus thermophilus, and Leuconostoc spp. all produced folate, while most Lactobacillus spp., with the exception of Lactobacillus plantarum, were not able to produce fo...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/aem.69.8.4542-4548.2003

    authors: Sybesma W,Starrenburg M,Tijsseling L,Hoefnagel MH,Hugenholtz J

    更新日期:2003-08-01 00:00:00

  • Inactivation of murine norovirus on a range of copper alloy surfaces is accompanied by loss of capsid integrity.

    abstract::Norovirus is one of the most common causes of acute viral gastroenteritis. The virus is spread via the fecal-oral route, most commonly from infected food and water, but several outbreaks have originated from contamination of surfaces with infectious virus. In this study, a close surrogate of human norovirus causing ga...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.03280-14

    authors: Warnes SL,Summersgill EN,Keevil CW

    更新日期:2015-02-01 00:00:00

  • Enhanced Alcaligenes faecalis Denitrification Rate with Electrodes as the Electron Donor.

    abstract::The utilization by Alcaligenes faecalis of electrodes as the electron donor for denitrification was investigated in this study. The denitrification rate of A. faecalis with a poised potential was greatly enhanced compared with that of the controls without poised potentials. For nitrate reduction, although A. faecalis ...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.00683-15

    authors: Wang X,Yu P,Zeng C,Ding H,Li Y,Wang C,Lu A

    更新日期:2015-08-15 00:00:00

  • Vanadium(V) reduction by Shewanella oneidensis MR-1 requires menaquinone and cytochromes from the cytoplasmic and outer membranes.

    abstract::The metal-reducing bacterium Shewanella oneidensis MR-1 displays remarkable anaerobic respiratory plasticity, which is reflected in the extensive number of electron transport components encoded in its genome. In these studies, several cell components required for the reduction of vanadium(V) were determined. V(V) redu...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/aem.70.3.1405-1412.2004

    authors: Myers JM,Antholine WE,Myers CR

    更新日期:2004-03-01 00:00:00

  • Formate-dependent growth and homoacetogenic fermentation by a bacterium from human feces: description of Bryantella formatexigens gen. nov., sp. nov.

    abstract::Formate stimulates growth of a new bacterium from human feces. With high formate, it ferments glucose to acetate via the Wood-Ljungdahl pathway. The original isolate fermented vegetable cellulose and carboxymethylcellulose, but it lost this ability after storage at -76 degrees C. 16S rRNA gene sequencing identifies it...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/aem.69.10.6321-6326.2003

    authors: Wolin MJ,Miller TL,Collins MD,Lawson PA

    更新日期:2003-10-01 00:00:00

  • Detection of T-2 toxin in Fusarium sporotrichioides-infected corn by enzyme-linked immunosorbent assay.

    abstract::A competitive enzyme-linked immunosorbent assay was used to screen for T-2 toxin in Fusarium sporotrichioides -infected corn. The assay detected T-2 toxin in diluted methanol extracts of corn samples at concentrations of 0.05 ng/ml. In infected corn samples, enzyme-linked immunosorbent assay and gas-liquid chromatogra...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.47.5.1161-1163.1984

    authors: Gendloff EH,Pestka JJ,Swanson SP,Hart LP

    更新日期:1984-05-01 00:00:00

  • Identification of Bifidobacterium strains by rRNA gene restriction patterns.

    abstract::Total DNA from 21 collection or industrial Bifidobacterium strains was cleaved with various restriction endonucleases. Following electrophoresis, the fragments were subjected to Southern blot hybridization with a heterologous [alpha-32P]dCTP-labeled rDNA (genes coding for rRNA) 23S gene probe. The ribosomal patterns a...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.60.5.1451-1458.1994

    authors: Mangin I,Bourget N,Bouhnik Y,Bisetti N,Simonet JM,Decaris B

    更新日期:1994-05-01 00:00:00

  • Isolation of Aeromonas spp. from water by using anaerobic incubation.

    abstract::A membrane filtration method incorporating a combination of anaerobic and aerobic incubation has been developed for the enumeration of Aeromonas spp. in drinking water. The use of anaerobic incubation improved the detection of Aeromonas spp. by reducing the growth of nonaeromonads. The confirmation rate of presumptive...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.55.9.2138-2140.1989

    authors: Cunliffe DA,Adcock P

    更新日期:1989-09-01 00:00:00

  • Role of chemotaxis in the ecology of denitrifiers.

    abstract::A modification of the Adler capillary assay was used to evaluate the chemotactic responses of several denitrifiers to nitrate and nitrite. Strong positive chemotaxis was observed to NO(3) and NO(2) by soil isolates of Pseudomonas aeruginosa, Pseudomonas fluorescens, and Pseudomonas stutzeri, with the peak response occ...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.49.1.109-114.1985

    authors: Kennedy MJ,Lawless JG

    更新日期:1985-01-01 00:00:00

  • Mosquito larvicidal activity of transgenic Anabaena strain PCC 7120 expressing combinations of genes from Bacillus thuringiensis subsp. israelensis.

    abstract::Various combinations of the genes cryIVA (cry4A), cryIVD (cry11A), and p20 from Bacillus thuringiensis subsp. israelensis were introduced into the nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120 by means of Escherichia coli-Anabaena shuttle vector pRL488p and were expressed under control of two tandem stro...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.63.12.4971-4974.1997

    authors: Xiaoqiang W,Vennison SJ,Huirong L,Ben-Dov E,Zaritsky A,Boussiba S

    更新日期:1997-12-01 00:00:00

  • Use of antibody responses against locus of enterocyte effacement (LEE)-encoded antigens to monitor enterohemorrhagic Escherichia coli infections on cattle farms.

    abstract::Enterohemorrhagic Escherichia coli (EHEC) is a significant zoonotic pathogen causing severe disease associated with watery and bloody diarrhea, hemorrhagic colitis, and the hemolytic-uremic syndrome (HUS) in humans. Infections are frequently associated with contact with EHEC-contaminated ruminant feces. Both natural a...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.01029-13

    authors: Joris MA,Vanrompay D,Verstraete K,De Reu K,De Zutter L,Cox E

    更新日期:2013-06-01 00:00:00

  • Comparison of genotypes and serotypes of Campylobacter jejuni isolated from Danish wild mammals and birds and from broiler flocks and humans.

    abstract::The incidence of human infection with Campylobacter jejuni is increasing in most developed countries and the reason for this is largely unknown. Although poultry meat is considered to be a major source, it is evident that other reservoirs exist, possibly common to humans and poultry. Environmental sources are believed...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.67.7.3115-3121.2001

    authors: Petersen L,Nielsen EM,Engberg J,On SL,Dietz HH

    更新日期:2001-07-01 00:00:00

  • Interactions between Pseudomonas aeruginosa and iodophor germicides in milking parlor udder wash water systems.

    abstract::In a field study of 29 dairy farms, Pseudomonas aeruginosa was isolated more frequently (P = 0.05) from milking parlor udder wash water systems containing iodophor germicides than from those with no germicide. Most available iodine (AI2) concentrations were below the recommended level of 25 ppm (25 microgram/ml). Rubb...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.57.2.568-572.1991

    authors: Hicks CR,Eberhart RJ,Erskine RJ,Spencer SB

    更新日期:1991-02-01 00:00:00

  • Colonization of the botanical environment by Klebsiella isolates of pathogenic origin.

    abstract::Growth, survival, and pathogenicity of Klebsiella growing in and on environmental foci were examined. Total coliforms present in raw wastes from pulp mills were in excess of 10(5)/ml, and 60 to 80% were Klebsiella. Fecal coliform counts ranged from 10(1) to 10(5)/ml. Klebsiella isolates from industrial effluents and a...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.34.5.557-563.1977

    authors: Knittel MD,Seidler RJ,Eby C,Cabe LM

    更新日期:1977-11-01 00:00:00

  • Intercity spread of echovirus 6 in Shandong Province, China: application of environmental surveillance in tracing circulating enteroviruses.

    abstract::Environmental surveillance is an effective approach in investigating circulating enteroviruses and had been conducted in the cities of Jinan and Linyi since February 2008 and April 2010, respectively. This study analyzed 46 sewage samples collected in the two cities in 2011 and found that echovirus 6 (E6) was the pred...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.01861-12

    authors: Tao Z,Song Y,Wang H,Zhang Y,Yoshida H,Ji S,Xu A,Song L,Liu Y,Cui N,Ji F,Li Y,Chen P,Xu W

    更新日期:2012-10-01 00:00:00

  • Competition Among Rhizobium spp. for Nodulation of Leucaena leucocephala in Two Tropical Soils.

    abstract::The successful nodulation of legumes by a Rhizobium strain is determined by the competitive ability of that strain against the mixture of other native and inoculant rhizobia. Competition among six Leucaena rhizobial strains in single and multistrain inoculants were studied. Field inoculation trials were conducted in a...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.48.1.5-9.1984

    authors: Moawad H,Bohlool BB

    更新日期:1984-07-01 00:00:00

  • Conditions for growing Mycoplasma canadense and Mycoplasma verecundum in a serum-free medium.

    abstract::Mycoplasma canadense and Mycoplasma verecundum were cultured in a serum-free medium containing bovine serum albumin, cholesterol, oleic acid, and palmitic acid in order to avoid the addition of horse serum. Growth was detected by measurement of A640 and by colony formation. The level of growth attained in this medium ...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.56.7.2259-2261.1990

    authors: Muñoz G,Sotomayor P

    更新日期:1990-07-01 00:00:00

  • Evaluation of MK filters for recovery of enteroviruses from tap water.

    abstract::The MK filter is an electropositively charged filter that can be used to concentrate enteroviruses from large volumes (400 to 1,000 liters) of water. This filter is less expensive than the commonly used 1MDS electropositive filter. In this study, we compared the recovery of poliovirus 1 (PV1) and that of coxsackieviru...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.60.6.1974-1977.1994

    authors: Ma JF,Naranjo J,Gerba CP

    更新日期:1994-06-01 00:00:00

  • Metabolic behavior of Lactococcus lactis MG1363 in microaerobic continuous cultivation at a low dilution rate.

    abstract::Minute amounts of oxygen were supplied to a continuous cultivation of Lactococcus lactis subsp. cremoris MG1363 grown on a defined glucose-limited medium at a dilution rate of 0.1 h(-1). More than 80% of the carbon supplied with glucose ended up in fermentation products other than lactate. Addition of even minute amou...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.67.6.2677-2682.2001

    authors: Jensen NB,Melchiorsen CR,Jokumsen KV,Villadsen J

    更新日期:2001-06-01 00:00:00

  • Effect of reactor turbulence on the binding-protein-mediated aspartate transport system in thin wastewater biofilms.

    abstract::This research documents an effect of reactor turbulence on the ability of gram-negative wastewater biofilm bacteria to actively transport l-aspartate via a binding-protein-mediated transport system. Biofilms which were not preadapted to turbulence and which possessed two separate and distinct aspartate transport syste...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.50.1.120-124.1985

    authors: Eighmy TT,Bishop PL

    更新日期:1985-07-01 00:00:00

  • Assessment of the environmental fate of the biological control agent of fire blight, Pseudomonas fluorescens EPS62e, on apple by culture and real-time PCR methods.

    abstract::The colonization of apple blossoms and leaves by Pseudomonas fluorescens EPS62e was monitored in greenhouse and field trials using cultivable cell counting and real-time PCR. The real-time PCR provided a specific quantitative method for the detection of strain EPS62e. The detection level was around 10(2) cells g (fres...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.72.4.2421-2427.2006

    authors: Pujol M,Badosa E,Manceau C,Montesinos E

    更新日期:2006-04-01 00:00:00

  • Multiplex reverse transcription-PCR for simultaneous detection of beet necrotic yellow vein virus, Beet soilborne virus, and Beet virus Q and their vector Polymyxa betae KESKIN on sugar beet.

    abstract::Three soilborne viruses transmitted by Polymyxa betae KESKIN in sugar beet have been described: Beet necrotic yellow vein virus (BNYVV), the agent of rhizomania, Beet soilborne virus (BSBV), and Beet virus Q (BVQ). A multiplex reverse transcription-PCR technique was developed to simultaneously detect BNYVV, BSBV, and ...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/aem.69.4.2356-2360.2003

    authors: Meunier A,Schmit JF,Stas A,Kutluk N,Bragard C

    更新日期:2003-04-01 00:00:00

  • Use of nuclear DNA restriction fragment length polymorphisms to analyze the diversity of the Aspergillus flavus group: A. flavus, A. parasiticus, and A. nomius.

    abstract::Recombinant DNA clones carrying high-copy or low-copy sequences from Aspergillus nidulans and Neurospora crassa were used to identify restriction fragment length polymorphisms (RFLPs) diagnostic for members of the A. flavus group: A. flavus, A. parasiticus, and A. nomius. These fungi were resolved into three distinct ...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.56.8.2453-2461.1990

    authors: Moody SF,Tyler BM

    更新日期:1990-08-01 00:00:00

  • Physiological adaptations involved in alkane assimilation at a low temperature by Rhodococcus sp. strain Q15.

    abstract::We examined physiological adaptations which allow the psychrotroph Rhodococcus sp. strain Q15 to assimilate alkanes at a low temperature (alkanes are contaminants which are generally insoluble and/or solid at low temperatures). During growth at 5 degrees C on hexadecane or diesel fuel, strain Q15 produced a cell surfa...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.65.7.2961-2968.1999

    authors: Whyte LG,Slagman SJ,Pietrantonio F,Bourbonnière L,Koval SF,Lawrence JR,Inniss WE,Greer CW

    更新日期:1999-07-01 00:00:00