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Items: 1 to 50 of 76

1.

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients.

Ravi A, Halstead FD, Bamford A, Casey A, Thomson NM, van Schaik W, Snelson C, Goulden R, Foster-Nyarko E, Savva GM, Whitehouse T, Pallen MJ, Oppenheim BA.

Microb Genom. 2019 Sep;5(9). doi: 10.1099/mgen.0.000293. Epub 2019 Sep 11.

2.

Gut Microbiota and Colonization Resistance against Bacterial Enteric Infection.

Ducarmon QR, Zwittink RD, Hornung BVH, van Schaik W, Young VB, Kuijper EJ.

Microbiol Mol Biol Rev. 2019 Jun 5;83(3). pii: e00007-19. doi: 10.1128/MMBR.00007-19. Print 2019 Aug 21. Review.

PMID:
31167904
3.

Enterococcus faecium genome dynamics during long-term asymptomatic patient gut colonization.

Bayjanov JR, Baan J, Rogers MRC, Troelstra A, Willems RJL, van Schaik W.

Microb Genom. 2019 Jul;5(7). doi: 10.1099/mgen.0.000277. Epub 2019 Jun 5.

4.

Do we really understand how faecal microbiota transplantation works?

Quraishi MN, McNally A, van Schaik W.

EBioMedicine. 2019 Apr;42:39. doi: 10.1016/j.ebiom.2019.03.024. Epub 2019 Mar 16. No abstract available.

5.

Prediction of the intestinal resistome by a three-dimensional structure-based method.

Ruppé E, Ghozlane A, Tap J, Pons N, Alvarez AS, Maziers N, Cuesta T, Hernando-Amado S, Clares I, Martínez JL, Coque TM, Baquero F, Lanza VF, Máiz L, Goulenok T, de Lastours V, Amor N, Fantin B, Wieder I, Andremont A, van Schaik W, Rogers M, Zhang X, Willems RJL, de Brevern AG, Batto JM, Blottière HM, Léonard P, Léjard V, Letur A, Levenez F, Weiszer K, Haimet F, Doré J, Kennedy SP, Ehrlich SD.

Nat Microbiol. 2019 Jan;4(1):112-123. doi: 10.1038/s41564-018-0292-6. Epub 2018 Nov 26.

PMID:
30478291
6.

Limited influence of hospital wastewater on the microbiome and resistome of wastewater in a community sewerage system.

Buelow E, Bayjanov JR, Majoor E, Willems RJ, Bonten MJ, Schmitt H, van Schaik W.

FEMS Microbiol Ecol. 2018 Jul 1;94(7). doi: 10.1093/femsec/fiy087.

PMID:
29767712
7.

In-depth resistome analysis by targeted metagenomics.

Lanza VF, Baquero F, Martínez JL, Ramos-Ruíz R, González-Zorn B, Andremont A, Sánchez-Valenzuela A, Ehrlich SD, Kennedy S, Ruppé E, van Schaik W, Willems RJ, de la Cruz F, Coque TM.

Microbiome. 2018 Jan 15;6(1):11. doi: 10.1186/s40168-017-0387-y.

8.

On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data.

Arredondo-Alonso S, Willems RJ, van Schaik W, Schürch AC.

Microb Genom. 2017 Aug 18;3(10):e000128. doi: 10.1099/mgen.0.000128. eCollection 2017 Oct.

9.

RNA-seq and Tn-seq reveal fitness determinants of vancomycin-resistant Enterococcus faecium during growth in human serum.

Zhang X, de Maat V, Guzmán Prieto AM, Prajsnar TK, Bayjanov JR, de Been M, Rogers MRC, Bonten MJM, Mesnage S, Willems RJL, van Schaik W.

BMC Genomics. 2017 Nov 21;18(1):893. doi: 10.1186/s12864-017-4299-9.

10.

Correction for Quainoo et al., "Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis".

Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL.

Clin Microbiol Rev. 2017 Nov 1;31(1). pii: e00082-17. doi: 10.1128/CMR.00082-17. Print 2018 Jan. No abstract available.

11.

Characterization of Enterococcus Isolates Colonizing the Intestinal Tract of Intensive Care Unit Patients Receiving Selective Digestive Decontamination.

Bello Gonzalez TDJ, Pham P, Top J, Willems RJL, van Schaik W, van Passel MWJ, Smidt H.

Front Microbiol. 2017 Aug 28;8:1596. doi: 10.3389/fmicb.2017.01596. eCollection 2017.

12.

Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis.

Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL.

Clin Microbiol Rev. 2017 Oct;30(4):1015-1063. doi: 10.1128/CMR.00016-17. Review. Erratum in: Clin Microbiol Rev. 2017 Nov 1;31(1):.

13.

Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects.

Buelow E, Bello González TDJ, Fuentes S, de Steenhuijsen Piters WAA, Lahti L, Bayjanov JR, Majoor EAM, Braat JC, van Mourik MSM, Oostdijk EAN, Willems RJL, Bonten MJM, van Passel MWJ, Smidt H, van Schaik W.

Microbiome. 2017 Aug 14;5(1):88. doi: 10.1186/s40168-017-0309-z.

14.

The Two-Component System ChtRS Contributes to Chlorhexidine Tolerance in Enterococcus faecium.

Guzmán Prieto AM, Wijngaarden J, Braat JC, Rogers MRC, Majoor E, Brouwer EC, Zhang X, Bayjanov JR, Bonten MJM, Willems RJL, van Schaik W.

Antimicrob Agents Chemother. 2017 Apr 24;61(5). pii: e02122-16. doi: 10.1128/AAC.02122-16. Print 2017 May.

15.

Challenges and opportunities for whole-genome sequencing-based surveillance of antibiotic resistance.

Schürch AC, van Schaik W.

Ann N Y Acad Sci. 2017 Jan;1388(1):108-120. doi: 10.1111/nyas.13310. Review.

PMID:
28134443
16.

Rapid resistome mapping using nanopore sequencing.

van der Helm E, Imamovic L, Hashim Ellabaan MM, van Schaik W, Koza A, Sommer MOA.

Nucleic Acids Res. 2017 May 5;45(8):e61. doi: 10.1093/nar/gkw1328.

17.

Genomic Characterization of Colistin Heteroresistance in Klebsiella pneumoniae during a Nosocomial Outbreak.

Halaby T, Kucukkose E, Janssen AB, Rogers MR, Doorduijn DJ, van der Zanden AG, Al Naiemi N, Vandenbroucke-Grauls CM, van Schaik W.

Antimicrob Agents Chemother. 2016 Oct 21;60(11):6837-6843. doi: 10.1128/AAC.01344-16. Print 2016 Nov.

18.

Complement resistance mechanisms of Klebsiella pneumoniae.

Doorduijn DJ, Rooijakkers SH, van Schaik W, Bardoel BW.

Immunobiology. 2016 Oct;221(10):1102-9. doi: 10.1016/j.imbio.2016.06.014. Epub 2016 Jun 16. Review.

19.

Global Emergence and Dissemination of Enterococci as Nosocomial Pathogens: Attack of the Clones?

Guzman Prieto AM, van Schaik W, Rogers MR, Coque TM, Baquero F, Corander J, Willems RJ.

Front Microbiol. 2016 May 26;7:788. doi: 10.3389/fmicb.2016.00788. eCollection 2016. Review.

20.

Genome-wide Screening Identifies Phosphotransferase System Permease BepA to Be Involved in Enterococcus faecium Endocarditis and Biofilm Formation.

Paganelli FL, Huebner J, Singh KV, Zhang X, van Schaik W, Wobser D, Braat JC, Murray BE, Bonten MJ, Willems RJ, Leavis HL.

J Infect Dis. 2016 Jul 15;214(2):189-95. doi: 10.1093/infdis/jiw108. Epub 2016 Mar 16.

PMID:
26984142
21.

The impact of host metapopulation structure on the population genetics of colonizing bacteria.

Numminen E, Gutmann M, Shubin M, Marttinen P, Méric G, van Schaik W, Coque TM, Baquero F, Willems RJ, Sheppard SK, Feil EJ, Hanage WP, Corander J.

J Theor Biol. 2016 May 7;396:53-62. doi: 10.1016/j.jtbi.2016.02.019. Epub 2016 Feb 23.

PMID:
26916623
22.

The N-terminal domain of the thermo-regulated surface protein PrpA of Enterococcus faecium binds to fibrinogen, fibronectin and platelets.

Guzmán Prieto AM, Urbanus RT, Zhang X, Bierschenk D, Koekman CA, van Luit-Asbroek M, Ouwerkerk JP, Pape M, Paganelli FL, Wobser D, Huebner J, Hendrickx AP, Bonten MJ, Willems RJ, van Schaik W.

Sci Rep. 2015 Dec 17;5:18255. doi: 10.1038/srep18255.

23.

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

de Been M, Pinholt M, Top J, Bletz S, Mellmann A, van Schaik W, Brouwer E, Rogers M, Kraat Y, Bonten M, Corander J, Westh H, Harmsen D, Willems RJ.

J Clin Microbiol. 2015 Dec;53(12):3788-97.

24.

Erratum to: Investigating the mobilome in clinically important lineages of Enterococcus faecium and Enterococcus faecalis.

Mikalsen T, Pedersen T, Willems R, Coque TM, Werner G, Sadowy E, van Schaik W, Jensen LB, Francia MV, Sundsfjord A, Hegstad K.

BMC Genomics. 2015 Sep 15;16(1):689. doi: 10.1186/s12864-015-1722-y. No abstract available.

25.

Deletions in a ribosomal protein-coding gene are associated with tigecycline resistance in Enterococcus faecium.

Niebel M, Quick J, Prieto AM, Hill RL, Pike R, Huber D, David M, Hornsey M, Wareham D, Oppenheim B, Woodford N, van Schaik W, Loman N.

Int J Antimicrob Agents. 2015 Nov;46(5):572-5. doi: 10.1016/j.ijantimicag.2015.07.009. Epub 2015 Aug 20.

PMID:
26364847
26.

Loss of Antibiotic Tolerance in Sod-Deficient Mutants Is Dependent on the Energy Source and Arginine Catabolism in Enterococci.

Ladjouzi R, Bizzini A, van Schaik W, Zhang X, Rincé A, Benachour A, Hartke A.

J Bacteriol. 2015 Oct;197(20):3283-93. doi: 10.1128/JB.00389-15. Epub 2015 Aug 10.

27.

Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions.

Versluis D, D'Andrea MM, Ramiro Garcia J, Leimena MM, Hugenholtz F, Zhang J, Öztürk B, Nylund L, Sipkema D, van Schaik W, de Vos WM, Kleerebezem M, Smidt H, van Passel MW.

Sci Rep. 2015 Jul 8;5:11981. doi: 10.1038/srep11981.

28.

The human gut resistome.

van Schaik W.

Philos Trans R Soc Lond B Biol Sci. 2015 Jun 5;370(1670):20140087. doi: 10.1098/rstb.2014.0087. Review.

29.

Investigating the mobilome in clinically important lineages of Enterococcus faecium and Enterococcus faecalis.

Mikalsen T, Pedersen T, Willems R, Coque TM, Werner G, Sadowy E, van Schaik W, Jensen LB, Sundsfjord A, Hegstad K.

BMC Genomics. 2015 Apr 10;16:282. doi: 10.1186/s12864-015-1407-6. Erratum in: BMC Genomics. 2015;16(1):689.

30.

Dissemination of cephalosporin resistance genes between Escherichia coli strains from farm animals and humans by specific plasmid lineages.

de Been M, Lanza VF, de Toro M, Scharringa J, Dohmen W, Du Y, Hu J, Lei Y, Li N, Tooming-Klunderud A, Heederik DJ, Fluit AC, Bonten MJ, Willems RJ, de la Cruz F, van Schaik W.

PLoS Genet. 2014 Dec 18;10(12):e1004776. doi: 10.1371/journal.pgen.1004776. eCollection 2014 Dec.

31.

Effects of selective digestive decontamination (SDD) on the gut resistome.

Buelow E, Gonzalez TB, Versluis D, Oostdijk EA, Ogilvie LA, van Mourik MS, Oosterink E, van Passel MW, Smidt H, D'Andrea MM, de Been M, Jones BV, Willems RJ, Bonten MJ, van Schaik W.

J Antimicrob Chemother. 2014 Aug;69(8):2215-23. doi: 10.1093/jac/dku092. Epub 2014 Apr 7.

PMID:
24710024
32.

Enterococcal Genomics.

Palmer KL, van Schaik W, Willems RJL, Gilmore MS.

In: Gilmore MS, Clewell DB, Ike Y, Shankar N, editors. Enterococci: From Commensals to Leading Causes of Drug Resistant Infection [Internet]. Boston: Massachusetts Eye and Ear Infirmary; 2014-.
2014 Feb 8.

33.

Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains.

Lebreton F, van Schaik W, McGuire AM, Godfrey P, Griggs A, Mazumdar V, Corander J, Cheng L, Saif S, Young S, Zeng Q, Wortman J, Birren B, Willems RJ, Earl AM, Gilmore MS.

MBio. 2013 Aug 20;4(4). pii: e00534-13. doi: 10.1128/mBio.00534-13.

34.

A LacI-family regulator activates maltodextrin metabolism of Enterococcus faecium.

Zhang X, Rogers M, Bierschenk D, Bonten MJ, Willems RJ, van Schaik W.

PLoS One. 2013 Aug 7;8(8):e72285. doi: 10.1371/journal.pone.0072285. eCollection 2013.

35.

The cell wall architecture of Enterococcus faecium: from resistance to pathogenesis.

Hendrickx AP, van Schaik W, Willems RJ.

Future Microbiol. 2013 Aug;8(8):993-1010. doi: 10.2217/fmb.13.66. Review.

PMID:
23902146
36.

Recent recombination events in the core genome are associated with adaptive evolution in Enterococcus faecium.

de Been M, van Schaik W, Cheng L, Corander J, Willems RJ.

Genome Biol Evol. 2013;5(8):1524-35. doi: 10.1093/gbe/evt111.

37.

The Enterococcus faecium enterococcal biofilm regulator, EbrB, regulates the esp operon and is implicated in biofilm formation and intestinal colonization.

Top J, Paganelli FL, Zhang X, van Schaik W, Leavis HL, van Luit-Asbroek M, van der Poll T, Leendertse M, Bonten MJ, Willems RJ.

PLoS One. 2013 May 31;8(5):e65224. doi: 10.1371/journal.pone.0065224. Print 2013.

38.

Functional genomic analysis of bile salt resistance in Enterococcus faecium.

Zhang X, Bierschenk D, Top J, Anastasiou I, Bonten MJ, Willems RJ, van Schaik W.

BMC Genomics. 2013 May 3;14:299. doi: 10.1186/1471-2164-14-299.

39.

Antibiotic resistant enterococci-tales of a drug resistance gene trafficker.

Werner G, Coque TM, Franz CM, Grohmann E, Hegstad K, Jensen L, van Schaik W, Weaver K.

Int J Med Microbiol. 2013 Aug;303(6-7):360-79. doi: 10.1016/j.ijmm.2013.03.001. Epub 2013 Mar 8. Review.

PMID:
23602510
40.

Identification of a genetic determinant in clinical Enterococcus faecium strains that contributes to intestinal colonization during antibiotic treatment.

Zhang X, Top J, de Been M, Bierschenk D, Rogers M, Leendertse M, Bonten MJ, van der Poll T, Willems RJ, van Schaik W.

J Infect Dis. 2013 Jun 1;207(11):1780-6. doi: 10.1093/infdis/jit076. Epub 2013 Feb 27.

PMID:
23447698
41.

Genomic transition of enterococci from gut commensals to leading causes of multidrug-resistant hospital infection in the antibiotic era.

Gilmore MS, Lebreton F, van Schaik W.

Curr Opin Microbiol. 2013 Feb;16(1):10-6. doi: 10.1016/j.mib.2013.01.006. Epub 2013 Feb 5. Review.

42.

Identification of CodY targets in Bacillus anthracis by genome-wide in vitro binding analysis.

Château A, van Schaik W, Joseph P, Handke LD, McBride SM, Smeets FM, Sonenshein AL, Fouet A.

J Bacteriol. 2013 Mar;195(6):1204-13. doi: 10.1128/JB.02041-12. Epub 2013 Jan 4.

43.

AsrR is an oxidative stress sensing regulator modulating Enterococcus faecium opportunistic traits, antimicrobial resistance, and pathogenicity.

Lebreton F, van Schaik W, Sanguinetti M, Posteraro B, Torelli R, Le Bras F, Verneuil N, Zhang X, Giard JC, Dhalluin A, Willems RJ, Leclercq R, Cattoir V.

PLoS Pathog. 2012;8(8):e1002834. doi: 10.1371/journal.ppat.1002834. Epub 2012 Aug 2.

44.

Restricted gene flow among hospital subpopulations of Enterococcus faecium.

Willems RJ, Top J, van Schaik W, Leavis H, Bonten M, Sirén J, Hanage WP, Corander J.

MBio. 2012 Jul 17;3(4):e00151-12. doi: 10.1128/mBio.00151-12. Print 2012.

45.

Genome-wide identification of ampicillin resistance determinants in Enterococcus faecium.

Zhang X, Paganelli FL, Bierschenk D, Kuipers A, Bonten MJ, Willems RJ, van Schaik W.

PLoS Genet. 2012 Jun;8(6):e1002804. doi: 10.1371/journal.pgen.1002804. Epub 2012 Jun 28.

46.

Hospital and community ampicillin-resistant Enterococcus faecium are evolutionarily closely linked but have diversified through niche adaptation.

de Regt MJ, van Schaik W, van Luit-Asbroek M, Dekker HA, van Duijkeren E, Koning CJ, Bonten MJ, Willems RJ.

PLoS One. 2012;7(2):e30319. doi: 10.1371/journal.pone.0030319. Epub 2012 Feb 17.

47.

CodY regulation is required for full virulence and heme iron acquisition in Bacillus anthracis.

Château A, van Schaik W, Six A, Aucher W, Fouet A.

FASEB J. 2011 Dec;25(12):4445-56. doi: 10.1096/fj.11-188912. Epub 2011 Sep 12.

PMID:
21911592
48.

IS element IS16 as a molecular screening tool to identify hospital-associated strains of Enterococcus faecium.

Werner G, Fleige C, Geringer U, van Schaik W, Klare I, Witte W.

BMC Infect Dis. 2011 Mar 31;11:80. doi: 10.1186/1471-2334-11-80.

49.

The recombinase IntA is required for excision of esp-containing ICEEfm1 in Enterococcus faecium.

Top J, Sinnige JC, Majoor EA, Bonten MJ, Willems RJ, van Schaik W.

J Bacteriol. 2011 Feb;193(4):1003-6. doi: 10.1128/JB.00952-10. Epub 2010 Dec 10.

50.

A multiresistance megaplasmid pLG1 bearing a hylEfm genomic island in hospital Enterococcus faecium isolates.

Laverde Gomez JA, van Schaik W, Freitas AR, Coque TM, Weaver KE, Francia MV, Witte W, Werner G.

Int J Med Microbiol. 2011 Feb;301(2):165-75. doi: 10.1016/j.ijmm.2010.08.015. Epub 2010 Oct 15.

PMID:
20951641

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