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Items: 1 to 50 of 53

1.

Ultrafast search of all deposited bacterial and viral genomic data.

Bradley P, den Bakker HC, Rocha EPC, McVean G, Iqbal Z.

Nat Biotechnol. 2019 Feb;37(2):152-159. doi: 10.1038/s41587-018-0010-1. Epub 2019 Feb 4.

PMID:
30718882
2.

Complete Genome Sequences of Four Salmonella enterica Strains (Including Those of Serotypes Montevideo, Mbandaka, and Lubbock) Isolated from Peripheral Lymph Nodes of Healthy Cattle.

Bugarel M, Cook PW, den Bakker HC, Harhay D, Nightingale KK, Loneragan GH.

Microbiol Resour Announc. 2019 Jan 10;8(2). pii: e01450-18. doi: 10.1128/MRA.01450-18. eCollection 2019 Jan.

3.

Pre-harvest internalization and surface survival of Salmonella and Escherichia coli O157:H7 sprayed onto different lettuce cultivars under field and growth chamber conditions.

Erickson MC, Liao JY, Payton AS, Cook PW, Den Bakker HC, Bautista J, Pérez JCD.

Int J Food Microbiol. 2019 Feb 16;291:197-204. doi: 10.1016/j.ijfoodmicro.2018.12.001. Epub 2018 Dec 4.

PMID:
30551016
4.

Genomic Diversity of Listeria monocytogenes Isolated from Clinical and Non-Clinical Samples in Chile.

Toledo V, den Bakker HC, Hormazábal JC, González-Rocha G, Bello-Toledo H, Toro M, Moreno-Switt AI.

Genes (Basel). 2018 Aug 2;9(8). pii: E396. doi: 10.3390/genes9080396.

5.

Molecular detection and quantification of viable probiotic strains in animal feedstuffs using the commercial direct fed microbial Lactobacillus animalis NP51 as a model.

Ayala DI, Chen JC, Bugarel M, Loneragan GH, den Bakker HC, Kottapalli KR, Brashears MM, Nightingale KK.

J Microbiol Methods. 2018 Jun;149:36-43. doi: 10.1016/j.mimet.2018.04.012. Epub 2018 Apr 17.

PMID:
29673790
6.

Molecular ecology of Listeria spp., Salmonella, Escherichia coli O157:H7 and non-O157 Shiga toxin-producing E. coli in pristine natural environments in Northern Colorado.

Ahlstrom CA, Manuel CS, Den Bakker HC, Wiedmann M, Nightingale KK.

J Appl Microbiol. 2018 Feb;124(2):511-521. doi: 10.1111/jam.13657.

PMID:
29215770
7.

Comparative Genomics Reveals the Diversity of Restriction-Modification Systems and DNA Methylation Sites in Listeria monocytogenes.

Chen P, den Bakker HC, Korlach J, Kong N, Storey DB, Paxinos EE, Ashby M, Clark T, Luong K, Wiedmann M, Weimer BC.

Appl Environ Microbiol. 2017 Jan 17;83(3). pii: e02091-16. doi: 10.1128/AEM.02091-16. Print 2017 Feb 1.

8.
9.

Carbapenem-Resistant Bacteria Recovered from Faeces of Dairy Cattle in the High Plains Region of the USA.

Webb HE, Bugarel M, den Bakker HC, Nightingale KK, Granier SA, Scott HM, Loneragan GH.

PLoS One. 2016 Jan 29;11(1):e0147363. doi: 10.1371/journal.pone.0147363. eCollection 2016.

10.

Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens.

Deng X, den Bakker HC, Hendriksen RS.

Annu Rev Food Sci Technol. 2016;7:353-74. doi: 10.1146/annurev-food-041715-033259. Epub 2016 Jan 11. Review.

PMID:
26772415
11.

Dissemination of the mcr-1 colistin resistance gene.

Webb HE, Granier SA, Marault M, Millemann Y, den Bakker HC, Nightingale KK, Bugarel M, Ison SA, Scott HM, Loneragan GH.

Lancet Infect Dis. 2016 Feb;16(2):144-5. doi: 10.1016/S1473-3099(15)00538-1. Epub 2015 Dec 18. No abstract available.

PMID:
26711363
12.

Determination of Evolutionary Relationships of Outbreak-Associated Listeria monocytogenes Strains of Serotypes 1/2a and 1/2b by Whole-Genome Sequencing.

Bergholz TM, den Bakker HC, Katz LS, Silk BJ, Jackson KA, Kucerova Z, Joseph LA, Turnsek M, Gladney LM, Halpin JL, Xavier K, Gossack J, Ward TJ, Frace M, Tarr CL.

Appl Environ Microbiol. 2015 Nov 20;82(3):928-38. doi: 10.1128/AEM.02440-15. Print 2016 Feb 1.

13.

Targeted Amplicon Sequencing for Single-Nucleotide-Polymorphism Genotyping of Attaching and Effacing Escherichia coli O26:H11 Cattle Strains via a High-Throughput Library Preparation Technique.

Ison SA, Delannoy S, Bugarel M, Nagaraja TG, Renter DG, den Bakker HC, Nightingale KK, Fach P, Loneragan GH.

Appl Environ Microbiol. 2015 Nov 13;82(2):640-9. doi: 10.1128/AEM.03182-15. Print 2016 Jan 15.

14.

Transcriptomic Analysis of the Adaptation of Listeria monocytogenes to Growth on Vacuum-Packed Cold Smoked Salmon.

Tang S, Orsi RH, den Bakker HC, Wiedmann M, Boor KJ, Bergholz TM.

Appl Environ Microbiol. 2015 Oct;81(19):6812-24. doi: 10.1128/AEM.01752-15. Epub 2015 Jul 24.

15.

Characterization of the cytolethal distending toxin (typhoid toxin) in non-typhoidal Salmonella serovars.

Rodriguez-Rivera LD, Bowen BM, den Bakker HC, Duhamel GE, Wiedmann M.

Gut Pathog. 2015 Jul 24;7:19. doi: 10.1186/s13099-015-0065-1. eCollection 2015.

16.

Whole-Genome Sequencing Allows for Improved Identification of Persistent Listeria monocytogenes in Food-Associated Environments.

Stasiewicz MJ, Oliver HF, Wiedmann M, den Bakker HC.

Appl Environ Microbiol. 2015 Sep 1;81(17):6024-37. doi: 10.1128/AEM.01049-15. Epub 2015 Jun 26.

17.

Molecular evolution patterns reveal life history features of mycoplasma-related endobacteria associated with arbuscular mycorrhizal fungi.

Toomer KH, Chen X, Naito M, Mondo SJ, den Bakker HC, VanKuren NW, Lekberg Y, Morton JB, Pawlowska TE.

Mol Ecol. 2015 Jul;24(13):3485-500. doi: 10.1111/mec.13250. Epub 2015 Jun 19.

PMID:
26011293
18.

Selection and Characterization of Phage-Resistant Mutant Strains of Listeria monocytogenes Reveal Host Genes Linked to Phage Adsorption.

Denes T, den Bakker HC, Tokman JI, Guldimann C, Wiedmann M.

Appl Environ Microbiol. 2015 Jul;81(13):4295-305. doi: 10.1128/AEM.00087-15. Epub 2015 Apr 17.

19.

Two Draft Genome Sequences of a New Serovar of Salmonella enterica, Serovar Lubbock.

Bugarel M, den Bakker HC, Nightingale KK, Brichta-Harhay DM, Edrington TS, Loneragan GH.

Genome Announc. 2015 Apr 16;3(2). pii: e00215-15. doi: 10.1128/genomeA.00215-15.

20.

Listeria booriae sp. nov. and Listeria newyorkensis sp. nov., from food processing environments in the USA.

Weller D, Andrus A, Wiedmann M, den Bakker HC.

Int J Syst Evol Microbiol. 2015 Jan;65(Pt 1):286-92. doi: 10.1099/ijs.0.070839-0. Epub 2014 Oct 23.

PMID:
25342111
21.

Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages.

Deng X, Desai PT, den Bakker HC, Mikoleit M, Tolar B, Trees E, Hendriksen RS, Frye JG, Porwollik S, Weimer BC, Wiedmann M, Weinstock GM, Fields PI, McClelland M.

Emerg Infect Dis. 2014 Sep;20(9):1481-9. doi: 10.3201/eid2009.131095.

22.

Rapid whole-genome sequencing for surveillance of Salmonella enterica serovar enteritidis.

den Bakker HC, Allard MW, Bopp D, Brown EW, Fontana J, Iqbal Z, Kinney A, Limberger R, Musser KA, Shudt M, Strain E, Wiedmann M, Wolfgang WJ.

Emerg Infect Dis. 2014 Aug;20(8):1306-14. doi: 10.3201/eid2008.131399.

23.

Genomic characterization of Salmonella Cerro ST367, an emerging Salmonella subtype in cattle in the United States.

Rodriguez-Rivera LD, Moreno Switt AI, Degoricija L, Fang R, Cummings CA, Furtado MR, Wiedmann M, den Bakker HC.

BMC Genomics. 2014 Jun 4;15:427. doi: 10.1186/1471-2164-15-427.

24.

Comparative genomic and morphological analyses of Listeria phages isolated from farm environments.

Denes T, Vongkamjan K, Ackermann HW, Moreno Switt AI, Wiedmann M, den Bakker HC.

Appl Environ Microbiol. 2014 Aug;80(15):4616-25.

25.

Listeria floridensis sp. nov., Listeria aquatica sp. nov., Listeria cornellensis sp. nov., Listeria riparia sp. nov. and Listeria grandensis sp. nov., from agricultural and natural environments.

den Bakker HC, Warchocki S, Wright EM, Allred AF, Ahlstrom C, Manuel CS, Stasiewicz MJ, Burrell A, Roof S, Strawn LK, Fortes E, Nightingale KK, Kephart D, Wiedmann M.

Int J Syst Evol Microbiol. 2014 Jun;64(Pt 6):1882-9. doi: 10.1099/ijs.0.052720-0. Epub 2014 Mar 5.

PMID:
24599893
26.

Genomic comparison of sporeforming bacilli isolated from milk.

Moreno Switt AI, Andrus AD, Ranieri ML, Orsi RH, Ivy R, den Bakker HC, Martin NH, Wiedmann M, Boor KJ.

BMC Genomics. 2014 Jan 14;15:26. doi: 10.1186/1471-2164-15-26.

27.

Salmonella bacteriophage diversity reflects host diversity on dairy farms.

Switt AI, den Bakker HC, Vongkamjan K, Hoelzer K, Warnick LD, Cummings KJ, Wiedmann M.

Food Microbiol. 2013 Dec;36(2):275-85. doi: 10.1016/j.fm.2013.06.014. Epub 2013 Jul 4.

28.

Genomic characterization provides new insight into Salmonella phage diversity.

Moreno Switt AI, Orsi RH, den Bakker HC, Vongkamjan K, Altier C, Wiedmann M.

BMC Genomics. 2013 Jul 17;14:481. doi: 10.1186/1471-2164-14-481.

29.

Evolutionary dynamics of the accessory genome of Listeria monocytogenes.

den Bakker HC, Desjardins CA, Griggs AD, Peters JE, Zeng Q, Young SK, Kodira CD, Yandava C, Hepburn TA, Haas BJ, Birren BW, Wiedmann M.

PLoS One. 2013 Jun 25;8(6):e67511. doi: 10.1371/journal.pone.0067511. Print 2013.

30.

Comparison of typing methods with a new procedure based on sequence characterization for Salmonella serovar prediction.

Ranieri ML, Shi C, Moreno Switt AI, den Bakker HC, Wiedmann M.

J Clin Microbiol. 2013 Jun;51(6):1786-97. doi: 10.1128/JCM.03201-12. Epub 2013 Apr 3.

31.

Genome sequencing identifies Listeria fleischmannii subsp. coloradonensis subsp. nov., isolated from a ranch.

den Bakker HC, Manuel CS, Fortes ED, Wiedmann M, Nightingale KK.

Int J Syst Evol Microbiol. 2013 Sep;63(Pt 9):3257-68. doi: 10.1099/ijs.0.048587-0. Epub 2013 Mar 22.

PMID:
23524352
32.

Complete Genome Sequence of the Porcine Strain Brachyspira pilosicoli P43/6/78(T.).

Lin C, den Bakker HC, Suzuki H, Lefébure T, Ponnala L, Sun Q, Stanhope MJ, Wiedmann M, Duhamel GE.

Genome Announc. 2013 Jan;1(1). pii: e00215-12. doi: 10.1128/genomeA.00215-12. Epub 2013 Feb 21.

33.

Ribosomal RNA gene diversity, effective population size, and evolutionary longevity in asexual glomeromycota.

Vankuren NW, den Bakker HC, Morton JB, Pawlowska TE.

Evolution. 2013 Jan;67(1):207-24. doi: 10.1111/j.1558-5646.2012.01747.x. Epub 2012 Aug 22.

PMID:
23289573
34.

Silage collected from dairy farms harbors an abundance of listeriaphages with considerable host range and genome size diversity.

Vongkamjan K, Switt AM, den Bakker HC, Fortes ED, Wiedmann M.

Appl Environ Microbiol. 2012 Dec;78(24):8666-75. doi: 10.1128/AEM.01859-12. Epub 2012 Oct 5.

35.

Listeria monocytogenes and hemolytic Listeria innocua in poultry.

Milillo SR, Stout JC, Hanning IB, Clement A, Fortes ED, den Bakker HC, Wiedmann M, Ricke SC.

Poult Sci. 2012 Sep;91(9):2158-63. doi: 10.3382/ps.2012-02292.

PMID:
22912449
36.

Identification and characterization of novel Salmonella mobile elements involved in the dissemination of genes linked to virulence and transmission.

Moreno Switt AI, den Bakker HC, Cummings CA, Rodriguez-Rivera LD, Govoni G, Raneiri ML, Degoricija L, Brown S, Hoelzer K, Peters JE, Bolchacova E, Furtado MR, Wiedmann M.

PLoS One. 2012;7(7):e41247. doi: 10.1371/journal.pone.0041247. Epub 2012 Jul 20.

37.

Equine stomachs harbor an abundant and diverse mucosal microbiota.

Perkins GA, den Bakker HC, Burton AJ, Erb HN, McDonough SP, McDonough PL, Parker J, Rosenthal RL, Wiedmann M, Dowd SE, Simpson KW.

Appl Environ Microbiol. 2012 Apr;78(8):2522-32. doi: 10.1128/AEM.06252-11. Epub 2012 Feb 3.

38.

FSL J1-208, a virulent uncommon phylogenetic lineage IV Listeria monocytogenes strain with a small chromosome size and a putative virulence plasmid carrying internalin-like genes.

den Bakker HC, Bowen BM, Rodriguez-Rivera LD, Wiedmann M.

Appl Environ Microbiol. 2012 Mar;78(6):1876-89. doi: 10.1128/AEM.06969-11. Epub 2012 Jan 13.

39.

Identification and characterization of psychrotolerant sporeformers associated with fluid milk production and processing.

Ivy RA, Ranieri ML, Martin NH, den Bakker HC, Xavier BM, Wiedmann M, Boor KJ.

Appl Environ Microbiol. 2012 Mar;78(6):1853-64. doi: 10.1128/AEM.06536-11. Epub 2012 Jan 13.

40.

Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica.

den Bakker HC, Moreno Switt AI, Govoni G, Cummings CA, Ranieri ML, Degoricija L, Hoelzer K, Rodriguez-Rivera LD, Brown S, Bolchacova E, Furtado MR, Wiedmann M.

BMC Genomics. 2011 Aug 22;12:425. doi: 10.1186/1471-2164-12-425.

41.

Listeriosis outbreak in dairy cattle caused by an unusual Listeria monocytogenes serotype 4b strain.

Bundrant BN, Hutchins T, den Bakker HC, Fortes E, Wiedmann M.

J Vet Diagn Invest. 2011 Jan;23(1):155-8.

PMID:
21217050
42.

Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss.

den Bakker HC, Cummings CA, Ferreira V, Vatta P, Orsi RH, Degoricija L, Barker M, Petrauskene O, Furtado MR, Wiedmann M.

BMC Genomics. 2010 Dec 2;11:688. doi: 10.1186/1471-2164-11-688.

43.

Listeria monocytogenes lineages: Genomics, evolution, ecology, and phenotypic characteristics.

Orsi RH, den Bakker HC, Wiedmann M.

Int J Med Microbiol. 2011 Feb;301(2):79-96. doi: 10.1016/j.ijmm.2010.05.002. Epub 2010 Aug 13. Review.

PMID:
20708964
44.

Salt stress phenotypes in Listeria monocytogenes vary by genetic lineage and temperature.

Bergholz TM, den Bakker HC, Fortes ED, Boor KJ, Wiedmann M.

Foodborne Pathog Dis. 2010 Dec;7(12):1537-49. doi: 10.1089/fpd.2010.0624. Epub 2010 Aug 14.

45.

A population genetics-based and phylogenetic approach to understanding the evolution of virulence in the genus Listeria.

den Bakker HC, Bundrant BN, Fortes ED, Orsi RH, Wiedmann M.

Appl Environ Microbiol. 2010 Sep;76(18):6085-100. doi: 10.1128/AEM.00447-10. Epub 2010 Jul 23.

46.

Clonality and recombination in the life history of an asexual arbuscular mycorrhizal fungus.

den Bakker HC, Vankuren NW, Morton JB, Pawlowska TE.

Mol Biol Evol. 2010 Nov;27(11):2474-86. doi: 10.1093/molbev/msq155. Epub 2010 Jun 20.

PMID:
20566475
47.

Multilocus sequence typing of outbreak-associated Listeria monocytogenes isolates to identify epidemic clones.

den Bakker HC, Fortes ED, Wiedmann M.

Foodborne Pathog Dis. 2010 Mar;7(3):257-65. doi: 10.1089/fpd.2009.0342.

PMID:
19911921
48.

Listeria marthii sp. nov., isolated from the natural environment, Finger Lakes National Forest.

Graves LM, Helsel LO, Steigerwalt AG, Morey RE, Daneshvar MI, Roof SE, Orsi RH, Fortes ED, Milillo SR, den Bakker HC, Wiedmann M, Swaminathan B, Sauders BD.

Int J Syst Evol Microbiol. 2010 Jun;60(Pt 6):1280-8. doi: 10.1099/ijs.0.014118-0. Epub 2009 Aug 10.

PMID:
19667380
49.

Lineage specific recombination rates and microevolution in Listeria monocytogenes.

den Bakker HC, Didelot X, Fortes ED, Nightingale KK, Wiedmann M.

BMC Evol Biol. 2008 Oct 8;8:277. doi: 10.1186/1471-2148-8-277.

50.

A phylogenetic study of Boletus section Boletus in Europe.

Beugelsdijk DC, van der Linde S, Zuccarello GC, den Bakker HC, Draisma SG, Noordeloos ME.

Persoonia. 2008 Jun;20:1-7. doi: 10.3767/003158508X283692. Epub 2008 Feb 1.

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