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Items: 1 to 50 of 57

1.

Whole genome sequencing uses for foodborne contamination and compliance: Discovery of an emerging contamination event in an ice cream facility using whole genome sequencing.

Allard MW, Strain E, Rand H, Melka D, Correll WA, Hintz L, Stevens E, Timme R, Lomonaco S, Chen Y, Musser SM, Brown EW.

Infect Genet Evol. 2019 Sep;73:214-220. doi: 10.1016/j.meegid.2019.04.026. Epub 2019 Apr 27. Review.

2.

Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance.

Timme RE, Strain E, Baugher JD, Davis S, Gonzalez-Escalona N, Sanchez Leon M, Allard MW, Brown EW, Tallent S, Rand H.

J Clin Microbiol. 2019 Apr 26;57(5). pii: e01816-18. doi: 10.1128/JCM.01816-18. Print 2019 May. Review.

3.

Utilizing the Public GenomeTrakr Database for Foodborne Pathogen Traceback.

Timme RE, Sanchez Leon M, Allard MW.

Methods Mol Biol. 2019;1918:201-212. doi: 10.1007/978-1-4939-9000-9_17.

PMID:
30580411
4.

Genetic Diversity of Salmonella and Listeria Isolates from Food Facilities.

Wang YU, Pettengill JB, Pightling A, Timme R, Allard M, Strain E, Rand H.

J Food Prot. 2018 Dec;81(12):2082-2089. doi: 10.4315/0362-028X.JFP-18-093.

PMID:
30485763
5.

Salmonella enterica Phylogeny Based on Whole-Genome Sequencing Reveals Two New Clades and Novel Patterns of Horizontally Acquired Genetic Elements.

Worley J, Meng J, Allard MW, Brown EW, Timme RE.

MBio. 2018 Nov 27;9(6). pii: e02303-18. doi: 10.1128/mBio.02303-18.

6.

GenomeTrakr proficiency testing for foodborne pathogen surveillance: an exercise from 2015.

Timme RE, Rand H, Sanchez Leon M, Hoffmann M, Strain E, Allard M, Roberson D, Baugher JD.

Microb Genom. 2018 Jul;4(7). doi: 10.1099/mgen.0.000185. Epub 2018 Jun 15.

7.

Resistome of carbapenem- and colistin-resistant Klebsiella pneumoniae clinical isolates.

Lomonaco S, Crawford MA, Lascols C, Timme RE, Anderson K, Hodge DR, Fisher DJ, Pillai SP, Morse SA, Khan E, Hughes MA, Allard MW, Sharma SK.

PLoS One. 2018 Jun 8;13(6):e0198526. doi: 10.1371/journal.pone.0198526. eCollection 2018.

8.

Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance.

Timme RE, Rand H, Shumway M, Trees EK, Simmons M, Agarwala R, Davis S, Tillman GE, Defibaugh-Chavez S, Carleton HA, Klimke WA, Katz LS.

PeerJ. 2017 Oct 6;5:e3893. doi: 10.7717/peerj.3893. eCollection 2017.

9.

Identification of Brucella genus and eight Brucella species by Luminex bead-based suspension array.

Lusk Pfefer TS, Timme R, Kase JA.

Food Microbiol. 2018 Apr;70:113-119. doi: 10.1016/j.fm.2017.09.015. Epub 2017 Sep 26.

PMID:
29173617
10.

Genomics of foodborne pathogens for microbial food safety.

Allard MW, Bell R, Ferreira CM, Gonzalez-Escalona N, Hoffmann M, Muruvanda T, Ottesen A, Ramachandran P, Reed E, Sharma S, Stevens E, Timme R, Zheng J, Brown EW.

Curr Opin Biotechnol. 2018 Feb;49:224-229. doi: 10.1016/j.copbio.2017.11.002. Epub 2017 Nov 21. Review.

PMID:
29169072
11.

Development of a Reference Standard Library of Chloroplast Genome Sequences, GenomeTrakrCP.

Zhang N, Ramachandran P, Wen J, Duke JA, Metzman H, McLaughlin W, Ottesen AR, Timme RE, Handy SM.

Planta Med. 2017 Dec;83(18):1420-1430. doi: 10.1055/s-0043-113449. Epub 2017 Jun 26.

PMID:
28651291
12.

Whole Genome and Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analyses of Listeria monocytogenes Isolates Associated with an Outbreak Linked to Cheese, United States, 2013.

Chen Y, Luo Y, Carleton H, Timme R, Melka D, Muruvanda T, Wang C, Kastanis G, Katz LS, Turner L, Fritzinger A, Moore T, Stones R, Blankenship J, Salter M, Parish M, Hammack TS, Evans PS, Tarr CL, Allard MW, Strain EA, Brown EW.

Appl Environ Microbiol. 2017 Jul 17;83(15). pii: e00633-17. doi: 10.1128/AEM.00633-17. Print 2017 Aug 1.

13.

The Public Health Impact of a Publically Available, Environmental Database of Microbial Genomes.

Stevens EL, Timme R, Brown EW, Allard MW, Strain E, Bunning K, Musser S.

Front Microbiol. 2017 May 9;8:808. doi: 10.3389/fmicb.2017.00808. eCollection 2017. No abstract available.

14.

TreeToReads - a pipeline for simulating raw reads from phylogenies.

McTavish EJ, Pettengill J, Davis S, Rand H, Strain E, Allard M, Timme RE.

BMC Bioinformatics. 2017 Mar 20;18(1):178. doi: 10.1186/s12859-017-1592-1.

15.

An analysis of Echinacea chloroplast genomes: Implications for future botanical identification.

Zhang N, Erickson DL, Ramachandran P, Ottesen AR, Timme RE, Funk VA, Luo Y, Handy SM.

Sci Rep. 2017 Mar 16;7(1):216. doi: 10.1038/s41598-017-00321-6.

16.

Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States.

Chen Y, Luo Y, Curry P, Timme R, Melka D, Doyle M, Parish M, Hammack TS, Allard MW, Brown EW, Strain EA.

PLoS One. 2017 Feb 6;12(2):e0171389. doi: 10.1371/journal.pone.0171389. eCollection 2017.

17.

Singleton Sequence Type 382, an Emerging Clonal Group of Listeria monocytogenes Associated with Three Multistate Outbreaks Linked to Contaminated Stone Fruit, Caramel Apples, and Leafy Green Salad.

Chen Y, Luo Y, Pettengill J, Timme R, Melka D, Doyle M, Jackson A, Parish M, Hammack TS, Allard MW, Brown EW, Strain EA.

J Clin Microbiol. 2017 Mar;55(3):931-941. doi: 10.1128/JCM.02140-16. Epub 2017 Jan 4.

18.

Genome Sequences of Multidrug-Resistant, Colistin-Susceptible and -Resistant Klebsiella pneumoniae Clinical Isolates from Pakistan.

Crawford MA, Timme R, Lomonaco S, Lascols C, Fisher DJ, Sharma SK, Strain E, Allard MW, Brown EW, McFarland MA, Croley T, Hammack TS, Weigel LM, Anderson K, Hodge DR, Pillai SP, Morse SA, Khan E, Hughes MA.

Genome Announc. 2016 Dec 15;4(6). pii: e01419-16. doi: 10.1128/genomeA.01419-16.

19.

Listeria monocytogenes in Stone Fruits Linked to a Multistate Outbreak: Enumeration of Cells and Whole-Genome Sequencing.

Chen Y, Burall LS, Luo Y, Timme R, Melka D, Muruvanda T, Payne J, Wang C, Kastanis G, Maounounen-Laasri A, De Jesus AJ, Curry PE, Stones R, K'Aluoch O, Liu E, Salter M, Hammack TS, Evans PS, Parish M, Allard MW, Datta A, Strain EA, Brown EW.

Appl Environ Microbiol. 2016 Nov 21;82(24):7030-7040. Print 2016 Dec 15.

20.

Draft Genome Sequences of 40 Salmonella enterica Serovar Typhimurium Strains Isolated from Humans and Food in Brazil.

Almeida F, Medeiros MI, Rodrigues DP, Payne J, Timme RE, Allard MW, Falcão JP.

Genome Announc. 2016 Sep 22;4(5). pii: e00892-16. doi: 10.1128/genomeA.00892-16.

21.

Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation.

Jackson BR, Tarr C, Strain E, Jackson KA, Conrad A, Carleton H, Katz LS, Stroika S, Gould LH, Mody RK, Silk BJ, Beal J, Chen Y, Timme R, Doyle M, Fields A, Wise M, Tillman G, Defibaugh-Chavez S, Kucerova Z, Sabol A, Roache K, Trees E, Simmons M, Wasilenko J, Kubota K, Pouseele H, Klimke W, Besser J, Brown E, Allard M, Gerner-Smidt P.

Clin Infect Dis. 2016 Aug 1;63(3):380-6. doi: 10.1093/cid/ciw242. Epub 2016 Apr 18.

22.

Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database.

Allard MW, Strain E, Melka D, Bunning K, Musser SM, Brown EW, Timme R.

J Clin Microbiol. 2016 Aug;54(8):1975-83. doi: 10.1128/JCM.00081-16. Epub 2016 Mar 23. Review.

23.

Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Give, Isolated from an Imported Chili Powder Product.

Wang H, Chen Y, Ayers S, Melka D, Laasri A, Payne JS, Zheng J, Son I, Timme R, Kastanis G, Hammack TS, Strain E, Allard MW, Evans PS, Brown EW.

Genome Announc. 2015 Jul 2;3(4). pii: e00726-15. doi: 10.1128/genomeA.00726-15.

24.

Draft Genome Sequences of Histamine-Producing Photobacterium kishitanii and Photobacterium angustum, Isolated from Albacore (Thunnus alalunga) and Yellowfin (Thunnus albacares) Tuna.

Bjornsdottir-Butler K, McCarthy SA, Dunlap PV, Timme RE, Benner RA Jr.

Genome Announc. 2015 Apr 30;3(2). pii: e00400-15. doi: 10.1128/genomeA.00400-15.

25.

Genome-wide methylation patterns in Salmonella enterica Subsp. enterica Serovars.

Pirone-Davies C, Hoffmann M, Roberts RJ, Muruvanda T, Timme RE, Strain E, Luo Y, Payne J, Luong K, Song Y, Tsai YC, Boitano M, Clark TA, Korlach J, Evans PS, Allard MW.

PLoS One. 2015 Apr 10;10(4):e0123639. doi: 10.1371/journal.pone.0123639. eCollection 2015.

26.

Characterization of Vibrio parahaemolyticus clinical strains from Maryland (2012-2013) and comparisons to a locally and globally diverse V. parahaemolyticus strains by whole-genome sequence analysis.

Haendiges J, Timme R, Allard MW, Myers RA, Brown EW, Gonzalez-Escalona N.

Front Microbiol. 2015 Feb 19;6:125. doi: 10.3389/fmicb.2015.00125. eCollection 2015.

27.

Characterization and evolution of Salmonella CRISPR-Cas systems.

Shariat N, Timme RE, Pettengill JB, Barrangou R, Dudley EG.

Microbiology. 2015 Feb;161(2):374-386. doi: 10.1099/mic.0.000005.

PMID:
28206902
28.

Characterization and evolution of Salmonella CRISPR-Cas systems.

Shariat N, Timme RE, Pettengill JB, Barrangou R, Dudley EG.

Microbiology. 2015 Feb;161(Pt 2):374-86. doi: 10.1099/mic.0.000005. Epub 2014 Dec 5.

PMID:
25479838
29.

First Fully Closed Genome Sequence of Salmonella enterica subsp. enterica Serovar Cubana Associated with a Food-Borne Outbreak.

Hoffmann M, Muruvanda T, Pirone C, Korlach J, Timme R, Payne J, Evans P, Meng J, Brown EW, Allard MW.

Genome Announc. 2014 Oct 30;2(5). pii: e01112-14. doi: 10.1128/genomeA.01112-14.

30.

Draft Genome Sequences of Clinical Vibrio parahaemolyticus Strains Isolated in Maryland (2010 to 2013).

Haendiges J, Timme R, Allard M, Myers RA, Payne J, Brown EW, Evans P, Gonzalez-Escalona N.

Genome Announc. 2014 Aug 7;2(4). pii: e00776-14. doi: 10.1128/genomeA.00776-14.

31.

The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica.

Pettengill JB, Timme RE, Barrangou R, Toro M, Allard MW, Strain E, Musser SM, Brown EW.

PeerJ. 2014 Apr 17;2:e340. doi: 10.7717/peerj.340. eCollection 2014.

32.

Complete Genome Sequence of a Multidrug-Resistant Salmonella enterica Serovar Typhimurium var. 5- Strain Isolated from Chicken Breast.

Hoffmann M, Muruvanda T, Allard MW, Korlach J, Roberts RJ, Timme R, Payne J, McDermott PF, Evans P, Meng J, Brown EW, Zhao S.

Genome Announc. 2014 Apr 3;2(2). pii: e00294-14. doi: 10.1128/genomeA.00294-14. No abstract available.

33.

Fully Assembled Genome Sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992.

Allard MW, Muruvanda T, Strain E, Timme R, Luo Y, Wang C, Keys CE, Payne J, Cooper T, Luong K, Song Y, Chin CS, Korlach J, Roberts RJ, Evans P, Musser SM, Brown EW.

Genome Announc. 2014 Apr 3;2(2). pii: e00293-14. doi: 10.1128/genomeA.00293-14. No abstract available.

34.

Whole-genome single-nucleotide-polymorphism analysis for discrimination of Clostridium botulinum group I strains.

Gonzalez-Escalona N, Timme R, Raphael BH, Zink D, Sharma SK.

Appl Environ Microbiol. 2014 Apr;80(7):2125-32. doi: 10.1128/AEM.03934-13. Epub 2014 Jan 24.

35.

Complete Genome Sequence of a Multidrug-Resistant Salmonella enterica Serovar Typhimurium var. 5- Strain Isolated from Chicken Breast.

Hoffmann M, Muruvanda T, Allard MW, Korlach J, Roberts RJ, Timme R, Payne J, McDermott PF, Evans P, Meng J, Brown EW, Zhao S.

Genome Announc. 2013 Dec 19;1(6). pii: e01068-13. doi: 10.1128/genomeA.01068-13. Erratum in: Genome Announc. 2014 Apr 03;2(2):null.

36.

Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters.

Timme RE, Pettengill JB, Allard MW, Strain E, Barrangou R, Wehnes C, Van Kessel JS, Karns JS, Musser SM, Brown EW.

Genome Biol Evol. 2013;5(11):2109-23. doi: 10.1093/gbe/evt159.

37.

Genome Sequences of Two Emerging Non-O157 Shiga Toxin-Producing Escherichia coli Strains.

Cao G, Ju W, Rump L, Zhao S, Zou L, Wang C, Strain E, Luo Y, Timme R, Allard M, Brown E, Meng J.

Genome Announc. 2013 May 16;1(3). pii: e00200-13. doi: 10.1128/genomeA.00200-13.

38.

Fully assembled genome sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992.

Allard MW, Muruvanda T, Strain E, Timme R, Luo Y, Wang C, Keys CE, Payne J, Cooper T, Luong K, Song Y, Chin CS, Korlach J, Roberts RJ, Evans P, Musser SM, Brown EW.

Genome Announc. 2013 Mar 21;1(2):e0008113. doi: 10.1128/genomeA.00081-13. Erratum in: Genome Announc. 2014 Apr 03;2(2):null.

39.

Draft Genome Sequence of a Clostridium botulinum Isolate from Water Used for Cooling at a Plant Producing Low-Acid Canned Foods.

Basavanna U, Gonzalez-Escalona N, Timme R, Datta S, Schoen B, Brown EW, Zink D, Sharma SK.

Genome Announc. 2013 Jan;1(1). pii: e00200-12. doi: 10.1128/genomeA.00200-12. Epub 2013 Feb 14.

40.

Genome Sequences of Salmonella enterica Serovar Heidelberg Isolates Isolated in the United States from a Multistate Outbreak of Human Salmonella Infections.

Hoffmann M, Luo Y, Lafon PC, Timme R, Allard MW, McDermott PF, Brown EW, Zhao S.

Genome Announc. 2013 Jan;1(1). pii: e00004-12. doi: 10.1128/genomeA.00004-12. Epub 2013 Jan 15.

41.

On the evolutionary history, population genetics and diversity among isolates of Salmonella Enteritidis PFGE pattern JEGX01.0004.

Allard MW, Luo Y, Strain E, Pettengill J, Timme R, Wang C, Li C, Keys CE, Zheng J, Stones R, Wilson MR, Musser SM, Brown EW.

PLoS One. 2013;8(1):e55254. doi: 10.1371/journal.pone.0055254. Epub 2013 Jan 30.

42.

Development of a locked nucleic acid real-time polymerase chain reaction assay for the detection of Pinus armandii in mixed species pine nut samples associated with dysgeusia.

Handy SM, Timme RE, Jacob SM, Deeds JR.

J Agric Food Chem. 2013 Feb 6;61(5):1060-6. doi: 10.1021/jf304223a. Epub 2013 Jan 23.

PMID:
23311709
43.

Phylogenetic analysis of non-O157 Shiga toxin-producing Escherichia coli strains by whole-genome sequencing.

Ju W, Cao G, Rump L, Strain E, Luo Y, Timme R, Allard M, Zhao S, Brown E, Meng J.

J Clin Microbiol. 2012 Dec;50(12):4123-7. doi: 10.1128/JCM.02262-12. Epub 2012 Oct 10.

44.

Erratum: Multigene phylogeny of the green lineage reveals the origin and diversification of land plants.

Finet C, Timme RE, Delwiche CF, Marletaz F.

Curr Biol. 2012 Aug 7;22(15):1456-7. No abstract available.

45.

Draft genome sequences of 21 Salmonella enterica serovar enteritidis strains.

Timme RE, Allard MW, Luo Y, Strain E, Pettengill J, Wang C, Li C, Keys CE, Zheng J, Stones R, Wilson MR, Musser SM, Brown EW.

J Bacteriol. 2012 Nov;194(21):5994-5. doi: 10.1128/JB.01289-12.

46.

Draft genome sequences of eight Salmonella enterica serotype newport strains from diverse hosts and locations.

Cao G, Zhao S, Strain E, Luo Y, Timme R, Wang C, Brown E, Meng J, Allard M.

J Bacteriol. 2012 Sep;194(18):5146. doi: 10.1128/JB.01171-12.

47.

Origin of strigolactones in the green lineage.

Delaux PM, Xie X, Timme RE, Puech-Pages V, Dunand C, Lecompte E, Delwiche CF, Yoneyama K, Bécard G, Séjalon-Delmas N.

New Phytol. 2012 Sep;195(4):857-71. doi: 10.1111/j.1469-8137.2012.04209.x. Epub 2012 Jun 27.

48.

Broad phylogenomic sampling and the sister lineage of land plants.

Timme RE, Bachvaroff TR, Delwiche CF.

PLoS One. 2012;7(1):e29696. doi: 10.1371/journal.pone.0029696. Epub 2012 Jan 13.

49.

Plants.

Delwiche CF, Timme RE.

Curr Biol. 2011 Jun 7;21(11):R417-22. doi: 10.1016/j.cub.2011.04.021. Review. No abstract available.

50.

Multigene phylogeny of the green lineage reveals the origin and diversification of land plants.

Finet C, Timme RE, Delwiche CF, Marlétaz F.

Curr Biol. 2010 Dec 21;20(24):2217-22. doi: 10.1016/j.cub.2010.11.035. Epub 2010 Dec 9. Erratum in: Curr Biol. 2012 Aug 7;22(15):1456-7.

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