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Draft Genome Sequences of Antimicrobial-Resistant Shigella Clinical Isolates from Pakistan.

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

Microbiol Resour Announc. 2019 Jul 25;8(30). pii: e00500-19. doi: 10.1128/MRA.00500-19.


All for one and one for all: the true potential of whole-genome sequencing.

Allard MW, Stevens EL, Brown EW.

Lancet Infect Dis. 2019 Jul;19(7):683-684. doi: 10.1016/S1473-3099(19)30172-0. Epub 2019 May 24. No abstract available.


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.


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.


Genomic surveillance links livestock production with the emergence and spread of multi-drug resistant non-typhoidal Salmonella in Mexico.

Delgado-Suárez EJ, Ortíz-López R, Gebreyes WA, Allard MW, Barona-Gómez F, Rubio-Lozano MS.

J Microbiol. 2019 Apr;57(4):271-280. doi: 10.1007/s12275-019-8421-3. Epub 2019 Feb 5.


The use of next generation sequencing for improving food safety: Translation into practice.

Jagadeesan B, Gerner-Smidt P, Allard MW, Leuillet S, Winkler A, Xiao Y, Chaffron S, Van Der Vossen J, Tang S, Katase M, McClure P, Kimura B, Ching Chai L, Chapman J, Grant K.

Food Microbiol. 2019 Jun;79:96-115. doi: 10.1016/ Epub 2018 Nov 17. Review.


Genome divergence and increased virulence of outbreak associated Salmonella enterica subspecies enterica serovar Heidelberg.

Antony L, Behr M, Sockett D, Miskimins D, Aulik N, Christopher-Hennings J, Nelson E, Allard MW, Scaria J.

Gut Pathog. 2018 Dec 24;10:53. doi: 10.1186/s13099-018-0279-0. eCollection 2018.


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.


Draft Genome Sequences of 57 Salmonella enterica Strains from Selected U.S. Swine Feed Mills.

Lomonaco S, Magossi G, Sanchez Leon M, Miller D, Kastanis GJ, Tallent SM, Allard MW, Brown EW, Trinetta V.

Microbiol Resour Announc. 2018 Nov 1;7(17). pii: e01191-18. doi: 10.1128/MRA.01191-18. eCollection 2018 Nov.


In-depth comparative analysis of Illumina® MiSeq run metrics: Development of a wet-lab quality assessment tool.

Kastanis GJ, Santana-Quintero LV, Sanchez-Leon M, Lomonaco S, Brown EW, Allard MW.

Mol Ecol Resour. 2019 Mar;19(2):377-387. doi: 10.1111/1755-0998.12973. Epub 2019 Jan 17.


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.


Genomics of Salmonella contaminating backyard production systems reveals persistence and transmission of genetically related Salmonella on a farm basis.

Toro M, Rivera D, Toledo V, Campos-Vargas R, Allard MW, Hamilton-West C, Moreno-Switt AI.

Zoonoses Public Health. 2018 Dec;65(8):1008-1014. doi: 10.1111/zph.12526. Epub 2018 Sep 27.


Genes significantly associated with lineage II food isolates of Listeria monocytogenes.

Pirone-Davies C, Chen Y, Pightling A, Ryan G, Wang Y, Yao K, Hoffmann M, Allard MW.

BMC Genomics. 2018 Sep 25;19(1):708. doi: 10.1186/s12864-018-5074-2.


Phylogenetic and antimicrobial resistance gene analysis of Salmonella Typhimurium strains isolated in Brazil by whole genome sequencing.

Almeida F, Seribelli AA, Medeiros MIC, Rodrigues DDP, de MelloVarani A, Luo Y, Allard MW, Falcão JP.

PLoS One. 2018 Aug 13;13(8):e0201882. doi: 10.1371/journal.pone.0201882. eCollection 2018.


Changing of the Genomic Pattern of Salmonella Enteritidis Strains Isolated in Brazil Over a 48 year-period revealed by Whole Genome SNP Analyses.

Campioni F, Cao G, Kastanis G, Janies DA, Bergamini AMM, Rodrigues DDP, Stones R, Brown E, Allard MW, Falcão JP.

Sci Rep. 2018 Jul 11;8(1):10478. doi: 10.1038/s41598-018-28844-6.


Whole genome sequencing reveals widespread distribution of typhoidal toxin genes and VirB/D4 plasmids in bovine-associated nontyphoidal Salmonella.

Delgado-Suárez EJ, Selem-Mojica N, Ortiz-López R, Gebreyes WA, Allard MW, Barona-Gómez F, Rubio-Lozano MS.

Sci Rep. 2018 Jun 29;8(1):9864. doi: 10.1038/s41598-018-28169-4.


Closed Genome Sequence of Clostridium botulinum Strain CFSAN064329 (62A).

Wentz TG, Yao K, Schill KM, Reddy NR, Skinner GE, Morrissey TR, Wang Y, Muruvanda T, Manickam G, Pillai CA, Thirunavukkarasu N, Hoffmann M, Hammack TS, Brown EW, Allard MW, Sharma SK.

Genome Announc. 2018 Jun 28;6(26). pii: e00528-18. doi: 10.1128/genomeA.00528-18.


Draft Genome Sequences of 112 Salmonella enterica Serovar Dublin Strains Isolated from Humans and Animals in Brazil.

Campioni F, Vilela FP, Cao G, Kastanis G, Miller D, Sanchez Leon M, Tiba-Casas MR, Fernandes SA, Rodrigues DDP, Costa RG, Allard MW, Falcão JP.

Genome Announc. 2018 Jun 14;6(24). pii: e00405-18. doi: 10.1128/genomeA.00405-18.


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.


Draft Genome Sequences of 116 Campylobacter jejuni Strains Isolated from Humans, Animals, Food, and the Environment in Brazil.

Frazão MR, Cao G, Medeiros MIC, Duque SDS, Leon MS, Allard MW, Falcão JP.

Genome Announc. 2018 Apr 19;6(16). pii: e00250-18. doi: 10.1128/genomeA.00250-18.


Draft Genome Sequences of 20 Salmonella enterica subsp. enterica Serovar Typhimurium Strains Isolated from Swine in Santa Catarina, Brazil.

Seribelli AA, Frazão MR, Gonzales JC, Cao G, Leon MS, Kich JD, Allard MW, Falcão JP.

Genome Announc. 2018 Apr 19;6(16). pii: e00232-18. doi: 10.1128/genomeA.00232-18.


Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases.

Piombo E, Sela N, Wisniewski M, Hoffmann M, Gullino ML, Allard MW, Levin E, Spadaro D, Droby S.

Front Microbiol. 2018 Apr 3;9:593. doi: 10.3389/fmicb.2018.00593. eCollection 2018.


Closed Genome Sequence of Chryseobacterium piperi Strain CTMT/ATCC BAA-1782, a Gram-Negative Bacterium with Clostridial Neurotoxin-Like Coding Sequences.

Wentz TG, Muruvanda T, Lomonaco S, Thirunavukkarasu N, Hoffmann M, Allard MW, Hodge DR, Pillai SP, Hammack TS, Brown EW, Sharma SK.

Genome Announc. 2017 Nov 30;5(48). pii: e01296-17. doi: 10.1128/genomeA.01296-17.


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.


CXC Chemokines Exhibit Bactericidal Activity against Multidrug-Resistant Gram-Negative Pathogens.

Crawford MA, Fisher DJ, Leung LM, Lomonaco S, Lascols C, Cannatelli A, Giani T, Rossolini GM, Doi Y, Goodlett DR, Allard MW, Sharma SK, Khan E, Ernst RK, Hughes MA.

MBio. 2017 Nov 14;8(6). pii: e01549-17. doi: 10.1128/mBio.01549-17.


Draft Genome Sequences of 64 Salmonella enterica Serotype Enteritidis Isolates Obtained from Wild Mice.

Guard J, Cao G, Kastanis GJ, Davison S, McClelland M, Sanchez Leon M, Zheng J, Brown E, Allard MW.

Genome Announc. 2017 Sep 7;5(36). pii: e00953-17. doi: 10.1128/genomeA.00953-17.


Draft Genome Sequences of Listeria monocytogenes Strains from Listeriosis Outbreaks Linked to Soft Cheese in Washington State.

Li Z, Marsland PA, Meek RT, Eckmann K, Allard MW, Pérez-Osorio AC.

Genome Announc. 2017 Sep 7;5(36). pii: e00936-17. doi: 10.1128/genomeA.00936-17.


Comparative Sequence Analysis of Multidrug-Resistant IncA/C Plasmids from Salmonella enterica.

Hoffmann M, Pettengill JB, Gonzalez-Escalona N, Miller J, Ayers SL, Zhao S, Allard MW, McDermott PF, Brown EW, Monday SR.

Front Microbiol. 2017 Aug 7;8:1459. doi: 10.3389/fmicb.2017.01459. eCollection 2017.


Draft Genome Sequences of Yersinia frederiksenii, Yersinia intermedia, and Yersinia kristensenii Strains from Brazil.

Imori PFM, Campioni F, Cao G, Kastanis G, Leon MS, Allard MW, Falcão JP.

Genome Announc. 2017 Aug 10;5(32). pii: e00780-17. doi: 10.1128/genomeA.00780-17.


Draft Genome Sequences of 256 Salmonella enterica subsp. enterica Serovar Enteritidis Strains Isolated from Humans, Food, Chickens, and Farm Environments in Brazil.

Campioni F, Cao G, Kastanis G, Sanchez Leon M, Bergamini AMM, Rodrigues DDP, Allard MW, Falcão JP.

Genome Announc. 2017 Jul 13;5(28). pii: e00399-17. doi: 10.1128/genomeA.00399-17.


Complete Genome Sequences of Two Salmonella enterica subsp. enterica Serovar Enteritidis Strains Isolated from Egg Products in the United States.

Hu L, Zhang G, Allard MW, Yao K, Stones R, Hoffmann M, Brown EW.

Genome Announc. 2017 Jun 29;5(26). pii: e00614-17. doi: 10.1128/genomeA.00614-17.


Whole genome sequencing analyses of Listeria monocytogenes that persisted in a milkshake machine for a year and caused illnesses in Washington State.

Li Z, Pérez-Osorio A, Wang Y, Eckmann K, Glover WA, Allard MW, Brown EW, Chen Y.

BMC Microbiol. 2017 Jun 15;17(1):134. doi: 10.1186/s12866-017-1043-1.


Complete Genome Sequences of Three Salmonella enterica subsp. enterica Serovar Saintpaul Isolates Associated with a 2013 Multistate Outbreak in the United States.

Yao K, Muruvanda T, Allard MW, Hoffmann M.

Genome Announc. 2017 Jun 1;5(22). pii: e00456-17. doi: 10.1128/genomeA.00456-17.


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.


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.


Complete Genome and Methylome Sequences of Salmonella enterica subsp. enterica Serovars Typhimurium, Saintpaul, and Stanleyville from the SARA/SARB Collection.

Yao K, Roberts RJ, Allard MW, Hoffmann M.

Genome Announc. 2017 Mar 16;5(11). pii: e00031-17. doi: 10.1128/genomeA.00031-17.


Multilocus sequence typing of Salmonella Typhimurium reveals the presence of the highly invasive ST313 in Brazil.

Almeida F, Seribelli AA, da Silva P, Medeiros MIC, Dos Prazeres Rodrigues D, Moreira CG, Allard MW, Falcão JP.

Infect Genet Evol. 2017 Jul;51:41-44. doi: 10.1016/j.meegid.2017.03.009. Epub 2017 Mar 10. No abstract available.


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.


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.


Molecular characterization of Salmonella Typhimurium isolated in Brazil by CRISPR-MVLST.

Almeida F, Medeiros MIC, Rodrigues DDP, Allard MW, Falcão JP.

J Microbiol Methods. 2017 Feb;133:55-61. doi: 10.1016/j.mimet.2016.12.020. Epub 2016 Dec 26.


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.


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.


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.


Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes.

Chen Y, Gonzalez-Escalona N, Hammack TS, Allard MW, Strain EA, Brown EW.

Appl Environ Microbiol. 2016 Sep 30;82(20):6258-6272. Print 2016 Oct 15.


The Future of Whole-Genome Sequencing for Public Health and the Clinic.

Allard MW.

J Clin Microbiol. 2016 Aug;54(8):1946-8. doi: 10.1128/JCM.01082-16. Epub 2016 Jun 15.


Whole Genome DNA Sequence Analysis of Salmonella subspecies enterica serotype Tennessee obtained from related peanut butter foodborne outbreaks.

Wilson MR, Brown E, Keys C, Strain E, Luo Y, Muruvanda T, Grim C, Jean-Gilles Beaubrun J, Jarvis K, Ewing L, Gopinath G, Hanes D, Allard MW, Musser S.

PLoS One. 2016 Jun 3;11(6):e0146929. doi: 10.1371/journal.pone.0146929. eCollection 2016.


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.


Complete Genome and Methylome Sequences of Salmonella enterica subsp. enterica Serovar Panama (ATCC 7378) and Salmonella enterica subsp. enterica Serovar Sloterdijk (ATCC 15791).

Yao K, Muruvanda T, Roberts RJ, Payne J, Allard MW, Hoffmann M.

Genome Announc. 2016 Mar 17;4(2). pii: e00133-16. doi: 10.1128/genomeA.00133-16.


Complete Genome and Methylome Sequences of Two Salmonella enterica spp.

Yao K, Muruvanda T, Roberts RJ, Payne J, Allard MW, Hoffmann M.

Genome Announc. 2016 Jan 21;4(1). pii: e01599-15. doi: 10.1128/genomeA.01599-15.


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.

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